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(Bio) Evolution: A Global Evolutionary Map (Tree of Life)
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PostPosted: Sun Mar 05, 2006 8:39 am    Post subject: (Bio) Evolution: A Global Evolutionary Map (Tree of Life) Reply with quote






A global evolutionary map reveals new insights into our last common ancestor
2 March 2006
European Molecular Biology Laboratory

In 1870 the German scientist Ernst Haeckel mapped the evolutionary relationships of plants and animals in the first 'tree of life'. Since then scientists have continuously redrawn and expanded the tree adding microorganisms and using modern molecular data, yet, many parts of the tree have remained unclear. Now a group at the European Molecular Biology Laboratory [EMBL] in Heidelberg has developed a computational method that resolves many of the open questions and produced what is likely the most accurate tree ever. The study, which appears in the current issue of the journal Science, gives some intriguing insights into the origins of bacteria and the last common universal ancestor of all life on earth today.

"DNA sequences of complete genomes provide us with a direct record of evolution", says Peer Bork, Associate Coordinator for Structural and Computational Biology at EMBL, whose group carried out the project. "For a long time the overwhelming amount of data [the human genome alone contains enough information to fill 200 telephone books] has made it very difficult to pinpoint the information needed for a high-resolution map of evolution. But our study shows how this challenge can be tackled by combining different computational methods in an automated process."

Bork's lab specialises in the computational analysis of genomes, and recently they applied this expertise to the tree of life. Since all organisms descend from the same ancestor, they share some common genes. Francesca Ciccarelli and Tobias Doerks of Bork's group managed to identify 31 genes with clear relatives in 191 organisms, ranging from bacteria to humans, to reconstruct their relationships.

"Even using such genes, you might get the wrong answer," says Ciccarelli. "Organisms inherit most genes from their parents, but over the course of evolution, a few have been obtained when organisms swapped genes with their neighbours in a process called horizontal gene transfer [HGT]. Obviously, the latter class of genes does not tell you anything about your ancestors. The trick was to identify and exclude them from the analysis."

"This procedure drastically reduced the 'noise' in the data, making it possible to identify as yet unknown details of early evolution," says Tobias Doerks. "For example, we now know that the first bacterium was probably a type called gram-positive and likely lived at high temperatures – suggesting that all life arose in hot environments."

The improved tree has also shed light on other research carried out by the group. Bork and colleagues are participating in projects that collect genetic material of unknown species en masse from environments such as farm soil and ocean floor. "With the new high-resolution tree in hand, it is now possible to classify genetic material from this unexplored microbial world and further our understanding of life on the planet."

Source Article
F. D. Ciccarelli, T. Doerks, C. von Mering, C. J. Creevey, B. Snel & P. Bork. Towards automatic reconstruction of a highly resolved tree of life. Science, 3 March 2006.

*************************************************************

Questions to explore further this topic:

What is the "Tree of Life" (other recent news)?

http://www.nsf.gov/od/lpa/news/02/pr0294.htm
http://www.spaceref.com/news/v.....?pid=19080
http://www.news.wisc.edu/11974.html
http://www.news.wisc.edu/newsp.....ltree.html

What is the "Tree of Life"?

http://tolweb.org/tree/
http://www.sciencemag.org/feature/data/tol/
http://ology.amnh.org/biodiver.....index.html
http://www.fossilmuseum.net/Tr.....n_page.htm
http://cas.bellarmine.edu/tiet.....n_and_.htm
http://www.nhc.ed.ac.uk/index.php?page=236

Archaea
http://www.sidwell.edu/us/scie.....b/Archaea/

Bacteria
http://www.sidwell.edu/us/scie...../Bacteria/

Eukarya
http://www.sidwell.edu/us/scie.....b/Eukarya/

What is a cladogram?

http://ology.amnh.org/biodiver.....ogram.html
http://ology.amnh.org/biodiver.....clado.html

An interactive "Tree of Life"

http://genome.jgi-psf.org/tre_home.html
http://evolution.berkeley.edu/.....tree.shtml

What is "geological time"?

http://www.fossilmuseum.net/Ge.....achine.htm
http://www.fossilmuseum.net/PaleobiologyVFM.htm
http://www.fossilmuseum.net/GeologicalHistory.htm

What is phylogeny?

http://www.ucmp.berkeley.edu/e.....phylo.html

Why is it important to assemble the "Tree of Life"?

http://www.nsf.gov/bio/pubs/reports/atol.pdf

What is the "origin of the species"?

http://www.bbc.co.uk/education.....osintr.htm

What is the theory of evolution?

http://www.pbs.org/wgbh/evolution/
http://evolution.berkeley.edu/

Becoming Human: A Documentary

http://www.becominghuman.org/

Evolution Teaching Resources

http://www.nas.edu/evolution/

Teaching Evolution

http://evolution.berkeley.edu/evosite/evohome.html
http://newton.nap.edu/html/evolution98/

Evolution is a Theory

http://www.livescience.com/oth.....50218.html

How Evolution Works

http://www.livescience.com/oth.....ience.html

The Missing Links in Human Evolution

http://www.livescience.com/hum.....links.html

What are vestigial organs?

http://www.livescience.com/ani.....rgans.html

Intelligent Design: An Ambiguous Assault on Evolution

http://www.livescience.com/hum....._main.html

Intelligent Design: The Death of Science

http://www.livescience.com/oth.....ience.html

Intelligent Design: Belief Posing as Theory

http://www.livescience.com/oth.....elief.html

Anti-evolution Attacks on the Rise

http://www.livescience.com/oth.....cases.html

GAMES

http://www.bbc.co.uk/sn/prehis.....sign.shtml


Last edited by adedios on Sat Jan 27, 2007 3:37 pm; edited 2 times in total
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PostPosted: Fri Apr 07, 2006 10:45 am    Post subject: New fossils fill the evolutionary gap Reply with quote

National Science Foundation
6 April 2006

New fossils fill the evolutionary gap between fish and land animals

Predator has sharp teeth, a crocodile-like head and flattened body
Working in rocks more than 375 million years old far above the Arctic Circle, paleontologists have discovered a remarkable new fossil species that represents the most compelling evidence yet of an intermediate stage between fish and early limbed animals.
The new species has a skull, neck, ribs, and parts of a fin that resemble the earliest limbed animals, called tetrapods. But the creature also has fins and scales like a fish.

"This animal is both fish and tetrapod. We jokingly call it a fishapod," said Neil Shubin of the University of Chicago. He and paleontologists from the Academy of Natural Sciences in Philadelphia, the University of Chicago, and Harvard University conducted the research. They report the finding in two papers published this week in the journal Nature.

"Paleontologists have known that animals first appeared on land in the Devonian Period," said Richard Lane, program director in the National Science Foundation (NSF)'s division of earth sciences, which funded the research. "To reach this evolutionary milestone, a skeletal progression from fish to land-roaming tetrapods would have been needed. Now we have new evidence of that progression."

The back of the animal's skull, neck, ribs and fins "are particularly tetrapod-like while the snout, lower jaws, and scale-cover are similar to those seen in closely related fish," Shubin said. The animal was a predator with sharp teeth, a crocodile-like head and a flattened body.

Scientists collected the fossils during four summer explorations on Ellesmere Island in Canada's Nunavut Territory. They turned to the people of Nunavut, who retain ownership of the fossils, for help in naming the new creature. The Nunavut Elders Council suggested the name "Tiktaalik" (tic-TA-lick), their word for a large, shallow-water fish.

At the time Tiktaalik lived, the Canadian Arctic region was part of a landmass that straddled the equator and had a subtropical climate. The deposits that produced the Tiktaalik fossils were left by stream systems meandering across wide floodplains.

