Labslink Research News

Dusting for prints from a fossil fish to understand evolutionary change

Wed, 27 Mar 2013 17:10:40 PDT

In 370 million-year-old red sandstone deposits in a highway roadcut, scientists have discovered a new species of armored fish in north central Pennsylvania. Fossils of armored fishes like this one, a phyllolepid placoderm, are known for the distinctive ornamentation of ridges on their exterior plates.......> Full story

great tool to find conference and courses

Sat, 28 Apr 2012 02:36:59 PDT

Hey guys

Some people working at the NKI (Netherlands Cancer Institute) have setup a
search engine for scientific meetings. check the description and the website
as well, if interested...
This website, called biomeeter (www.biomeeter.com) is really well done as it
gives a nice overview of the upcoming meetings organized, and the search can
be done by field or keyword, or even by location (as it's always possible to
combine business with pleasure ;-)).
Another great characteristic of Biomeeter is that you can add yourself
meetings to the website and share the info. And last but not least: you can
get informed with an email alert about upcoming meetings in your field.
So, check it out and if you like it, spread the word in your lab and
institute!

Rare fungus kills endangered rattlesnakes in southern Illinois

Tue, 21 Feb 2012 18:08:29 PDT

he eastern massasauga rattlesnake (Sistrurus catenatus catenatus), a candidate for protection under the federal Endangered Species Act, suffers from habitat loss and environmental stresses wherever it is found, said University of Illinois.......> Full story

Road runoff spurring spotted salamander evolution

Wed, 01 Feb 2012 17:15:55 PDT

Spotted salamanders exposed to contaminated roadside ponds are adapting to their toxic environments, according to a Yale paper in Scientific Reports. This study provides the first documented evidence that a vertebrate has adapted to the negative effects of roads apparently by evolving rapidly.......> Full story

German research team targets 'at risk' data on biodiversity

Mon, 19 Dec 2011 16:52:02 PDT

A new German-based project is setting out to rescue biodiversity data at risk of being lost, because they are not integrated in institutional databases, are kept in outdated digital storage systems, or are not properly documented.......> Full story

They call it 'guppy love': UCLA biologists solve an evolution mystery

Wed, 23 Nov 2011 16:54:59 PDT

Guppies in the wild have evolved over at least half-a-million years — long enough for the males' coloration to have changed dramatically. Yet a characteristic orange patch on male guppies has remained remarkably stable, though it could have become redder or more yellow. Why has it stayed the same hue of orange over such a long period of time?.......> Full story

Tiny fossil fragment reveals giant-but-ugly-truth

Fri, 14 Oct 2011 17:53:06 PDT

New research from the Universities of Portsmouth and Leicester has identified a small fossil fragment at the Natural History Museum, London as being part of a giant pterosaur – setting a new upper limit for the size of winged and toothed animals. Dr David Martill from the University of Portsmouth and Dr David Unwin from the University of Leicester examined the fossil - which consisted of the tip of a pterosaur snout that had been in the Museum collections since 1884. Their identification of the fossil as being part of the world's largest toothed pterosaur has been published in Cretaceous Research. Dr Unwin, from the School of Museum Studies at the University of Leicester, said: "Our study showed that the fossil represented a huge individual with a wingspan that might have reached 7 metres. This is far larger than, for example, any modern bird, although some extinct birds may have reached 6 metres in wingspan. "What this research shows is that some toothed pterosaurs reached truly spectacular sizes and, for now, it allows us to put a likely upper limit on that size – around 7 metres in wingspan." Dr Martill, from the University of Portsmouth, added: "It's an ugly looking specimen, but with a bit of skill you can work out just exactly what it was. All we have is the tip of the upper jaws - bones called the premaxillae, and a broken tooth preserved in one socket. "Although the crown of the tooth has broken off, its diameter is 13mm. This is huge for a pterosaur. Once you do the calculations you realise that the scrap in your hand is a very exciting discovery. "The specimen was placed in the collections of London's Natural History Museum by Sir Richard Owen, perhaps the world's greatest vertebrate palaeontologist. In his day, Owen reconstructed a giant New Zealand Moa from a single bone. We might never achieve Owen's calibre, but it is nice to think that we are following in his footsteps." Pterosaurs are flying reptiles, famously seen in Jurassic Park, that lived in the Mesozoic Era alongside dinosaurs between 210 and 65 million years ago. There are six or seven major groups of toothed pterosaurs, but in this study the researchers focused on just one: the ornithocheirids. Unlike other toothed groups, all of which were of relatively modest size (wingspans at most of 2 or 3 metres), they are known to have achieved very large and possibly even giant sizes with wingspans of 6 meters or more. Ornithocheirids were specialised fish-feeding pterosaurs that used a fiercesome set of teeth in the tips of the jaws, to grab their prey as they flew low and slow over the surface of the water. Dr Unwin said: "We found that, generally speaking, large ornithocheirids reached wingspans of 5 or 6 metres which was consistent with previous ideas about this group. However, we also came across one fossil, collected in the mid-19th century from a deposit in Cambridgeshire called the Cambridge Greensand that seemed to be unusually large. "This fossil, now in the collections of the Natural History Museum, London, consisted of the tip of a pterosaur snout. The shape of the snout and the broken-off tooth that it contained allowed us to identify the new find as belonging to Coloborhynchus capito, a very rare ornithocheirid represented only by a few fossil fragments from the Cambridge Greensand. Calculating the original size of the animal based on just a fragment is difficult, but we were able to take advantage of some recent finds in Brazil of almost complete skeletons of ornithocheirids that are closely related to the Cambridge Greensand jaw fragment." "Our study showed that the fossil did indeed represent a very large individual with a wingspan that might have reached 7 metres." Significantly, though, this is still far short of the giant size achieved by some toothless pterosaurs. Several species of a group called azhdarchids achieved wingspans of around 10 metres. The challenge for the researchers now is to try to understand why some groups, such as azhdarchids, reached these giant sizes, while toothed forms, such as the ornithocheirids, did not. Teeth are heavy, so part of the explanation may lie in weight reduction by losing these. Dr Unwin said: "This research is important because it helps us to better understand patterns of evolution over millions of years, and in groups that are now extinct. At a more general level, it feeds into TV documentaries such as the current series 'Dinosaur Planet' on BBC1, ensuring that they have the 'ring of authenticity' that ensures successful reception, by experts and the lay public alike. Indeed, these programs are enormously popular, as viewing figures show, allowing us to comfort ourselves with the thought that the research we carry out is helping to satisfy the interests of a not insignificant portion of the viewing public. "For Dave Martill and I, this was to some extent the 'bread and butter' stuff that we do everyday. But it's this slow piling up of data and, critically, its connection into our general understanding, that leads to the really big discoveries. Dave likes to refer to the fossil as the ugliest fossil he ever studied, and I can see his point, but as I did my PhD on Cambridge Greensand pterosaurs they have a special place in my affections and, no matter how ugly, I still love them."

Sexual selection by sugar molecule helped determine human origins

Mon, 10 Oct 2011 16:44:19 PDT

Researchers at the University of California, San Diego School of Medicine say that losing the ability to make a particular kind of sugar molecule boosted disease protection in early hominids, and may have directed the evolutionary emergence of our ancestors, the genus Homo. The findings, published in this week's early online edition of the Proceedings of the National Academy of Sciences, are among the first evidence of a novel link between cell surface sugars, Darwinian sexual selection, and immune function in the context of human origins Sialic acids are sugar molecules found on the surfaces of all animal cells, where they serve as vital contact points for interaction with other cells and with the surrounding environment, including as targets for invasive pathogens. For millions of years, the common ancestors of humans and other apes shared a particular kind of sialic acid known as N-glycolylneuraminic acid or Neu5Gc. Then, for reasons possibly linked to a malarial parasite (http://health.ucsd.edu/news/2005/Pages/09_08_Varki.aspx) that bound Neu5Gc, a gene mutation three million or so years ago inactivated the human enzyme involved in making the molecule. Instead, humans began producing more of a slightly different form of sialic acid called Neu5Ac, the precursor of Neu5Gc. "This occurred at about the same time as early humans were apparently becoming major predators in their environment," said Pascal Gagneux, PhD, an evolutionary biologist and associate professor of cellular and molecular medicine at UC San Diego. "It's hard to be sure exactly what happened because evolution works on so many things simultaneously, but the change in sialic acid meant that early humans developed an immune response to Neu5Gc. It became viewed by their immune systems as foreign, something to be destroyed. At about the same time, they started eating red meat, a major source of Neu5Gc, which may have further stimulated the immune response." Gagneux and colleagues say this strong immune reaction to Neu5Gc likely had a profound effect upon early human reproduction. In all mammals, the biological costs of pregnancy for the female can be huge, sometimes even life-threatening, and so it behooves females to ensure only the best-matching sperm successfully fertilize an egg. The scientists hypothesized that anti-Neu5Gc antibodies would target Neu5Gc-positive sperm or fetal tissues in early humans, kill them and thus reduce the chances of reproductive success. The researchers tested the idea by exposing chimpanzee sperm, whose cell surface sugars are more than half non-human sialic acids, to human anti-Neu5Gc antibodies. The antibodies bound and killed the ape sperm in vitro. The scientists then mated female mice genetically altered to lack Neu5Gc and immunized to produce anti-Neu5Gc antibodies with Neu5Gc-positive males. The fertility rate for the females was measurably lower due to pre-zygotic incompatibility – the anti-sperm effects of female antibodies. "Over time, this incompatibility would reduce and then eliminate individuals with Neu5Gc," said Gagneux. "Oddly enough, based on our theoretical model, the process works faster when the fertility rate is only slightly decreased, rather than producing 100 percent infertility." Gagneux noted that the findings add further weight to the concept of "speciation by infection," in which a combination of infectious diseases suffered by a particular population could predispose that population to diverge from other populations due to reproductive incompatibility. In the case of early humans, one driver may have been female immunity to Neu5Gc. Previous studies (http://ucsdnews.ucsd.edu/newsrel/health/Varki%208%2022.htm) have shown that the loss of Neu5Gc occurred about two to three million years ago, which happens to be about the time of emergence of Homo ergaster/erectus, the likely ancestor of humans. "We suggest that the immune mechanism described here was involved in the origin of the genus Homo," said study co-author Ajit Varki, MD, professor of medicine and cellular and molecular medicine and director of the Center for Academic Research and Training in Anthropogeny at UC San Diego.

Aquatic fish jump into picture of evolutionary land invasion

Fri, 07 Oct 2011 17:45:07 PDT

Research sometimes means looking for one thing and finding another. Such was the case when biology professor Alice Gibb and her research team at Northern Arizona University witnessed a small amphibious fish, the mangrove rivulus, jump with apparent skill and purpose out of a small net and back into the water......> Full story

Researchers greatly improve evolutionary Tree of Life for mammals

Thu, 22 Sep 2011 17:51:03 PDT

An international research team led by biologists at the University of California, Riverside and Texas A&M University has released for the first time a large and robust DNA matrix that has representation for all mammalian families. The matrix – the culmination of about five years of painstaking research – has representatives for 99 percent of mammalian families, and covers not only the earliest history of mammalian diversification but also all the deepest divergences among living mammals. "This is the first time this kind of dataset has been put together for mammals," said Mark Springer, a professor of biology at UC Riverside, who co-led the research project with William Murphy, an associate professor of genetics at Texas A&M. "Until now, no one has been able to assemble this kind of matrix, based on DNA sequences from many different genes, to examine how the different families of mammals are related to each other. This dataset, with all the sequences we generated, provides a large and reliable foundation – a springboard – for biologists to take the next leap in this field of work. We can now progress from phylogeny that has representatives for all the different mammalian families to phylogenies that have representatives for genera and species." Phylogeny is the history of organismal lineages as they change through time. A vast evolutionary tree, called the Tree of Life, represents the phylogeny of organisms, the genealogical relationships of all living things. As most introductory biology textbooks will show, organisms are biologically classified according to a hierarchical system characterized by seven main taxonomic ranks: kingdom, phylum or division, class, order, family, genus, species. For example, humans are known taxonomically as Homo sapiens. Their genus is Homo, the family is Hominidae, the order is Primates and the class is Mammalia. To date divergence times on their phylogeny of mammalian families, Springer and colleagues used a "relaxed molecular clock." This kind of molecular clock allows for the use of multiple rates of evolution instead of using one rate of evolution that governs all branches of the Tree of Life. They also used age estimates for numerous fossil mammals to calibrate their time tree. "We need to have calibrations to input into the analysis so that we know, for example, that elephants and their nearest relatives have been separate from each other since at least the end of the Paleocene – more than 55 million years ago," Springer said. "We were able to put together a diverse assemblage of fossil calibrations from different parts of the mammalian tree, and we used it in conjunction with molecular information to assemble the most robust time tree based on sequenced data that has been developed to date." Study results appear today (Sept. 22) in Science Express. "This study is the beginning of a larger plan to use large molecular data sets and sophisticated techniques for dating and estimating rates of diversification to resolve much larger portions of the mammalian tree, ultimately including all described species, as well as those that have gone recently extinct or for which only museum material may be available," Murphy said. "Only then can we really begin to understand the role of the environment and events in earth history in promoting the generation of living biodiversity. This phylogeny also serves as a framework to understand the history of the unique changes in the genome that underlie the vast morphological diversity observed in the more than 5400 living species of mammals." Springer explained that the research team looked for spikes in the diversification history of mammals and used an algorithm to determine whether the rate of diversification was constant over time or whether there were distinct pulses of rate increases or decreases. The researchers found an increase in the diversification rate 80-82 million years ago, which corresponds to the time – specifically, the end of the Cretaceous Terrestrial Revolution – when a lot of different orders were splitting from each other. "This is when flowering plants diversified, which provided opportunities for the diversification of small mammals," Springer said. Springer and colleagues also detected a second spike in the diversification history of mammals at the end of the Cretaceous – 65.5 million years ago, when dinosaurs, other large terrestrial vertebrates, and many marine organisms went extinct, opening up a vast ecological space. "Such ecological voids can get filled quickly," Springer explained. "We see that in mammals, even though different orders such as primates and rodents split from each other back in the Cretaceous, the orders did not diversify into their modern representations until after the Cretaceous, 65.5 million years ago. The void seems to have facilitated the radiation – that is, branching in conjunction with change – of different orders of several mammals into the adaptive zones they occupy today. After the Cretaceous, we see increased diversification, with some lineages becoming larger and more specialized." The researchers stress that their time tree is a work in progress. In the next two years, they expect to construct a supermatrix, also based on gene sequences, and include the majority of living mammalian species. The current work incorporates 164 mammalian species. "Our phylogeny, underpinned by a large number of genes, sets the stage for us to understand how the different mammalian species are related to each other," Springer said. "That will help us understand when these species diverged from each other. It will allow us to look for taxonomic rates of increase or decrease over time in different groups in various parts of the world so that we can understand these diversification rate changes in relationship to important events in Earth's history – such as the diversification of flowering plants and changes associated with climatic events. Researchers routinely make use of phylogenies in diverse fields such as ecology, physiology, and biogeography, and the new phylogeny for mammalian families provides a more accurate framework for these studies. "When you understand how taxa are related to each other," Springer added, "you can start to understand which changes at the genome level underpin key morphological changes associated with, say, flight and echolocation in bats or loss of teeth in toothless mammals. In other words, you can pinpoint key molecular changes that are associated with key morphological changes. This would be extremely difficult, if not altogether impossible, without the kind of robust molecular phylogeny we have developed." The research team also reports that their results contradict the "delayed rise of present-day mammals" hypothesis. According to this hypothesis, introduced by a team of scientists in a 2007 research paper, the ancestors of living mammals underwent a pulse of diversification around 50 million years ago, possibly in response to the extinction of archaic mammals that went extinct at the end of the Paleocene (around 56 million years ago). The earlier extinction event around 65.5 million years ago, which resulted in the demise of the dinosaurs, had no effect on the diversification of the ancestors of extant mammals, according to the 2007 research paper. "Our analysis shows that the mass extinction event 65.5 million years ago played an important role in the early diversification and adaptive radiation of mammals," Springer said. "The molecular phylogeny we used to develop the matrix is far more reliable and accurate, and sets our work apart from previous studies."

