Simpler Times: Did an Earlier Genetic Molecule Predate DNA and RNA?

ScienceDaily (Jan. 9, 2012) — In the chemistry of the living world, a pair of nucleic acids -- DNA and RNA -- reign supreme. As carrier molecules of the genetic code, they provide all organisms with a mechanism for faithfully reproducing themselves as well as generating the myriad proteins vital to living systems.

Yet according to John Chaput, a researcher at the Center for Evolutionary Medicine and Informatics, at Arizona State University's Biodesign Institute^®, it may not always have been so.

Chaput and other researchers studying the first tentative flickering of life on earth have investigated various alternatives to familiar genetic molecules. These chemical candidates are attractive to those seeking to unlock the still-elusive secret of how the first life began, as primitive molecular forms may have more readily emerged during the planet's prebiotic era.

One approach to identifying molecules that may have acted as genetic precursors to RNA and DNA is to examine other nucleic acids that differ slightly in their chemical composition, yet still possess critical properties of self-assembly and replication as well as the ability to fold into shapes useful for biological function.

According to Chaput, one interesting contender for the role of early genetic carrier is a molecule known as TNA, whose arrival on the primordial scene may have predated its more familiar kin. A nucleic acid similar in form to both DNA and RNA, TNA differs in the sugar component of its structure, using threose rather than deoxyribose (as in DNA) or ribose (as in RNA) to compose its backbone.

In an article released online January 9 in the journal Nature Chemistry, Chaput and his group describe the Darwinian evolution of functional TNA molecules from a large pool of random sequences. This is the first case where such methods have been applied to molecules other than DNA and RNA, or very close structural analogues thereof. Chaput says "the most important finding to come from this work is that TNA can fold into complex shapes that can bind to a desired target with high affinity and specificity." This feature suggests that in the future it may be possible to evolve TNA enzymes with functions required to sustain early life forms.

Nearly every organism on earth uses DNA to encode chunks of genetic information in genes, which are then copied into RNA. With the aid of specialized enzymes known as polymerases, RNA assembles amino acids to form essential proteins. Remarkably, the basic functioning of the genetic code remains the same, whether the organism is a snail or a senator, pointing to a common ancestor in the DNA-based microbial life already flourishing some 3.5 billion years ago.

Nevertheless, such ancestors were by this time quite complex, leading some scientists to speculate about still earlier forms of self-replication. Before DNA emerged to play its dominant role as the design blueprint for life, a simpler genetic world dominated by RNA may have prevailed. The RNA world hypothesis as it's known alleges that ribonucleic acid (RNA) acted to store genetic information and catalyze chemical reactions much like a protein enzyme, in an epoch before DNA, RNA and proteins formed the integrated system prevalent today throughout the living world.

While the iconic double helix of DNA is formed from two complimentary strands of nucleotides, attached to each other by base pairing in a helical staircase, RNA is single-stranded. The two nucleic acids DNA and RNA are named for the type of sugar complex that forms each molecule's sugar-phosphate backbone -- a kind of molecular thread holding the nucleotide beads together.

Could a simpler, self-replicating molecule have existed as a precursor to RNA, perhaps providing genetic material for earth's earliest organisms? Chaput's experiments with the nucleic acid TNA provide an attractive case. To begin with, TNA uses tetrose sugars, named for the four-carbon ring portion of their structure. They are simpler than the five-carbon pentose sugars found in both DNA and RNA and could assemble more easily in a prebiotic world, from two identical two-carbon fragments.

This advantage in structural simplicity was originally thought to be an Achilles' heel for TNA, making its binding behavior incompatible with DNA and RNA. Surprisingly, however, research has now shown that a single strand of TNA can indeed bind with both DNA and RNA by Watson-Crick base pairing -- a fact of critical importance if TNA truly existed as a transitional molecule capable of sharing information with more familiar nucleic acids that would eventually come to dominate life.

In the current study, Chaput and his group use an approach known as molecular evolution to explore TNA's potential as a genetic biomolecule. Such work draws on the startling realization that fundamental Darwinian properties -- self-replication, mutation and selection -- can operate on non-living chemicals.

Extending this technique to TNA requires polymerase enzymes that are capable of translating a library of random DNA sequences into TNA. Once such a pool of TNA strands has been generated, a process of selection must successfully identify members that can perform a given function, excluding the rest. As a test case, the team hoped to produce through molecular evolution, a TNA strand capable of acting as a high-specificity, high-affinity binding receptor for the human protein thrombin.

They first attempted to demonstrate that TNA nucleotides could attach by complementary base pairing to a random sequence of DNA, forming a hybrid DNA-TNA strand. A DNA polymerase enzyme assisted the process. Many of the random sequences, however, contained repeated sections of the guanine nucleotide, which had the effect of pausing the transcription of DNA into TNA. Once random DNA libraries were built excluding guanine, a high yield of DNA-TNA hybrid strands was produced.

The sequences obtained were 70 nucleotides in length, long enough Chaput says, to permit them to fold into shapes with defined binding sites. The DNA-TNA hybrids were then incubated with the target molecule thrombin. Sequences that bound with the target were recovered and amplified through PCR. The DNA portion was removed and used as a template for further amplification, while the TNA molecules displaying high-affinity, high specificity binding properties were retained.

Additionally, the binding affinity of the evolved and selected TNA molecules was tested against two other common proteins, for which they displayed no affinity, strengthening the case that a highly specific binding molecule had resulted from the group's directed evolution procedure.

Chaput suggests that issues concerning the prebiotic synthesis of ribose sugars and the non-enzymatic replication of RNA may provide circumstantial evidence of an earlier genetic system more readily produced under primitive earth conditions. Although solid proof that TNA acted as an RNA precursor in the prebiotic world may be tricky to obtain, Chaput points to the allure of this molecule as a strong candidate, capable of storing information, undergoing selection processes and folding into tertiary structures that can perform complex functions. This result provides the motivation to explore TNA as an early genetic system.

Chaput is optimistic that major questions about the prebiotic synthesis of TNA, its role in the origin and early evolution of life on earth, and eventual genetic takeover by RNA will, over time, be answered.

http://www.sciencedaily.com/releases/2012/01/120109103029.htm

Most Recent European Great Ape Discovered

ScienceDaily (Jan. 13, 2012) — Based on a hominid molar, scientists from Germany, Bulgaria and France have documented that great apes survived in Europe in savannah-like landscapes until seven million years ago.