"This kind of shallow stream system seems to be where many features of land-living animals first arose," said Ted Daeschler of the Academy of Natural Sciences in Philadelphia. "The species shows that evolution from life in water to life on land happened gradually in fish in shallow water."

The skeletal structure of Tiktaalik and the nature of the deposits where it was found suggest an animal that lived on the water bottom, in the shallows, and perhaps even out of the water for short periods.

"The skeleton of Tiktaalik indicates that it could support its body under the force of gravity whether in very shallow water or on land," said Farish Jenkins of Harvard University. "This represents a critical early phase in the evolution of all limbed animals, including us."

The project was also funded by the National Geographic Society, an anonymous donor, and the researchers' institutions. The team also relied on geological mapping by the Geological Survey of Canada.


###
NSF-PR 06-055

The National Science Foundation (NSF) is an independent federal agency that supports fundamental research and education across all fields of science and engineering, with an annual budget of $5.58 billion. NSF funds reach all 50 states through grants to nearly 1,700 universities and institutions. Each year, NSF receives about 40,000 competitive requests for funding, and makes nearly 10,000 new funding awards. The NSF also awards over $400 million in professional and service contracts yearly.

Receive official NSF news electronically through the e-mail delivery and notification system, MyNSF (formerly the Custom News Service). To subscribe, visit http://www.nsf.gov/mynsf/ and fill in the information under "new users".

Useful NSF Web Sites:
NSF Home Page: http://www.nsf.gov
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PostPosted: Fri Apr 07, 2006 10:55 am    Post subject: Controversial findings help explain evolution of life Reply with quote

Oregon State University
7 April 2006

Controversial findings help explain evolution of life

CORVALLIS, Ore. – Chemists at Oregon State University have pioneered a controversial theory about how supposedly-stable DNA bases can be pushed into a "dark state" in which they are highly vulnerable to damage from ultraviolet radiation – an idea that has challenged some of the most basic concepts of modern biochemistry.
The theory, not long ago dismissed as impossible by much of the science community, has just in recent months begun to garner increasing interest, and is being confirmed by other studies.

And though it began as scientific heresy, the findings could help explain how the presence of water was the key to the evolution of life on Earth, making it possible for life to emerge from what was once a hostile and unforgiving primordial soup of chemicals and radiation.

More and more research is being focused on this area since a study proving the existence of this "dark state" was published by OSU researchers in the Journal of Physical Chemistry – even though other journals had repeatedly rejected the findings because they were too radical.

"The findings of our studies did not fit most people's preconceived notions about how DNA molecules work, so they assumed we had to be wrong," said Wei Kong, an OSU professor of chemistry. "The critics seemed very sure of themselves, and we had a lot of sleepless nights."

"But just since last summer this has been a key point of discussion at several conferences and caused quite an excitement, as people see the data," Kong said. "Among other things, it helps to explain how water, or something else serving the same role, could have helped lead to the evolution of life."

The core of the debate, Kong said, relates to the behavior of the nucleic acid bases – adenine, thymine, guanine and cytosine - that as A-T and G-C base pairs form DNA and ultimately become the blueprint for all living things. One of the most basic premises of biochemistry is that these nucleic acid bases are very stable, as they would have to be to prevent rampant mutations and make an organized genetic structure possible.

But studies at OSU, which were done with highly sophisticated electron spectroscopy, showed that the alleged stability of the nucleic acid bases in DNA is largely a myth.

"In their biological form, surrounded by other hydrogen-bonded bases, it's true that the nucleic acids which make up DNA are stable," Kong said. "But we found that living things, in their totality, provide an environment which creates that stability, through attachments within base pairs and/or with neighboring bases. These attachments allow damaging photonic energy to be released as heat. But a DNA base as an isolated molecule, just by itself, does not have that stability."

In a compelling experiment, OSU scientists probed the fate of nucleic acid bases after laser irradiation in the ultraviolet range. They found that the molecules – which react extraordinarily fast to ultraviolet light insults – could by themselves spend 20-300 nanoseconds in an unstable, vibrating "dark state" in which they could easily mutate and not fully recover from photonic damage.

The lifetime of the dark state is not long – a nanosecond is one billionth of a second. But it's more than enough time for DNA mutations to happen, Kong said. And the existence of this dark state raised questions about how life ever could have begun, given that the genetic carriers were so easily mutated or destroyed during this very brief but very vulnerable time.

"When the bases of DNA were first being formed billions of years ago, the atmosphere was actually quite hostile," Kong said. "It was a period prior to any protective ozone layer on Earth and the ultraviolet radiation was very strong. So if primordial DNA bases were forced into this vulnerable dark state, they should have incurred large amounts of photochemical damage that would have made the very survival of these bases difficult, let alone further evolution of life."

Except for one other finding, that is.

According to OSU research, the "dark state" essentially disappears in the presence of water. So if water were present, the earliest DNA bases would have been able to survive and eventually help form the basis for ever-more-complex life forms.

"In modern biological forms, it's not essential that water be present for DNA to have stability," Kong said. "There are other mechanisms that now exist in biology to accomplish that, and complex biological processes are possible that don't always require water. But in its most basic form, we now know that DNA bases are not stable and they are highly vulnerable to UV-induced damage."

The findings suggest, Kong said, how water could have been an absolutely essential compound to allow early DNA bases to remain stable, resist mutation, and ultimately allow for the evolution of life.

OSU researchers were the first to propose the "dark state" model and prove its existence.

"What this is really telling us is that life is a unified process," Kong said. "It's not just a group of DNA bases, but it's also the physical environment in which they exist. Later on, as life became more evolved, there were other ways to achieve genetic stability. But at first, it simply may not have been possible without water."
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PostPosted: Mon May 01, 2006 6:01 pm    Post subject: Evolution Occurs Faster at the Equator Reply with quote

Evolution Occurs Faster at the Equator
By Ker Than
LiveScience Staff Writer
posted: 01 May 2006
05:00 pm ET

Plants and animals living in warm, tropical climates evolve faster than those living in more temperate zones, a new study suggests.

The finding, detailed in the May 2 issue of the journal for the Proceedings of the National Academy of Sciences, could help explain why rainforests have such rich biodiversity compared to other parts of the planet.

A census of all the plants and animals around the world would reveal that species richness is uneven: it is highest in the tropics, the regions of Earth near the equator, and lower the closer one goes toward the planet's poles.

What's going on

To investigate the reasons for this trend, Shane Wright of the University of Auckland, New Zealand, and colleagues looked at the rate of molecular evolution for 45 tropical plants and compared it to that of related species living at more temperate latitudes.

The researchers examined the rate at which DNA bases in the plants' genetic code are substituted. Like characters in a four-letter alphabet, bases are DNA molecules arranged to spell out instructions for building proteins. If one of the letters—A, T, G or C—become substituted with another, the instructions can change and a dysfunctional or entirely new and useful protein can be produced.

The researchers found that tropical plants had more than twice the rate of base substitution compared to their temperate cousins.

How it works

The finding supports a theory put forth by biologist Klaus Rohde in 1992 that climate can have a powerful effect on how fast organisms evolve and branch off into new species. Scientists think it works like this:

Warmer temperatures speed up metabolism by allowing chemical reactions to occur at a faster rate, but this increased efficiency comes at a price: it produces higher quantities of charged atoms or molecules called "free radicals," which can damage proteins—including DNA. Higher metabolism also speeds up DNA replication, which is just another chemical reaction, and this can increase the number of copying mistakes that can occur.

