The Evolution Project

Ohio HOPE

2006-08-10T12:58:00.000-05:00

A few days ago we mentioned a new group in Ohio that will be helping promote pro-science candidates for the Ohio Board of Ed, and especially helping to bust "Ohio's answer to Connie Morris." Well, HOPE has webpage now, so you can click over there and help support their important work.

How western Kansas became K-State country, and how we can make it evolution country

2006-08-09T14:53:00.000-05:00

KU Country? | LJWorld.com:

Craig Miner’s latest book, “Next Year Country: Dust to Dust in Western Kansas, 1890-1940,” was featured in Monday’s Journal-World. In the book, Miner, a history professor at Wichita State University, chronicles the peaks and valleys of western Kansas, where harsh weather often spelled the difference between success and failure for the agricultural economy.

While compiling the history, Miner turned up several clues about why residents of the western two-thirds of the state have a good feeling about K-State. The school set up experiment stations across the area to test crop varieties and develop new hybrids that were resistant to pests and drought.

K-State, the railroads and the local Farm Bureaus took information on the road, traveling to different cities giving lectures and sharing information about better agriculture techniques for men and home economics for women.

I see nothing to suggest that a similar strategy, reaching out to the more distant communities and showing the value of science and evolutionary biology to people in rural Kansas couldn't bring the western part of the state as firmly onto the side of Darwin as they are of the Wildcats.

Request for help

2005-11-07T20:21:00.000-06:00

I haven't had the time to deal with TEP lately, but I hate to see it languish. Would anyone like to help me out?

678: The Living Worlds Hypothesis

2005-10-05T02:47:00.000-05:00

In this interview David Grinspoon posits a hypothesis about the way life could have evolved on Titan. It's a testable hypothesis.

677: A Prize Bug

2005-10-05T02:39:00.000-05:00

A Prize Bug:

As scientists got to know the global variation of Helicobacter better, they began to discover a remarkable pattern. They mapped out an evolutionary tree of the strains of the bacteria and found that it lined up very well with the migrations of humans over the past 50,000 years. One study looked at the Ladakh province of northern India. Muslims and Buddhists have coexisted there for 1000 but remain isolated from one another. It turns out that Muslim Ladakhs only carry a European strain of Helicobacter, while Buddhists carry a mix of European and East Asian bugs. In Peru, Indians who have lived in relative isolation from European colonists carry Helicobacter that is akin to the bugs in East Asia, a major source of migration into the New World. Peruvians from the cities, on the other hand, carried European Helicobacter. It appears that Helicobacter existed in our species before humans began to move beyond Africa, and was then carried around the world as our ancestors traveled the globe. But exactly how long ago this parasite first made its home in us remains to be discovered.

Scientists have a long way to go in order to understand the full evolutionary story of Helicobacter. Many ethnic groups have yet to be sampled, and the evolutionary contortions of their bacteria have yet to be documented. This work promises to offer some guidance about what we should do about this remarkable bug. Antibiotics can wipe it out, but that doesn't necessarily mean we should eradicate it from our species. It produces some proteins that kill other microbes, and one study suggested that it reduces the chances of children getting diarrhoea. Other studies have suggested that while Helicobacter causes some kinds of cancer, not having it increases the chances of other kinds. It's possible that a long coevolution has made Helicobacter part parasite, part mutualist--much the same as intestinal worms may have prevented our ancestors from getting allergies. It's even possible that Helicobacter's high-speed evolution allowed it to become more parasitic in some parts of the world and more mutualistic in others. Before we decide on its future, it will serve us well to understand Helicobacter's past.

This is the bacterium that won Marshall and Warren this year's Nobel Prize. Understanding its evolution gives insight into the diseases it causes and prevents, and our own species' history.