Using human genomes to illuminate the mysteries of early human history

Wed, 21 Sep 2011 17:23:25 PDT

Cornell researchers have developed new statistical methods based on the complete genome sequences of people alive today to shed light on events at the dawn of human history.......> Full story

A 'jumping gene's' preferred targets may influence genome evolution

Tue, 06 Sep 2011 17:25:55 PDT

The human genome shares several peculiarities with the DNA of just about every other plant and animal. Our genetic blueprint contains numerous entities known as transposons, or "jumping genes," which have the ability to move from place to place on the chromosomes within a cell. An astounding 50% of human DNA comprises both active transposon elements and the decaying remains of former transposons that were active thousands to millions of years ago before becoming damaged and immobile. If all of this mobile and formerly mobile DNA were not mysterious enough, every time a plant, animal or human cell prepares to divide, the chromosome regions richest in transposon-derived sequences, even elements long deceased, are among the last to duplicate. The reason for their delayed duplication, if there is one, has eluded biologists for more than 50 years. New research led by Carnegie's Allan Spradling and published online this week by Proceedings of the National Academy of Sciences provides potential insight into both these enigmas. The scientists used the fruit fly, Drosophila melanogaster, one of the premier "model" organisms for studying genome structure and gene function. They focused on one particular transposon, called the P element, which has an unsurpassed ability to move that has stimulated its widespread use by Drosophila researchers. Remarkably, P elements have only been present in Drosophila melanogaster for about 80 years, at which time they were acquired from the genome of a distantly related fruit fly species by an unknown process. P elements remain highly "infective" today. Adding just one copy to the genome of one fly causes all the flies in a laboratory population with which it breeds to acquire 30 to 50 P elements within a few generations. The original goal of the Spradling team's research was not to understand how transposons spread or genomes evolve, but something much simpler: To learn why P elements insert at some locations in the genome but not in others. Spradling and his colleagues, who oversee the NIH-funded Drosophila "Gene Disruption Project" used a database containing more than 50,000 genomic sites where P elements have inserted. They built this exceptional database over the last 20 years. P elements insert into DNA very selectively. Nearly 40% of new jumps occur within just 300 genes and always near the beginning of the gene. But the genes seemed to have nothing in common. When these sites were compared to data about the Drosophila genome, particularly recent studies of Drosophila genome duplication, the answer became clear. What many P insertion sites share in common is an ability to function as starting sites or "origins" for DNA duplication. This association between P elements and the machinery of genome duplication suggested that they can coordinate their movement with DNA replication. Spradling and his team propose that P elements—and likely other transposons as well—use a replication connection to spread more rapidly through genomes. These elements would only transpose after replicating, and then preferentially insert themselves into portions of DNA that have not yet become activated. This would allow them to duplicate twice rather than just once during the genome duplication cycle. If the elements get a late start, however, only the last segments of the chromosome to duplicate will be left for their second duplication. This explains tendency of such regions to be transposon-rich. However, the researchers found that two other Drosophila transposons, known as piggyBac and Minos, do not insert at replication origins, so this mechanism is far from universal. Furthermore, Spradling cautioned that it is particularly difficult to experimentally test hypotheses about evolution. "By gaining insight into one specific transposon's movements, we may have begun to glimpse mechanisms that have profoundly influenced genome evolution for nearly all animals" Spradling commented.

Genetic map of African-Americans to aid study of diseases, human evolution

Wed, 20 Jul 2011 17:17:37 PDT

A group of researchers from the University of Oxford, Harvard Medical School and the University of Mississippi Medical Center has constructed the world's most detailed genetic map, a tool scientists can use to better understand the roots of disease and how DNA is passed generationally to create diversity in the human species. About 5,000 Jackson-area volunteers were included in a group of nearly 30,000 African-Americans whose genetic information the scientists used to create the map. The map pinpoints genome locations where people splice together DNA from their mothers and fathers to produce sperm or eggs. That process, known as recombination, mixes DNA from the person's parents and passes it on to his or her children. Almost every prior genetic map was developed in people of European ancestry. The new map is the first built in African-Americans. "The world's best genetic map is now built in African-Americans," said David Reich, professor of genetics at Harvard Medical School, who co-led the study with Simon Myers, a lecturer in statistics at the University of Oxford. "This map, built in 30,000 African-Americans who are from studies of heart disease and cancer, has a resolution so high it is now the world's most accurate map." The findings will be published in the July 21 edition of Nature. Dr. James Wilson, UMMC professor of medicine and the study's coordinator, said the map holds promise for both broad, genome-wide applications and narrowly focused, single-disease research. "The map will be helpful in finding the genetic roots of any disease that's affected by inheritance – which is virtually every disease," he said. For example, studies have shown certain diseases, such as hypertension, affect African-Americans at greater rates than whites, even with other variables like age, weight and socioeconomic level accounted for. The map could be used to better understand why. A surprise was that the map turned out to be different than those based on people of European and other non-African ancestries. "The landscape of recombination has shifted in African-Americans compared with Europeans," said Anjali Hinch, the study's first author and a post-graduate student at the Oxford University's Wellcome Trust Centrefor Human Genetics. Wilson said the African-American genome has become distinct because of recombination in the U.S. during the past two to three centuries. "African-Americans are a genetically distinguishable group from other continental populations," he said. "African-Americans differ from their African ancestors in that most of them also have genes from European ancestors." The researchers knew that going into the project. But once they analyzed the breakpoints where recombination occurs in African-American genomes, an unexpected difference appeared. "Over half of African-Americans carry a version of the biological machinery for recombination that is different to that in Europeans. As a result, African-Americans experience recombination where it almost never occurs in Europeans," Myers said. Scientists have only recently begun to explore the genetic differences between individuals and populations — and the roles those differences play in human health. In that respect, the first draft of the human genome, completed a decade ago, was only a starting point for understanding the genetic origins of disease. As researchers begin to parse those differences, a crucial tool is a genetic map, as it determines how some groups of genetic differences tend to be inherited together. Recombination, together with mutation, accounts for all the genetic (and thus physical) variety we see within species. But while mutation refers to the errors introduced into single locations within genomes when cells divide, recombination refers to the process by which huge chunks of chromosomes are stitched together during sexual reproduction. A key to the success of genetic maps is that this stitching occurs only at specific locations in the genome. In a landmark set of papers, Myers and his colleagues previously identified a particular DNA code, or motif, that attracted the recombination machinery. Knowing the motif, a string of 13 DNA letters, researchers could zero in on the exact locations where recombination typically occurred—the "recombination hotspots." "When recombination goes wrong, it's known that this can lead to mutations causing congenital diseases, for example diseases like Charcot-Marie-Tooth disease, or certain anemias. We found the same 13-base motif marking many of these disease-mutation sites," said Myers. Reich, who is also a senior associate member of the Broad Institute, said the places in the genome where there are recombination hotspots can also be disease hotspots. "Charting recombination hotspots can thus bring us to the places in the genome that cause disease," he said. The researchers discovered that the 13 base-pair motif responsible for many hotspots in Europeans accounts for only two-thirds as much recombination in African-Americans. They connected the remaining third to a new motif of 17 base pairs, which is recognized by a version of the recombinational machinery that occurs almost exclusively in people of African ancestry. These findings are expected to help researchers understand the roots of congenital conditions that occur more often in African-Americans (due to mutations at the hotspots that are more common in African-Americans), and also to help discover new disease genes in all populations, because of the ability to map these genes more precisely. The new map is so accurate specifically because so many African-Americans have both African and European genes, due to racial mixing during the last couple of hundred years. Reich and Myers are experts in analyzing genetic data to reconstruct the mosaic of regions of African and European genetic ancestry in DNA of modern African-Americans. Using a computer program Reich and Myers wrote specifically to sort the massive amounts of data, Hinch identified places in the genomes of the 30,000 people where switches occurred between African and European ancestry, detecting about 70 per person. These switches correspond to recombination events in the last couple of hundred years, resulting in the more than 2 million recombination events that the researchers used to build the map. The study was only possible because of collaboration from 81 co-authors from many institutions, using DNA samples from five large studies that had previously been carried out to study common diseases such as heart disease and cancer, funded by the National Institutes of Health, the Department of Defense, and many private foundations. "All the co-authors worked together in an incredibly collegial way to put together the enormous set of samples and high quality genetic data that made this study a success," Wilson said.

Sniffing out lymphoma by turning dogs into humans

Wed, 06 Apr 2011 19:23:29 PDT

Researchers at North Carolina State University are narrowing the search for genes involved in non-Hodgkin lymphoma – by turning dogs into humans. Humans and dogs don’t just share companionship and living space, they also share a similar genetic makeup. Additionally, they share the same types of cancer, including lymphoma. Dr. Matthew Breen, professor of genomics at NC State, uses canines as a genetic model for studying lymphoma because purebred dogs of the same breed have less genetic variation among them than humans do, making it easier to pinpoint areas on canine chromosomes that may be involved with cancer.......> Full story

UCSB scientists get glimpse of how the 'code' of life may have emerged

Thu, 24 Mar 2011 03:17:58 PDT

A portion of the "code" of life has been unraveled by a UC Santa Barbara graduate student from the town of Jojutla, Mexico. Annia Rodriguez worked with John Perona, professor in UCSB's Department of Chemistry and Biochemistry, to decipher intramolecular communication within a large RNA-protein enzyme responsible for expressing the genetic code for the amino acid glutamine. To their surprise, the experiments by Rodriguez captured a partial glimpse of how the genetic coding of life may have emerged. The results of the study are published in the journal Structure, published by CELL. Life is based on the ability of all living cells to convert the genetic information in DNA, into the specific sequences of amino acids that make up the proteins that are the cell's workhorses. The key reaction in this decoding process is the attachment of a particular amino acid to one end of a small RNA molecule known as a transfer RNA. The enzyme that catalyzes this amino acid-RNA attachment is the aminoacyl-tRNA synthetase. Rodriguez performed many laborious experiments in which she removed portions of the aminoacyl-tRNA synthetase that interact with the anticodon stem of the transfer RNA, far from the part of the enzyme that binds the amino acid. Using a biochemical approach known as rapid chemical quench kinetics, Rodriguez discovered that when she made these changes to the enzyme, the binding of the amino acid to the protein was strengthened, even though the amino acid binds far away from the positions where the changes were made. "It is totally counterintuitive," said Perona. "Imagine if you had a car, and you took out a gear, and the car went faster. Why would you want that gear if it makes your car go slower?" In all, Rodriguez found that separately removing seven different "gears" from a distant part of the molecule each caused the amino acid to bind more tightly to the aminoacyl-tRNA synthetase. Perona explained that this provides the first systematic analysis demonstrating long-range communication in an enzyme that depends on RNA for its function. "So what we think is going on is that these enzyme-RNA interactions far from the amino acid binding site evolved together with the needs of the cell to respond to subtle cues from its environment – especially in terms of how much amino acid is available," said Perona. "It makes sense in terms of evolution." Rodriguez is the first in her family to pursue a Ph.D., which she will complete this year. Now 28 years old, she began her career as a nurse in Cuernavaca, Mexico. Then she went on to obtain a B.S. in biochemical engineering at the Instituto Tecnológico de Zacatepec. Graduation from her undergraduate program called for work at a research institution and she chose UCSB. Upon graduation, Rodriguez was offered a prestigious five-year scholarship with Mexico's Consejo Nacional de Ciencia y Technología (CONACYT) to continue her studies at UCSB. Although her current research is not focused specifically on human health, Rodriguez said: "My interest in biochemistry started because I wanted to know the mechanisms by which drugs and medications worked inside the human body. I wanted to learn not just the signs and symptoms of disease, but how diseases are developed in a molecular level."

First image of protein residue in 50 million year old reptile skin

Wed, 23 Mar 2011 03:50:30 PDT

Published in the journal Royal Society Proceedings B: Biology, the brightly-coloured image shows the presence of amides – the organic compounds, or building blocks of life – in the ancient skin of a reptile, found in the 50 million year-old rocks of the Green River Formation in Utah, USA. This image had never been seen by the human eye, until a team led by Dr Roy Wogelius and Dr Phil Manning used state-of-the-art infra-red technology at The University of Manchester to reveal and map the fossilized soft tissue of a beautifully-preserved reptile. These infra-red maps are backed up by the first ever element-specific maps of organic material in fossil skin generated using X-rays at the Stanford synchrotron in the USA, also by the Manchester researchers. Chemical details are clear enough that the scientists, from the School of Earth, Atmospheric and Environmental Sciences, are even able to propose how this exceptional preservation occurs. When the original compounds in the skin begin to break down they can form chemical bonds with trace metals, and under exceptional conditions these trace metals act like a 'bridge' to minerals in the sediments. This protects the skin material from being washed away or decomposing further. Geochemist Roy Wogelius: "The mapped distributions of organic compounds and trace metals in 50 million year old skin look so much like maps we've made of modern lizard skin as a check on our work, it is sometimes hard to tell which is the fossil and which is fresh." "These new infra-red and X-ray methods reveal intricate chemical patterns that have been overlooked by traditional methods for decades." The new images are compelling, and represent the next step in the academics' research programme to use modern analytical chemistry and 21st century techniques to understand how such remarkable preservation occurs, and ultimately to discover the chemistry of ancient life. These new results imply that trace metal inventories and patterns in ancient reptile skin, even after fossilisation, can indeed be compared to modern reptiles. The infra-red light causes vibrations in the fossilized skin, and a map of where these vibrations occur can be obtained from a fossil by using a trick: a tiny crystal (like an old phonograph record stylus) which moves from point-to-point in a programmable grid across the surface. At each point where the tiny crystal touches the fossil, an infra-red beam that shines through the crystal reflects off of the crystal base, but a small amount of the beam probes beyond the interface- and if organic compounds are present, they absorb portions of the beam and change the reflected signal. This allows the team to non-destructively map large fossils which do not themselves transmit or reflect the beam – a revolutionary process for paleontologists. Nick Edwards, first author on the publication, said: "The ability to chemically analyse rare and precious fossils such as these without the need to remove material and destroy them is an important and long overdue addition to field of palaeontology. "Hopefully this will provide future opportunities to unlock the information stored in other similarly preserved specimens." Dr Manning said: "Here physics, palaeontology and chemistry have collided to yield incredible insight to the building blocks of fossilized soft tissue. "The results of this study have wider implications, such as understanding what happens to buried wastes over long periods of time. The fossil record provides us with a long-running experiment, from which we can learn in order to help resolve current problems."