Together, damage to DNA by free radicals and replication mistakes could result in mutations that, over time and through natural selection pressures, can form new species.
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PostPosted: Sun May 21, 2006 9:33 am    Post subject: 'Hobbit' Fossil From Flores, Indonesia Reply with quote

Scientists Scuttle Claims That 'Hobbit' Fossil From Flores, Indonesia, Is A New Hominid
Field Museum
19 May 2006

When scientists found 18,000-year-old bones of a small, humanlike creature on the Indonesian island of Flores in 2003, they concluded that the bones represented a new species in the human family tree that they named Homo floresiensis. Their interpretation was widely accepted by the scientific community and heralded by the popular press around the world. Because of its very short stature, H. floresiensis was soon dubbed the "Hobbit."


Full article:

http://www.sciencedaily.com/re.....100438.htm
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PostPosted: Sat May 27, 2006 10:26 am    Post subject: Assembling the Tree of Life Reply with quote

Assembling the Tree of Life
31 May 2006
Emily Sohn

It's easy to see how you're related to your parents, grandparents, brothers, sisters, and cousins. It's not so easy to see how you're related to apple trees, worms, or elephants.
From algae to zebras, all living things on Earth have a common ancestor. The Tree of Life Project aims to show how these species are related to one another by putting them into a family tree. Biologists and other scientists all over the world are working to identify and sort Earth's organisms—from plants to microbes to animals, living or extinct—to see how they fit together.


Full article:

http://www.sciencenewsforkids......ature1.asp
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PostPosted: Mon Jun 12, 2006 7:01 pm    Post subject: Parallel evolution: proteins do it, too Reply with quote

June 12, 2006
Jianzhi Zhang
University of Michigan



Parallel evolution: proteins do it, too
ANN ARBOR, Mich.—Wings, spines, saber-like teeth—nature and the fossil record abound with examples of structures so useful they've evolved independently in a variety of animals. But scientists have debated whether examples of so-called adaptive, parallel evolution also can be found at the level of genes and proteins.

In the June 11 issue of Nature Genetics, evolutionary biologist Jianzhi (George) Zhang presents evidence for one such instance in a gene for an enzyme that helps leaf-eating monkeys digest their food.

"We know that parallel, or convergent, evolution is very common at the level of morphology—birds can fly, insects can fly, bats can fly, and they've all evolved this capability independently. But at the DNA and protein sequence level, it's very rare to find parallel evolution. This paper provides a real example," said Zhang, an associate professor of ecology and evolutionary biology.

The new work builds on previous research in which Zhang showed that the duplication of a gene encoding a pancreatic enzyme helped Asian colobine monkeys cope with an unusual diet.

"Colobines are different from other monkeys in that they primarily eat leaves rather than fruit or insects, and leaves are very difficult to digest," Zhang said. The monkeys manage with a digestive system similar to a cow's. Bacteria in the gut ferment the leaves and take up nutrients that are released in the process. The monkeys, in turn, digest the bacteria to recover the nutrients, such as protein and ribonucleic acid (RNA), a particularly important source of nitrogen in leaf eaters.

Zhang focused his attention on RNASE1, a pancreatic enzyme that breaks down bacterial RNA. Most primates have one gene encoding the enzyme, but he found that the douc langur, a colobine from Asia, has two—one encodes RNASE1, and its duplicate encodes a new enzyme, RNASE1B. The duplicate enzyme, it turns out, works better than the original in the acidic conditions of the colobine small intestine, making it more efficient at recovering nutrients from bacteria.

Zhang's initial analysis showed that the duplication occurred about four million years ago, some nine million years after the two main groups of colobines—Asian and African—split into separate lineages. To confirm that the duplication occurred after the split, he analyzed DNA samples from an African colobine known as the guereza or colobus monkey.

"We sequenced the gene, and to our surprise we found not one, not two, but three RNASE1 genes," Zhang said. "Further analysis showed that the duplications in African monkeys and Asian monkeys were separate, independent events." Next, Zhang wanted to know if the duplications resulted in similar functional changes in the enzyme. Just as in the Asian colobine, the duplicated genes in African colobines functioned more efficiently at the typical acidity level of the colobine small intestine, he found.

"Then our question was whether the similar functional changes were due to identical amino acid changes at the protein sequence level," Zhang said. "Indeed, we found three amino acid changes that were identical in the two lineages. They occurred independently, but they were identical." Additional experiments confirmed that the three, independent, parallel amino acid changes were responsible for the change in enzyme function.

In both Asian and African colobines, the original, less efficient, gene is not discarded after duplication. But why, Zhang wondered.

"The guess is that the old copy is still doing something important," he said. "RNASE1 has another function, which is to degrade double-stranded RNA. Double-stranded RNA is not normally found in food, but it's found in some viruses, so the old gene may be useful in defending against viral infection." Zhang checked the new and old genes in both lineages and found the same pattern: the new genes have lost the ability to degrade double-stranded RNA, but the older genes have kept it.

"So it looks like, after gene duplication, there is a division of labor," Zhang said. "Before duplication, the gene is supposed to do both jobs: digestion and degrading double-stranded RNA. After duplication, one copy seems to retain the activity of degrading double-stranded RNA while the other copy has adapted to changed pH in the small intestine so it can better digest food."

Even after clearly demonstrating parallel evolution in this case, Zhang believes the phenomenon is uncommon at the protein sequence level. However, he proposes a list of criteria in the Nature Genetics paper that he and other researchers can use to test apparent examples in the future.

The work was funded by National Institutes of Health.
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PostPosted: Thu Jul 13, 2006 6:17 pm    Post subject: Darwin's Finches Evolve Before Scientists' Eyes Reply with quote

Darwin's Finches Evolve Before Scientists' Eyes

By Sara Goudarzi
LiveScience Staff Writer
posted: 13 July 2006
02:00 pm ET



For the first time scientists have observed in real-time evolutionary changes in one species driven by competition for resources from another.

In a mere two decades, one of Charles Darwin's finch species, Geospiza fortis, reduced its beak size to better equip itself to consume small sized seeds, scientists report in the July 14 issue of the journal Science.

The finch once had its own kingdom on the Galapagos Island of Daphne Major. It had its pick of seeds to eat. But the arrival of another species of finch about 20 years ago, and additional food competition from a drought on the island in 2003, changed everything.

"When there is a severe drought on a small island, natural selection occurs," said study co-author Peter Grant of Princeton University.

The new larger species ate the larger and harder seeds on the island, food that the biggest members of the native finch clan normally ate.

"The recent immigrant species had almost eaten the supply of food themselves, so they almost went extinct," Grant said. "The resident species, the species that was there before the new species arrived, underwent a large shift toward small size in beaks."

Typically, the small members of the species can't crack the larger seeds. But with the depletion of the larger seeds, the small-beaked population, which could reach the smaller feed and needed less food to meet its daily energy needs, had a better survival rate.

This type of evolutionary change is known as character displacement.

"It's a very important one in studies of evolution because it shows that species interact for food and undergo evolutionary change, which minimizes further evolution," Grant said. 'It has not been possible to observe the whole process from start to finish in nature."
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PostPosted: Tue Jul 25, 2006 6:22 am    Post subject: Human Ancestors May Have Hit the Ground Running Reply with quote

Human Ancestors May Have Hit the Ground Running

By Charles Q. Choi
Special to LiveScience
posted: 24 July 2006
01:36 pm ET



New findings raise the interesting possibility that the step from a tree-dwelling ape to a terrestrial biped might not have been as drastic as previously thought.

Scientists find muscles gibbons use for climbing and swinging through trees might also help the apes run.

Humans are the upright apes, but much remains unknown as to how our ancestors first found their footing. To shed light on the past, Evie Vereecke at the University of Antwerp in Belgium and her colleagues looked at how modern cousins of humanity such as gibbons and bonobos amble.

For two months, Vereecke's team monitored how four white-handed gibbons at a local zoo strode at speeds ranging from strolls to sprints across a 13-foot-long walkway surrounded with video cameras and loaded with scientific instruments such as force plates and pressure mats.