676: Fitting in: Newly evolved genes adopt a variety of strategies to remain in the gene pool

2005-10-05T02:35:00.000-05:00

The Panda's Thumb: Fitting in: Newly evolved genes adopt a variety of strategies to remain in the gene pool:

To determine the basis for the persistence of functional gene duplicates in the genome, three scientists at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich have collaborated on the largest systematic analysis of duplicated gene function to date. Using an integrative combination of computational and experimental approaches, they classified duplicate pairs of genes involved in yeast metabolism into four functional categories: (1) back-up, where a duplicate gene copy has acquired the ability to compensate in the absence of the other copy, (2) subfunctionalization, where a duplicate copy has evolved a completely new, non-overlapping function, (3) regulation, where the differential regulation of duplicates fine-tunes pathway usage, and (4) gene dosage, where the increased expression provided by the duplicate gene copy augments production of the corresponding protein.

Their results, which appear in the October issue of the journal Genome Research, indicate that no single role prevails but that all four of the mechanisms play a substantial role in maintaining duplicate genes in the genome.

Gene duplication is a major source of novel material for evolution.

675: The words of the world

2005-10-05T02:32:00.000-05:00

The Panda's Thumb: The words of the world:

A study in Science has returned biological methods to linguistic evolution in a reversal of history, and concluded that one can, within limits, reconstruct the history of language.

Charles Darwin was not the first person to suppose that historical evolution could be recognised by homologies and represented by tree diagrams. That honour goes to Sir William Jones in 1797, although the tree idea was later.

Jones argued that one could compare cognate terms and infer a historical relationship between languages and this has become the foundation of modern philology. For example, words that are based on the idea of “knowing” (including, as it happens, “idea”) generate a tree of Indo-European languages. [And like biological evolution, there are “creationists” who think that all language was created in Sanskrit.]

Now, a study in Science has returned biological methods to linguistic evolution in a reversal of history, and come up with some interesting conclusions.

Evolution gives insight into linguistics.

674: New dolphin species discovered

2005-10-05T02:29:00.000-05:00

New dolphin species in Australia.

673: How A Zebra Lost Its Stripes: Rapid Evolution Of The Quagga

2005-10-05T02:27:00.000-05:00

How A Zebra Lost Its Stripes: Rapid Evolution Of The Quagga:

In the past, the quagga has alternatively been described as a species and a subspecies of the Plains zebra.These researchers asked how and when the quagga diverged from all the remaining related horses, zebras, and asses. They compared the genetics, coat color and habitats of existing zebras with related extinct species.

The mitochondrial DNA markers from 13 museum specimens, including the only skeleton in museum collections, which is at Yale's Peabody Museum of Natural History, showed that quagga likely diverged from Plains zebra about 120,000 to 290,000 years ago during the Ice Age. These results suggest that the quagga descended from a population of plains zebras that became isolated and the distinct quagga body type and coloring evolved rapidly.

This study reveals that the Ice Age was important not just in Europe and North America, but also in Africa.

"The rapid evolution of coat color in the quagga could be explained by disrupted gene flow because of geographical isolation, an adaptive response to a drier habitat, or a combination of both of the two forces," said Caccone.

Thanks to afarensis for the tip.

672: Autoimmune overload may damage HIV-infected brain | Science Blog

2005-10-05T02:24:00.000-05:00

Autoimmune overload may damage HIV-infected brain | Science Blog:

Researchers studying the evolution of the human immunodeficiency virus (HIV) in the brain have found that the body's own defenses may cause HIV-related dementia.

Publishing in the Sept. 2005 issue of the Journal of Virology, the researchers show that HIV in the temporal lobe mutates at a rate 100 times faster than in other parts of the body, triggering white blood cells to continually swarm to attack the infection. The associated overcrowding and inflammation appear to cause the dementia.

Earlier studies had suggested that the build-up of white blood cells could lead to HIV-related dementia, but this is the first study to track the probable mechanism.

The findings could lead to new treatments that target HIV-infected white blood cells, perhaps one day countering the brain wasting that will affect as many as 15 percent of the nearly 40 million people around the world who are infected with the virus.

Evolution, saving lives.