A seven million year old pre-molar of a hominid discovered near the Bulgarian town of Chirpan documents that great apes survived longer in Europe than previously believed. An international team of scientists from the Bulgarian Academy of Science, the French Centre National de la Recherche Scientifique, and Madelaine Böhme from the Senckenberg Center for Human Evolution and Paleoenvironment at the University of Tübingen was involved in the project. The new discovery may cause a revision in our understanding of some major steps in hominid evolution.

To date scientists have assumed that great apes went extinct in Europe at least 9 million years ago because of changing climatic and environmental conditions. Under the direction of Nikolai Spassov from the National Museum of Natural Science in Sofia, Bulgaria, the molar was discovered in Upper Miocene fluvial sediments near Chirpan. The morphology and the great thickness of the tooth enamel point to a hominid fossil. The age of the fossiliferous sands at 7 million years reveals the fossil to be most recent known great ape from continental Europe.

Until now, the most recent fossil was that of a 9.2 million year old specimen of Ouranopithecus macedonensis from Greece. Hominids therefore were thought to have disappeared from Europe prior to 9 million years ago. At this time, European terrestrial ecosystems had been changed from mostly evergreen and lush forests to savannah-like landscapes with a seasonal climate. It had been thought that great apes, which typically consume fruits, were unable to survive this change due to a seasonal deficiency of fruits.

The scientists found animals typical of a savannah in the fossil-bearing layer: several species of elephants, giraffes, gazelles, antelopes, rhinos, and saber-toothed cats. This discovery suggests that European hominids were able to adapt to the seasonal climate of a savannah-like ecosystem. This conclusion is further corroborated by electron microscope analysis of the tooth's masticatory surface, which reveals that the Bulgarian hominid had consumed hard and abrasive objects like grass, seeds, and nuts. In this respect, the feeding behavior of this animal resembles that of later African hominids from about 4 million years ago (e.g. australopithecids like 'Lucy').

„We now also need to rethink where the origin of humans took place," says Professor Madelaine Böhme of the University of Tübingen. So far, most scientists believe that human evolution happened exclusively in Africa and that humans migrated from Africa to other continents. "There is increasing evidence, however, that a significant part of human evolution happened outside Africa, in Europe and western Asia."

That migration plays a major role in early hominid evolution was documented by paleontologists from the Senckenberg Center for Human Evolution and Paleoenvironment in June 2011, when they presented an early Eurasian hominid. A further piece to the puzzle had furthermore been an isolated molar tooth excavated southwest of Sigmaringen, Germany, and dated to 17 million years ago. The Tübingen group of paleoclimatologists led by Böhme reconstructed the climate at this time and demonstrated that great apes dispersed at this time under a tropical-subtropical and humid climate from Africa into Europe. Together, both investigations document an at least 10 million year lasting population of great apes in Europe and a significant evolution from fruit-eaters to harder object feeders.

http://www.sciencedaily.com/releases/2012/01/120113210347.htm

Evolution Is Written All Over Your Face

ScienceDaily (Jan. 11, 2012) — Why are the faces of primates so dramatically different from one another?

UCLA biologists working as "evolutionary detectives" studied the faces of 129 adult male primates from Central and South America, and they offer some answers in research published Jan. 11, in the early online edition of the journal Proceedings of the Royal Society B. The faces they studied evolved over at least 24 million years, they report.

"If you look at New World primates, you're immediately struck by the rich diversity of faces," said Michael Alfaro, a UCLA associate professor of ecology and evolutionary biology and the senior author of the study. "You see bright red faces, moustaches, hair tufts and much more. There are unanswered questions about how faces evolve and what factors explain the evolution of facial features. We're very visually oriented, and we get a lot of information from the face."

Some of theprimate species studied are solitary, while others live in groups that can include dozens or even hundreds of others.

The life scientists divided each face into 14 regions; coded the color of each part, including the hair and skin; studied the patterns and anatomy of the faces; and gave each a "facial complexity" score. They studied how the complexity of primate faces evolved over time and examined the primates' social systems. To assess how facial colors are related to physical environments, they analyzed environmental variables, using the longitude and latitude of primates' habitats as a proxy for sun exposure and temperature. They also used statistical methods to analyze the evolutionary history of the primate groups and when they diverged from one another.

"We found very strong support for the idea that as species live in larger groups, their faces become more simple, more plain," said lead author Sharlene Santana, a UCLA postdoctoral scholar in ecology and evolutionary biology and a postdoctoral fellow with UCLA's Institute for Society and Genetics. "We think that is related to their ability to communicate using facial expressions. A face that is more plain could allow the primate to convey expressions more easily.

"Humans have pretty bare faces, which may allow us to see facial expressions more easily than if, for example, we had many colors in our faces."

The researchers' finding that faces are more simple in larger groups came as a surprise.

"Initially, we thought it might be the opposite," Santana said. "You might expect that in larger groups, faces would vary more and have more complex parts that would allow one individual to identify any member of that group. That is not what we found. Species that live in larger groups live in closer proximity to one another and tend to use facial expressions more than species in smaller groups that are more spread out. Being in closer proximity puts a stronger pressure on using facial expressions."

"This finding suggests that facial expressions are increasingly important in large groups," said co-author Jessica Lynch Alfaro, associate director of the UCLA Institute for Society and Genetics. "If you're highly social, then facial expressions matter more than having a highly complex pattern on your face. "

The evolutionary biologists also found that when primates live in environment with more species that are closely related, their faces are more complex, regardless of their group size. This finding is consistent with their need to recognize individuals of other closely related species that live in the same habitat to avoid interbreeding, Santana said.

Santana, Lynch Alfaro and Alfaro present the first quantitative evidence linking social behavior to the evolution of facial diversity and complexity in primates, and they also show that ecology controls aspects of facial patterns.

As species live closer to the equator, the skin and hair around their eyes get darker, the biologists report. They also found that regions of the face around the nose and mouth get darker when species live in humid environments and denser forests and that facial hair gets longer as species live farther from the equator and the climate gets colder, which may be related to regulating body temperature.

"This is a good start toward understanding facial diversity," Alfaro said. "There was not a good idea before about what aspects of faces were shaped by which evolutionary pressure. Sharlene [Santana] has been able to say what social complexity, social behavior and ecology are doing to faces."

In the future, Santana, Lynch Alfaro and Alfaro may use computer facial-recognition software to help quantify the faces in a more sophisticated way. They also plan to study the faces of carnivores, including big cats.

Previous studies, they noted, have found that primate species with moustaches and beards (such as No. 11 and No. 9 in the accompanying image) tend to look poker-faced; they don't move their faces much when they communicate, compared with other species (such as No. 4).

Alfaro praised Santana's ability to answer some of these difficult evolutionary questions.

