Rise in Oxygen Drove Evolution of Animal Life 550 Million Years Ago

ScienceDaily (Dec. 18, 2010) — Researchers funded by the Biotechnology and Biological Sciences Research Council (BBSRC) at the University of Oxford have uncovered a clue that may help to explain why the earliest evidence of complex multicellular animal life appears around 550 million years ago, when atmospheric oxygen levels on the planet rose sharply from 3% to their modern day level of 21%.


Original image of Trichoplax adhaerens. (Credit: Copyright Karolin von der Chevallerie, University of Hannover)

The team, led by Professor Chris Schofield, has found that humans share a method of sensing oxygen with the world's simplest known living animal -- Trichoplax adhaerens -- suggesting the method has been around since the first animals emerged around 550 million years ago.

This discovery, published in the January 2011 edition of EMBO Reports, throws light on how humans sense oxygen and how oxygen levels drove the very earliest stages of animal evolution.

Professor Schofield said "It's absolutely necessary for any multicellular organism to have a sufficient supply of oxygen to almost every cell and so the atmospheric rise in oxygen made it possible for multicellular organisms to exist.

"But there was still a very different physiological challenge for these organisms than for the more evolutionarily ancient single-celled organisms such as bacteria. Being multicelluar means oxygen has to get to cells not on the surface of the organism. We think this is what drove the ancesters of Trichoplax adhaerens to develop a system to sense a lack of oxygen in any cell and then do something about it."

The oxygen sensing process enables animals to survive better at low oxygen levels, or 'hypoxia'. In humans this system responds to hypoxia, such as is caused by high altitudes or physical exertion, and is very important for the prevention of stroke and heart attacks as well as some types of cancer.

Trichoplax adhaerens is a tiny seawater organism that lacks any organs and has only five types of cells, giving it the appearance of an amoeba. By analysing how Trichoplax reacts to a lack of oxygen, Oxford researcher Dr Christoph Loenarz found that it uses the same mechanism as humans -- in fact, when the key enzyme from Trichoplax was put it in a human cell, it worked just as well as the human enzyme usually would.

They also looked at the genomes of several other species and found that this mechanism is present in multi-cellular animals, but not in the single-celled organisms that were the precursors of animals, suggesting that the mechanism evolved at the same time as the earliest multicellular animals

Defects in the most important human oxygen sensing enzyme can cause polycythemia -- an increase in red blood cells. This latest work could also open up new approaches to develop therapies for this disorder.

Professor Douglas Kell, Chief Executive, BBSRC said "Understanding how animals -- and ultimately humans -- evolved is essential to our ability to pick apart the workings of our cells. Knowledge of normal biological processes underpins new developments that can improve quality of life for everyone. The more skilful we become in studying the evolution of some of our most essential cell biology, the better our chances of ensuring long term health and well being to match the increase in average lifespan in the UK and beyond."

http://www.sciencedaily.com/releases/2010/12/101217145647.htm

New Fossil Site in China Shows Long Recovery of Life from the Largest Extinction in Earth's History

ScienceDaily (Dec. 22, 2010) — A major new fossil site in south-west China has filled in a sizeable gap in our understanding of how life on this planet recovered from the greatest mass extinction of all time, according to a paper co-authored by Professor Mike Benton, in the School of Earth Sciences, and published in the Proceedings of the Royal Society B. The work is led by scientists from the Chengdu Geological Center in China.



An ichthyosaur, a one-meter long fish-eating reptile -- from the new fossil site in China. (Credit: Image courtesy of University of Bristol)

Some 250 million years ago, at the end of the time known as the Permian, life was all but wiped out during a sustained period of massive volcanic eruption and devastating global warming. Only one in ten species survived, and these formed the basis for the recovery of life in the subsequent time period, called the Triassic. The new fossil site -- at Luoping in Yunnan Province -- provides a new window on that recovery, and indicates that it took about 10 million years for a fully-functioning ecosystem to develop.