671: Save the Flowers

2005-10-04T23:40:00.000-05:00

Save the Flowers: Science News Online, Sept. 24, 2005:

No one knows what's responsible for this waning of fragrance by roses and other ornamental-flower varieties, including carnations and chrysanthemums, but scientists who investigate floral scent suspect that the flower breeding that's led to an estimated 18,000 rose cultivars in an ever-widening spectrum has run roughshod over fragrance.

"Pigment compounds are derived from the same biochemical precursors [as scent compounds are], so it makes sense that if you make more of one you get less of the other," notes floral-scent biochemist and geneticist Eran Pichersky of the University of Michigan in Ann Arbor.

Floral scent may be dwindling because breeders for the $30 billion ornamental-flower industry pay scant attention to this most emblematic attribute of flowers.

Evolution is a story of trade-offs. This is a testable evolutionary hypothesis.

Thanks to BoingBoing for the tip.

644-670: Evolutionary Game Theory

2005-09-28T18:42:00.000-05:00

A few words on Evolutionary Game Theory:

About a month ago, Michael asked me to give my opinion on an article on cheating viruses and game theory. Coincidentally, I had to write a referee report on a paper about evolutionary game theory (EGT) only recently, so I have collected further material and ideas about this topic which I would like to share with you:

Jörgen Weibull's paper "What have we learned from Evolutionary Game Theory so far?" provides a great non-technical introduction to EGT. It gives a first idea of what EGT is all about. I very much appreciated the reference list of this paper as well. In Evolutionary game dynamic, Josef Hofbauer and Karl Sigmund dig a little deeper and provide some interesting insights into the relationship between systems of differential equations (inclusions) and special equilibrium refinements (notable ESS and ES). Finally, I would like to draw your attention to Daniel Friedman's paper "On economic applications of evolutionary game theory". This paper is also non-technical and its objective is to make the general ideas behind an evolutionary game theoretic model more tranparent. As the title suggests, Friedman gives a nice outline of how these ideas can be incorporated into economic models.

Links are omitted, but click through and check out the ways that evolutionary logic is used by economists.

643: Insight into our sight: A new view on the evolution of the eye lens

2005-09-26T14:06:00.000-05:00

Via Stranger Fruit, Insight into our sight: A new view on the evolution of the eye lens:

Fish, frogs, birds and mammals all experience image-forming vision, thanks to the fact that their eyes all express crystallins and form a lens; however, the vertebrates' nearest invertebrate relatives, such as sea squirts, have only simple eyes that detect light but are incapable of forming an image. This has lead to the view that the lens evolved within the vertebrates early in vertebrate evolution, and it raises a long-standing question in evolutionary biology: How could a complex organ with such special physical properties have evolved?

In their new work, Shimeld and colleagues approached this question by examining the evolutionary origin of one crystallin protein family, known as the ß?-crystallins. Focusing on sea squirts, invertebrate cousins of the vertebrate lineage, the researchers found that these creatures possess a single crystallin gene, which is expressed in its primitive light-sensing system. The identification of the sea squirt's crystallin strongly suggests that it is the single gene from which the vertebrate ß?-crystallins evolved.

The researchers also found that, remarkably, expression of the sea squirt crystallin gene is controlled by genetic elements that also respond to the factors that control lens development in vertebrates: The researchers showed that when regulatory regions of the sea squirt gene are transferred to frog embryos, these regulatory elements drive gene expression in the tadpoles' own visual system, including the lens. This strongly suggests that prior to the evolution of the lens, there was a regulatory link between two tiers of genes: those that would later become responsible for controlling lens development, and those that would help give the lens its special physical properties. This combination of genes appears to have then been co-opted in an early vertebrate during the evolution of its visual system, giving rise to the lens.

Common descent, testable evolutionary predictions and evaluating evolutionary hypotheses. Cool.

642: Evolving modularity

2005-09-26T13:01:00.000-05:00

John Hawks explains Why organisms are modular. Very neat simulations by Kashtan and Alon on the evolution of circuits in varying environment.

641: Researchers Find How Malaria Parasite Disperses From Red Blood Cells | Science Blog

2005-09-19T11:57:00.000-05:00

Researchers Find How Malaria Parasite Disperses From Red Blood Cells | Science Blog:

Researchers at the National Institute of Child Health and Human Development have determined the sequence in which the malaria parasite disperses from the red blood cells it infects. The National Institute of Child Health and Human Development is one of the National Institutes of Health.