"Sharlene has tested ideas that have been virtually impossible to test before," he said. "She has found a clever way to implicate the degree of sociality as contributing to the diversity of faces. Social behavior explains some aspects of facial diversity."

Santana also devised a way to test a theory that has been in the biological literature for decades but had never been tested before. As a lineage diverges and species accumulate, a series of changes in facial coloration and body coloration emerges. The theory she was able to test suggests that once a species evolves to have a certain color, such as hair color, the change is irreversible and it cannot evolve back to a previous color in its lineage. Santana found this theory to be wrong.

"The idea in biology that evolutionary change is irreversible is rejected very strongly by our data," Alfaro said.

Lessons for human faces?

Does the study have implications for the evolution of human faces?

The findings do suggest, Alfaro said, that an important factor in shaping human faces is the premium on making unambiguous facial expressions.

"Humans don't have all these elaborate facial ornamentations, but we do have the ability to communicate visually with facial expressions," Alfaro said. "Does reduced coloration complexity create a blank palate for visual expressions that can be conveyed more easily? That is an idea we are testing."

Santana's research is funded by fellowships from the National Science Foundation and UCLA's Institute for Society and Genetics.

http://www.sciencedaily.com/releases/2012/01/120111223744.htm

Bacteria's Move from Sea to Land May Have Occurred Much Later Than Thought

ScienceDaily (Dec. 22, 2011) — Research by University of Tennessee, Knoxville, faculty has discovered that bacteria's move from sea to land may have occurred much later than thought. It also has revealed that the bacteria may be especially useful in bioenergy research.

Igor Jouline, UT-Oak Ridge National Laboratory joint faculty professor of microbiology and researcher at ORNL's Joint Institute for Computational Sciences, performed a genome sequence analysis of the soil bacteria Azospirillum, a species' whose forebearers made the sea-to-land move. The analysis indicates the shift may have occurred only 400 million years ago, rather than approximately two billion years earlier, as originally thought.

Published in the journal PLoS Genetics, Jouline calculated the timing of the sea-land transition through studies of genome sequences of two species of Azospirillum, a terrestrial genus with almost exclusively aquatic relatives.

Jouline conducted his research with Kristin Wuichet and Leonid Sukharnikov of the Department of Microbiology, Gladys Alexandre of Department of Biochemistry, Cellular, and Molecular Biology, and Kirill Borziak, a graduate student in the ORNL-UT Genome Science and Technology program.

"In the absence of fossil records for bacteria, it is hard to estimate when and how bacteria transitioned from sea to land," said Jouline. "Using genome sequencing and analysis of bacteria of the genus Azospirillum, which colonizes roots of important cereals and grasses, we show that these organisms transitioned from aquatic environments to land approximately at the same time that plants appeared on land -- 400 million years ago."

Jouline said the Azospirillum lineage the team studied has obtained nearly half of its genome from terrestrial organisms, which suggests the much later water-land transition, which coincides with the first appearance of plants on land.

The study is of interest to researchers beyond its evolutionary significance. Azospirillum is currently used as a biofertilizer for grasses and some other plants. Commercial fertilizers containing the bacteria are available world wide.

"Because these bacteria colonize roots of grasses and improve their growth and development, they might be important for bioenergy research," Jouline said.

"Switchgrass is one of the most important potential sources of bioethanol. In this study, we have shown that genomes of Azospirillum contain as many cellulolytic enzymes as those from known effective cellulose degrading bacteria," he said. "We have also demonstrated experimentally that azospirilla do degrade cellulose, especially the strain that can penetrate grass roots."

The team also included Greg Hurst of the ORNL Chemical Sciences Division; research groups from Pasteur Institute in Paris, France, universities of Lyon and Toulouse in France, University of Sydney in Australia, and the National University of Mexico; and Florence Wisniewski-Dye from the University of Lyon.

The research was supported with funding from the National Science Foundation and the Department of Energy's Office of Science.

http://www.sciencedaily.com/releases/2011/12/111222195017.htm

Molecular 'Culprit' in Rise of Planetary Oxygen

ScienceDaily (Jan. 10, 2012) — A turning point in the history of life occurred 2 billion to 3 billion years ago with the unprecedented appearance and dramatic rise of molecular oxygen. Now researchers report they have identified an enzyme that was the first -- or among the first -- to generate molecular oxygen on Earth.

The new findings, reported in the journal Structure, build on more than a dozen previous studies that aim to track the molecular evolution of life by looking for evidence of that history in present-day protein structures. These studies, led by University of Illinois crop sciences and Institute for Genomic Biology professor Gustavo Caetano-Anollés, focus on structurally and functionally distinct regions of proteins -- called folds -- that are part of the universal toolkit of living cells.

Protein folds are much more stable than the sequences of amino acids that compose them, Caetano-Anollés said. Mutations or other changes in sequence often occur without disrupting fold structure or function. This makes folds much more reliable markers of long-term evolutionary patterns, he said.

In the new study, Caetano-Anollés, working with colleagues in China and Korea, tackled an ancient mystery: Why did some of the earliest organisms begin to generate oxygen, and why?

"There is a consensus from earth scientists that about 2.4 billion years ago there was a big spike in oxygen on Earth," Caetano-Anollés said. They generally agree that this rise in oxygen, called the Great Oxygenation Event, was tied to the emergence of photosynthetic organisms.

"But the problem now comes with the following question," he said. "Oxygen is toxic, so why would a living organism generate oxygen? Something must have triggered this."

The researchers looked for answers in the "molecular fossils" that still reside in living cells. They analyzed protein folds in nearly a thousand organisms representing every domain of life to assemble a timeline of protein history. Their timeline for this study was limited to single-fold proteins (which the researchers believe are the most ancient), and was calibrated using microbial fossils that appeared in the geologic record at specific dates.

The analysis revealed that the most ancient reaction of aerobic metabolism involved synthesis of pyridoxal (the active form of vitamin B6, which is essential to the activity of many protein enzymes) and occurred about 2.9 billion years ago. An oxygen-generating enzyme, manganese catalase, appeared at the same time.

Other recent studies also suggest that aerobic (oxygen-based) respiration began on Earth 300 to 400 million years before the Great Oxidation Event, Caetano-Anollés said. This would make sense, since oxygen production was probably going on for a while before the spike in oxygen occurred.

Catalases convert hydrogen peroxide to water and oxygen. The researchers hypothesize that primordial organisms "discovered" this enzyme when trying to cope with an abundance of hydrogen peroxide in the environment. Some geochemists believe that hydrogen peroxide was abundant at this time as a result of intensive solar radiation on glaciers that covered much of Earth.