The gibbons collaborated well, "especially when you rewarded them with some raisins," Vereecke said.

For the full article:

http://www.livescience.com/ani.....lking.html
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PostPosted: Sun Aug 13, 2006 8:06 am    Post subject: U.S. Lags World in Grasp of Genetics and Acceptance of Evol. Reply with quote

U.S. Lags World in Grasp of Genetics and Acceptance of Evolution

By Ker Than
LiveScience Staff Writer
posted: 10 August 2006
02:01 pm ET



A comparison of peoples' views in 34 countries finds that the United States ranks near the bottom when it comes to public acceptance of evolution. Only Turkey ranked lower.

Among the factors contributing to America's low score are poor understanding of biology, especially genetics, the politicization of science and the literal interpretation of the Bible by a small but vocal group of American Christians, the researchers say.

“American Protestantism is more fundamentalist than anybody except perhaps the Islamic fundamentalist, which is why Turkey and we are so close,” said study co-author Jon Miller of Michigan State University.

For the full article:

http://www.livescience.com/hum....._rank.html
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PostPosted: Sat Sep 09, 2006 10:47 pm    Post subject: Modern humans, not Neandertals, may be evolution's 'odd man Reply with quote

Modern humans, not Neandertals, may be evolution's 'odd man out'
Washington University in St. Louis
7 September 2006

Looking incorrectly at Neandertals
Could it be that in the great evolutionary "family tree," it is we Modern Humans, not the brow-ridged, large-nosed Neandertals, who are the odd uncle out?

New research published in the August, 2006 journal Current Anthropology by Neandertal and early modern human expert, Erik Trinkaus, professor of anthropology at Washington University in St. Louis, suggests that rather than the standard straight line from chimps to early humans to us with Neandertals off on a side graph, it's equally valid, perhaps more valid based on what the fossils tell us, that the straight line should be from the common ancestor to the Neandertals, and the Modern Humans should be the branch off that.

Trinkaus has spent years examining the fossil record and began to realize that maybe researchers have been looking at our ancient ancestors the wrong way.

Trinkaus combed through the fossil record, identifying traits which seemed to be genetic markers – those not greatly influenced by environment, life ways and wear and tear. He was careful to examine traits that appear to be largely independent of each other to avoid redundancy.

"I wanted to see to what extent Neandertals are derived, that is distinct, from the ancestral form. I also wanted to see the extent to which modern humans are derived relative to the ancestral form," Trinkaus says. "What I came up with is that modern humans have about twice as many uniquely derived traits than do the Neandertals."

"In the broader sweep of human evolution," says Trinkaus, "the more unusual group is not Neandertals, whom we tend to look at as strange, weird and unusual, but it's us - Modern Humans. The more academic implication of this research is that we should not be trying to explain the Neandertals, which is what most people have tried to do, including myself, in the past. We wonder why Neandertals look unusual and we want to explain that. What I'm saying is that we've been asking the wrong questions."

The most unusual characteristics throughout human anatomy occur in Modern Humans, argues Trinkaus. "If we want to better understand human evolution, we should be asking why Modern Humans are so unusual, not why the Neandertals are divergent. Modern Humans, for example, are the only people who lack brow ridges. We are the only ones who have seriously shortened faces. We are the only ones with very reduced internal nasal cavities. We also have a number of detailed features of the limb skeleton that are unique.

"Every paleontologist will define the traits a little differently," Trinkaus admits. "If you really wanted to, you could make the case that Neandertals look stranger than we do. But if you are reasonably honest about it, I think it would be extraordinarily difficult to make Neandertals more derived than Modern Humans."

###
Full text of the article is located online at, http://www.journals.uchicago.e.....13.web.pdf
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PostPosted: Sat Sep 09, 2006 10:54 pm    Post subject: Genetic Surprise Confirms Neglected 70-Year-Old Evolutionary Reply with quote

September 8, 2006
University of Rochester

Genetic Surprise Confirms Neglected 70-Year-Old Evolutionary Theory

Biologists at the University of Rochester have discovered that an old and relatively unpopular theory about how a single species can split in two turns out to be accurate after all, and acting in nature.

The finding, reported in today's issue of Science, reveals that scientists must reassess the processes involved in the origin of species. The beginnings of speciation, suggests the paper, can be triggered by genes that change their locations in a genome.

"In the 1930s there was speculation that parts of chromosomes that switch from one location to another might cause a species to split into two different species," says John Paul Masly, lead author of the paper and doctoral student at the University of Rochester. "Showing that it was more than an academic idea was difficult, and required a bit of luck. Other genetic causes of speciation are clearly documented in nature, and it wasn't until we had the ability to sequence whole genomes that we could even attempt to investigate the question."

Curiously, the hypothesis nearly died twice.

Theodosius Dobzhansky, a well-known evolutionary geneticist, studied fruit flies in the infant days of genetic research in 1930. He mapped out how it might be possible for sections of chromosomes to relocate themselves in a genome. Those mobile sections can cause sterility in inter-species hybrids, which can act as a speciation pressure.

In theory, the idea was sound, but scientists long debated whether it actually happened in nature. Eventually a competing theory involving the gradual accumulation of mutations was shown to occur in nature so often that geneticists largely dismissed the moving gene hypothesis.

"We knew going into this that it was a risky experiment," says Masly. "But we hoped we could pull it off."

Over the span of the six-year project, the prospects of bolstering the controversial evolutionary idea looked increasingly bleak.

Masly brought together two species of fruit fly—the workhorses of the genetics world—to see what genes were active when they were crossbred. One species, Drosophila melanogaster, had its genome already sequenced, making that part of the job much easier. The second species, Drosophila simulans, was still in the process of being sequenced, which meant much of the work had to be done by hand by Masly and his collaborators.

Masly knew that chromosome #4 on melanogaster held a gene that was somehow very important for fertility—information found earlier by Rochester biologist H. Allen Orr. Crossbreeding the flies proved tricky because a few million years of evolution separated the species, but after a few nudges the flies produced what Masly was looking for—a sterile male.

This is when Dobzhansky's 70-year-old hypothesis nearly died for good.

The reigning theory of speciation says that the genes causing hybrid sterility must have diverged slowly by normal evolutionary changes. To determine if this was true, Masly had only to look at chromosome #4 and find the gene on it that caused the hybrid sterility.

But there was no gene there.

"Something was all wrong. We couldn't find the gene and we were this close to giving up on the whole project"
"There was a great, 'Oh no,' moment," says Masly. "I'd been working on this for six years and it was starting to look like it was all for nothing. Something was all wrong. We couldn't find the gene and we were this close to giving up on the whole project."

But once again, insights from the past came into play. Masly and Orr, Masly's advisor and professor of biology at the University of Rochester, were talking one day when Orr suddenly recalled an off-hand comment from a scientist named Hermann J. Muller in a paper 60 years earlier. Muller speculated that perhaps since the sterility in the flies is so recessive—meaning it's almost completely non-functional—perhaps the gene in question has jumped clear off the chromosome.

"It had never occurred to us that the gene might have moved right off chromosome #4 in simulans," says Masly. As the simulans' genome was newly sequenced, Masly called a colleague, geneticist Corbin D. Jones, a co-author of the paper and Rochester graduate, who was studying the simulans genome.

Over the phone one day in the lab, Jones told Masly what his analysis turned up.

"You're not going to believe this, but you're right," said Jones. "It's not on the fourth chromosome. It's on the third."

"That was really exciting," says Masly. "It was completely unexpected and it made the cause of this hybrid's sterility very simple; the gene's on number four in one species and on number three in the other, so when you mate the two, every now and then you'll get a male with a combination that includes no gene at all. These guys are sterile because they completely lack a gene that's necessary for fertility."