…

“It’s extremely important to learn about all aspects of the malaria parasite’s life cycle, ” said Duane Alexander, M.D., Director of the NICHD. “The parasite is growing resistant to the drugs used to treat it, and new information is essential for developing strategies to protect against the disease.”

Evolution is at work in the resistance to drugs, but also explains how the parasite is so well adapted to parasitism.

Technorati Tags: evolution

640: Stressed Cells Spark DNA Repair Missteps And Speed Evolution

2005-09-18T23:17:00.000-05:00

Thanks to afarensis for point out Stressed Cells Spark DNA Repair Missteps And Speed Evolution:

When Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, first published her finding that the mutation rate increased in bacteria stressed by starvation, sometimes resulting in a rare change that benefited the bacteria, it was controversial.

In a report in the current issue of the journal Molecular Cell, she and her colleagues describe not only how it happens but also show that this only occurs at a special time and place in the stressed cells.

Research on evolution that reveals how cancer works, how the body fights it, and how new mutations arise.

Technorati Tags: evolution

639: Mitochondrial DNA adaptations in living human populations

2005-09-18T17:08:00.000-05:00

Mitochondrial DNA adaptations in living human populations:

populations in northern latitudes today are enriched for a number of mtDNA haplogroups that are likely adaptive to cold. Today, these haplogroups (as a class) are largely protective against degenerative diseases of aging, possibly because they reduce oxygen free radical production. But they are also more susceptible to disorders of energy metabolism, because they reduce ATP production.

Needless to say, this says some interesting things about the relationship of longevity and energy metabolism in recent human populations.

Human evolution and the trade-offs between longevity and energy efficiency.

Technorati Tags: evolution

638: Part Human, Part Virus

2005-09-18T17:03:00.000-05:00

Part Human, Part Virus: Corante > The Loom >:

Here’s the history as they now see it: the free-living, oxygen-breathing ancestors of mitochondria were infected with some nasty T3/T7 viruses. Most of the time the viruses were fatal. But some mutant tried to replicate itself inside a proto-mitochondrion and failed. Its genes were trapped in the genome of its host. Its host was able to reproduce, and one of its descendants took up residence inside the cell of a eukaryote. At some point after this merger, a mutation caused the virus’s DNA and RNA copying genes to come back online. They took over the job of making these molecules, and the mitochondria’s own genes for this job were later stripped out of its genome.

Viruses, endosymbionts, and the evolution of eukaryotes.

Technorati Tags: evolution

637: For Fossil Hunters, Gobi Is No Desert - New York Times

2005-09-14T23:20:00.000-05:00

For Fossil Hunters, Gobi Is No Desert - New York Times:

It has been the paleontologists' boast, never disputed, that this particular forbidding stretch of the Gobi holds the world's richest and most diverse deposits of dinosaur and early mammal remains from 80 million years ago, a critical time for life in the Cretaceous geologic period.

Four years had passed since paleontologists of the American-Mongolian expedition last pitched camp at Ukhaa Tolgod ("brown hills" in Mongolian), scene of their greatest triumphs. They were lured back last month, as surely as gold prospectors to the mother lode, by the expectation that the site has more to yield.

Hunting early fossils. Evolution at work.

Technorati Tags: evolution

636: Immune system has evolved to prevent autoimmune disease | Science Blog

2005-09-14T17:12:00.000-05:00

Immune system has evolved to prevent autoimmune disease | Science Blog:

New research finds the human immune system has foregone evolutionary changes that would allow it to produce better antibodies in less time because the improved antibodies would be far more likely to attack the body's own tissues. The Rice University study finds the immune system has evolved a near-perfect balance for producing antibodies that are both effective against pathogens and unlikely to cause autoimmune disease.