"In the glacial melt waters you would have a high concentration of hydrogen peroxide and that would be gradually exposing a number of the primitive organisms (alive at that time)," Caetano-Anollés said. The appearance of manganese catalase, an enzyme that degrades hydrogen peroxide and generates oxygen as a byproduct, makes it a likely "molecular culprit for the rise of oxygen on the planet," he said.

The research team included scientists from the Korea Research Institute of Bioscience and Biotechnology; Huazhong Agricultural University, China; and Shandong University of Technology, China.

http://www.sciencedaily.com/releases/2012/01/120110140216.htm

Death Anxiety Prompts People to Believe in Intelligent Design, Reject Evolution, Study Suggests

ScienceDaily (Mar. 30, 2011) — Researchers at the University of British Columbia and Union College (Schenectady, N.Y.) have found that people's death anxiety can influence them to support theories of intelligent design and reject evolutionary theory.

Existential anxiety also prompted people to report increased liking for Michael Behe, intelligent design's main proponent, and increased disliking for evolutionary biologist Richard Dawkins.

The lead author is UBC Psychology Asst. Prof. Jessica Tracy with co-authors Joshua Hart, assistant professor of psychology at Union College, and UBC psychology PhD student Jason Martens.

Published in the March 30 issue of the journal PLoS ONE, their paper is the first to examine the implicit psychological motives that underpin one of the most heated debates in North America. Despite scientific consensus that intelligent design theory is inherently unscientific, 25 per cent of high school biology teachers in the U.S. devote at least some class time to the topic of intelligent design. And in Canada, for example, Alberta passed a law in 2009 that may allow parents to remove children from courses covering evolution.

British evolutionary biologist Prof. Dawkins, like the majority of scientists, argues that life's origins are best explained by Charles Darwin's theory of natural selection. However, intelligent design advocates such as Prof. Behe, a U.S. author and biochemist, assert that complex biochemical and cellular structures are too complex to be explained by evolutionary mechanisms and should be attributed to a supernatural creator.

"Our results suggest that when confronted with existential concerns, people respond by searching for a sense of meaning and purpose in life," says Tracy. "For many, it appears that evolutionary theory doesn't offer enough of a compelling answer to deal with these big questions."

The researchers carried out five studies with 1,674 U.S. and Canadian participants of different ages and a broad range of educational, socioeconomic and religious backgrounds.

In each study, participants were asked to imagine their own death and write about their subsequent thoughts and feelings, or they were assigned to a control condition: imagining dental pain and writing about that.

The participants were then asked to read two similarly styled, 174-word excerpts from the writings of Behe and Dawkins, which make no mention of religion or belief, but describe the scientific and empirical support for their respective positions.

After going through these steps, participants who imagined their own death showed greater support for intelligent design and greater liking for Behe, or a rejection of evolution theory coupled with disliking for Dawkins, compared to participants in the control condition.

However, the research team saw reversed effects during the fourth study which had a new condition. Along with writings by Behe and Dawkins, there was an additional passage by Carl Sagan. A cosmologist and science writer, Sagan argues that naturalism -- the scientific approach that underlies evolution, but not intelligent design -- can also provide a sense of meaning. In response, these participants showed reduced belief in intelligent design after being reminded of their own mortality.

Tracy says, "These findings suggest that individuals can come to see evolution as a meaningful solution to existential concerns, but may need to be explicitly taught that taking a naturalistic approach to understanding life can be highly meaningful."

Similar results emerged in the fifth study, carried out entirely with natural science students at graduate and undergraduate levels. After thinking about death, these participants also showed greater support for the theory of evolution and liking of Dawkins, compared to control participants.

The researchers say these findings indicate a possible means of encouraging students to accept evolution and reject intelligent design.

"Natural science students have been taught to view evolutionary theory as compatible with the desire to find a greater sense of meaning in life," says Tracy. "Presumably, they already attain a sense of existential meaning from evolution."

The study received support from the Social Science and Humanities Research Council of Canada and the Michael Smith Foundation for Health Research.

http://www.sciencedaily.com/releases/2011/03/110330192201.htm

Evolution: Not Only the Fittest Survive

ScienceDaily (Mar. 29, 2011) — Darwin's notion that only the fittest survive has been called into question by new research published in the journal Nature. A collaboration between the Universities of Exeter and Bath in the UK, with a group from San Diego State University in the US, challenges our current understanding of evolution by showing that biodiversity may evolve where previously thought impossible.


Bacteria growing on a Petri plate. (Credit: iStockphoto/Monika Wisniewska)

The work represents a new approach to studying evolution that may eventually lead to a better understanding of the diversity of bacteria that cause human diseases.

Conventional wisdom has it that for any given niche there should be a best species, the fittest, that will eventually dominate to exclude all others.

This is the principle of survival of the fittest. Ecologists often call this idea the `competitive exclusion principle' and it predicts that complex environments are needed to support complex, diverse populations.

Professor Robert Beardmore, from the University of Exeter, said: "Microbiologists have tested this principle by constructing very simple environments in the lab to see what happens after hundreds of generations of bacterial evolution, about 3,000 years in human terms. It had been believed that the genome of only the fittest bacteria would be left, but that wasn't their finding. The experiments generated lots of unexpected genetic diversity."

This test tube biodiversity proved controversial when first observed and had been explained away with claims that insufficient time had been allowed to pass for a clear winner to emerge.

The new research shows the experiments were not anomalies.

Professor Laurence Hurst, of the University of Bath, said: "Key to the new understanding is the realization that the amount of energy organisms squeeze out of their food depends on how much food they have. Give them abundant food and they use it inefficiently. When we combine this with the notion that organisms with different food-utilizing strategies are also affected in different ways by genetic mutations, then we discover a new principle, one in which both the fit and the unfit coexist indefinitely."

Dr Ivana Gudelj, also from the University of Exeter, said: "The fit use food well but they aren't resilient to mutations, whereas the less efficient, unfit consumers are maintained by their resilience to mutation. If there's a low mutation rate, survival of the fittest rules, but if not, lots of diversity can be maintained.

"Rather nicely, the numbers needed for the principle to work accord with those enigmatic experiments on bacteria. Their mutation rate seems to be high enough for both fit and unfit to be maintained."

Dr. David Lipson of San Diego State University, concluded: "Earlier work showed that opposing food utilization strategies could coexist in complex environments, but this is the first explanation of how trade-offs, like the one we studied between growth rate and efficiency, can lead to stable diversity in the simplest possible of environments."

http://www.sciencedaily.com/releases/2011/03/110327191044.htm

Was Israel the Birthplace of Modern Humans?