"The Luoping site dates from the Middle Triassic and contains one of the most diverse marine fossil records in the world," said Professor Benton. "It has yielded 20,000 fossils of fishes, reptiles, shellfish, shrimps and other seabed creatures. We can tell that we're looking at a fully recovered ecosystem because of the diversity of predators, most notably fish and reptiles. It's a much greater diversity than what we see in the Early Triassic -- and it's close to pre-extinction levels."

Reinforcing this conclusion is the complexity of the food web, with the bottom of the food chains dominated by species typical of later Triassic marine faunas -- such as crustaceans, fishes and bivalves -- and different from preceding ones.

Just as important is the 'debut' of top predators -- such as the long-snouted bony fish Saurichthys, the ichthyosaur Mixosaurus, the sauropterygian Nothosaurus and the prolacertiform Dinocephalosaurus -- that fed on fishes and small predatory reptiles.

Professor Shixue Hu of the Chengdu Group said: "It has taken us three years to excavate the site, and we moved tonnes of rock. Now, with thousands of amazing fossils, we have plenty of work for the next ten years!"

"The fossils at Luoping have told us a lot about the recovery and development of marine ecosystems after the end-Permian mass extinction," said Professor Benton. "There's still more to be discovered there, and we hope to get an even better picture of how life reasserted itself after the most catastrophic global event in the history of our planet."

http://www.sciencedaily.com/releases/2010/12/101222093204.htm

Africa Has Two Elephant Species, Genetic Analysis Confirms

ScienceDaily (Dec. 22, 2010) — Contrary to the belief of many scientists (as well as many members of the public), new research confirms that Africa has two -- not one -- species of elephant. Scientists from Harvard Medical School, the University of Illinois, and the University of York in the United Kingdom used genetic analysis to prove that the African savanna elephant and the smaller African forest elephant have been largely separated for several million years.



Top: Forest elephants (shown) in Africa have now been confirmed as a new species of elephant and have been distinguished from the larger savanna elephant in Africa. Bottom: Africa's savanna elephant (shown) is as different from Africa's forest elephant as Asian elephants are to mammoths, says a new study in PLoS Biology. (Credit: Forest elephant photo by Nicholas Georgiadis; Savanna elephant photo by A. Schaefer)

The researchers, whose findings appear online in PLoS Biology, compared the DNA of modern elephants from Africa and Asia to DNA that they extracted from two extinct species: the woolly mammoth and the mastodon. Not only is this the first time that anyone has generated sequences for the mastodon nuclear genome, but it is also the first time that the Asian elephant, African forest elephant, African savanna elephant, the extinct woolly mammoth, and the extinct American mastodon have been looked at together.

"Experimentally, we had a major challenge to extract DNA sequences from two fossils -- mammoths and mastodons -- and line them up with DNA from modern elephants over hundreds of sections of the genome," says research scientist Nadin Rohland of the Department of Genetics at Harvard Medical School.

According to David Reich, associate professor in the same department, "The surprising finding is that forest and savanna elephants from Africa -- which some have argued are the same species -- are as distinct from each other as Asian elephants and mammoths."

Researchers only had DNA from a single elephant in each species, but had collected enough data from each genome to traverse millions of years of evolution to the time when elephants first diverged from each other.

"The divergence of the two species took place around the time of the divergence of the Asian elephant and woolly mammoths," says Professor Michi Hofreiter, who specializes in the study of ancient DNA in the Department of Biology at York. "The split between African savanna and forest elephants is almost as old as the split between humans and chimpanzees. This result amazed us all."

The possibility that the two might be separate species was first raised in 2001, but this is the most compelling scientific evidence so far that they are indeed distinct.

Previously, many naturalists believed that African savanna elephants and African forest elephants were two populations of the same species, despite the significant size differences. The savanna elephant has an average shoulder height of 3.5 meters whereas the forest elephant has an average shoulder height of 2.5 meters. The savanna elephant weighs between six and seven tons, roughly double the weight of the forest elephant.

DNA analysis revealed a wide range of genetic diversity within each species. The savanna elephant and woolly mammoth have very low genetic diversity, Asian elephants have medium diversity, and forest elephants have very high diversity. Researchers believe that this is due to varying levels of reproductive competition among males.