The findings will be published in the journal Physical Review Letters. They are based on a new model of the immune system that is the first to simulate the hierarchical nature of the body's immune response. The model predicts that chronic infections may lead to autoimmune diseases, a scenario that has been proposed as a cause of some rheumatic diseases like arthritis.

Mmmm, evolution. There are constraints on evolution and our immune system is (clearly) not perfect.

635: How bodies and plants repair UV damaged DNA | Science Blog

2005-09-14T17:10:00.000-05:00

How bodies and plants repair UV damaged DNA | Science Blog:

For the first time, researchers have observed exactly how some cells are able to repair DNA damage caused by the sun's ultraviolet (UV) radiation.

The Ohio State University study revealed how the enzyme photolyase uses energy from visible light to repair UV damage.

This enzyme is missing in all mammals, including humans, although all plants and all other animals have it. Greater understanding of how photolyase works could one day lead to drugs that help repair UV damage in human DNA.

…

Scientists believe that all placental mammals lost the ability to make this enzyme some 170 million years ago, said Zhong, an assistant professor of physics and adjunct assistant professor of chemistry and biochemistry at Ohio State.

That's why humans, mice, and all other mammals are particularly vulnerable to cancer-causing UV rays from the sun. But the rest of the animal kingdom – insects, fish, birds, amphibians, marsupials, and even bacteria, viruses and yeast – retained a greater ability to repair such damage.

Common descent!

634: In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times

2005-09-14T17:05:00.000-05:00

In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times:

Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior.

Scientists sequenced the DNA of a chimpanzee named Clint and compared it with that of humans.

The comparison pinpoints the genetic differences that have arisen in the two species since they split from a common ancestor some six million years ago.

The realization that chimpanzees hold a trove of information about human evolution and nature comes at a time when they and other great apes are under harsh pressures in their native habitat. Their populations are dwindling fast as forests are cut down and people shoot them for meat. They may soon disappear from the wild altogether, primatologists fear, except in the few sanctuaries that have been established.

Chimpanzees and people possess almost identical sets of genes, so the genes that have changed down the human lineage should hold the key to what makes people human.

Common descent and human evolution!

633: Brain May Still Be Evolving, Studies Hint - New York Times

2005-09-14T16:58:00.000-05:00

Brain May Still Be Evolving, Studies Hint - New York Times:

Two genes involved in determining the size of the human brain have undergone substantial evolution in the last 60,000 years, researchers say, leading to the surprising suggestion that the brain is still undergoing rapid evolution.

The discovery adds weight to the view that human evolution is still a work in progress, since previous instances of recent genetic change have come to light in genes that defend against disease and confer the ability to digest milk in adulthood.

It had been widely assumed until recently that human evolution more or less stopped 50,000 years ago.

This surprises no one, in fact. I've got a stack of cases where humans are evolving, ranging from lactose intolerance to mutations which conferred protection against the Plague and now protect some people against HIV.

Don't read this to mean that particular alleles necessarily are "genetically smarter" or anything like that. It may mean that or it may not, all they are showing is change, another name for evolution.

632: The Tubercular Hominid

2005-08-22T12:29:00.000-05:00

The Tubercular Hominid: Corante > The Loom >:

French researchers have found that people in Djibouti carry strains of TB that are significantly different than anything seen before. They have many more genetic differences than have been found in human TB strains from anywhere else in the world. Yet they are more closely related to other human TB than to the Mycobacterium species that infect cattle and other animals. The scientists then turned the mutations of the Djibouti strains into a molecular clock. They estimate that the ancestor of today's human TB existed some three million years. The results have just been published in the new open access journal PLOS Pathogens.

If tuberculosis was infecting our ancestors three million years ago, it was infecting early, small-brained hominids. All of the hominids known from that time lived in Africa, and hominids would not be found outside the continent for over a million years. Our own species is believed to have evolved much later in Africa, and to have spread to Asia and Europe roughly 50,000 years ago. So it's telling that all these ancient strains are found in Africa, not far from some of the richest lodes of hominid fossils in Ethiopia. The genetic diversity of these bacteria reflects the genetic diversity of living Africans.

The evolution of TB.