Evolutionary 'winners' and 'losers' revealed in collaborative study

Wed, 23 Mar 2011 03:47:30 PDT

In a study that literally analyzed competing bacteria fighting it out to the death, a University of Houston (UH) researcher and his colleagues identified evolutionary 'winners' and 'losers.' Continuing research to understand the basis of these fates may become a useful tool is designing roadblocks to antibiotic resistance. In collaboration with scientists at Michigan State University (MSU), UH evolutionary biologist Timothy Cooper and his graduate student Utpala Shrestha were co-authors on a paper titled "Second-Order Selection for Evolvability in a Large Escherichia coli Population." The report appeared March 18 in Science, the world's leading journal of original scientific research, global news and commentary. "The project found that bacteria growing for thousands of generations in an environment containing glucose as the only food had evolved to be better at getting better," Cooper said. "We found that two lineages of bacteria arose and competed in a single experimental population. The lineage that initially grew more slowly, yet had the potential to evolve more rapidly, was the evolutionary 'winner.' This is surprising because it's usually thought that competition is decided by what competitors can do now and not what they are capable of in the future." As genetic changes occurred, making some individuals better competitors on the glucose food, other individuals that did not quickly get their own beneficial mutations were outcompeted and went extinct. Down the line, understanding the benefits of evolving quickly like this will be a useful tool to predict such things as antibiotic resistance and the evolution of infectious disease. Cooper said this knowledge may one day help scientists design intervention strategies that make the evolution of these traits less likely to occur. The work done by Cooper and Shrestha at UH established the specific genetic changes occurring during this bacterial evolution experiment that caused the change in their ability to evolve further. They discovered the genetic change that was important for determining which bacteria would prevail and which were destined to become extinct. "Our collaborators isolated individual bacteria from a population that had evolved for 500 generations and sequenced their entire DNA genome to determine all the changes that had occurred," Cooper said. "By isolating these changes and adding them in defined combinations back into the original ancestral strain, we were able to determine their individual effects." Reminiscent of Aesop's lesson that 'slow and steady wins the race,' Cooper adds that even bacteria can benefit from a long-term view, with their experiment showing that bacteria that adapted, slowly but consistently, outcompeted those that initially grew quickly but then ran out of ways to improve. With much of his work based on experimental evolution, which is the lab-based study of evolving populations, Cooper's motivation for this experiment comes from wanting to understand the factors involved in evolution of organisms to better fit their environments. Using bacterial and computational experimental systems he aims to identify and integrate these mechanisms and examine how they depend on genetic and environmental factors. "Bacteria provide an ideal model system to address these questions, because they evolve so quickly, undergoing thousands of generations in only a few years," Cooper said. "Additionally, we can now sequence their entire genomes and determine the genetic changes that lead to improvements in their ability to grow." Funded by the National Science Foundation and the Defense Advanced Research Projects Agency, this work was a multidisciplinary effort done in collaboration with researchers in zoology, microbiology and molecular genetics at MSU. In addition to UH's Cooper and Shrestha, the MSU team consisted of Richard Lenski, Jeffrey Barrick, Robert Woods and Mark Kauth. Woods has since moved on to the University of Michigan and Barrick is currently at the University of Texas at Austin.

UF researcher: Flowering plant study 'catches evolution in the act'

Fri, 18 Mar 2011 03:49:41 PDT

A new University of Florida study shows when two flowering plants are crossed to produce a new hybrid, the new species' genes are reset, allowing for greater genetic variation. Researchers say the study, to be published March 17 in Current Biology, could lead to a better understanding of how to best grow more stable and higher yielding agricultural crops. "We caught evolution in the act," said Doug Soltis, a distinguished professor in UF's biology department and study co-author. "New and diverse patterns of gene expression may allow the new species to rapidly adapt in new environments." The study shows the new plant species had relaxed control of gene expression in its earliest generations. But today, after 80 years of evolution, control has been regained, allowing for the production of different patterns of gene expression in different plants. The new species was remade in UF greenhouses as well as studied in its natural habitat. Researchers analyzed Tragopogon miscellus, a species in the daisy family that originated naturally through hybridization in the northwest U.S. about 80 years ago. The new species formed when two species introduced from Europe mated to produce a hybrid offspring. The species mated before in Europe, but the hybrids were never successful. However, in America something new happened – the number of chromosomes in the hybrid spontaneously doubled, and at once it became larger than its parents and quickly spread. "No one had extended this to natural populations and the rapidity at which this can occur, and that's pretty astonishing," said Jonathan Wendel, professor and chairman of the department of ecology, evolution, and organismal biology at Iowa State University. "That species is such a beautiful model for that." Hybridization with chromosome doubling is a prominent mode of species formation and through this study scientists can better understand how different plant groups originated. "Understanding the impacts this process has on genome structure may help understand how best to breed crops for high and stable yields," said study co-author Pat Schnable, director of the Center for Plant Genomics at Iowa State University. Before discovering their relaxed gene expression, the team had expected the artificial hybrids to exhibit a combination of the parents' genes, said study co-author Pam Soltis, curator of molecular systematics and evolutionary genetics at the Florida Museum of Natural History on the UF campus. "What we found was a surprise," said lead author Richard Buggs of Queen Mary University of London, who worked on the study as a postdoctoral researcher at the Florida Museum. "It's as if hybridization and chromosome doubling hit a reset button on gene expression, turning them all on -- this could allow subsequent generations to experiment by switching off different genes." The expression of the hybrid plant's genes in all tissues at all times allowed natural selection to shape what would emerge generations later, Pam Soltis said. With this form of hybridization, there is the opportunity for parental patterns to be equalized, as if the hybrid has a fresh chance to exhibit a wide variety of genetic expressions over time. Its two parent species, Tragopogon dubius and Tragopogon pratensis, were introduced to the U.S. in the 1920s. The researchers started making the artificial hybrids in 2004 and the plants take about one year to grow from seed to being able to produce seeds, Pam Soltis said. "Tragopogon miscellus is unique because we actually know when it originated," Pam Soltis said. "Museum collections tell us when the parent species were introduced, allowing us to infer the age of the hybrid species." The researchers studied 144 duplicated gene pairs from the 40-generation-old Tragogogon miscellus, whose common name is goatsbeard. Because the flower of the plant only blooms for a few hours in the morning, it is often referred to as "John-go-to-bed-at-noon." It looks like a daisy except for being either purple or yellow in color. "The Soltises are showing at the genetic level how this really important process of genome doubling generates new biological diversity," Wendel said. "This leads to new questions and the design of new experiments that can help us understand the ecological and evolutionary consequences of the genetic changes they're observing."

'Fly tree of life' mapped, adds big branch of evolutionary knowledge

Tue, 15 Mar 2011 03:18:45 PDT

Calling it the "new periodic table for flies," researchers at North Carolina State University and collaborators across the globe have mapped the evolutionary history of flies, providing a framework for further comparative studies on the insects that comprise more than 10 percent of all life on Earth. The research, published today in the online edition of Proceedings of the National Academy of Sciences, plugs gaps in the 260-million-year history of the fly order Diptera, says Dr. Brian Wiegmann, NC State professor of entomology and primary investigator of the fly tree of life project. While providing the most comprehensive picture of fly life over the ages, the tree should allow scientists to tease out answers to other puzzling questions about flies, like how some traits, such as blood feeding, appeared and reappeared many times across millions of years of evolution. The results of future studies based on the information provided by the tree may have important impacts on human health and the environment; flies have a substantial impact on society as vectors of killer diseases like malaria, as agricultural pests, and as important pollinators and decomposers. "Flies have a long history of evolutionary success in all sorts of environments," Wiegmann says. "For example, there are fly larvae that live in petroleum, in hot springs, in the gills of land crabs, on the dung of millipedes and within bee hives. The fly tree of life allows us to learn more about both the pattern and the process of evolutionary change, and to make predictions about new discoveries." Using the most complete set of fly genetic and structural anatomy data ever collected, the paper shows that members of the oldest, still-living fly families are rare, anatomically strange flies with long legs and long wings that grow up in fast-flowing mountain waters. "Flies' origins and evolutionary history began in wet environments," Wiegmann says. "As flies diversified, they became more well-suited to terrestrial life. In general, they have flexible life histories that have allowed them to flourish in opportunistic ways." Life on Earth has emerged in bursts of diversification, and fly evolution mirrors this process: flies became more diverse in three large episodes occurring at 220, 180 and 65 million years ago. Just as dinosaurs were becoming extinct, flies and moths were experiencing the largest diversification of animals that has occurred in the past 65 million years. The paper also shows the number of times that different fly lifestyles evolved; there are 12 different and independent occasions when flies began feeding on blood, for example, and 18 times when, ironically, flies lost their wings. Some results were surprising. The study showed that the nearest relatives of Drosophila, the fruit fly that many key scientific discoveries have been based on, are two unusual parasites: bee lice, wingless flies that live on honey bees; and Cryptochetidae, flies used as biological controls of crop pests. "Flies are more ecologically diverse than any other organism," Wiegmann says. "There are so many different kinds – 152,000 named species – and they do so many different things that they've been a particularly difficult puzzle for scientists. We still haven't found all the flies that exist, so there are still some surprises out there. But this work unlocks some of the mysteries of the fly evolutionary tree and adds a major branch to the tree of life for all living things."

Missing DNA makes us human

Thu, 10 Mar 2011 03:28:49 PDT

Chimpanzees and humans are minimally different genetically, but the small differences are what make us human, according to a team of researchers who identified segments of non-coding DNA missing in humans that exist in chimpanzees and other animals. "The technology now lets us look at the genomes of humans and other mammals and find sites where humans are unique," said Philip Reno, assistant professor of anthropology, Penn State. "We can now correlate that information with specific human physical characteristics." DNA is composed of gene segments that code for proteins and non-coding segments that initiate and regulate the work of the coding segments. While the coding segments are important, the non-coding segments are the control mechanism of the organism. Without changing the coding gene, increasing or decreasing the amount the gene is expressed can have significant influence on what the organism looks like and how it functions. The researchers, while at Stanford University, first compared the human genome with that of chimpanzees and other mammals to locate areas of complete deletion in the human genome. "We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signaling and neural function," the researchers report in today's (Mar. 7) issue of Nature. One sequence missing in humans is next to the androgen receptor gene. The absence of this particular region of non-coding DNA may have two consequences -- the human loss of sensory whiskers and small keratinous spines on the penis. "We often think of brain size and bipedalism as key characteristics of what makes us human," said Reno. "But another difference is our sexual behavior." He notes that chimpanzees have quick intercourse because the male chimpanzees are in a competition to see which male can fertilize the one receptive female. This situation occurs when many males copulate with one or a few females. The chimpanzee's penile spines, because they are tactile, may enhance this rapid copulation. Human ancestors, however, likely evolved to favor pair-bonding relationships and group living. The loss of penile spines may have prolonged intercourse to reinforce the pair bond where partners are beneficial for the successful raising of offspring. "We now have the genetic sequence of three separate Neanderthal individuals," said Reno. "Looking at these same non-coding areas, the Neanderthal genome lacks them as well." The absence of these non-coding locations in Neanderthal positions the DNA losses to between 7 million years ago, when human ancestors split from chimpanzees, and 800,000 years ago, when human ancestors split from Neanderthal. Another area of non-coding DNA the researchers found missing in humans was near a tumor suppressor gene expressed in the brain. "During development of mammals, a lot of neurons die in the formation of the brain," said Reno. "The absence of this sequence down regulates expression of the gene that leads to cell death and leads to larger brains." The researchers suggest that they can test other locations associated with human-specific characteristics using functional studies like those used in this research.

Skin color: Handy tool for teaching evolution

Mon, 21 Feb 2011 03:27:49 PDT

Variations in skin color provide one of the best examples of evolution by natural selection acting on the human body and should be used to teach evolution in schools, according to a Penn State anthropologist. "There is an inherent level of interest in skin color and for teachers, that is a great bonus -- kids want to know," said Nina Jablonski, professor and head, Department of Anthropology, Penn State. "The mechanism of evolution can be completely understood from skin color." Scientists have understood for years that evolutionary selection of skin pigmentation was caused by the sun. As human ancestors gradually lost their pelts to allow evaporative cooling through sweating, their naked skin was directly exposed to sunlight. In the tropics, natural selection created darkly pigmented individuals to protect against the sun. Ultraviolet B radiation produces vitamin D in human skin, but can destroy folate. Folate is important for the rapid growth of cells, especially during pregnancy, when its deficiency can cause neural tube defects. Destruction of folate and deficiencies in vitamin D are evolutionary factors because folate-deficient mothers produce fewer children who survive, and vitamin D-deficient women are less fertile than healthy women. Dark skin pigmentation in the tropics protects people from folate destruction, allowing normal reproduction. However, because levels of ultraviolet B are high year round, the body can still produce sufficient vitamin D. As humans moved out of Africa, they moved into the subtropics and eventually inhabited areas up to the Arctic Circle. North or south of 46 degrees latitude -- Canada, Russia, Scandinavia, Western Europe and Mongolia -- dark-skinned people could not produce enough vitamin D, while lighter-skinned people could and thrived. Natural selection of light skin occurred. The differences between light-skinned and dark-skinned people are more interesting than studying changes in the wing color of moths or, the most commonly used evolutionary example, bacterial colonies, according to Jablonski. Adaptation to the environment through evolutionary change becomes even more interesting when looking at the mechanism of tanning. "In the middle latitudes tanning evolved multiple times as a mechanism to partly protect humans from harmful effect of the sun," Jablonski told attendees at the annual meeting of the American Association for the Advancement of Science today (Feb. 20) in Washington, D.C. Tanning evolved for humans so that when ultraviolet B radiation increases in early spring, the skin gradually darkens. As the sun becomes stronger, the tan deepens. During the winter, as ultraviolet B wanes, so does the tan, allowing appropriate protection against folate destruction but sufficient vitamin D production. Tanning evolved in North Africa, South America, the Mediterranean and most of China. Natural variation in skin color due to natural selection can be seen in nearly every classroom in the U.S. because humans now move around the globe far faster than evolution can adjust for the sun. The idea that variation in skin color is due to where someone's ancestors originated and how strong the sun was in those locations is inherently interesting, Jablonski noted. "People are really socially aware of skin color, intensely self-conscious about it," she said. "The nice thing about skin color is that we can teach the principles of evolution using an example on our own bodies and relieve a lot of social stress about personal skin color at the same time." Jablonski noted that the ability to tan developed in a wide variety of peoples and while the outcome, tanablity, is the same, the underlying genetic mechanisms are not necessarily identical. She also noted that depigmentated skin also developed at least three times through different genetic mechanisms. Students who never tan, will also understand why they do not and that they never will.