"We now have to treat the forest and savanna elephants as two different units for conservation purposes," says Alfred Roca, assistant professor in the Department of Animal Sciences at the University of Illinois. "Since 1950, all African elephants have been conserved as one species. Now that we know the forest and savanna elephants are two very distinctive animals, the forest elephant should become a bigger priority for conservation purposes."

This research was funded by the Max Planck Society and by a Burroughs Wellcome Career Development Award in Biomedical Science.

http://www.sciencedaily.com/releases/2010/12/101221172244.htm

Fossil Finger Bone Yields Genome of a Previously Unknown Human Relative

ScienceDaily (Dec. 22, 2010) — A 30,000-year-old finger bone found in a cave in southern Siberia came from a young girl who was neither an early modern human nor a Neanderthal, but belonged to a previously unknown group of human relatives who may have lived throughout much of Asia during the late Pleistocene epoch. Although the fossil evidence consists of just a bone fragment and one tooth, DNA extracted from the bone has yielded a draft genome sequence, enabling scientists to reach some startling conclusions about this extinct branch of the human family tree, called "Denisovans" after the cave where the fossils were found.

The findings are reported in the Dec. 23 issue of Nature by an international team of scientists, including many of the same researchers who earlier this year published the Neanderthal genome. Coauthor Richard Green of the University of California, Santa Cruz, played a lead role in the analysis of the genome sequence data, for which a special portal was designed on the UCSC Genome Browser. The team was led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

By comparing the Denisovan genome sequence with the genomes of Neanderthals and modern humans, the researchers determined that the Denisovans were a sister group to the Neanderthals, descended from the same ancestral population that had separated earlier from the ancestors of present-day humans. The study also found surprising evidence of Denisovan gene sequences in modern-day Melanesians, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians, just as Neanderthals appear to have interbred with the ancestors of all modern-day non-Africans.

"The story now gets a bit more complicated," said Green, an assistant professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz. "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neanderthals, we now see these very intertwined story lines with more players and more interactions than we knew of before."

The Denisovans appear to have been quite different both genetically and morphologically from Neanderthals and modern humans. The tooth found in the same cave as the finger bone shows a morphology that is distinct from Neanderthals and modern humans and resembles much older human ancestors, such as Homo habilis and Homo erectus. DNA analysis showed that the tooth and the finger bone came from different individuals in the same population.

The finger bone was found in 2008 by Russian scientists in Denisova Cave, an archaeological site in southern Siberia. Pääbo, who had worked with the Russian scientists before, obtained the bone for his research on ancient DNA. In Leipzig, researchers extracted DNA from the bone and sequenced the mitochondrial genome, a smaller DNA sequence separate from the chromosomal DNA and easier to obtain from ancient samples. The results, published earlier this year, showed a surprising divergence from the mitochondrial genomes of Neanderthals and modern humans, and the team quickly began working to sequence the nuclear genome.

"It was fortuitous that this discovery came quickly on the heels of the Neanderthal genome, because we already had the team assembled and ready to do another similar analysis," Green said. "This is an incredibly well-preserved sample, so it was a joy to work with data this nice. We don't know all the reasons why, but it is almost miraculous how well-preserved the DNA is."

The relationship between Denisovans and present-day Melanesians was a completely unexpected finding, he said. The comparative analysis, which included genome sequences of individuals from New Guinea and Bougainville Island, indicates that genetic material derived from Denisovans makes up about 4 to 6 percent of the genomes of at least some Melanesian populations. The fact that Denisovans were discovered in southern Siberia but contributed genetic material to modern human populations in Southeast Asia suggests that their population may have been widespread in Asia during the late Pleistocene, said David Reich of Harvard Medical School, who led the population genetic analysis.

It is not clear why fossil evidence had not already revealed the existence of this group of ancient human relatives. But Green noted that the finger bone was originally thought to be from an early modern human, and the tooth resembles those of other ancient human ancestors. "It could be that other samples are misclassified," he said. "But now, by analyzing DNA, we can say more definitively what they are. It's getting easier technically to do this, and it's a great new way to extract information from fossil remains."