ScienceDaily (Dec. 31, 2010) — It has long been believed that modern humans emerged from the continent of Africa 200,000 years ago. Now Tel Aviv University archaeologists have uncovered evidence that Homo sapiens roamed the land now called Israel as early as 400,000 years ago -- the earliest evidence for the existence of modern humans anywhere in the world.



It has long been believed that modern humans emerged from the continent of Africa 200,000 years ago.

The findings were discovered in the Qesem Cave, a pre-historic site located near Rosh Ha'ayin that was first excavated in 2000. Prof. Avi Gopher and Dr. Ran Barkai of Tel Aviv University's Department of Archaeology, who run the excavations, and Prof. Israel Hershkowitz of the university's Department of Anatomy and Anthropology and Sackler School of Medicine, together with an international team of scientists, performed a morphological analysis on eight human teeth found in the Qesem Cave.

This analysis, which included CT scans and X-rays, indicates that the size and shape of the teeth are very similar to those of modern humans. The teeth found in the Qesem Cave are very similar to other evidence of modern humans from Israel, dated to around 100,000 years ago, discovered in the Skhul Cave in the Carmel and Qafzeh Cave in the Lower Galilee near Nazareth. The results of the researchers' findings are being published in the American Journal of Physical Anthropology.

Reading the past

Qesem Cave is dated to a period between 400,000 and 200,000 years ago, and archaeologists working there believe that the findings indicate significant evolution in the behavior of ancient humans. This period of time was crucial in the history of humankind from cultural and biological perspectives. The teeth that are being studied indicate that these changes are apparently related to evolutionary changes taking place at that time.

Prof. Gopher and Dr. Barkai noted that the findings related to the culture of those who dwelled in the Qesem Cave -- including the systematic production of flint blades; the regular use of fire; evidence of hunting, cutting and sharing of animal meat; mining raw materials to produce flint tools from subsurface sources -- reinforce the hypothesis that this was, in fact, innovative and pioneering behavior that may correspond with the appearance of modern humans.

An unprecedented discovery

According to researchers, the discoveries made in the Qesem Cave may overturn the theory that modern humans originated on the continent of Africa. In recent years, archaeological evidence and human skeletons found in Spain and China also undermined this proposition, but the Qesem Cave findings because of their early age is an unprecedented discovery.

Excavations at Qesem Cave continue and the researchers hope to uncover additional finds that will enable them to confirm the findings published up to now and to enhance our understanding of the evolution of humankind -- especially the emergence of modern man.

http://www.sciencedaily.com/releases/2010/12/101230123554.htm

Oxygen-Free Early Oceans Likely Delayed Rise of Life on Planet

ScienceDaily (Jan. 10, 2011) — Geologists at the University of California, Riverside have found chemical evidence in 2.6-billion-year-old rocks that indicates that Earth's ancient oceans were oxygen-free and, surprisingly, contained abundant hydrogen sulfide in some areas.

"We are the first to show that ample hydrogen sulfide in the ocean was possible this early in Earth's history," said Timothy Lyons, a professor of biogeochemistry and the senior investigator in the study, which appears in the February issue of Geology. "This surprising finding adds to growing evidence showing that ancient ocean chemistry was far more complex than previously imagined and likely influenced life's evolution on Earth in unexpected ways -- such as, by delaying the appearance and proliferation of some key groups of organisms."

Ordinarily, hydrogen sulfide in the ocean is tied to the presence of oxygen in the atmosphere. Even small amounts of oxygen favor continental weathering of rocks, resulting in sulfate, which in turn gets transported to the ocean by rivers. Bacteria then convert this sulfate into hydrogen sulfide.

How then did the ancient oceans contain hydrogen sulfide in the near absence of oxygen, as the 2.6-million-year-old rocks indicate? The UC Riverside-led team explains that sulfate delivery in an oxygen-free environment can also occur in sufficient amounts via volcanic sources, with bacteria processing the sulfate into hydrogen sulfide.

Specifically, Lyons and colleagues examined rocks rich in pyrite -- an iron sulfide mineral commonly known as fool's gold -- that date back to the Archean eon of geologic history (3.9 to 2.5 billion years ago) and typify very low-oxygen environments. Found in Western Australia, these rocks have preserved chemical signatures that constitute some of the best records of the very early evolutionary history of life on the planet.

The rocks formed 200 million years before oxygen amounts spiked during the so-called "Great Oxidation Event" -- an event 2.4 billion years ago that helped set the stage for life's proliferation on Earth.

"Our previous work showed evidence for hydrogen sulfide in the ocean more than 100 million years before the first appreciable accumulation of oxygen in the atmosphere at the Great Oxidation Event," Lyons said. "The data pointing to this 2.5 billion-year-old hydrogen sulfide are fingerprints of incipient atmospheric oxygenation. Now, in contrast, our evidence for abundant 2.6 billion-year-old hydrogen sulfide in the ocean -- that is, another 100 million years earlier -- shows that oxygen wasn't a prerequisite. The important implication is that hydrogen sulfide was potentially common for a billion or more years before the Great Oxidation Event, and that kind of ocean chemistry has key implications for the evolution of early life."

Clint Scott, the first author of the research paper and a former graduate student in Lyons's lab, said the team was also surprised to find that the Archean rocks recorded no enrichments of the trace element molybdenum, a key micronutrient for life that serves as a proxy for oceanic and atmospheric oxygen amounts.

The absence of molybdenum, Scott explained, indicates the absence of oxidative weathering of the continental rocks at this time (continents are the primary source of molybdenum in the oceans). Moreover, the development of early life, such as cyanobacteria, is determined by the amount of molybdenum in the ocean; without this life-affirming micronutrient, cyanobacteria could not become abundant enough to produce large quantities of oxygen.

"Molybdenum is enriched in our previously studied 2.5 billion-year-old Archean rocks, which ties to the earliest hints of atmospheric oxygenation as a harbinger of the Great Oxidation Event," Scott said. "The scarcity of molybdenum in rocks deposited 100 million years earlier, however, reflects its scarcity also in the overlying water column. Such metal deficiencies suggest that cyanobacteria were probably struggling to produce oxygen when these rocks formed.

"Our research has important implications for the evolutionary history of life on Earth," Scott added, "because biological evolution both initiated and responded to changes in ocean chemistry. We are trying to piece together the cause-and-effect relationships that resulted, billions of years later, in the evolution of animals and, ultimately, humans. This is really the story of how we got here."

The first animals do not appear in the fossil record until around 600 million years ago -- almost two billion years after the rocks studied by Scott and his team formed. The steady build-up of oxygen, which began towards the end of the Archean, played a key role in the evolution of new life forms.