Subtle shifts, not major sweeps, drove human evolution

Fri, 18 Feb 2011 03:22:27 PDT

The most popular model used by geneticists for the last 35 years to detect the footprints of human evolution may overlook more common subtle changes, a new international study finds. Classic selective sweeps, when a beneficial genetic mutation quickly spreads through the human population, are thought to have been the primary driver of human evolution. But a new computational analysis, published in the February 18, 2011 issue of Science, reveals that such events may have been rare, with little influence on the history of our species. By examining the sequences of nearly 200 human genomes, research led by Ryan Hernandez, PhD, assistant professor of Bioengineering and Therapeutic Sciences at the University of California at San Francisco, found new evidence arguing against selective sweeps as the dominant mode of human adaptation. The reversal suggests that smaller changes in multiple genes may have been the primary driver of changes in human phenotypes, and that new models are needed to retrace the genetic steps of evolution. "Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome," said Molly Przeworski, PhD, professor of Human Genetics and Ecology & Evolution at the University of Chicago and co-senior author of the paper. "It suggests that human adaptation, like most common human diseases, has a complex genetic architecture." Under the classic selective sweep model, a new, advantageous gene appears and quickly spreads through the population. Because of its rapid rise, the gene becomes fixed in the genome with less variation than a gene that spread more slowly and was subject to the shuffling effects of recombination. Geneticists have used this model to look for genetic segments surrounded by "troughs" of low variation, the theoretical footprint of a selective sweep. Applying the model has identified more than 2,000 genes – roughly 10 percent of the human genome – suggesting that selective sweeps were a frequent occurrence that drove the evolution of humans away from their primate ancestors. "The selective sweep model was introduced in 1974 and has pretty much been the central model ever since," Przeworski said. "It is fair to say that it is the model behind almost every scan for selection done to date, in humans or in other organisms." However, areas of low diversity around gene segments might also be produced by other evolutionary mechanisms. To test whether selective sweeps were the predominant cause of these troughs, a group of scientists from the University of Chicago, the University of California at San Francisco, Hebrew University of Jerusalem, and the University of Oxford used data from179 subjects in the 1000 Genomes Project, an international effort to catalogue human variation. "This is really a groundbreaking dataset that allowed this type of analysis to be done for the very first time," Hernandez said. The research team looked at genes with human-specific substitutions, where the nucleotide sequence is different from close primate relatives. In some cases, the new sequence switches an amino acid in the protein the gene encodes, a replacement that likely improved the protein's function. In other genes, the sequence change is "synonymous," coding for the same amino acid as before and leaving the protein's function unperturbed. Under the classic selective sweep model, genetic diversity would be lower surrounding the first group of mutations, those that produced beneficial changes in function, because of their quick spread. But when the two groups were compared, the troughs of low diversity were similar for genes that produce functional changes and genes with synonymous substitutions that do not. The result suggests that classic selective sweeps could not have been the most common cause of these low diversity troughs, leaving the door open for other modes of evolution. "Phenotypic variation in humans isn't as simple as we thought it would be," Hernandez said. "The idea that human adaptation might proceed by single changes at the amino acid level is quite a nice idea, and it's great that we have a few concrete examples of where that occurred, but it's too simplistic a view." Further evidence against common selective sweeps was provided by comparing genome variation in different populations. Because Nigerian, European, and Chinese/Japanese populations separated roughly 100,000 years ago and subsequently adapted to different environments, frequent selective sweeps would be expected to fix clear genetic differences between the populations. However, comparing genomes of different populations from the 1000 Genomes Project detected only subtle differences in allele frequencies, representative of small changes over time rather than rapid sweeps. "It dovetails quite well with findings coming out of medical mapping studies, which also suggest that many loci of small effect influence disease risk," Przeworski said. "These findings call into question how much more there is to find using the selective sweep approach, and should also make us skeptical of how many of the findings to date will turn out to be validated."

Biological anthropologists question claims for human ancestry

Thu, 17 Feb 2011 03:22:41 PDT

"Too simple" and "not so fast" suggest biological anthropologists from the George Washington University and New York University about the origins of human ancestry. In the upcoming issue of the journal Nature, the anthropologists question the claims that several prominent fossil discoveries made in the last decade are our human ancestors. Instead, the authors offer a more nuanced explanation of the fossils' place in the Tree of Life. They conclude that instead of being our ancestors the fossils more likely belong to extinct distant cousins. "Don't get me wrong, these are all important finds," said co-author Bernard Wood, University Professor of Human Origins and professor of Human Evolution Anatomy at GW and director of its Center for the Advanced Study of Hominid Paleobiology. "But to simply assume that anything found in that time range has to be a human ancestor is naïve." The paper, "The evolutionary context of the first hominins," reconsiders the evolutionary relationships of fossils named Orrorin, Sahelanthropus and Ardipithecus, dating from four to seven million years ago, which have been claimed to be the earliest human ancestors. Ardipithecus, commonly known as "Ardi," was discovered in Ethiopia and was found to be radically different from what many researchers had expected for an early human ancestor. Nonetheless, the scientists who made the discovery were adamant it is a human ancestor. "We are not saying that these fossils are definitively not early human ancestors," said co-author Terry Harrison, a professor in NYU's Department of Anthropology and director of its Center for the Study of Human Origins. "But their status has been presumed rather than adequately demonstrated, and there are a number of alternative interpretations that are possible. We believe that it is just as likely or more likely that they are fossil apes situated close to the ancestry of the living great ape and humans." The authors are skeptical about the interpretation of the discoveries and advocate a more nuanced approach to classifying the fossils. Wood and Harrison argue that it is naïve to assume that all fossils are the ancestors of creatures alive today and also note that shared morphology or homoplasy – the same characteristics seen in species of different ancestry – was not taken into account by the scientists who found and described the fossils. For example, the authors claim that for Ardipithecus to be a human ancestor, one must assume that homoplasy does not exist in our lineage, but is common in the lineages closest to ours. The authors suggest there are a number of potential interpretations of these fossils and that being a human ancestor is by no means the simplest, or most parsimonious explanation. The scientific community has long concluded that the human lineage diverged from that of the chimpanzee six to eight million years ago. It is easy to differentiate between the fossils of a modern-day chimpanzee and a modern human. However, it is more difficult to differentiate between the two species when examining fossils that are closer to their common ancestor, as is the case with Orrorin, Sahelanthropus, and Ardipithecus. In their paper, Wood and Harrison caution that history has shown how uncritical reliance on a few similarities between fossil apes and humans can lead to incorrect assumptions about evolutionary relationships. They point to the case of Ramapithecus, a species of fossil ape from south Asia, which was mistakenly assumed to be an early human ancestor in the 1960s and 1970s, but later found to be a close relative of the orangutan. Similarly, Oreopithecus bambolii, a fossil ape from Italy shares many similarities with early human ancestors, including features of the skeleton that suggest that it may have been well adapted for walking on two legs. However, the authors observe, enough is known of its anatomy to show that it is a fossil ape that is only distantly related to humans, and that it acquired many "human-like" features in parallel. Wood and Harrison point to the small canines in Ardipithecus and Sahelanthropus as possibly the most convincing evidence to support their status as early human ancestors. However, canine reduction was not unique to the human lineage for it occurred independently in several lineages of fossil apes (e.g., Oreopithecus, Ouranopithecus and Gigantopithecus) presumably as a result of similar shifts in dietary behavior.

MU, ASU researchers' discovery could change views of human evolution

Fri, 11 Feb 2011 03:35:45 PDT

Feet arches give humans a spring in their steps, shock absorbing abilities, and stiff platforms to propel themselves forward, allowing them to walk upright consistently. Now, researchers at the University of Missouri and Arizona State University have found proof that arches existed in a predecessor to the human species that lived more than 3 million years ago. This discovery could change scientists' views of human evolution. The study is being published this week in Science. Carol Ward, an MU researcher in the Department of Pathology and Anatomical Sciences at the MU School of Medicine, and William Kimbel and Donald Johanson, director and founding director of the Institute of Human Origins at Arizona State University, studied a 3.2 million-year-old fourth metatarsal of Australopithecus afarensis. A team from the Institute of Human Origins and National Museum of Ethiopia led by Kimbel discovered the fossil in Hadar, Ethiopia. The species is often referred to as "Lucy," the nickname of the most complete fossil skeleton of the species to be discovered. The foot bone suggests that these hominids had stiff, arched feet, similar to humans. Australopithecus afarensis had smaller brains and stronger jaws than humans, and scientists have known the animals walked upright on two feet. However, researchers have not known whether Lucy and her kin were more versatile creatures than humans and spent time climbing through the trees. "Now that we know Lucy and her relatives had arches in their feet, this affects much of we know about them, from where they lived to what they ate and how they avoided predators," said Ward, professor of integrative anatomy. "The development of arched feet was a fundamental shift toward the human condition, because it meant giving up the ability to use the big toe for grasping branches, signaling that our ancestors had finally abandoned life in the trees in favor of life on the ground." With human-like arches in its feet, Australopithecus afarensis was able to roam the countryside and leave the forest to forage for food when necessary. With its strong jaws, Australopithecus also could eat several types of food, including fruit, seeds, nuts and roots. Combining their strong jaws and their new skill of walking, Lucy and her relatives were able to live in open areas as well as wooded ones. Australopithecus was a new kind of hominin, fundamentally different from earlier species like Ardipithecus ramidus, which preceded Lucy and was not committed to walking upright on the ground. Instead, Ardipithecus ramidus moved on all four feet or upright depending on the situation, and had powerful grasping feet. "Arches in the feet are a key component of human-like walking because they absorb shock and also provide a stiff platform so that we can push off from our feet and move forward," Ward said. "People today with 'flat feet' who lack arches have a host of joint problems throughout their skeletons. Understanding that the arch appeared very early in our evolution shows that the unique structure of our feet is fundamental to human locomotion. If we can understand what we were designed to do and the natural selection that shaped the human skeleton, we can gain insight into how our skeletons work today. Arches in our feet were just as important for our ancestors as they are for us." "This fourth metatarsal is the only one known of A. afarensis and is a key piece of evidence for the early evolution of the uniquely human way of walking," Kimbel said. "The ongoing work at Hadar is producing rare parts of the skeleton that are absolutely critical for understanding how our species evolved."

Death in the bat caves: UC Davis experts call for action against fast-moving disease

Thu, 03 Feb 2011 03:25:03 PDT

A team of wildlife experts led by UC Davis called today for a national fight against a new fungus that has killed more than 1 million bats in the eastern United States and is spreading fast throughout North America. "If we lose bats, we lose keystone species in some communities, predators that consume enormous numbers of insects, and beautiful wildlife species that are important parts of North America's biodiversity," said Janet Foley, a UC Davis professor of veterinary medicine at the Center for Vectorborne Diseases. Foley and her co-authors' call to action appears today online in the Early View section of the journal Conservation Biology. Bats are essential members of natural ecosystems, hunting insects, pollinating plants and scattering seeds, Foley said. "Bats do the jobs at night that birds do during the day. But because they are most active in darkness, few people are aware of how many bats live around us and how valuable they are." The new fungal disease has been named "white-nose syndrome." Scientists think the fungus, which normally lives in soil, somehow traveled to cave walls where bats hibernate in winter and began infecting the animals' facial skin and wing membranes. Sick bats appear to be coated with frost. They fly more than normal, which uses up fat reserves, and also lose water at a faster rate than normal. Disoriented, they move to exposed places, such as cave entrances. Eventually, they starve, freeze or die of dehydration. The first infected bats were found by a cave explorer near Albany, N.Y., in February 2006. Since then, infected bats have been found northward to Ontario and Quebec in Canada, south to Tennessee and west to Oklahoma. The authors write that they expect white-nose syndrome to cross the Rocky Mountains and enter California in the next several years. There are 23 species of bats in California that hibernate in caves, and so are vulnerable to white-nose syndrome. Foley said the fungus does not appear to be a threat to people or animals other than bats. The National Wildlife Health Center, a program of the U.S. Geological Survey, identified the white-nose fungus, Geomyces destructans, in 2007. "In the three years since its discovery, white-nose syndrome has changed the focus of bat conservation in North America," said Foley. "A national response is required, and our epidemiological roadmap is designed to help emerging state and national plans to combat white-nose syndrome across the United States." Foley and her collaborators developed their recommendations at a workshop in Colorado in August funded by the National Park Service. The authors' recommendations include: an outbreak investigation network that would establish a standard diagnosis and case definitions; bat population monitoring; and improved public awareness of the problem. "Scientists, policy makers and members of the public will all have a voice in the coming debate over the best course of action," Foley said. They also call for further studies of chemical and biological agents known to kill the fungus but not yet proven safe for bats, as well as study of treatments for similar diseases.

Newly discovered dinosaur likely father of Triceratops

Tue, 01 Feb 2011 03:19:22 PDT

Triceratops and Torosaurus have long been considered the kings of the horned dinosaurs. But a new discovery traces the giants' family tree further back in time, when a newly discovered species appears to have reigned long before its more well-known descendants, making it the earliest known member of its family. The new species, called Titanoceratops after the Greek myth of the Titans, rivaled Triceratops in size, with an estimated weight of nearly 15,000 pounds and a massive eight-foot-long skull. Titanoceratops, which lived in the American southwest during the late Cretaceous period around 74 million years ago, is the earliest known triceratopsin, suggesting the group evolved its large size more than five million years earlier than previously thought, according to Nicholas Longrich, the paleontologist at Yale who made the discovery.......> Full story

Gene 'relocation' key to most evolutionary change in bacteria

Fri, 28 Jan 2011 03:29:08 PDT

In a new study, scientists at the University of Maryland and the Institut Pasteur show that bacteria evolve new abilities, such as antibiotic resistance, predominantly by acquiring genes from other bacteria. The researchers new insights into the evolution of bacteria partly contradict the widely accepted theory that new biological functions in bacteria and other microbes arise primarily through the process of gene duplication within the same organism. Their just released study will be published in the open-access journal PLoS Genetics on January 27. Microbes live and thrive in incredibly diverse and harsh conditions, from boiling or freezing water to the human immune system. This remarkable adaptability results from their ability to quickly modify their repertoire of protein functions by gaining, losing and modifying their genes. Microbes were known to modify genes to expand their repertoire of protein families in two ways: via duplication processes followed by slow functional specialization, in the same way as large multicellular organisms like us, and by acquiring different genes directly from other microbes. The latter process, known as horizontal gene transfer, is notoriously conspicuous in the spread of antibiotic resistance, turning some bacteria into drug-resistant 'superbugs' such as MRSA (methicillin-resistant Staphylococcus aureus), a serious public health concern. The researchers examined a large database of microbial genomes, including some of the most virulent human pathogens, to discover whether duplication or horizontal gene transfer was the most common expansion method. Their study shows that gene family expansion can indeed follow both routes, but unlike in large multicellular organisms, it predominantly takes place by horizontal transfer. First author Todd Treangen, a postdoctoral researcher in the University of Maryland Center for Bioinformatics and Computational Biology and co-author Eduardo P. C. Rocha of the Institut Pasteur conclude that because microbes invented the majority of life's biochemical diversity -- from respiration to photosynthesis --, "the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families."