In the light of the Neanderthal and Denisovan genomes, a new, more complex picture is emerging of the evolutionary history of modern humans and our extinct relatives. According to Green, there was probably an ancestral group that left Africa between 300,000 and 400,000 years ago and quickly diverged, with one branch becoming the Neanderthals who spread into Europe and the other branch moving east and becoming Denisovans. When modern humans left Africa about 70,000 to 80,000 years ago, they first encountered the Neanderthals, an interaction that left traces of Neanderthal DNA scattered through the genomes of all non-Africans. One group of humans later came in contact with Denisovans, leaving traces of Denisovan DNA in the genomes of humans who settled in Melanesia.

"This study fills in some of the details, but we would like to know much more about the Denisovans and their interactions with human populations," Green said. "And you have to wonder if there were other populations that remain to be discovered. Is there a fourth player in this story?"

The paper's 28 coauthors include scientists from Germany, Spain, China, Russia, Canada, and the United States. Reich and Green are among seven coauthors credited with contributing equally to this work. This research was supported by the Max Planck Society, the Krekeler Foundation, the U.S. National Institutes of Health, and the U.S. National Science Foundation.

http://www.sciencedaily.com/releases/2010/12/101222131119.htm

Separation Between Neanderthal and Homo Sapiens Might Have Occurred 500,000 Years Earlier, DNA from Teeth Suggests

ScienceDaily (June 23, 2010) — The separation of Neanderthal and Homo sapiens might have occurred at least one million years ago, more than 500.000 years earlier than previously believed, according to new DNA-based analyses.

A doctoral thesis conducted at the National Center for Research on Human Evolution (Centro Nacional de Investigación sobre la Evolución Humana), associated with the University of Granada, analyzed the teeth of almost all species of hominids that have existed during the past 4 million years. Quantitative methods were employed, and they managed to identify Neanderthal features in ancient European populations.

The main purpose of this research, whose author is Aida Gómez Robles, was to reconstruct the history of evolution of the human species using the information provided by the teeth, which are the most numerous and best preserved remains of the fossil record. To this purpose, a large sample of dental fossils from different sites in Africa, Asia and Europe was analyzed. The morphological differences of each dental class were assessed and the ability of each tooth to identify the species to which its owner belonged was analyzed.

The researcher concluded that it is possible to correctly determine the species to which an isolated tooth belonged with a success rate ranging from 60% to 80%. Although these values are not very high, they increase as different dental classes from the same individual are added. That means that if several teeth from the same individual are analyzed, the probability of correctly identifying the species can reach 100%.

Aida Gómez Robles explains that, from all the species of hominids currently known, "none of them has a probability higher than 5% to be the common ancestor of Neanderthals and Homo sapiens. Therefore, the common ancestor of this lineage is likely to have not been discovered yet."

Computer Simulation

What is innovative about this study is that computer simulation was employed to observe the effects of environmental changes on morphology of the teeth. Similar studies had been conducted on the evolution and development of different groups of mammals, but never on human evolution.

Additionally, the research conducted at CENIEH and at the University of Granada is pioneering -- together with recent studies based on the shape of the skull -- in using mathematical methods to make an estimation of the morphology of the teeth of common ancestors in the evolutionary tree of the human species. "However, in this study, only dental morphology was analyzed. The same methodology can be used to rebuild other parts of the skeleton of that species, which would provide other models that would serve as a reference for future comparative studies of new fossil finds."

To carry out this study, Gómez Robles employed fossils from a number of archaeological-paleontological sites, such as that of the Gran Colina and the Sima de los Huesos, located in Atapuerca range (Burgos, Spain), and the site of Dmanisi in the Republic of Georgia. She also studied different fossil collections by visiting international institutions as the National Museum of Georgia, the Institute of Human Paleontology and the Museum of Mankind in Paris, the European Research Centre Tautavel (France), the Senckenberg Institute Frankfurt, the Museum of Natural History in Berlin, the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing and the Museum of Natural History in New York and Cleveland.