The gene, called JYAlpha, is one of the same genes that is essential for sperm motility in the flies, as well as in humans and other mammals.

Masly's work shows a back door through which speciation can start. If the right genes jump around in the genome, a population can begin creating individuals that can't successfully mate with the general population. If other speciation pressures, like geographic isolation, are added to the mix, the pressure may be enough to split one species into two new species.

When asked if JYAlpha may be responsible for melanogaster and simulans' initial split a few million years ago, Masly replied, "That's lost to history."

Fortunately, the theory isn't.

This research was funded by the National Science Foundation, the Canadian Institutes of Health Research, and the National Institutes of Health.
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PostPosted: Wed Sep 13, 2006 1:29 pm    Post subject: Survival of the fittest? Not so fast Reply with quote

Survival of the fittest? Not so fast
STAR SCIENCE By Eduardo A. Padlan, Ph.D.
The Philippine STAR 09/14/2006
http://www.philstar.com/philst.....144402.htm

The phrase "survival of the fittest" was coined by Herbert Spencer, a
British social philosopher, to accentuate the differences in survivability
of the different social classes. Inevitably, the notion fed into the belief
of the existence of more advanced individuals and cultures, and served to
justify colonization (of "inferior" societies) and imperialism.

To Spencer, the concept was equivalent to what Charles Darwin was then
calling "natural selection, or the preservation of favored races in the
struggle for life." The phrase was later adopted and widely used by Charles
Darwin himself. The phrase can be applied, not only to individuals and
groups, but to cells and molecules as well.

Survival and perpetuation of one's genes are every organism's most immediate
goals. There is an unending struggle for survival among the many organisms
in our world and the most able to compete - the "fittest" - have the highest
chances of winning. The many different organisms that can be found in our
world today are the result of eons of change, competition, and selection of
the "fittest" (in other words, evolution), and the present-day organisms
represent the forms that are best adapted to the prevailing conditions.

Who are the "fittest"? Are they the strongest? The healthiest? The most
intelligent? All of the preceding? None of the preceding? In fact, the
"prevailing conditions" are what define who are the "fittest" (and who will
survive).

In a situation where there is shortage of food, those who do not require
much food - the smaller individuals - will more likely survive. In
situations where there is competition for territory, the better fighters -
the bigger and stronger, or those who have better weapons - will more likely
win.

If two individuals - one fat, one lean - are dumped in the ocean, one will
probably float while hardly moving a muscle, whereas the other may sink
straight to the bottom. If instead they are dumped in lion country, the cats
will more likely end up feasting on meat generously marbled with fat,
instead of lean meat. (I'm obviously trying to be funny here.)

But really it all depends on the "prevailing conditions."

That is true also in the cellular and molecular world of biology. The
"fittest" among the molecules and cells, the ones chosen by Nature to
prevail and to persist, are defined by the circumstances. Let me illustrate.


Recognition is the hallmark of biology. Biological molecules and cells do
not associate randomly - otherwise, our world will be chaotic. Rather,
molecules (and cells) interact specifically with the entities (other
molecules and cells) they are meant to interact with. There is a pattern to
which we conform. There is order and structure. In situations where
molecules are meant to bind one another, the molecules which best fit each
other and whose interaction serves the intended purpose would be expected to
be favored and kept during the course of evolution.

A part of us in which recognition is very important is our immune system.
The system has to be able to distinguish between beneficial and harmful
(food is good, germs are bad) - we tolerate the first, we rid ourselves of
the second. The system also has to be able to distinguish between our own
cells (and molecules) and foreign cells (and substances) - we leave our own
cells alone, we kill the invaders. How does the immune system accomplish
this?

Three types of molecules are primarily responsible for immune recognition:
the antibodies, the T cell receptors (TCRs) for antigen, and the Major
Histocompatibility Complex (MHC) molecules. A membrane form of antibodies is
initially found on the surface of B lymphocytes (cells that complete their
differentiation in the bone marrow) and then a soluble form of antibodies is
secreted after the B cells have gone through several cycles of development
(maturation). The TCRs are found on the surface of T lymphocytes (cells that
complete their differentiation in the thymus and of which two types will be
mentioned here: the helper T cell and the killer T cell). MHC molecules are
present on the surface of all cells, except those which no longer synthesize
protein (for example, red blood cells). Two types of MHC molecules are of
interest here: MHC Class I, which is recognized by killer T cells, and MHC
Class II, which is recognized by helper T cells.

When they are first formed (in B cells and found in membrane form on the
surface of the cells), antibodies have low affinity (strength of binding)
and are not specific for anything (binding is said to be specific if it is
to only one ligand). When a foreign substance (antigen) gets inside us,
there may be B cells that by chance are able to bind to it, even though only
weakly. Those B cells will internalize the antigen, break it up into pieces
(peptides) and then display the peptides on their surface, bound to MHC
Class II molecules. Helper T cells will then come along and if there is a
helper T cell whose TCR can bind to the MHC:peptide complex, the T cell will
then secrete molecules directed at the B cell, causing the latter to divide.
When a B cell divides, its antibody genes undergo hypermutation (mutation at
a very rapid rate). Once again, by chance, antibodies on the daughter B
cells may bind the antigen - more strongly this time. Those daughter B cells
are then "selected," because of their higher affinity, to be activated by
helper T cells. The cycle is repeated until, in the end, we have B cells
producing antibodies that are specific for the antigen and are able to bind
to it with high affinity. The "best" antibodies then are characterized by
high affinity for antigen. (B cells that bind to our own molecules are
"killed" before they leave the bone marrow.)

For TCRs, the criterion for which are the "best" is quite different. TCRs
bind to both the MHC molecule AND the bound peptide. If the binding of the
TCR to the MHC molecule is too strong, a helper T cell could activate a B
cell that is not displaying the right peptide, or kill the cell, if the T
cell is of the killer type and the MHC molecule is of Class I; either of
these events would be disastrous. The "best" TCRs then are characteraized by
only medium-strength affinity. (As in the case of B cells, T cells that bind
to our own peptides are "killed" before they leave the thymus.)

Many other examples abound that demonstrate that there is no easy answer to
the question of what constitutes "fitness." So if someone asks which
individuals, cultures, organisms or molecules are the "fittest" and best
suited for survival, a good response would be: "It depends."
* * *
Eduardo A. Padlan has a Ph.D. in Biophysics and was a research scientist at
the (US) National Institutes of Health until his retirement in 2000. He is
currently an Adjunct Professor in the Marine Science Institute, College of
Science, University of the Philippines Diliman. He is a Corresponding Member
of the National Academy of Science and Technology, Philippines. He can be
reached at epadlan@aol.com or at edpadlan@yahoo.com.
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PostPosted: Fri Nov 17, 2006 8:44 am    Post subject: Reply with quote

Short Legs Win Evolution Battle

By Jeanna Bryner
LiveScience Staff Writer
posted: 16 November 2006
02:01 pm ET

In a reptilian version of "Survivor," lizards with longer legs ultimately get booted from islands by their short-legged opponents.

Countering the widespread view of evolution as an eon-long process, evolutionary biologists discovered that when island lizards were exposed to a new predator, natural selection occurred in a six-month period, first favoring longer and then shorter hind legs.

The findings are detailed in the Nov. 17 issue of the journal Science.

Brown anolis (Anolis sagrei) lizards spend much of their time on the ground. But as previous studies have shown, when a ground-dwelling, predatory lizard is introduced, the anoles scamper up trees. They switch to an arboreal lifestyle to escape being eaten.