Altered gene protects some African-Americans from coronary artery disease

Fri, 28 Jan 2011 03:21:22 PDT

A team of scientists at Johns Hopkins and elsewhere has discovered that a single alteration in the genetic code of about a fourth of African-Americans helps protect them from coronary artery disease, the leading cause of death in Americans of all races. Researchers found that a single DNA variation - having at least one so-called guanine nucleotide in a base pair instead of a combination without any guanine - on a gene already linked to higher risk of coronary disease in other races is linked in blacks to decreased risk. Specifically, the study showed that otherwise healthy African-American men and women with the alternative genetic code had a fivefold reduction in the likelihood that their arteries would narrow or clog. For African-Americans who inherited two copies of the guanine gene variant, one from each parent, the risk reduction was even more dramatic. They were 10 times less likely to have coronary heart disease, which disproportionately afflicts a greater number of African-Americans than whites or any other ethnic group. Nearly 17 million Americans have an arterial problem plaguing the heart, causing a half-million deaths, annually. "What we think we have here is the first confirmed hereditary link to cardiovascular disease among African-Americans and it is a protective one," says senior study investigator and health epidemiologist Diane Becker, M.P.H., Sc.D. "This newly found link in African-Americans was not only protective instead of harmful but was also found at a precise location on gene CDKN2B, a gene close to the single base pair modification tied to other increased risk of coronary artery disease in other races." Becker emphasizes that only an estimated quarter of blacks have the protective CDKN2B code, and only 6 percent have two copies, so "while a lot of African-Americans have this protective genetic modification, most do not." Advance testing for the genetic marker, she says, could ultimately in the future assist physicians in risk-stratifying those without inherited protection so they could be monitored more closely for early signs and symptoms of disease. The findings are set to appear in the Journal of Human Genetics online Jan. 27. Becker, a professor at both the Johns Hopkins University School of Medicine and Hopkins' Bloomberg School of Public Health, and a team that included researchers at Duke and Emory universities, also say their results, based on blood analysis from 548 black men and women in the Baltimore region and confirmed in several hundred more in the Atlanta and Durham, N.C., regions, help explain why earlier studies found potentially dangerous genetic connections to this type of heart disease in Caucasians, Hispanics and Asians, but failed to find a negative tie-in to the disease in blacks. Earlier studies, says Becker, had involved genome-wide reviews in multiracial populations and taken "a needle in the haystack approach" to finding that one change in a string of some 58,000 base pairs, in a chromosomal region known as 9p21. That region, which includes CDKN2B, is associated with higher rates of coronary disease in non-blacks. The team's latest analysis was successful, she believes, because it had a large and sufficiently broadly based black volunteer population. The study group comprised men and women between the ages of 26 and 60. Investigators also focused on the 9p21 region and a subsection of genetic material within called ANRIL that overlaps and is closely held to CDKN2B, but away from the deleterious genetic variant found earlier. Johns Hopkins cardiologist Brian Kral, M.D., M.P.H., says the abundance of activity in this particular region of the genome, including CDK2NB and ANRIL, suggests that everyday replication of this zone could play a more fundamental, underlying role in the progression of coronary artery disease in all races. Kral, an assistant professor at Johns Hopkins and its Heart and Vascular Institute. was co-lead investigator of the latest study, along with Hopkins genetic epidemiologist Rasika Mathias, Sc.D. The team next plans to further investigate the ANRIL subregion of 9p21 to see if any single genetic changes speed up or slow down progression of coronary diseases. Blood samples for the genetic analysis came from a larger study being led by Becker of some 4,000 people from white and African-American ethnic backgrounds. Called the Genetic Study of Atherosclerosis Risk (GeneSTAR), under way at Johns Hopkins since 1983, it involves participants who were all healthy upon enrollment, with no existing symptoms of heart disease. All were monitored for at least five years with periodic check-ups to see who developed heart disease and who did not. Each had a sibling or a parent who had a history of coronary artery disease or some other symptom of blocked arteries, such as chest pain or shortness of breath. The latest study was based on results collected through 2007, by which time 35 black study participants had suffered some form of heart attack or needed an angioplasty or X-ray scan of the heart's blood vessels to confirm or rule out arterial blockages.

Test shows dinosaurs survived mass extinction by 700,000 years

Fri, 28 Jan 2011 03:19:48 PDT

University of Alberta researchers determined that a fossilized dinosaur bone found in New Mexico confounds the long established paradigm that the age of dinosaurs ended between 65.5 and 66 million years ago. The U of A team, led by Larry Heaman from the Department of Earth and Atmospheric Sciences, determined the femur bone of a hadrosaur as being only 64.8 million years old. That means this particular plant eater was alive about 700,000 years after the mass extinction event many paleontologists believe wiped all non-avian dinosaurs off the face of earth, forever. Heaman and colleagues used a new direct-dating method called U-Pb (uranium-lead) dating. A laser beam unseats minute particles of the fossil, which then undergo isotopic analysis. This new technique not only allows the age of fossil bone to be determined but potentially can distinguish the type of food a dinosaur eats. Living bone contains very low levels of uranium but during fossilization (typically less than 1000 years after death) bone is enriched in elements like uranium. The uranium atoms in bone decay spontaneously to lead over time and once fossilization is complete the uranium-lead clock starts ticking. The isotopic composition of lead determined in the hadrosaur's femur bone is therefore a measure of its absolute age. Currently, paleontologists date dinosaur fossils using a technique called relative chronology. Where possible, a fossil's age is estimated relative to the known depositional age of a layer of sediment in which it was found or constrained by the known depositional ages of layers above and below the fossil-bearing horizon. However, obtaining accurate depositional ages for sedimentary rocks is very difficult and as a consequence the depositional age of most fossil horizons is poorly constrained. A potential weakness for the relative chronology approach is that over millions of years geologic and environmental forces may cause erosion of a fossil-bearing horizon and therefore a fossil can drift or migrate from its original layer in the strata. The researchers say their direct-dating method precludes the reworking process. It's widely believed that a mass extinction of the dinosaurs happened between 65.5 and 66 million years ago. It's commonly believed debris from a giant meteorite impact blocked out the Sun, causing extreme climate conditions and killing vegetation worldwide. Heaman and his research colleagues say there could be several reasons why the New Mexico hadrosaur came from a line of dinosaurs that survived the great mass extinction events of the late Cretaceous period (KT extinction event). Heaman says it's possible that in some areas the vegetation wasn't wiped out and a number of the hadrosaur species survived. The researchers also say the potential survival of dinosaur eggs during extreme climatic conditions needs to be explored. Heaman and his colleagues believe if their new uranium-lead dating technique bears out on more fossil samples then the KT extinction paradigm and the end of the dinosaurs will have to be revised.

Ancient body clock discovered that helps to keep all living things on time

Thu, 27 Jan 2011 03:23:27 PDT

The mechanism that controls the internal 24-hour clock of all forms of life from human cells to algae has been identified by scientists. Not only does the research provide important insight into health-related problems linked to individuals with disrupted clocks – such as pilots and shift workers – it also indicates that the 24-hour circadian clock found in human cells is the same as that found in algae and dates back millions of years to early life on Earth. Two new studies out today in the journal Nature from the Universities of Cambridge and Edinburgh give insight into the circadian clock which controls patterns of daily and seasonal activity, from sleep cycles to butterfly migrations to flower opening. One study, from the University of Cambridge's Institute of Metabolic Science, has for the first time identified 24-hour rhythms in red blood cells. This is significant because circadian rhythms have always been assumed to be linked to DNA and gene activity, but – unlike most of the other cells in the body – red blood cells do not have DNA. Akhilesh Reddy, from the University of Cambridge and lead author of the study, said: "We know that clocks exist in all our cells; they're hard-wired into the cell. Imagine what we'd be like without a clock to guide us through our days. The cell would be in the same position if it didn't have a clock to coordinate its daily activities. "The implications of this for health are manifold. We already know that disrupted clocks – for example, caused by shift-work and jet-lag – are associated with metabolic disorders such as diabetes, mental health problems and even cancer. By furthering our knowledge of how the 24-hour clock in cells works, we hope that the links to these disorders – and others – will be made clearer. This will, in the longer term, lead to new therapies that we couldn't even have thought about a couple of years ago." For the study, the scientists, funded by the Wellcome Trust, incubated purified red blood cells from healthy volunteers in the dark and at body temperature, and sampled them at regular intervals for several days. They then examined the levels of biochemical markers – proteins called peroxiredoxins – that are produced in high levels in blood and found that they underwent a 24-hour cycle. Peroxiredoxins are found in virtually all known organisms. A further study, by scientists working together at the Universities of Edinburgh and Cambridge, and the Observatoire Oceanologique in Banyuls, France, found a similar 24-hour cycle in marine algae, indicating that internal body clocks have always been important, even for ancient forms of life. The researchers in this study found the rhythms by sampling the peroxiredoxins in algae at regular intervals over several days. When the algae were kept in darkness, their DNA was no longer active, but the algae kept their circadian clocks ticking without active genes. Scientists had thought that the circadian clock was driven by gene activity, but both the algae and the red blood cells kept time without it. Andrew Millar of the University of Edinburgh's School of Biological Sciences, who led the study, said: "This groundbreaking research shows that body clocks are ancient mechanisms that have stayed with us through a billion years of evolution. They must be far more important and sophisticated than we previously realised. More work is needed to determine how and why these clocks developed in people – and most likely all other living things on earth – and what role they play in controlling our bodies."

With cloud computing, the mathematics of evolution may get easier to learn

Sun, 23 Jan 2011 04:56:40 PDT

An innovative, educational computing platform developed by University at Buffalo faculty members and hosted by the cloud (remote, high-capacity, scalable servers) is helping UB students understand parts of evolutionary biology on an entirely new level. Soon, high-school and middle-school students will benefit from the same tool as well. Pop! World, developed by UB faculty members with a $250,000 National Science Foundation grant, takes advantage of cloud computing, which allows programs to run on remote servers instead of through departmental or institutional servers. That feature allows resource-intensive programs to serve many users regardless of their physical location without sacrificing speed or quality of service. "The cloud serves as a way to distribute resources for free without limits on how many people can access it and with no regard to what kind of computer you are downloading to," says Jessica Poulin, PhD, research assistant professor in the Department of Biological Sciences in the College of Arts and Sciences, who developed Pop! World with principal investigator Bina Ramamurthy, PhD, research associate professor in the Department of Computer Science and Engineering in the School of Engineering and Applied Sciences, and Katharina Dittmar, PhD, assistant professor of biological sciences. "Everybody can get there." UB faculty members designed Pop! World because they wanted to get college students more excited about population genetics; they also wanted to maintain the university's unique freshman lab requirements at a time when resources are growing more scarce. UB is one of the few universities in the U.S. that encourages freshmen interested in biology to begin experiencing labs during their first semester on campus. "We put our freshmen right into labs because students who might otherwise be lost from the major are captivated when they get to do science," Poulin says. "When you sit in a lecture hall with 400 people and someone is talking about flatworms, what do you care? Despite the logistical difficulties, and the intense demands on staff time, we think that getting freshmen into labs is one of our department's great strengths. We didn't want to discontinue it." At the same time, Poulin says that it is difficult to convey the main concepts of population genetics at this level, particularly those that are mathematically demanding. Hired in 2008 to revamp UB's evolutionary biology curriculum for Bio 200, Poulin says that the department was seeking ways to maintain and improve the course and the lab for students without requiring additional resources, such as teaching assistants. "Almost all of evolutionary theory can be mathematically modeled if you know enough information to begin with," she says. "If you enter the correct parameters into the computer, the computer will tell you what will happen after one generation or a thousand generations. I wanted students to be exposed to something that made them feel they were actually watching evolution happen. I wanted it to be captivating." While some computational tools exist to help students with population genetics -- the mathematical analysis of evolution -- the result is often nothing more dramatic than a line graph. "Our students grew up in the Internet age surrounded by MP3 players, wireless phones and social networking apps," says Ramamurthy, "so the visual aspects of Pop! World are certainly very appealing to them." The UB team programmed Pop! World in Adobe Flash, which lends a highly visual, nearly tactile look to the program. While the current version illustrates evolution with red and green lizards, it is highly adaptable, so it can be used with any population of organisms. It also is highly scalable, so that it can be made more complex, to serve the needs of population genetics researchers, or less complex, to serve the needs of middle- and high-school students. A preliminary version of Pop! World is running on the Google App Engine Cloud. It can be accessed by going to http://popworld15.appspot.com/. With the help of the NSF grant, the UB team is now creating a sophisticated version of the tool, expected to be available by Fall 2011. "Our idea was to use general principles of population genetics not only to convey the principle in the context of evolutionary biology but to make sure that students understand visually what's happening with the mathematics behind it," explains Dittmar. When an early version of Pop! World was used to teach evolutionary biology last summer, students and teaching assistants responded enthusiastically. "The TAs loved it because it facilitated their explanations of a very complicated problem," Poulin says. "Pop! World gives students the visual background they need to understand complex mathematical problems," Dittmar adds. "And it works kind of like a video game, which serves the current population of undergrads well." That visual appeal is also expected to go far with middle-school and high-school biology students, groups the UB team hopes to excite about evolution; by spring, they expect to have completed a modified version for them as well. By making evolutionary biology more visually appealing and, thus, more accessible, Poulin hopes that Pop! World will make evolution itself a more appealing subject for secondary schools to teach. "There's a huge disconnect," she says. "The universities all accept evolution as fact. It's not a question. But many high schools and middle schools don't want to touch it. They don't want to deal with the politics of it." Her hope is that the visual and educational appeal of Pop! World and the ease of using it will begin to change that situation. The UB team's grant, "A Cloud-enabled Evolutionary Genetics Learning Tool for Engaging the Cyber-savvy Generation" (NSF OCI CI-Team 1041280) from the NSF's Office of Cyberinfrastructure, will run for two years.

Inventions of evolution: What gives frogs a face

Fri, 14 Jan 2011 03:33:21 PDT

“Don't be a frog!“ people say in jest when someone hesitates instead of acting straight away. However to be called a frog should actually be a reason to strengthen one's self-confidence. After all frogs are real winners – at least from the point of view of evolutionary biology: Nearly 6.000 species are known today. “In terms of numbers frogs are superior to all the other amphibians, and even mammals“, says Professor Dr. Lennart Olsson from the Friedrich Schiller University Jena (Germany). Professor Olsson's research group for Systematic Zoology examines these animals’s special secret of success. “We are interested in how the frogs developed in such a great variety and which evolutionary new development is responsible for making frogs so particularly successful“, Jennifer Schmidt from Olsson's team explains........> Full story

Punctuated evolution in cancer genomes

Fri, 07 Jan 2011 03:26:16 PDT

Remarkable new research overthrows the conventional view that cancer always develops in a steady, stepwise progression. It shows that in some cancers, the genome can be shattered into hundreds of fragments in a single cellular catastrophe, wreaking mutation on a massive scale. The scars of this chromosomal crisis are seen in cases from across all the common cancer types, accounting for at least one in forty of all cancers. The phenomenon is particularly common in bone cancers, where the distinctively ravaged genome is seen in up to one in four cases. The team looked at structural changes in the genomes of cancer samples using advanced DNA sequencing technologies. In some cases, they found dramatic structural changes affecting highly localised regions of one or a handful of chromosomes that could not be explained using standard models of DNA damage. "The results astounded us," says Dr Peter Campbell, from the Cancer Genome Project at the Wellcome Trust Sanger Institute and senior author on the paper. "It seems that in a single cell in a single event, one or more chromosomes basically explode – literally into hundreds of fragments. "In some instances – the cancer cases – our DNA repair machinery tries to stick the chromosomes back together but gets it disastrously wrong. Out of the hundreds of mutations that result, several promote the development of cancer." Cancer is typically viewed as a gradual evolution, taking years to accumulate the multiple mutations required to drive the cancer's aggressive growth. Many cancers go through phases of abnormal tissue growth before eventually developing into malignant tumours. The new results add an important new insight, a new process that must be included in our consideration of cancer genome biology. In some cancers, a chromosomal crisis can generate multiple cancer-causing mutations in a single event. "We suspect catastrophes such as this might happen occasionally in the cells of our body," says Dr Andy Futreal, Head of Cancer Genetics and Genomics at the Wellcome Trust Sanger Institute and an author on the paper. "The cells have to make a decision – to repair or to give up the ghost. "Most often, the cell gives up, but sometimes the repair machinery sticks bits of genome back together as best it can. This produces a fractured genome riddled with mutations which may well have taken a considerable leap along the road to cancer." The new genome explosions caused 239 rearrangements on a single chromosome in one case of colorectal cancer. The damage was particularly common in bone cancers, where it affected five of twenty samples. In one of these samples the team found three cancer genes that they believe were mutated in a single event: all three are genes that normally suppress cancer development and when deleted or mutated can lead to increased cancer development. "The evidence suggests that a single cellular crisis shatters a chromosome or chromosomes," says Professor Mike Stratton, Director of the Wellcome Trust Sanger Institute and an author on the paper, "and that the DNA repair machinery pastes them back together in a highly erroneous order. "It is remarkable that, not only can a cell survive this crisis, it can emerge with a genomic landscape that confers a selective advantage on the clone, promoting evolution towards cancer." The team propose two possible causes of the damage they see. First, they suggest it might occur during cell division, when chromosomes are packed into a condensed form. Ionizing radiation can cause breaks like those seen. The second proposition is that attrition of telomeres – the specialized genome sequences at the tips of chromosomes – causes genome instability at cell division.