"Future research needs to focus on whether sulfidic and oxygen-free conditions were prevalent throughout the Archean, as our model predicts," Scott said.

Lyons and Scott were accompanied on this project by Christopher Reinhard from UCR; Andrey Bekker from the University of Manitoba, Canada; Bernhard Schnetger from Oldenburg University, Germany; Bryan Krapež from the Curtin University of Technology, Western Australia; and Douglas Rumble III from the Carnegie Institution of Washington, Washington, DC. Currently, Scott is a postdoctoral researcher at McGill University, Canada.

Funding for this work came from the National Science Foundation, the NASA Exobiology Program, the NASA Astrobiology Institute, and through a Canadian National Sciences and Engineering Research Council Discovery Grant.

http://www.sciencedaily.com/releases/2011/01/110110151016.htm

Widespread, Persistent Oxygen-Poor Conditions in Earth's Ancient Oceans Impacted Early Evolution of Animals

ScienceDaily (Jan. 6, 2011) — The conventional view of the history of the Earth is that the oceans became oxygen-rich to approximately the degree they are today in the Late Ediacaran Period (about 600 million years ago) after staying relatively oxygen-poor for the preceding four billion years. But biogeochemists at the University of California, Riverside have found evidence that shows that the ocean went back to being "anoxic" or oxygen-poor around 499 million years ago, soon after the first appearance of animals on the planet, and remained anoxic for 2-4 million years. What's more, the researchers suggest that such anoxic conditions may have been commonplace over a much broader interval of time, with their data capturing a particularly good example.



Researcher Benjamin Gill near the top of a stratigraphic section at Lawsons Cove, Utah. (Credit: Steve Bates.)

The researchers argue that such fluctuation in the ocean's oxygenation state is the most likely explanation for what drove the rapid evolutionary turnover famously recognized in the fossil record of the Cambrian Period (540 to 488 million years ago).

They report in the Jan. 6 issue of Nature that the transition from a generally oxygen-rich ocean during the Cambrian to the fully oxygenated ocean we have today was not a simple turn of the switch, as has been widely accepted until now.

"Our research shows the ocean fluctuated between oxygenation states 499 million years ago," said co-author Timothy Lyons, a professor of biogeochemistry, whose lab led the research, "and such fluctuations played a major, perhaps dominant, role in shaping the early evolution of animals on the planet by driving extinction and clearing the way for new organisms to take their place."

Oxygen is a staple for animal survival, but not for the many bacteria that thrive in and even demand life without oxygen.

Understanding how the environment changed over the course of Earth's history can clue scientists to how exactly life evolved and flourished during the critical, very early stages of animal evolution.

"Life and the environment in which it lives are intimately linked," said Benjamin Gill, the first author of the research paper, who worked in Lyons's lab as a graduate student. Gill explained that when the ocean's oxygenation states changed rapidly in Earth's history, some organisms were not able to cope. Further oceanic oxygen affects cycles of other biologically important elements such as iron, phosphorus and nitrogen.

"Disruption of these cycles is another way to drive biological crises," he said. "Thus both directly and indirectly a switch to an oxygen-poor state of the ocean can cause major extinction of species."

The researchers are now working on finding an explanation for why the oceans became oxygen-poor about 499 million years ago.

"What we have found so far is evidence that it happened," Gill said. "We have the 'effect,' but not the 'cause.' The oxygen-poor state persisted for 2-4 million years, likely until the enhanced burial of organic matter, originally derived from oxygen-producing photosynthesis, resulted in the accumulation of more oxygen in the atmosphere and ocean. As a kind of negative feedback, the abundant burial of organic material facilitated by anoxia may have bounced the ocean to a more oxygen-rich state."

Gill stressed that understanding past events in Earth's distant history can help refine our view of changes happening on the planet presently.

"Today, some sections of the world's oceans are becoming oxygen-poor -- the Chesapeake Bay and the so-called 'dead zone' in the Gulf of Mexico are just two examples," he said. "We know the Earth went through similar scenarios in the past. Understanding the ancient causes and consequences can provide essential clues to what the future has in store for our ocean."

In the study, Lyons, Gill and their team examined the carbon, sulfur and molybdenum contents of rocks they collected from localities in the United States, Sweden, and Australia. Combined, these analyses allowed the team to infer the amount of oxygen present in the ocean at the time the limestones and shales were deposited. By looking at successive rock layers, they were able to compile the biogeochemical history of the ocean.

Lyons and Gill were joined in the research by Seth A. Young of Indiana University, Bloomington; Lee R. Kump of Penn State University; Andrew H. Knoll of Harvard University; and Matthew R. Saltzman of Ohio State University. Currently, Gill is a postdoctoral researcher at Harvard University.

The study was funded by a grant from the U.S. National Science Foundation.

http://www.sciencedaily.com/releases/2011/01/110105131743.htm

Neandertals’ Extinction Not Caused by Deficient Diets, Tooth Analysis Shows

ScienceDaily (Jan. 1, 2011) — Researchers from George Washington University and the Smithsonian Institution have discovered evidence to debunk the theory that Neandertals' disappearance was caused in part by a deficient diet -- one that lacked variety and was overly reliant on meat. After discovering starch granules from plant food trapped in the dental calculus on 40-thousand-year-old Neandertal teeth, the scientists believe that Neandertals ate a wide variety of plants and included cooked grains as part of a more sophisticated, diverse diet similar to early modern humans.

Neandertal teeth from Shanidar cave. (Credit: George Washington University)

"Neandertals are often portrayed as very backwards or primitive," said Amanda Henry, lead researcher and a post-doctoral researcher at GW. "Now we are beginning to understand that they had some quite advanced technologies and behaviors."

Dr. Henry made this discovery together with Alison Brooks, professor of anthropology and international affairs at GW, and Dolores Piperno, a GW research professor and senior scientist and curator of archaeobotany and South American archaeology at the Smithsonian National Museum of Natural History, Washington D.C., and Smithsonian Tropical Research Institute, Panama.

The discovery of starch granules in the calculus on Neandertal teeth provides direct evidence that they made sophisticated, thoughtful food choices and ate more nutrient-rich plants, for example date palms, legumes and grains such as barley. Until now, anthropologists have hypothesized that Neandertals were outlived by early modern humans due in part to the former's primitive, deficient diet, with some scientists arguing Neandertals' diets were specialized for meat-eating. As such, during major climate swings Neandertals could be outcompeted by early humans who incorporated diverse plant foods available in the local environment into their diets.