The results of this research were disclosed in two articles published in Journal of Human Evolution (2007 and 2008), and they will also be thoroughly presented within a few months.

http://www.sciencedaily.com/releases/2010/06/100623104436.htm

More Than Skin Deep, Tanning Product of Sun's Rays

ScienceDaily (June 22, 2010) — People who remain pale and never tan can blame their distant ancestors for choosing to live in the northern reaches of the globe and those who easily achieve a deep tan can thank their ancestors for living in the subtropical latitudes, according to Penn State anthropologists.



People who remain pale and never tan can blame their distant ancestors for choosing to live in the northern reaches of the globe and those who easily achieve a deep tan can thank their ancestors for living in the subtropical latitudes, according to Penn State anthropologists. (Credit: iStockphoto/Yuliyan Velchev)

"The variation of ultraviolet radiation, especially in the middle and high latitudes is great," said Nina Jablonski, professor of anthropology and chair of Penn State's anthropology department. "Tanning has evolved multiple times around the world as a mechanism to partly protect humans from harmful effects of ultraviolet radiation."

Jablonski, working with George Chaplin, senior research associate in anthropology and an expert in geographic information systems, looked at the way the sun illuminates different parts of the Earth. They looked at levels and angles of incidence of both ultraviolet A and B radiation at various latitudes. Ultraviolet B radiation is much more variable than ultraviolet A as latitude increases due to atmospheric scattering of the light and absorption by oxygen.

Ultraviolet B radiation produces vitamin D in human skin. Ultraviolet radiation can, however, destroy folate. Folate is important for the rapid growth of cells, especially during pregnancy where its deficiency can cause neural tube defects.

"What we now recognize is that some of the medical problems seen in darkly pigmented people may be linked at some level to vitamin D deficiency," said Jablonski. "Things like certain types of cancer in darkly pigmented people and in people who use a lot of sunscreen or always stay inside could be partly related to vitamin D deficiency."

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, where human ancestors evolved and where both ultraviolet radiations are high throughout the year, natural selection created darkly pigmented individuals to protect against the sun.

"Past arguments about the selective value of dark pigmentation focused on the protective effects of melanin against sunburn, skin cancer, and overproduction of vitamin D. These factors can no longer be considered significant selective pressures," the Jablonski and Chaplin report in a recent issue of the Proceedings of the National Academy of Sciences.

Sunburn and most skin cancers do not alter an individual's ability to procreate, so they are not selection factors. The human body also has a mechanism to prevent overproduction of vitamin D.

Previously, the researchers concluded that dark skin pigmentation in the tropics protects people from folate destruction by ultraviolet B, but, because levels of ultraviolet B are high year round, the skin can still allow enough in to manufacture vitamin D.

As humans moved out of Africa, they moved into the subtropics and eventually inhabited areas up to the Arctic Circle. Ultraviolet radiation in these areas is neither consistent nor strong. North or south of 46 degrees latitude, which includes all of Canada, Russia, Scandinavia, Western Europe and Mongolia, there is insufficient ultraviolet B through most of the year to produce vitamin D. Populations in these areas evolved to have little skin pigmentation.

In the latitudes between 23 and 46 degrees, an area that encompasses North Africa, South America, the Mediterranean and most of China, ultraviolet B radiation is much more variable. Heavily pigmented skin in the winter would block the development of vitamin D, and lightly pigmented skin during the summer would allow destruction of folate.

"We actually demonstrate that in those middle latitudes where highly fluctuating levels of ultraviolet radiation occur throughout the year, tanning has evolved multiple times as a mechanism to partly protect humans from harmful effect of the sun," said Jablonski.

The tanning process evolved for humans who by and large were naked all the time. As the ultraviolet B radiation began to increase in the early spring, the skin would begin to gradually darken. As the sun became stronger, the tan became deeper. During the winter, as ultraviolet B waned, so did the tan, allowing Vitamin D production and protecting folate.

The researchers note 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. They also note that depigmentated skin also developed at least three times through different genetic mechanisms.

Implications for today focus on the fact that depigmented people now live in tropical and subtropical areas where besides getting sunburned they run the risk of losing folate. Highly pigmented people live in higher latitudes where they may become vitamin D deficient, especially if they use sunscreens.