What triggers mass extinctions? Study shows how invasive species stop new life

Sat, 01 Jan 2011 03:16:55 PDT

An influx of invasive species can stop the dominant natural process of new species formation and trigger mass extinction events, according to research results published today in the journal PLoS ONE. The study of the collapse of Earth's marine life 378 to 375 million years ago suggests that the planet's current ecosystems, which are struggling with biodiversity loss, could meet a similar fate. Although Earth has experienced five major mass extinction events, the environmental crash during the Late Devonian was unlike any other in the planet's history. The actual number of extinctions wasn't higher than the natural rate of species loss, but very few new species arose. "We refer to the Late Devonian as a mass extinction, but it was actually a biodiversity crisis," said Alycia Stigall, a scientist at Ohio University and author of the PLoS ONE paper........>Full story

SU scientists find that in the evolutionary mating game, brawn and stealth rule

Fri, 24 Dec 2010 07:12:17 PDT

When prowling for a hook up, it's not always the good-looker who gets the girl. In fact, in a certain species of South American fish, brawn and stealth beat out colorful and refined almost every time. In a series of published studies of a South American species of fish (Poecilia parae), which are closely related to guppies, Syracuse University scientists have discovered how the interplay between male mating strategies and predator behavior has helped preserve the population's distinctive color diversity over the course of time. The third study in the series was published Dec. 23 in BMC Evolutionary Biology, a publication of BioMed Central, London. The studies were supported in part by grants from the National Science Foundation (NSF). "Poecilia parae are an ideal model for investigating how genetic diversity originates and is maintained within a species," says study author Jorge Luis Hurtado-Gonzales, a Ph.D. candidate in the Department of Biology in SU's College of Arts and Sciences. "The findings may help us better understand how to protect biodiversity in larger ecosystems." Hurtado-Gonzales' co-author is J. Albert C. Uy of the University of Miami. Like guppies, Poecilia parae sexually reproduce and their offspring are born live. Unlike guppies, in which no two males have exactly the same color patterns, Poecilia parae males come in five, genetically determined colors—red, yellow, blue, parae (clear with a black stripe), and immaculata (drab gray that mimics the color of immature females). When found in the wild, the abundance of each color group represented in the total population is relatively constant despite the fact that females prefer to mate with the more striking reds and yellows. "If females prefer red and yellow males, then one would think that red and yellow would dominate and the other colors would phase out over time," Hurtado-Gonzales says. "However, red and yellow are the rarest colors found in the wild." The most recent study in BMC Evolutionary Biology found that while females prefer reds and yellows they go for the winner of fin-to-fin combat in a significant number of cases. In the study, the larger parae almost always prevailed, thus gaining a mating advantage despite its less-than-desirable coloration. Immaculatas, which are the smallest males, generally shunned the showy displays of violence and were mostly ignored by all but yellow males. The larger yellows almost always defeated immaculatas, stopping them from approaching females. "In the absence of male-to-male competition, we found that females will almost always choose a red male," Hurtado-Gonzales says. "However, if the red loses a fight, the female will generally seek out the winner. In most cases, that is the larger parae, which is the most dominant male." Immaculatas compensate for their lack of physical prowess and attractiveness through a mating strategy that relies on stealth. In a 2009 study published in the journal Animal Behavior, Hurtado-Gonzales found that the immaculatas' drab color provides camouflage that enables them to stealthy mate with females while the more colorful red males were wooing them. Females are promiscuous and will mate with multiple males. Additionally, immaculatas have developed larger testes, which produce more sperm, providing a post-mating advantage in the race to fertilize female eggs. Finally, in a study published earlier this year in the Journal of Evolutionary Biology, produced by the European Society for Evolutionary Biology, Hurtado-Gonzales found that a common predator of Poecilia parae prefers to dine on reds and yellows, most likely because their striking colors make them easier to see. This predatory disadvantage contributes to the lower numbers of reds and yellows in the overall population. "It seems that within an evolutionary scale, the less attractive males persist in the population over their more attractive counterparts by evolving unique, but likely equally effective mating strategies," Hurtado-Gonzales says. "Therefore, the maintenance of multiple colors may result from the interaction between predator control of attractive males (reds and yellows) and the ability of less attractive males to exploit other areas of sexual selection, including male dominance, sneak behavior, and sperm competition." A forthcoming study will focus on how blue males gain a mating advantage. Early results indicate that blues exploit habitats in which blue light waves maximize their attractiveness to females and possibly limit their vulnerability to predators.

Genome of extinct Siberian human sheds new light on modern human origins

Thu, 23 Dec 2010 03:26:33 PDT

The sequencing of the nuclear genome from an ancient finger bone found in a Siberian cave shows that the cave dwellers were neither Neandertals nor modern humans. An international team of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany) has sequenced the nuclear genome from a finger bone of an extinct hominin that is at least 30,000 years old and was excavated by archaeologists from the Russian Academy of Sciences in Denisova Cave in southern Siberia, Russia, in 2008. A team at Harvard Medical School led the population-genetics analysis. These findings are published in the December 23 issue of Nature. Earlier this year Svante Pääbo and his colleagues showed that the mitochondrial DNA from the finger bone displayed an unusual sequence suggesting that it came from an unknown ancient hominin form. Now, using techniques the researchers developed to sequence the Neandertal genome earlier this year, they have sequenced the nuclear genome from the bone. The researchers found that the individual was female and came from a group of hominins that shared an ancient origin with Neandertals, but subsequently diverged. They call this group of hominins Denisovans. Unlike Neandertals, Denisovans did not contribute genes to all present-day Eurasians. However, Denisovans share an elevated number of genetic variants with modern-day Papua New Guinean populations, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians. In addition, a Denisovan tooth found in the same cave shows a morphology that is distinct from Neandertals and modern humans and resembles much older hominin forms. Bence Viola, a scientist at the Max Planck Institute of Evolutionary Anthropology comments, "The tooth is just amazing. It allows us to connect the morphological and genetic information." David Reich, an associate professor at Harvard Medical School who led the population genetic analysis, says, "The fact that Denisovans were discovered in Southern Siberia but contributed genetic material to modern human populations from New Guinea suggests that Denisovans may have been widespread in Asia during the Late Pleistocene." According to Svante Pääbo of the Max Planck Institute of Evolutionary Anthropology, "In combination with the Neandertal genome sequence, the Denisovan genome suggests a complex picture of genetic interactions between our ancestors and different ancient hominin groups."

Without intervention, Mariana crow to become extinct in 75 years

Tue, 21 Dec 2010 03:32:07 PDT

Researchers from the University of Washington say the Mariana crow, a forest crow living on Rota Island in the western Pacific Ocean, will go extinct in 75 years. The extinction could happen almost twice as soon as previously believed. The crow's extinction can be prevented with a bird management program that focuses on helping fledgling birds reach their first birthday, said James Ha, UW research associate professor in psychology. Ha examined survival rates in 97 Mariana crows – Corvus kubaryi – that had been tracked between 1990 and 2010 by researchers. He found that 40 percent of fledgling crows made it to their first birthday. The rapid decline of young birds is twice what researchers previously estimated. "It's the first year of survival that's the most crucial," said Ha, lead author of a report on the research. "If only 40 percent of fledglings survive their first year, then we predict the species will go extinct in 75 years." Ha and his co-authors published the report in the current issue of Bird Conservation International. The 75-year extinction estimate is according to a population model that factors in the estimated number of existing Mariana crows – 330 – with the 40 percent first-year survival rate, average number of fledglings per nest and fertility of female birds. Using this model, Ha found that 91 birds would exist in 20 years and that in 75 years the species would be extinct. Previously, biologists believed that the first-year survival rate of Mariana crows was higher, around 60 to 80 percent. When Ha used those estimates in his population model, the outlook was not as grim for the birds. At 60 percent first-year survival rate, Mariana crows would dwindle to 218 birds in 20 years and become extinct in 133 years. And an 80 percent first-year survival rate projects that in 20 years there would be 453 birds, a growing population that would avoid extinction. "According to the population model, if we can boost fledgling survival from 40 percent to 70 percent, the Mariana crows will be fine," Ha said. Of the about 35 crow species, Mariana crows are considered rare and classified as critically endangered. Weighing about a half of a pound, Mariana crows are 40 percent smaller than other crows, such as the Northwest crow. Monogamously-mating, Mariana crows live exclusively on Rota Island, populated by about 1,200 people and located 56 miles northeast of Guam. Rota is a U.S. territory and is up for consideration as a U.S. national park. Ha and Renee Ha, co-author of the report and UW research scientist in psychology, fear that Rota faces the same avian demise as Guam, which has no forest birds. Brown tree snakes introduced to the island after World War II wiped out native birds, such as the Guam flycatcher and the Rufous fantail. The Has suspect that the uncontrolled increase of feral cats on Rota is leading to the decrease of Mariana crows, much like brown tree snakes led to the disappearance of forest birds on Guam. The researchers say that a captive rearing program could save the Mariana crows. They hope to set up a rearing facility where they could incubate eggs from the wild, raise the fledglings until their first birthday and then release the grown birds into nesting sites on the island.

Research shows that environmental factors limit species diversity

Tue, 21 Dec 2010 03:21:36 PDT

It's long been accepted by biologists that environmental factors cause the diversity—or number—of species to increase before eventually leveling off. Some recent work, however, has suggested that species diversity continues instead of entering into a state of equilibrium. But new research on lizards in the Caribbean not only supports the original theory that finite space, limited food supplies, and competition for resources all work together to achieve equilibrium; it builds on the theory by extending it over a much longer timespan. The research was done by Daniel Rabosky of the University of California, Berkeley and Richard Glor of the University of Rochester who studied patterns of species accumulation of lizards over millions of years on the four Caribbean islands of Puerto Rico, Jamaica, Hispaniola, and Cuba. Their paper is being published December 21 in the journal, Proceedings of the National Academy of Sciences. Glor and Rabosky focused on species diversity—the number of distinct species of lizards—not the number of individual lizards. "Geographic size correlates to diversity," said Glor. "In general, the larger the area, the greater the number of species that can be supported. For example, there are 60 species of Anolis lizards on Cuba, but far fewer species on the much smaller islands of Jamaica and Puerto Rico." There are only 6 species on Jamaica and 10 on Puerto Rico. Ecologists Robert MacArthur of Princeton University and E.O. Wilson of Harvard University established the theory of island biogeography in the 1960s to explain the diversity and richness of species in restricted habitats, as well as the limits on the growth in number of species. Glor said the MacArthur-Wilson theory was developed for ecological time-scales, which encompass thousands of years, while his work with Rabosky extends the concepts over a million years. "MacArthur and Wilson recognized the macroevolutionary implications of their work," explained Glor, "but focused on ecological time-scales for simplicity." Historically, biologists needed fossil records to study patterns of species diversification of lizards on the Caribbean islands. But advances in molecular methodology allowed Glor and Rabosky to use DNA sequences to reconstruct evolutionary trees that show the relationships between species. The two scientists found that species diversification of lizards on the four islands reached a plateau millions of years ago and has essentially come to an end. Glor said the extent and quality of the data used in the research allowed him and Rabosky to show that species diversification of lizards on the islands was not continuing and had indeed entered a state of equilibrium. "When we look at other islands and continents that vary in species richness," said Glor, "we can't just consider rates of accumulation; we need to look at the plateau points." Glor emphasizes that a state of equilibrium does not mean that the evolution of a species comes to an end. Lizards will continue to adapt to changes in their environment, but they are not expected to develop in a way that increases the number of species within a habitat. Glor believes his work with Rabosky represents the "final word" on the importance of limits on species diversity over the rate of speciation when explaining the species-area relationship in anole lizards.

Scientists decipher 3 billion-year-old genomic fossils

Mon, 20 Dec 2010 03:31:36 PDT

About 580 million years ago, life on Earth began a rapid period of change called the Cambrian Explosion, a period defined by the birth of new life forms over many millions of years that ultimately helped bring about the modern diversity of animals. Fossils help palaeontologists chronicle the evolution of life since then, but drawing a picture of life during the 3 billion years that preceded the Cambrian Period is challenging, because the soft-bodied Precambrian cells rarely left fossil imprints. However, those early life forms did leave behind one abundant microscopic fossil: DNA. Because all living organisms inherit their genomes from ancestral genomes, computational biologists at MIT reasoned that they could use modern-day genomes to reconstruct the evolution of ancient microbes. They combined information from the ever-growing genome library with their own mathematical model that takes into account the ways that genes evolve: new gene families can be born and inherited; genes can be swapped or horizontally transferred between organisms; genes can be duplicated in the same genome; and genes can be lost. The scientists traced thousands of genes from 100 modern genomes back to those genes' first appearance on Earth to create a genomic fossil telling not only when genes came into being but also which ancient microbes possessed those genes. The work suggests that the collective genome of all life underwent an expansion between 3.3 and 2.8 billion years ago, during which time 27 percent of all presently existing gene families came into being. Eric Alm, a professor in the Department of Civil and Environmental Engineering and the Department of Biological Engineering, and Lawrence David, who recently received his Ph.D. from MIT and is now a Junior Fellow in the Harvard Society of Fellows, have named this period the Archean Expansion. Because so many of the new genes they identified are related to oxygen, Alm and David first thought that the emergence of oxygen might be responsible for the Archean Expansion. Oxygen did not exist in the Earth's atmosphere until about 2.5 billion years ago when it began to accumulate, likely killing off vast numbers of anerobic life forms in the Great Oxidation Event. "The Great Oxidation Event was probably the most catastrophic event in the history of cellular life, but we don't have any biological record of it," says Alm. Closer inspection, however, showed that oxygen-utilizing genes didn't appear until the tail end of the Archean Expansion 2.8 billion years ago, which is more consistent with the date geochemists assign to the Great Oxidation Event. Instead, Alm and David believe they've detected the birth of modern electron transport, the biochemical process responsible for shuttling electrons within cellular membranes. Electron transport is used to breathe oxygen and by plants and some microbes during photosynthesis when they harvest energy directly from the sun. A form of photosynthesis called oxygenic photosynthesis is believed to be responsible for generating the oxygen associated with the Great Oxidation Event, and is responsible for the oxygen we breathe today. The evolution of electron transport during the Archean Expansion would have enabled several key stages in the history of life, including photosynthesis and respiration, both of which could lead to much larger amounts of energy being harvested and stored in the biosphere. "Our results can't say if the development of electron transport directly caused the Archean Expansion," says David. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems." David and Alm also went on to investigate how microbial genomes evolved after the Archean Expansion by looking at the metals and molecules associated with the genes and how those changed in abundance over time. They found an increasing percentage of genes using oxygen, and enzymes associated with copper and molybdenum, which is consistent with the geological record of evolution. "What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of living organisms," says Alm. "And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail."