Drs. Henry, Brooks and Piperno's discovery suggests otherwise. The researchers discovered starch granules in dental calculus, which forms when plaque buildup hardens, on the fossilized teeth of Neandertal skeletons excavated from Shanidar Cave in Iraq and Spy Cave in Belgium. Starch granules are abundant in most human plant foods, but were not known to survive on fossil teeth this old until this study. The researchers' findings indicate that Neandertals' diets were more similar to those of early humans than originally thought. The researchers also determined from alterations they observed in the starch granules that Neandertals prepared and cooked starch-rich foods to make them taste better and easier to digest.

"Neandertals and early humans did not visit the dentist," said Dr. Brooks. "Therefore, the calculus or tartar remained on their teeth, preserving tiny clues to the previously unknown plant portion of their diets."

Dr. Henry is currently a post-doctoral researcher in the Columbian College of Arts and Sciences Hominid Paleobiology program at the George Washington University, where she also received her Ph.D. in Jan. 2010. Her research focuses on the uses of plant foods by human ancestors. In Jan. 2011, Dr. Henry will begin leading an independent research group focusing on the evolution of human diet at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Dr Brooks' research focuses on the evolution of modern human behavior. Dr. Piperno is a pioneer in the detection and study of plant microfossils and the evolution of human diets.

"This significant finding provides new insight on the plight of the Neandertals," said Peg Barratt, dean of GW's Columbian College of Arts and Sciences. "It's also an excellent example of our dynamic partnership with the Smithsonian to further advance learning and discovery."

The research was supported by a National Science Foundation IGERT award, a Wenner Gren Foundation doctoral dissertation award, a Smithsonian Institution pre-doctoral fellowship, a National Science Foundation HOMINID award to the Smithsonian Institution and a selective excellence award from the George Washington University.

http://www.sciencedaily.com/releases/2010/12/101230113723.htm

Heat Helped Hasten Life's Beginnings on Earth, Research Suggests

ScienceDaily (Dec. 5, 2010) — There has been controversy about whether life originated in a hot or cold environment, and about whether enough time has elapsed for life to have evolved to its present complexity.


Lava flow. (Credit: USGS)

But new research at the University of North Carolina at Chapel Hill investigating the effect of temperature on extremely slow chemical reactions suggests that the time required for evolution on a warm earth is shorter than critics might expect.

The findings are published in the Dec. 1, 2010, online early edition of the Proceedings of the National Academy of Sciences.

Enzymes, proteins that jump-start chemical reactions, are essential to life within cells of the human body and throughout nature. These molecules have gradually evolved to become more sophisticated and specific, said lead investigator Richard Wolfenden, PhD, Alumni Distinguished Professor of biochemistry and biophysics at the UNC School of Medicine.

To appreciate how powerful modern enzymes are, and the process of how they evolved, scientists need to know how quickly reactions occur in their absence.

Wolfenden's group measured the speed of chemical reactions, estimating that some of them take more than 2 billion years without an enzyme.

In the process of measuring slow reaction rates, "it gradually dawned on us that the slowest reactions are also the most temperature-dependent," Wolfenden said.

In general, the amount of influence temperature has on reaction speeds varies drastically, the group found. In one slow reaction, for instance, raising the temperature from 25 to 100 degrees Celsius increases the rate 10 million fold. "That is a shocker," Wolfenden said. "That's what's going to surprise people most, as it did me."

That is surprising, Wolfenden said, because a textbook rule in chemistry -- for more than a century -- has been that the influence of temperature is modest. In particular, a doubling in reaction rate occurs when the temperature rises 10 degree Celsius, according to experiments done in 1866.

High temperatures were probably a crucial influence on reaction rates when life began forming in hot springs and submarine vents, Wolfenden said. Later, the cooling of the earth provided selective pressure for primitive enzymes to evolve and become more sophisticated, the Wolfenden's group hypothesizes.

Using two different reaction catalysts -- which are not protein enzymes but that may have resembled early precursors to enzymes -- the group put the hypothesis to the test. The catalyzed reactions are indeed far less sensitive to temperature, compared with reactions that are accelerated by catalysts. The results are consistent with our hypothesis, Wolfenden said.

Wolfenden's group plans to test the hypothesis using other catalysts. In the meantime, these findings are likely to influence how scientists think of the first primitive forms of life on earth, and may affect how researchers design and enhance the power of artificial catalysts, he added.

Study co-authors from UNC are Randy Stockbridge, PhD, Charles Lewis, Jr., PhD and research specialist Yang Yuan, MS. Support for the research came from the National Institute of General Medicine, a component of the National Institutes of Health.

http://www.sciencedaily.com/releases/2010/12/101202124321.htm

Sewage Water Bacteria: 'Missing Link' in Early Evolution of Life on Earth?

ScienceDaily (Nov. 27, 2010) — A common group of bacteria found in acid bogs and sewage treatment plants has provided scientists with evidence of a 'missing link' in one of the most important steps in the evolution of life on Earth -- the emergence of cells with a nucleus containing DNA (eukaryotic cells).


New research shows that PVC (Planctomycetes, Verrucomicrobiae, Chlamydiae) bacteria -- members of which are commonly found in today's sewage treatment plants or acid bogs -- represent an intermediate type of cell structure. (Credit: iStockphoto/Viktor Balabanov).

For billions of years, bacteria (single celled organisms without a nucleus) were the only cellular life form on Earth. Then, about 1.6 to 2.1 billion years ago, eukaryotic cells emerged. These cells (with a nucleus) heralded the evolution of multi-cellular life on Earth including: plants, insects, animals and humans.

Until now scientists have been unable to identify an 'ancestral cell' linking the early prokaryotes with the later eukaryotes, so fusion theory -- where two cells merge to form a new cell -- is often put forward to explain the appearance of these new cell types.

But new findings by scientists from University College Dublin, Ireland, and the European Molecular Biology Laboratory in Heidelberg, Germany, published in Science (Nov. 26, 2010), have put paid to the fusion theory explanation, and suggest that an intermediate or 'missing link' cell did exist all those billions of years ago.

"Our discovery means that the appearance of eukaryotic cells on Earth can be explained by Darwinian evolution over billions of years rather than a 'big bang' fusion theory," says cell biologist Dr Emmanuel Reynaud from University College Dublin, one of the co-authors of the scientific paper.

"Our analysis shows that PVC [Planctomycetes, Verrucomicrobiae, Chlamydiae] bacteria, members of which are commonly found in today's sewage treatment plants or acid bogs, represent an intermediate type of cell structure. They are slightly bigger than other known bacteria, and they also divide more slowly."