For the full article:

http://www.livescience.com/ani....._legs.html
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PostPosted: Sat Dec 09, 2006 2:02 pm    Post subject: Finding an answer to Darwin’s Dilemma Reply with quote

Finding an answer to Darwin’s Dilemma
Thursday December 07, 2006
Queen's University

Oxygen may be the clue to first appearance of large animals, says Queen’s prof

The sudden appearance of large animal fossils more than 500 million years ago – a problem that perplexed even Charles Darwin and is commonly known as “Darwin’s Dilemma” – may be due to a huge increase of oxygen in the world’s oceans, says Queen’s paleontologist Guy Narbonne, an expert in the early evolution of animals and their ecosystems.

In 2002, Dr. Narbonne and his research team found the world’s oldest complex life forms between layers of sandstone on the southeastern coast of Newfoundland. This pushed back the age of Earth’s earliest known complex life to more than 575 million years ago, soon after the melting of the massive “snowball” glaciers. New findings reported today shed light on why, after three billion years of mostly single-celled evolution, these large animals suddenly appeared in the fossil record.

In a paper published on-line in Science Express, Dr. Narbonne’s team argues that a huge increase in oxygen following the Gaskiers Glaciation 580 million years ago corresponds with the first appearance of large animal fossils on the Avalon Peninsula in Newfoundland.

Now for the first time, geochemical studies have determined the oxygen levels in the world’s oceans at the time these sediments accumulated in Avalon. “Our studies show that the oldest sediments on the Avalon Peninsula, which completely lack animal fossils, were deposited during a time when there was little or no free oxygen in the world’s oceans,” says Dr. Narbonne. “Immediately after this ice age there is evidence for a huge increase in atmospheric oxygento at least 15 per cent of modern levels, and these sediments also contain evidence of the oldest
large animal fossils.”

Also on the research team are Don Canfield (University of Southern Denmark) and Simon Poulton (Newcastle University, U.K.). Geochemical studies by Drs. Canfield and Poulton included measurements of iron speciation and sulphur isotopes to determine the oxygen levels in the world’s oceans at the time these sediments accumulated in Avalon.

The close connection between the first appearance of oxygenated conditions in the world’s oceans and the first appearance of large animal fossils confirms the importance of oxygen as a trigger for the early evolution of animals, the researchers say. They hypothesize that melting glaciers increased the amount of nutrients in the ocean and led to a proliferation of single-celled organisms that liberated oxygen through photosynthesis. This began an evolutionary radiation that led to complex communities of filter-feeding animals, then mobile bilateral animals, and ultimately to the Cambrian “explosion” of skeletal animals 542 million years ago.
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PostPosted: Tue Jan 30, 2007 7:11 am    Post subject: Does evolution select for faster evolvers? Reply with quote

Rice University

Does evolution select for faster evolvers?

Horizontal gene transfer adds to complexity, speed of evolution
HOUSTON, Jan. 29, 2007 -- It's a mystery why the speed and complexity of evolution appear to increase with time. For example, the fossil record indicates that single-celled life first appeared about 3.5 billion years ago, and it then took about 2.5 billion more years for multi-cellular life to evolve. That leaves just a billion years or so for the evolution of the diverse menagerie of plants, mammals, insects, birds and other species that populate the earth.

New studies by Rice University scientists suggest a possible answer; the speed of evolution has increased over time because bacteria and viruses constantly exchange transposable chunks of DNA between species, thus making it possible for life forms to evolve faster than they would if they relied only on sexual selection or random genetic mutations.

"We have developed the first exact solution of a mathematical model of evolution that accounts for this cross-species genetic exchange," said Michael Deem, the John W. Cox Professor in Biochemical and Genetic Engineering and professor of physics and astronomy.

The research appears in the Jan. 29 issue of Physical Review Letters.

Past mathematical models of evolution have focused largely on how populations respond to point mutations – random changes in single nucleotides on the DNA chain, or genome. A few theories have focused on recombination – the process that occurs in sexual selection when the genetic sequences of parents are recombined.

Horizontal gene transfer (HGT) is a cross-species form of genetic transfer. It occurs when the DNA from one species is introduced into another. The idea was ridiculed when first proposed more than 50 years ago, but the advent of drug-resistant bacteria and subsequent discoveries, including the identification of a specialized protein that bacteria use to swap genes, has led to wide acceptance in recent years.

"We know that the majority of the DNA in the genomes of some animal and plant species – including humans, mice, wheat and corn – came from HGT insertions," Deem said. "For example, we can trace the development of the adaptive immune system in humans and other jointed vertebrates to an HGT insertion about 400 million years ago."

The new mathematical model developed by Deem and visiting professor Jeong-Man Park attempts to find out how HGT changes the overall dynamics of evolution. In comparison to existing models that account for only point mutations or sexual recombination, Deem and Park's model shows how HGT increases the rate of evolution by propagating favorable mutations across populations.

Deem described the importance of horizontal gene transfer in the work in a January 2007 cover story in the Physics Today, showing how HGT compliments the modular nature of genetic information, making it feasible to swap whole sets of genetic code – like the genes that allow bacteria to defeat antibiotics.

"Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species," Deem said.

###
The research is supported by the Defense Advanced Research Projects Agency.
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PostPosted: Tue Jan 30, 2007 7:21 am    Post subject: FSU anthropologist confirms 'Hobbit' indeed a separate speci Reply with quote

Florida State University
29 January 2007

FSU anthropologist confirms 'Hobbit' indeed a separate species

Dean Falk led international team in brain analysis of ancient hominid
TALLAHASSEE, Fla. -- After the skeletal remains of an 18,000-year-old, Hobbit-sized human were discovered on the Indonesian island of Flores in 2003, some scientists thought that the specimen must have been a pygmy or a microcephalic — a human with an abnormally small skull.

Not so, said Dean Falk, a world-renowned paleoneurologist and chair of Florida State University's anthropology department, who along with an international team of experts created detailed maps of imprints left on the ancient hominid's braincase and concluded that the so-called Hobbit was actually a new species closely related to Homo sapiens.

Now after further study, Falk is absolutely convinced that her team was right and that the species cataloged as LB1, Homo floresiensis, is definitely not a human born with microcephalia — a somewhat rare pathological condition that still occurs today. Usually the result of a double-recessive gene, the condition is characterized by a small head and accompanied by some mental retardation.

"We have answered the people who contend that the Hobbit is a microcephalic," Falk said of her team's study of both normal and microcephalic human brains published in the Jan. 29 issue of the journal PNAS (Proceedings of the National Academy of Sciences of the United States).

The debate stemmed from the fact that archaeologists had found sophisticated tools and evidence of a fire near the remains of the 3-foot-tall adult female with a brain roughly one-third the size of a contemporary human.

"People refused to believe that someone with that small of a brain could make the tools. How could it be a sophisticated new species?"

But that's exactly what it is, according to Falk, whose team had previously created a "virtual endocast" from a three-dimensional computer model of the Hobbit's braincase, which reproduces the surface of the brain including its shape, grooves, vessels and sinuses. The endocasts revealed large parts of the frontal lobe and other anatomical features consistent with higher cognitive processes.

"LB1 has a highly evolved brain," she said. "It didn't get bigger, it got rewired and reorganized, and that's very interesting."

In this latest study, the researchers compared 3-D, computer-generated reconstructions of nine microcephalic modern human brains and 10 normal modern human brains. They found that certain shape features completely separate the two groups and that Hobbit classifies with normal humans rather than microcephalic humans in these features. In other ways, however, Hobbit's brain is unique, which is consistent with its attribution to a new species.

Comparison of two areas in the frontal lobe, the temporal lobe and the back of the brain show the Hobbit brain is nothing like a microcephalic's and is advanced in a way that is different from living humans. In fact, the LB1 brain was the "antithesis" of the microcephalic brain, according to Falk, a finding the researchers hope puts this part of the Hobbit controversy to rest.