What 'pine' cones reveal about the evolution of flowers

Wed, 15 Dec 2010 03:21:02 PDT

From southern Africa's pineapple lily to Western Australia's swamp bottlebrush, flowering plants are everywhere. Also called angiosperms, they make up 90 percent of all land-based, plant life. New research published this week in the Proceedings of the National Academy of Sciences provides new insights into their genetic origin, an evolutionary innovation that quickly gave rise to many diverse flowering plants more than 130 million years ago. Moreover, a flower with genetic programming similar to a water lily may have started it all. "Water lilies and avocado flowers are essentially 'genetic fossils' still carrying genetic instructions that would have allowed the transformation of gymnosperm cones into flowers," said biologist Doug Soltis, co-lead researcher at the University of Florida in Gainesville.......> Full story

Loss of species large and small threatens human health

Thu, 02 Dec 2010 03:22:37 PDT

The loss of biodiversity—from beneficial bacteria to charismatic mammals—threatens human health. That's the conclusion of a study published this week in the journal Nature by scientists who study biodiversity and infectious diseases. The work reveals a critical connection between conservation and disease. Species losses in ecosystems such as forests and fields result in increases in pathogens—disease-causing organisms—the researchers found. The animals, plants, and microbes most likely to disappear as biodiversity is lost are often those that buffer infectious disease transmission. Those that remain tend to be species that magnify the transmission of infectious diseases like West Nile virus, Lyme disease, and hantavirus. "We knew of specific cases in which declines in biodiversity increase the incidence of disease," says Felicia Keesing, an ecologist at Bard College in Annandale, N.Y., and first author of the paper. "But we've learned that the pattern is much more general: biodiversity loss tends to increase pathogen transmission across a wide range of infectious disease systems." The pattern holds true for various types of pathogens—viruses, bacteria, fungi—and for many types of hosts, whether humans, other animals, or plants. "When a clinical trial of a drug shows that it works," says Keesing, "the trial is halted so the drug can be made available. In a similar way, the protective effect of biodiversity is clear enough that we need to implement policies to preserve it now." In the case of Lyme disease, says co-author Richard Ostfeld of the Cary Institute of Ecosystem Studies in Millbrook, N.Y., "strongly buffering species like the opossum are lost when forests are fragmented, but white-footed mice thrive. The mice increase numbers of both the blacklegged tick vector and the pathogen that causes Lyme disease." Scientists don't yet know, Ostfeld says, why the most resilient species—"the last ones standing when biodiversity is lost"—are the ones that also amplify pathogens. Preserving natural habitats, the authors argue, is the best way to prevent this effect. Global biodiversity has declined at an unprecedented pace since the 1950s. Current extinction rates are estimated at 100 to 1,000 times higher than in past epochs, and are projected to increase at least a thousand times more in the next 50 years. Expanding human populations can increase contact with novel pathogens through activities such as land-clearing for agriculture and hunting for wildlife. Identifying the variables involved in infectious disease emergence is difficult but critical, says co-author Andrew Dobson of Princeton University. Biodiversity is an important factor, but so are land use changes and human population growth and behavior, he says. "When biological diversity declines and contact with humans increases, you have a perfect recipe for infectious disease outbreaks." The authors call for careful monitoring of areas in which large numbers of domesticated animals are raised or fish are farmed. "That would reduce the likelihood of an infectious disease jumping from wildlife to livestock, then to humans," says Keesing. For humans and other species to remain healthy, it will take more than a village—we need an entire planet, the scientists say, one with its diversity thriving.

Study: Ecological effects of biodiversity loss underestimated

Wed, 01 Dec 2010 03:19:42 PDT

Children aren't the only youngsters who are picky eaters: More than half of all species are believed to change their diets -- sometimes more than once -- between birth and adulthood. And a new study by ecologists at Rice University and the University of California, Santa Barbara, finds this pattern has major implications for the survival of threatened species and the stability of natural ecosystems. With thousands of species facing Earth's sixth major mass extinction, there is little doubt that the planet's biodiversity is in rapid decline. But many questions remain about how natural ecosystems will respond to the lost diversity. The new study, published online this week in Ecology Letters, challenges one of the standard assumptions that ecologists have used for decades to analyze the effects of biodiversity loss on ecosystems. That assumption -- that all food resources used by a species are interchangeable among all members of the species -- fails to account for the fact that diets change as young animals develop into adults, said Rice ecologist Volker Rudolf, one of the study's co-authors. The findings by Rudolf and co-author Kevin Lafferty suggest that changing dietary needs within species have important implications for ecosystem health. "If a species has three resources in an ecosystem, and we take away one, conventional wisdom suggests that that species should be fine," said Rudolf, assistant professor in ecology and evolutionary biology. "But if the missing resource is crucial for a particular developmental stage of the species, that just doesn't work. You can't take away all of the adults, for example, or all of the larvae, and assume that the species will persist." He said the new study was made possible by a wealth of information from recent datasets collected by Lafferty and colleagues at UC Santa Barbara. The datasets cover seven food webs --each representing the network of connections between dozens and, in some cases, hundreds of species in an ecosystem. Rudolf said Lafferty's food webs include data about specific resource requirements for particular developmental stages within species, in some instances for as many as 50 percent of the species in the ecosystem. "With this data, we were able to estimate the percentage of resources that are actually shared among developmental stages," Rudolf said. "In addition, we were able to show how this affects the stability of natural ecosystems. "We found that in most food webs, the individual stages of a species typically share less than 50 percent of their resources," he said. "And within certain subgroups, like metamorphic species, that number is sometimes less than 10 percent." The researchers used the information to formulate computer models that simulated how the loss of species affects natural ecosystems. One important implication of the finding is that natural ecosystems are much less stable than previously assumed, and many at-risk species may face an even greater likelihood of becoming extinct than ecologists previously thought. "Our results suggest that the increasing loss of biodiversity -- due to changing climate, habitat destruction and other causes -- will likely have much more devastating effects on natural communities and result in a greater number of species extinctions than previously believed," Rudolf said.

Ancient wind held secret of life and death

Tue, 30 Nov 2010 03:24:31 PDT

The mystery of how an abundance of fossils have been marvellously preserved for nearly half a billion years in a remote region of Africa has been solved by a team of geologists from the University of Leicester's Department of Geology. They have established that an ancient wind brought life to the region – and was then instrumental in the preservation of the dead. Sarah Gabbott, Jan Zalasiewicz and colleagues investigated a site near the Table Mountains in South Africa. Their findings are published in the latest issue of the journal Geology. Sarah Gabbott said: "Near Table Mountain in South Africa lies one of the world's most mysterious rock layers. Just a few metres thick, and almost half a billion years old, it contains the petrified remains of bizarre early life-forms, complete with eyes and guts and muscles. "We investigated why these animals are so marvellously preserved, when most fossils are just fragments of bone and shell? The answer seems to lie in a bitter wind, blowing off a landscape left devastated by a massive ice-cap." Gabbott and Zalasiewicz added that microscopic analysis of the shale layers using a specially designed 'Petroscope', obtained with funding from the Royal Society, revealed remarkable and so far unique structures – myriads of silt grains, neatly wrapped in the remains of marine algae. The authors state: "The silt grains are sedimentary aliens - much bigger than the marine mud flakes in which they are embedded. They could only have been blown by fierce glacial winds on to the sea surface from that distant landscape. Arriving thick and fast, they carried nutrients into the surface waters, fuelling its prolific life. The deep waters, though, were overwhelmed by rotting, sinking vegetation, becoming stagnant and lifeless – ideal conditions to preserve the animal remains, down to their finest details. A cold wind, here, was key to both life and death."

Size of mammals exploded after dinosaur extinction

Mon, 29 Nov 2010 03:17:43 PDT

Researchers demonstrate that the extinction of dinosaurs 65 million years ago made way for mammals to get bigger - about a thousand times bigger than they had been. The study, which is published in the prestigious journal Science, is the first to show this new pattern of increased body size of mammals after the exit of the dinosaurs. "Basically, the dinosaurs disappear and all of a sudden there is nobody else eating the vegetation. That's an open food source and mammals start going for it, and it's more efficient to be an herbivore when you're big," says paper co-author Dr. Jessica Theodor, associate professor in the Department of Biological Sciences at the University of Calgary. Theodor says as well as confirming the dramatic growth in mammalian size after the dinosaurs, the study shows that the ecosystem is able to reset itself relatively quickly. "You lose dinosaurs 65 million years ago, and within 25 million years the system is reset to a new maximum for the animals that are there in terms of body size. That's actually a pretty short time frame, geologically speaking," she says. "That's really rapid evolution." Theodor says mammals grew from a maximum of about 10 kilograms when they were sharing the earth with dinosaurs to a maximum of 17 tonnes afterwards. "Nobody has ever demonstrated that this pattern is really there. People have talked about it but nobody has ever gone back and done the math," says Theodor one of the 20 researchers from around the world who worked on the study. "We went through every time period and said OK, for this group of mammals what's the biggest one? And then we estimated its body mass." In order to document how big mammals grew after the 'competitive release' caused by the extinction of dinosaurs, researchers collected data on the maximum size for major groups of land mammals on each continent, including Perissodactyla, odd-toed ungulates such as horses and rhinos; Proboscidea, which includes elephants, mammoth and mastodon; Xenarthra, the anteaters, tree sloths, and armadillos; as well as a number of other extinct groups. The results give clues as to what sets the limits on mammal size on land; the amount of space available to each animal and the climate they live in. The colder the climate, the bigger the mammals seem to get, as bigger animals conserve heat better. It also shows that no one group of mammals dominates the largest size class – the absolute largest mammal belongs to different groups over time and space.

In fending off diseases, plants and animals are much the same, research shows

Fri, 19 Nov 2010 03:23:25 PDT

It may have been 1 billion years since plants and animals branched apart on the evolutionary tree but down through the ages they have developed strikingly similar mechanisms for detecting microbial invasions and resisting diseases. This revelation was arrived at over a period of 15 years by teams of researchers from seemingly disparate fields who have used classical genetic studies to unravel the mysteries of disease resistance in plants and animals, according to a historical overview that will appear in the Nov. 19 issue of the journal Science. The report, written by Pamela Ronald, a UC Davis plant pathologist, and Bruce Beutler, an immunologist and mammalian geneticist at The Scripps Research Institute, describes how researchers have used common approaches to tease apart the secrets of immunity in species ranging from fruit flies to rice. It also forecasts where future research will lead. "Increasingly, researchers will be intent on harnessing knowledge of host sensors to advance plant and animal health," said Ronald, who was a co-recipient of the 2008 U.S. Department of Agriculture's National Research Initiative Discovery Award for work on the genetic basis of flood tolerance in rice. "Some of the resistance mechanisms that researchers will discover will likely serve as new drug targets to control deadly bacteria for which there are currently no effective treatments," she said. At the heart of this research saga are receptors -- protein molecules usually found on cell membranes -- that recognize and bind to specific molecules on invading organisms, signaling the plant or animal in which the receptor resides to mount an immune response and fend off microbial infection and disease. Beutler and Ronald have played key roles in this chapter of scientific discovery. In 1995, Ronald identified the first such receptor -- a rice gene known as known as Xa21 -- and in 1998, Beutler identified the gene for the first immune receptor in mammals -- a mouse gene known as TLR4. Their overview in Science includes illustrated descriptions of the disease-resistance or immunity pathways in the mouse, Drosophila fruit fly, rice and a common research plant known as Arabidopsis. These represent the immune defense systems of vertebrates, insects, monocotyledons (grass-like plants) and dicotyledons (plants like beans that have two seed leaves.) The researchers note that plant biologists led the way in discovering receptors that sense and respond to infection. The 1980s brought about an intense hunt for the genes that control production of the receptor proteins, followed by an "avalanche" of newly discovered receptor genes and mechanisms in the 1990s. Another milestone included discovery in 2000 of the immune receptor in Arabidopsis known as FLS2 -- which demonstrated that a plant receptor could bind to a molecule that is present in many different microbial invaders. The review also discuses how plant and animal immune responses have evolved through the years and which mechanisms have remained the same. While the past 15 years have been rich in significant discoveries related to plant and animal immunity, Beutler and Ronald are quick to point out that researchers have just scratched the surface. "If you think of evolution as a tree and existing plant and animal species as the leaves on the tips of the tree's branches, it is clear that we have examined only a few of those leaves and have only a fragmentary impression of what immune mechanisms exist now and were present in the distant past," said Beutler, an elected member of the U.S. National Academy of Sciences. He and Ronald predict that, as results from new gene sequencing projects become available, scientists will likely find that some plant and animal species emphasize specific resistance mechanisms while having little use for others. For example, the researchers point out that the Drosophila's immune system depends on only one immunologically active receptor, known as the Toll receptor, to sense invasion by fungi and gram-positive bacteria. In contrast, Arabidopsis has dozens of sensors to protect against microbial infections and rice has hundreds. Ronald and Beutler project that many surprises will be uncovered by future research as it probes the disease-resistance mechanisms of other species.

DNA reveals origins of first European farmers

Wed, 10 Nov 2010 03:22:14 PDT

A team of international researchers led by ancient DNA experts from the University of Adelaide has resolved the longstanding issue of the origins of the people who introduced farming to Europe some 8000 years ago. A detailed genetic study of one of the first farming communities in Europe, from central Germany, reveals marked similarities with populations living in the Ancient Near East (modern-day Turkey, Iraq and other countries) rather than those from Europe. Project leader Professor Alan Cooper, Director of the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide, says: "This overturns current thinking, which accepts that the first European farming populations were constructed largely from existing populations of hunter-gatherers, who had either rapidly learned to farm or interbred with the invaders." The results of the study have been published today in the online peer-reviewed science journal PLoS Biology. "We have finally resolved the question of who the first farmers in Europe were – invaders with revolutionary new ideas, rather than populations of Stone Age hunter-gatherers who already existed in the area," says lead author Dr Wolfgang Haak, Senior Research Associate with ACAD at the University of Adelaide. "We've been able to apply new, high-precision ancient DNA methods to create a detailed genetic picture of this ancient farming population, and reveal that it was radically different to the nomadic populations already present in Europe. "We have also been able to use genetic signatures to identify a potential route from the Near East and Anatolia, where farming evolved around 11,000 years ago, via south-eastern Europe and the Carpathian Basin (today's Hungary) into Central Europe," Dr Haak says. The project involved researchers from the University of Mainz and State Heritage Museum in Halle, Germany, the Russian Academy of Sciences and members of the National Geographic Society's Genographic Project, of which Professor Cooper is a Principal Investigator and Dr Haak is a Senior Research Associate. The ancient DNA used in this study comes from a complete graveyard of Early Neolithic farmers unearthed at the town of Derenburg in Saxony-Anhalt, central Germany. "This work was only possible due to the close collaboration of archaeologists excavating the skeletons, to ensure that no modern human DNA contaminated the remains, and nicely illustrates the potential when archaeology and genetics are combined," says Professor Kurt Werner Alt from the collaborating Institute of Anthropology in Mainz, Germany.