"It is a conspiracy of modernity," said Jablonski. "The rapidity at which we can move long distances and live far away from our ancestral homelands. The fact that we can live and work indoors. All this has happened within the last 500 years and especially within the last 200 years."

http://www.sciencedaily.com/releases/2010/06/100621125137.htm

3.6 Million-Year-Old Relative of 'Lucy' Discovered: Early Hominid Skeleton Confirms Human-Like Walking Is Ancient

ScienceDaily (June 21, 2010) — Meet "Lucy's" Great-Grandfather. Cleveland Museum of Natural History Curator and Head of Physical Anthropology Dr. Yohnannes Haile-Selassie led an international team that discovered and analyzed a 3.6 million-year-old partial skeleton found in Ethiopia. The early hominid is 400,000 years older than the famous "Lucy" skeleton and is significantly larger in size. Research on the new specimen reveals that advanced human-like, upright walking occurred much earlier in the evolutionary timeline than previously thought.

Haile-Selassie is the first author of the initial analysis of the specimen, which will be published in the online early edition of the Proceedings of the National Academy of Sciences during the week of June 21, 2010.

The partial skeleton belongs to "Lucy's" species, Australopithecus afarensis. It was found in the Woranso-Mille area of Ethiopia's Afar region by a team led by Haile-Selassie that excavated of the skeleton over five years following the discovery in 2005 of the lower arm bone. The team recovered the most complete clavicle and one of the most complete shoulder blades ever found in the human fossil record. A significant portion of the rib cage was also found.

The specimen was nicknamed "Kadanuumuu" (kah-dah-nuu-muu) by the authors. This means "big man" in the Afar language and reflects its large size. The male hominid stood between 5 to 5 ½ feet tall, while "Lucy" stood only 3 ½ feet tall.

"This individual was fully bipedal and had the ability to walk almost like modern humans," said Haile-Selassie. "As a result of this discovery, we can now confidently say that 'Lucy' and her relatives were almost as proficient walking on two legs as we are, and that the elongation of our legs came earlier in our evolution that previously thought."

He explained, "All of our understanding of Australopithecus afarenis' locomotion was dependent on 'Lucy.' Because she was an exceptionally small female with absolutely short legs, this gave some researchers the impression that she was not fully adapted to upright walking. This new skeleton falsifies that impression because if 'Lucy's' frame had been as large as this specimen, her legs would also have been proportionally longer."

Kent State University Professor Dr. C. Owen Lovejoy was a co-author of the research and helped analyze the skeleton. When comparing it to "Lucy," Lovejoy said, "They both have pelves, a complete lower limb bone and elements of the forelimb, vertebral column and thorax. However, the new specimen has more complete ribs and a nearly complete scapula, which tells us much more about body form in Australopithecus afarensis than 'Lucy' was able to alone."

Authors of the research include Cleveland scientists Dr. Bruce Latimer, interim director of the Center for Human Origins of the Institute for the Science of Origins at Case Western Reserve University, and Dr. Beverly Saylor, associate professor of geological sciences at Case Western Reserve University. Other co-authors are from Addis Ababa University in Ethiopia, Berkeley Geochronology Center and Stanford University.

Australopithecus afarenis is the best-known direct early human ancestor. Until now, the only partial skeleton assigned to this species was "Lucy," a 3.2 million-year-old female individual, which was discovered in 1974 by a team led by then Museum curator Dr. Donald Johanson.

The analysis of "Kadanuumuu" indicates that the shoulder and rib cage of this species were different from those of chimpanzees. "These findings further confirm what we concluded from the 'Ardi' specimen -- that chimpanzees have undergone a great deal of specialized evolution since we shared a last common ancestor with them," said Lovejoy.

"Ardi," or Ardipithecus ramidus is a 4.4 milion-year-old hominid species that was unveiled in October 2009 by a team that included Haile-Selassie, Lovejoy, and Museum scientists and associate researchers Dr. Linda Spurlock, Dr. Bruce Latimer and Dr. Scott Simpson. "Ardi" was named by the journal Science as breakthrough discovery of the year. Click here to find out more about "Ardi."

http://www.sciencedaily.com/releases/2010/06/100621151119.htm