It's time to move on to other important questions, Falk said, namely the origin of this species that co-existed at the same time that Homo sapiens was presumed to be the Earth's sole human inhabitant.

"It's the $64,000 question: Where did it come from?" she said. "Who did it descend from, who are its relatives, and what does it say about human evolution? That's the real excitement about this discovery."


###
Falk's co-authors on the PNAS paper, "Brain shape in human microcephalics and Homo floresiensis," are Charles Hildebolt, Kirk Smith and Fred Prior of the Washington University School of Medicine in St. Louis; M.J. Morwood of the University of New England in Australia; Thomas Sutikna, E. Wayhu Saptomo and Jatmiko of the Indonesian Centre for Archaeology in Indonesia; Herwig Imhof of the Medical University of Vienna, Austria; and Horst Seidler of the University of Vienna, Austria.
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PostPosted: Fri Feb 16, 2007 8:10 am    Post subject: Researchers untangle nature of 'regressive evolution' in cav Reply with quote

New York University
15 February 2007

Researchers untangle nature of 'regressive evolution' in cavefish

"Regressive evolution," or the reduction of traits over time, is the result of either natural selection or genetic drift, according to a study on cavefish by researchers at New York University's Department of Biology, the University of California at Berkeley's Department of Integrative Biology, and the Harvard Medical School. Previously, scientists could not determine which forces contributed to regressive evolution in cave-adapted species, and many doubt the role of natural selection in this process. Darwin himself, who famously questioned the role of natural selection in eye loss in cave fishes, said, "As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse."

The research appears in the most recent issue of the journal Current Biology.

Cave adaptations have evolved in many species independently, and each cave species can be considered a replicate of the same evolutionary experiment that asks how species change in perpetual darkness. This makes cavefish a rich source for the examination of the evolutionary process.

In this study, the researchers examined the genetic basis of regressive evolution in the eyes and pigmentation of Mexican cavefish. To do so, they mapped the quantitative trait loci (QTL) determining differences in eye and lens sizes as well as the melanophore—or pigment cell—number between cave and surface fish. These QTL represent genes where new mutations arose in cave populations. To better understand the genetic basis for regressive evolution, they focused on two alternative explanations for regression: natural selection, in which beneficial DNA mutations become more common over time, and genetic drift, in which the frequencies of these mutations can rise or fall over time due solely to statistical variation.

Their results suggested that eyes and pigmentation regressed through different mechanisms. Mutations in cave populations that affected eye or lens size invariably caused size reductions. This observation is consistent with evolution by natural selection and inconsistent with evolution by genetic drift. By contrast, mutations in cave populations that affected pigmentation sometimes caused increases instead of decreases in pigment cell density, consistent with evolution by random processes and genetic drift.

Allaying Darwin's doubts about the role of natural selection in eye loss, the researchers suggest that the high metabolic cost of maintaining the retina is the source of selection against eyes in the cave. By contrast, no such great cost is associated with pigmentation—thus, the two traits regress for different reasons.
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PostPosted: Sat Feb 24, 2007 8:35 am    Post subject: First Humans: Time of Origin Pinned Down Reply with quote

First Humans: Time of Origin Pinned Down

By Robin Lloyd
LiveScience Senior Editor
posted: 23 February 2007
01:21 pm ET

The lineages of humans and chimpanzees, our closest relatives, diverged from one another about 4.1 million years ago, according to a new estimate that is said to be far more precise than previous ranges for this critical evolutionary moment.

However, the claim is a bad match with previous estimates based on fossil evidence and other genetic work.

Asger Hobolth of North Carolina State University and his colleagues arrived at the new estimate of " the time we became human," or the time in the past when descendents of the human-chimp ancestor split into human and chimp, by statistically comparing DNA from four regions of the human, chimp and gorilla genomes.

For the full article:

http://www.livescience.com/hum.....split.html
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PostPosted: Wed Mar 14, 2007 7:17 am    Post subject: Darwin's famous finches and Venter's marine microbes Reply with quote

Salk Institute

Darwin's famous finches and Venter's marine microbes
13 March 2007

LA JOLLA, CA -- Although the Galápagos finches were to play a pivotal role in the inception of Darwin’s theory of evolution through natural selection, he had no inkling of their significance when he collected them during his voyage on the HMS Beagle.

Similarly, it is hard to predict the impact the vast amount of marine microbial DNA – collected during the Sorcerer II Global Ocean Sampling Expedition by J. Craig Venter, Ph.D., and his team – will have on our understanding of the natural world.

"If anything, this is just the beginning," says Gerard Manning, Ph.D., director of the Razavi Newman Center for Bioinformatics at the Salk Institute for Biological Studies. "We’re starting to explore this trove of sequences now, but it may be decades before we fully understand it all."

Just like the famous ornithologist John Gould who had to classify the Galápagos finches before they led Darwin on the right track, Manning and many others have been busy during the last couple of months wading through roughly 7.7 million sequenced snippets of sea-borne genomic DNA to impose order on the flood of data and to classify the identified proteins.

Their findings are detailed in series of papers, published in this week’s online edition of the journal Public Library of Science Biology (www.plos.org).

The authors are plying the rapidly emerging trade of metagenomics (also known as environmental genomics) that seeks to examine genomic snapshots taken directly from the environment.

"Metagenomics allows us to sample the 99 percent of all bacteria that won’t grow in the lab," explains Manning. "GOS opens a huge window into biological and genomic diversity and, within this diversity, to better understand many of the fundamentals of biology." he adds.

Expanding the universe of protein families

But instead of whole genomes, metagenomics produces a whole grab bag of bits and pieces for which scientists have to develop new methods to extract meaning. In one of the papers, an array of scientists, spearheaded by first author Shibu Yooseph, Ph.D., and his colleagues at the Craig Venter Institute, compared every DNA fragment with every other available DNA fragment to produce clusters of related sequences. This exhaustive analysis predicted more than 6 million proteins in the GOS data – nearly twice the number of all proteins ever described before – and laid the groundwork for further studies.

Manning, a co-author on Yooseph’s paper, looked at the other side of the coin. He ran all the public sequences and GOS data against Pfam, a collection of signature profiles for all known protein families. Each of these profiles is an average of all known members of a certain protein family.

"Instead of starting with a human kinase to find a bacterial kinase, for example, you start with all of them together, which makes the search much more sensitive, but also very computationally expensive," Manning says. "We did almost 350 million comparisons, which is probably an order of magnitude or two more than anybody has ever done before."

Manning and co-author Yufeng Zhai, Ph.D., a bioinformatics programmer in the Razavi Newman Center for Bioinformatics at the Salk, could only accomplish this rather gargantuan task with the help of Time Logic, a company in Carlsbad, California. The company specializes in hardware that accelerates genomic searches. "We only have one of their accelerators, but Time Logic stepped up and lent us eight more," says Manning. The final computation took two weeks, but would have taken well over a century on a traditional computer.

The Salk scientists could assign over half of all GOS sequences to known protein families, and discovered that certain protein profiles are more popular in the ocean or on land. For example, gram-positive bacteria are best known for their hardy spores, but this ability has been entirely lost in their marine relatives.. Flagella, whip-like extensions propelling bacteria forward and pili, short extensions used to exchange genetic material between bacteria (also known as microbial sex), are also less frequent in marine environments.

"By comparing our findings with the Yooseph clusters, we also discovered hundreds of new gene families that hadn’t even been seen before," says Zhai and adds that by adding the diverse GOS data to known profiles, "we were able to make them more sensitive and diverse, and so increase their power to categorize novel sequences."