Human-specific evolution in battling bugs and building babies

Fri, 05 Nov 2010 03:34:48 PDT

Although human and chimpanzee immune systems have many identical components, this is not the case for the family of killer cell immunoglobulin-like receptors (KIR) controlling white blood cells known as natural killer (NK) cells. Published in the open-access journal PloS Genetics on November 4, a paper by Stanford University researchers describes qualitative KIR differences, acquired after humans and chimpanzees separated 6 million years ago and mainly a consequence of innovation in the human line. These differences open up an exciting avenue for explaining the differential susceptibility of humans and chimpanzees to devastating infectious diseases such as HIV/AIDS and malaria. While immunological research has increasingly concentrated on the inbred laboratory mouse for the last half century, mice actually represent a poor model for human KIR because their NK cell receptors are so disparate from the simian primate counterparts. As a result, the researchers looked at chimpanzee KIR so that they could accurately compare them with the well-characterized human versions. NK cells serve in both immune defense and reproduction; they contribute to early defense against infection and are implicated during the early phase of pregnancy, when uterine NK cells orchestrate enlargement of maternal arteries that will supply blood to the placenta and nourish the fetus. These vital NK cell functions seem subject to variable and competing selective pressures that have driven rapid KIR evolution and produced striking differences between humans and chimpanzees, as closely related as they are. These distinctions derive from adaptations in the human line in response to selective pressures on human NK cells due to the competing needs of defense and reproduction. Whereas chimpanzees have a potent battery of KIR that appears aimed at fighting infection, the human KIR represent a functional compromise between battling bugs and building babies.

Forces for cancer spread: Genomic instability and evolutionary selection

Thu, 28 Oct 2010 03:34:39 PDT

In new research published today, researchers uncover evolution in action in cancer cells. They show the forces of evolution in pancreatic tumours mean that not only is cancer genetically different between different patients, but each new focus of cancer spread within a patient has acquired distinct mutations. Effectively, ten different foci of cancer spread are ten different, but related, tumours. The complexity of pancreatic cancer genetics uncovered in this work helps to explain the difficulty of treating the disease but also strengthens the need for improved methods for early diagnosis Pancreatic cancer is an aggressive malignancy with only two or three patients in one hundred living beyond five years from first diagnosis. The spread – metastasis – of the tumour is thought to be relatively symptomless in most patients until the disease is advanced. "We have always known that pancreatic cancer is a particularly aggressive disease," says Dr Peter Campbell, from the Wellcome Trust Sanger Institute and first author on the paper. "This study illustrates why it is so challenging. Each metastasis is its own tumour, each evolving, each striving for dominance, each adapting to life outside the pancreas. When we treat cancer that has spread through the body, we're not just treating one tumour, we might be treating tens of genetically distinct tumours." The researchers, from the Wellcome Trust Sanger Institute, near Cambridge, UK and the Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins Medical Institutions, Baltimore, USA, looked at cancers in 13 patients who died from pancreatic cancer. They mapped rearrangements in the genomes of cancer samples: in some cases, they looked at several metastases from a patient. They discovered that pancreatic cancer genomes often contain a distinctive pattern of genome rearrangement that possibly reflects changes to repair mechanisms in the cancer cells. The pattern of mutation events is dramatically different to that found in breast cancer, for example. "With each study, cancer genomes are being revealed in their intricate complex detail," says Dr Andy Futreal, Head of Cancer Genetics and Genomics at the Wellcome Trust Sanger Institute and a senior author on the paper. "Genome instability is common in cancer, but this study has further revealed the dynamic nature of that instability and its role in spread of disease in the patient – with instability being an engine of selection that allows the tumour to adapt to new sites in the body. "We can see a root of common lesions – about half of the mutations are shared across metastases. Metastatic cancer is therefore like a family: the different deposits of tumour are genetically related to one another, as brothers, sisters and cousins are, but also have distinguishing genetic features that make them individual. Identifying and targeting the shared mutations with drugs is likely to be a route to more effective treatment." In a companion study Dr Iacobuzio-Donahue and her colleagues show that single-letter mutations show a similarly complex pattern. The team on that paper suggest that there might be a long time lag from the first cancer-causing mutations in the primary tumour to the violent and rapid metastasis of late-stage disease. Both papers suggest that the galloping mutation rate that develops produces cells that, because of specific mutations they acquire, can colonize other organs. Different combinations of active genes are needed to survive in different tissues. This is a return to the 120-year-old seed and soil hypothesis that some organs provide particularly fertile ground for particular cancer cells to grow. This work shows that even in one person's cancer, clones of cells can evolve genomes specialised for life in defined organs. The researchers emphasize that the shared mutations common to many early-stage pancreatic cancers could provide a route to discovery of new drug targets. In addition, the long time between the initial genetic changes in the developing primary cancer and spread to other organs might offer a window in which early diagnosis could detect disease while it is still curable by surgery. The patients for these studies were recruited to a programme established by Dr Iacobuzio-Donahue in Baltimore to develop new understanding of this difficult tumour type. Patients with terminal pancreatic cancer discuss with the team the aims of the research and choose whether or not to provide samples after their death. "We are so grateful to all patients who have discussed this programme," explains Dr Iacobuzio-Donahue from the Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins Medical Institutions, Baltimore, Maryland and a senior author on the paper. "In times of tremendous personal difficulty, they and their families and friends have taken steps to help others, with the hope we can improve diagnosis and treatments in the future. The sacrifices they have made are now fundamentally improving our understanding of how pancreatic cancer develops and spreads. "This is a research paper, but we are all of us aware that there are real people behind these samples."

60 Utahns are among landmark large-scale genome sequencing study

Thu, 28 Oct 2010 03:30:28 PDT

Just seven months after University of Utah geneticists took part in a landmark study that sequenced for the first time the genome of an entire Utah family, U of U researchers have taken part in another historic study that is the first large-scale genome sequencing project – 179 people representing three continents – and 60 Utahns played a major role in this study, too. Published Wednesday, Oct. 27, 2010, in Nature, the study demonstrates how quickly the science of genome sequencing is expanding – first from individuals, then to families, and now to large groups of people representing distinct geographic and ethnic populations, according to Lynn B. Jorde, Ph.D., professor and chair of human genetics in the U of U School of Medicine and a senior investigator and co-author on the study. Rapid-fire technological advances and highly sophisticated computers are giving geneticists the ability to sequence the genomes of increasingly larger groups of people at lower costs, and this study is an example of the research that breakthroughs in technology enable. It highlights as well the significant role Utahns have played in groundbreaking genetics studies. "This study provides the first large-scale inventory of human genetic diversity," Jorde said. "It also is a good example of how Utahns have helped researchers worldwide. Genetics studies keep coming back to Utah." The study is part of the 1000 Genomes Project Consortium – an international collaboration of hundreds of geneticists from dozens of laboratories with the goals of cataloging the range of genetic diversity found in people worldwide and characterizing 95 percent of the most common genetic mutations found in humans. Along with being the first large-scale genome-sequencing project, the study made several important findings, including confirmation of earlier work of Jorde's lab group and scientists at the Institute for Systems Biology in Seattle that gave the first direct estimate of the rate of genetic mutation in humans; providing evidence of recent natural selection in new genes; discovering a number of genetic mutations that occur often enough to be considered among the most common in humans; and identifying new "mobile elements" – DNA sequences that randomly reshuffle in the genome. Earlier this year, Jorde, who is on the 1000 Genomes Project steering committee, was part of the team that was the first to sequence the genome of an entire family – two parents and two children who live in Utah. As part of that study, published in March in Science, he estimated the rate at which genetic mutations are passed from generation to generation at 60 – meaning each parent passes 30 genetic mutations to their offspring. Most gene mutations are harmless, but understanding the rate at which mutations are passed among generations is an essential part of understanding the human biological clock, according to Jorde. To confirm his estimated mutation rate, which was half of what had been estimated previously by indirect methods, researchers in the current study sequenced the genomes of two families of three people each. "We were delighted that the mutation rate estimate obtained from the 1000 Genomes Project was exactly the same as our estimate," Jorde said. In the large-scale sequencing phase of the project – in which the genomes of 60 Utahns representing Northern Europe; 60 Nigerians representing Africa; and 30 Chinese and 30 Japanese people representing Southeast Asia were sequenced – the researchers identified a number of new genes that appear to have undergone recent natural selection. That mirrors another study from Jorde's lab, published in Science in July of this year, that showed evidence of genetic natural selection within the past 5,000 to 10,000 years that enables the people of Tibet to thrive in the low-oxygen environment of extremely high altitudes. Finding further proof of natural selection in a broader diversity of people in the current study provides evidence to answer another basic question about humans: are we still evolving? "These studies provide an unequivocal answer – yes," Jorde said. The 60 Utahns in the project were part of a number of families who 30 years ago volunteered for a U of U study investigating how genetic variations are passed in families. As they sequenced the genomes of those three population groups, the researchers also discovered a number of genetic mutations that occur often enough – defined as being found in greater than 1 percent of people – to be considered common gene mutations. With the discovery of these new gene mutations, more than 15 million DNA variations have been identified in the human genome and the researchers believe the 1000 Genomes Project has reached its goal of identifying 95 percent of common genetic mutations. That's a major step that provides a reference of genetic variation for researchers worldwide trying to unravel the genetic bases of countless diseases, according to Jorde. "People now have a catalog for comparing their research results," he said. "Our ultimate goal is to use this information to understand the causes of disease." In a third phase of the study, researchers including Jin chuan Xing, Ph.D., a postdoctoral fellow in Jorde's lab, looked at the DNA of 697 people and discovered new "mobile elements" – DNA sequences that pop up randomly in peoples' genomes. Although the function of mobile elements is unknown, they comprise half the human genome and are believed to help propel evolution. This was the first study to look at mobile elements in a large population of people, Xing said. "We discovered a lot of new ones," he said. "This will help us look at how mobile elements assemble."

World's vertebrates face increasing risk of extinction

Wed, 27 Oct 2010 03:31:27 PDT

A new assessment conducted by 174 scientists from around the world underscores a growing concern about the health of the world's biodiversity, quantifying the rate of decline among vertebrate species on a global scale for the first time. The team's results support the idea that our planet is currently experiencing its sixth mass extinction—nearly one fifth of all known vertebrate species are currently classified as Threatened on the International Union for the Conservation of Nature (IUCN) Red List, and an average of 52 species of mammals, birds, and amphibians move one category closer to extinction each year. The team, which includes California Academy of Sciences mammalogist Dr. Galen Rathbun, notes that over the past four decades, species extinction rates have exceeded normal background rates by two to three orders of magnitude. However, the team reports that species losses and declines would have been 20% worse in the absence of conservation efforts to protect threatened species. Thus, while current conservation efforts remain insufficient to offset the main drivers of biodiversity loss—including habitat loss, over-exploitation, and invasive alien species—targeted conservation efforts have had a measurable positive impact on the planet's vertebrate species. The research is reported in the October 26 issue of Science Express, the website for the journal Science (publication in the print version of Science will follow at a later date). The study used data for 25,000 species from The IUCN Red List of Threatened Species™ to investigate the status of the world's vertebrates (mammals, birds, amphibians, reptiles and fishes) and how this status has changed over time. Their results indicate that approximately 20% of the worlds vertebrates are currently classified as Threatened (assigned the IUCN Red List status of Critically Endangered, Endangered, or Vulnerable), including 25% of all mammals, 13% of birds, 22% of reptiles, 41% of amphibians, 33% of cartilaginous fishes, and 15% of bony fishes. While vertebrates comprise just 3% of the known species on Earth, they play vital roles in their ecosystems and have great cultural and economic significance for humans. The new report demonstrates that these species continue to decline at an alarming rate, particularly in tropical areas. Global patterns of rising extinction risk are most marked in Southeast Asia, where agricultural expansion, logging, and hunting are the primary forces behind accelerating extinction rates. California Academy of Sciences mammalogist Dr. Galen Rathbun contributed data to the report on the status of the members of the Afrotheria supercohort, an ancient group of African mammals that includes elephants, sea cows, hyraxes, sengis (also known as elephant-shrews), tenrecs, golden moles and aardvarks. Of the 83 species currently recognized in this supercohort, 30 are considered Threatened, and an additional eight species are considered data deficient—these species are quite possibly threatened, but scientists don't know enough about their distribution to be able to assign them a status. Therefore, somewhere between 36% and 46% of the world's Afrotheria species are currently threatened with extinction. The Afrotheria supercohort represents one of the world's major mammalian evolutionary radiations. By one count, the seven groups that make up the Afrotheria represent nearly a third of all the living orders of mammals. However, the number of species within this supercohort is relatively low, totaling only about 1.5% of the world's mammals. This means that with relatively few species extinctions, entire groups of afrotherian mammals would cease to exist, thus terminating over 100 million years of evolution in Africa and drastically reducing that region's biodiversity. "Almost any loss within the Afrotheria supercohort would be profound in terms of its evolutionary significance, because the members of this group carry such unique genes," says Rathbun. "Like many other groups, the afrotherian mammals are threatened predominantly by habitat loss and habitat degradation. For instance, all four of the forest-dwelling sengis are threatened with extinction, because the forests in Africa are rapidly disappearing." While habitat loss and degradation are the primary drivers of rising extinction rates around the world, they are not the only culprits. The study authors noted several new threats that have emerged in recent years, including the use of a veterinary drug called diclofenac, an anti-inflammatory drug similar to ibuprofen that was introduced to the veterinary market on the Indian subcontinent in the early 1990s. While cattle can tolerate high doses of the drug, it soon became apparent that Asian vultures cannot—shortly after feeding on dead livestock treated with diclofenac, the birds die from renal failure. Since 1992, the population of Oriental White-backed Vultures has declined by more than 99%. Based on the current trends, scientists estimate that the Oriental White-backed Vulture will be extinct in the wild in less than a decade. The only hope for the bird's survival is to establish an aggressive captive breeding program, which would enable scientists to reintroduce vultures to the wild once diclofenac is no longer in use. California Academy of Sciences ornithologist Dr. David Mindell has been studying genetic diversity in current and historical Oriental White-backed Vulture populations to help guide these captive breeding efforts and assess species status of the bird's closest relatives. His research has provided a clear course of action for ensuring that this species survives with a healthy, diverse gene pool. Captive breeding programs are just one of the conservation strategies that are helping to mitigate species extinctions. The study authors also found evidence of notable conservation successes through legislation to limit hunting, establishment of new protected areas, and efforts to remove invasive alien species. "The stark reality of accelerating species losses can lead to a feeling of hopelessness," says Mindell, Dean of Science at the California Academy of Sciences. "However, the IUCN data analyzed in this assessment show that concerted efforts by biologists and conservationists can make a positive difference in slowing rates of endangerment. Hopefully, these findings will bolster existing efforts at conservation—and spawn new initiatives as well."