"The structure of PVC suggests that it is an ancestor of a 'missing link' cell which connected prokaryotic to eukaryotic cells along an evolutionary path all those billions of years ago," says Dr Damien P Devos from the European Molecular Biology Laboratory, Heidelberg, Germany, who co-authored the scientific paper.

http://www.sciencedaily.com/releases/2010/11/101126094444.htm

Age Doesn't Matter: New Genes Are as Essential as Ancient Ones

ScienceDaily (Dec. 16, 2010) — New genes that have evolved in species as little as one million years ago -- a virtual blink in evolutionary history -- can be just as essential for life as ancient genes, startling new research has discovered.


The development process for Drosophila melanogaster stopped at the pharate stage when the new gene G32376 was knocked down. This gene originated 18 million years ago. (Credit: Manyuan Long Lab/University of Chicago)

Evolutionary biologists have long proposed that the genes most important to life are ancient and conserved, handed down from species to species as the "bread and butter" of biology. New genes that arise as species split off from their ancestors were thought to serve less critical roles -- the "vinegar" that adds flavor to the core genes.

But when nearly 200 new genes in the fruit fly species Drosophila melanogaster were individually silenced in laboratory experiments at the University of Chicago, more than 30 percent of the knockdowns were found to kill the fly. The study, published December 17 in Science, suggests that new genes are equally important for the successful development and survival of an organism as older genes.

"A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."

The study used technology called RNA interference to permanently block the transcription of each targeted gene into its functional product from the beginning of a fly's life. Of the 195 young genes tested, 59 were lethal (30 percent), causing the fly to die during its development. When the same method was applied to a sample of older genes, a statistically similar figure was found: 86 of 245 genes (35 percent) were lethal when silenced.

Because the young genes tested only appeared between 1 and 35 million years ago, the data suggests that new genes with new functions can become an essential part of a species' biology much faster than previously thought. A new gene may become indispensable by forming interactions with older genes that control important functions, said Sidi Chen, University of Chicago graduate student and first author of the study.

"New genes come in and quickly interact with older genes, and if that interaction is favorable by helping the organism survive or reproduce better, it is favored by natural selection and stays in the genome," Chen said. "After a while, it becomes essential, and the organism literally cannot live without the gene any more. It's something like love: You fall in love with someone and then you cannot live without them."

The indispensable nature of new genes also questions long-held beliefs about the shared features of development across different species. In 1866, German zoologist Ernst Haeckel famously hypothesized that "ontogeny recapitulates phylogeny" after observing that the early steps of development are shared by animals as different as fly and man.

Biologists subsequently predicted and confirmed that the same ancient, essential genes would be the conductors of this early development in all species. This principle enabled the use of model organisms, including flies, mice, and rats, to be used for research on the mechanisms of human disease.

Intriguingly, in the new study, deleting many of the new genes causes flies to die during middle or late stages of development, while older genes were lethal during early development. So while ancient genes essential for the early steps of development are shared, newer genes unique to each species may take over the later developmental stages that make each species unique. For example, many new genes in the study were found to be involved with metamorphosis, the mid-life stage that drastically transforms the body plan in animals.

"This may change the way we view the developmental program," Long said. "Each species has a different species-specific developmental program shaped by natural selection, and we can no longer say that from Drosophila to humans the development of different organisms is just encoded by the same genetic program. The story is much more complicated than what we used to believe."

As such, a full understanding of biological diversity may require a new focus on genes unique to each organism.

"I think it has important implications on human health," Chen said. "Animal models have proven to be very useful and important for dissecting human disease. But if our intuition is correct, some important health information for humans will reside in the unique parts of the human genome."

The newfound importance of young genes and unique developmental programs may have a dramatic impact on the field, Long said. The discovery will also inspire new research directions examining how quickly new genes can become essential and their exact role in species-specific development.

"Biologists have long assumed, quite reasonably, that ancient genes have survived natural selection because they are essential to life and that new genes are generally less critical to an organism's development," said Irene Eckstrand, PhD, who manages Dr. Long's and other evolutionary biology grants at the National Institutes of Health. "This important study suggests that this assumption is flawed, unlocking new questions that could lead to a deeper understanding of evolutionary processes and their impact on human health."

The work was funded by grants from the National Institute of General Medical Sciences, the National Science Foundation, and the Chicago Biomedical Consortium.

http://www.sciencedaily.com/releases/2010/12/101216142523.htm

Molecular Fossil: Crystal Structure Shows How RNA, One of Biology's Oldest Catalysts, Is Made

ScienceDaily (Dec. 17, 2010) — In today's world of sophisticated organisms proteins are the stars. They are the indispensible catalytic workhorses, carrying out the processes essential to life. But long, long ago ribonucleic acid (RNA) reigned supreme.

Now Northwestern University researchers have produced an atomic picture that shows how two of these very old molecules interact with each other. It is a rare glimpse of the transition from an ancient, RNA-based world to our present, protein-catalyst dominated world.

The scientists are the first to show the atomic details of how ribonuclease P (RNase P) recognizes, binds and cleaves transfer RNA (tRNA). They used the powerful X-rays produced by the Advanced Photon Source at Argonne National Laboratory to obtain images from crystals formed by these two RNA molecules. The result is a snapshot of one of the most complex models of a catalytic RNA and its target.

Details of the structure will be published Nov. 14 by the journal Nature.

"RNA is an ancient molecule, but it is pretty sophisticated," said Alfonso Mondragón, professor of molecular biosciences in the Weinberg College of Arts and Sciences. He led the research. "Our crystal structure shows that it has many of the properties we ascribe to modern molecules. RNA is a catalyst that has much of the versatility and complexity of modern-day proteins."

For billions of years and still to this day, the function of RNase P -- found in nearly all organisms, from bacteria to humans -- has been to cleave transfer tRNA. If the tRNA is not cleaved, it is not useful to the cell.

"We knew this important chemistry happened, that RNA acts as a catalyst, but we didn't know exactly how until now," Mondragón said. "We now have a better understanding of how RNA works."

RNase P is formed by a large RNA core plus a small protein, illustrating the evolutionary shift from an RNA world toward a protein-dominated world. The protein helps recognize the tRNA, but most of the recognition occurs through RNA-RNA interactions involving shape complementarity and also base pairing.

The structure shows that once RNase P recognizes tRNA, it docks and, assisted by metal ions, cuts one chemical bond. This matures the tRNA, producing a smaller RNA molecule that now can contribute to fundamental processes in the cell. The RNA-based enzyme does this over and over, cutting each tRNA in exactly the same place every time.

"The discovery nearly 30 years ago that RNA molecules can have a catalytic function raised the idea that maybe RNA was the first molecule," Mondragón said. "Our work reinforces this notion of the existence of an RNA world when life first began."

http://www.sciencedaily.com/releases/2010/11/101114161935.htm

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