Diversity of microbial kinases

In a separate study, Manning, Zhai, and first author Natarajan Kannan, Ph.D., a postdoctoral researcher in the lab of HHMI investigator and UCSD professor Susan S. Taylor, Ph.D., traded the breadth of the ocean survey for the depth of a single protein domain. They zoomed in on kinases, extremely well studied enzymes, which control every aspect of eukaryotic cell biology and are important cancer drug targets. They control the activity of proteins and small molecules by attaching tiny phosphate groups to them. By contrast, much less has been known about their bacterial counterparts.

Again and again, the researchers combed the GOS data for bacterial kinases, each time rebuilding their domain profiles by including the new members found in the previous round. All in all, they dug up 45,000 protein kinase sequences that fell into 20 distinct families, of which the eukaryotic protein kinases are just one. The additional 19 families spanned a huge range and included several that had never been described before.

"Prokaryotic protein-like kinases were considered to be some sort of niche players, but actually they are more prevalent and widespread than histidine kinases," explains Manning. Bacteria were thought to rely mostly on histidine kinases, which are structurally different from protein kinases, for all their signaling needs.

Even though the different kinase families had very little similarity in their sequence, it emerged that 10 key residues were conserved in almost all kinase families, fingering them as being at the core of what it means to be a kinase. Seven of those had been previously known to be important in human kinases, but the other three were unexpected finds.

The other surprising finding was just how innovative and plastic the different families were, even with these core residues, as one or another family had found ways to eliminate any but one of the 10 key residues. Using structural modeling, and patterns of sequence conservation, Kannan was able to show that loss of one key residue could be compensated by changes around other conserved regions of the protein, and that some of these changes in bacterial kinases are also seen in specific human kinases.

Says Manning, "By looking at all these very distant microbial relatives we can understand more even about human kinases and their relationship to cancer and other diseases. We go out into the ocean, we find all this diversity and analyzing what’s new and what’s not new reflects back on the things we thought we knew well."

Research done at the Salk Institute was supported by the Razavi-Newman Foundation.

Sorcerer II Global Ocean Sampling Expedition

The circumnavigating Sorcerer II Expedition, named after the sailboat J. Craig Venter transformed into a marine research vessel, was inspired in part by the journeys of the HMS Beagle and the HMS Challenger in the nineteenth century. But unlike those pioneering expeditions, the Sorcerer II team led by J. Craig Venter and a globe-spanning network of collaborators are after tiny microbes, classifying the species they encounter not by their appearance but by their unique genetic code.

The current studies analyze samples collected from surface waters during the first phase (or first third) of the voyage, which led the Sorcerer II from Newfoundland through the Panama Canal and Galapagos Island on to French Polynesia. Venter’s crew siphoned seawater through a series of increasingly fine filters to collect the microbes, which they sent back to the J. Craig Venter Institute in Maryland.

In the lab, the scientists shredded the collected genetic material in millions of random snippets and then determined their sequence. Based on overlapping sequences, computer programs can then assemble longer stretches and merge them into longer pieces of a genome. These so-called "scaffolds" are a treasure trove for a diverse group of scientists, who try to squeeze as much information as possible from the largest metagenomic dataset ever collected. For more information about the expedition, please go to: the J. Craig Venter Institute (URL: www.sorcerer2expedition.org and www.venterinstitute.org)

###
About the Salk Institute:

The Salk Institute for Biological Studies in La Jolla, California, is an independent nonprofit organization dedicated to fundamental discoveries in the life sciences, the improvement of human health, and the training of future generations of researchers. Jonas Salk, M.D., whose polio vaccine all but eradicated the crippling disease poliomyelitis in 1955, opened the Institute in 1965 with a gift of land from the City of San Diego and the financial support of the March of Dimes.
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PostPosted: Fri Mar 16, 2007 8:13 am    Post subject: Surprising Pace of Evolution and Extinction Revealed Reply with quote

Surprising Pace of Evolution and Extinction Revealed

By Ker Than
LiveScience Staff Writer
posted: 15 March 2007
02:00 pm ET

New species of birds and mammals evolve faster at high latitudes than in the tropics, but they also go extinct faster, a new study suggests.

The finding, detailed in the March 16 issue of the journal Science, could help explain why biodiversity in the tropics is so much greater compared with other parts of the world.

Researchers Jason Weir and Dolph Schluter of the University of British Columbia in Canada mapped the genetic family tree of more than 300 mammal and bird species in the Americas over the past 10 million years.

For the full article:

http://www.livescience.com/ani.....s_evo.html
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PostPosted: Thu Mar 22, 2007 9:49 am    Post subject: Predators Stifle Rapid Evolution of Prey Reply with quote

Predators Stifle Rapid Evolution of Prey

By Ker Than
LiveScience Staff Writer
posted: 21 March 2007
01:00 pm ET

Evolution, normally viewed as a slow, steady process, can occur in rapid fits and starts with one species splitting into several lineages in a relatively short period of time. Now scientists have identified two factors that influence these bursts of new species.

Called adaptive radiation, the relatively swift emergence of new species is known to occur in isolated ecosystems, such as remote islands, or following mass extinctions. But details about what drives this process have remained murky.

Two new studies, detailed in the March 22 issue of the journal Nature, suggest predator-prey relationships, as well as the timing and relative order of a species' arrival into a new environment, can greatly affect how rapidly this branching process occurs.

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http://www.livescience.com/ani.....ation.html
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PostPosted: Wed Mar 28, 2007 10:20 am    Post subject: Study Explains Why We're Not All Beautiful Reply with quote

Study Explains Why We're Not All Beautiful

By Andrea Thompson
LiveScience Staff Writer
posted: 28 March 2007
09:47 am ET

A new study explains why we aren't all born with Brad Pitt’s perfectly chiseled features or Angelina Jolie’s pouty lips.

A long-standing thorn in the side of biologists has been the difficulty in accounting for the enormous variation between individuals when sexual selection by females for the most attractive mates should quickly spread the “best” genes through a population.

“It is a major problem for evolutionary biology,” said study team leader Marion Petrie of Newcastle University.

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http://www.livescience.com/hum.....radox.html
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PostPosted: Sat May 12, 2007 6:34 am    Post subject: A Grove of Evolutionary Trees Reply with quote

Week of May 12, 2007; Vol. 171, No. 19

A Grove of Evolutionary Trees
Julie J. Rehmeyer

An oceanographer buys a piece of whale flesh at a market in Japan. The clerk assures her the meat comes from a Baird's beaked whale, which is legal to hunt under certain circumstances. The scientist takes the meat to her lab, performs a DNA analysis of it, and finds that it is in fact an endangered right whale. Killing a right whale is a crime.

When the oceanographer reports her findings to the International Whaling Commission, the commissioners ask her one question: how certain are you?

Until recently, a scientist would not have been able to give a rigorous answer. The analysis depends on the scientist's understanding of the evolutionary relationships among different species of whales, and statisticians didn't know how to analyze the tree-shaped graphs that express those relationships.

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http://sciencenews.org/article.....thtrek.asp
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PostPosted: Thu May 24, 2007 11:36 am    Post subject: An Evolving Debate about Evolution Reply with quote

An Evolving Debate about Evolution
By David Masci, Senior Research Fellow, Pew Forum on Religion & Public Life

posted: 23 May 2007 03:28 pm ET

The evolution controversy, traditionally a state and local issue, has vaulted into the national political arena, making a surprise appearance at the first Republican presidential candidate debate on May 3 and garnering a large amount of press attention in the days following the event. Whether the evolution debate will continue to play even a minor role in the 2008 presidential campaign is an open question. Still, the fact that the issue was raised at all in a national context and that the incident was widely reported is significant, demonstrating how recent high profile battles over teaching evolution in public schools have increased people's awareness of the controversy.


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http://www.livescience.com/str.....ution.html
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