631: Worm ideal model for studying viruses in humans | Science Blog

2005-08-18T11:17:00.000-05:00

Worm ideal model for studying viruses in humans | Science Blog:

For years researchers throughout the world have studied C. elegans because many aspects of its biology, such as genetics, development and the workings of neurons, mirror the biology of humans. However, no viruses were known to infect the millimeter-long roundworm so it was not used as a model for studying viral infections.

The Nature paper now shows that UC Riverside researchers have developed a strain of the worm, C. elegans, in which an animal virus could replicate, allowing them to map the delicate dance of action and reaction between virus and host.

The UCR team has shown that virus replication in the worm triggers an antiviral response known as RNA silencing or RNA interference (RNAi). RNAi specifically breaks down the virus’ RNA. Virus RNA creates proteins that allow the virus to function. The virus responds by producing a protein acting as a suppressor of RNAi to shut down the host’s antiviral response. Virus infection did not occur when the viral RNAi suppressor was made inactive by genetic mutations in the host system.

C. elegans’ RNAi system is considered a “blanket system,” meaning that it has parallels in humans, making the worm model discovered by Ding and his colleagues a valuable tool in studying the way viruses interact with hosts. This tool may speed the discovery of treatments for virus-caused diseases that plague humans.

“The RNAi machinery is very similar between humans and C. elegans, and human viruses such as Influenza A virus and HIV are known to produce RNAi suppressors,” Ding said. “So now, the question is can we treat human viral diseases using chemical inhibitors of viral RNAi suppressors?”

Common descent and the evolutionary arms race between viruses and their hosts.

Ohio science

2005-08-17T22:16:00.000-05:00

At Thoughts from Kansas.

630: Scientists Crack 40-year-old DNA Puzzle And Point To 'Hot Soup' At The Origin Of Life

2005-08-17T20:55:00.000-05:00

Scientists Crack 40-year-old DNA Puzzle And Point To 'Hot Soup' At The Origin Of Life:

In a paper published in the Journal of Molecular Evolution this week, researchers from the University of Bath describe a new theory which they believe could solve a puzzle that has baffled scientists since they first deciphered the language of DNA almost 40 years ago.

…

why there should be 64 words in the DNA dictionary which translate into just 20 amino acids, and why a process that is more complex than it needs to be should have evolved in the first place, has puzzled scientists for the last 40 years.

Dozens of scientists have suggested theories to solve the puzzle, but these have been quickly discounted or failed to explain some of the other quirks in protein synthesis.

…

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.

The new theory builds on an original idea suggested by Francis Crick - one of the discoverers of the structure of DNA - that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident “frozen in time”.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes - but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.

By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids - explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.

“When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today,” said Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.

“This simple theory explains many unresolved features of the current genetic code. No one has ever been able to do this before, so we are very excited.”

The theory also explains how the structure of the genetic code maximises error tolerance. For instance, ‘slippage’ in the translation process tends to produce another amino acid with the same characteristics, and explains why the DNA code is so good at maintaining its integrity.

“This is important because these kinds of mistakes can be fatal for an organism,” said Dr van den Elsen. “None of the older theories can explain how this error tolerant structure might have arisen.”

The new theory also highlights two amino acids that can be excluded from the doublet system and are likely to be relatively recent ‘acquisitions’ by the genetic code. As these amino acids - glutamine and asparagine - are unable to hold their shape in high temperatures, this suggests that heat prevented them from being acquired by the code at some point in the past.

Research into the evolution of DNA, and evolutionary hypotheses to be tested.

629: The Questionable Authority: Applications of Evolution 1 - The Erythrina Gall Wasp

2005-08-17T20:40:00.000-05:00

The Questionable Authority: Applications of Evolution 1 - The Erythrina Gall Wasp:

At the moment, there is a new invasive species that is making the news here in Hawai'i: a species of "gall wasp" that has been wrecking havoc on trees of the genus Erythrina in Singapore, Taiwan, and a number of other places was found in a valley on Oahu in April. Since then, it has been found in a large number of other places on Oahu, and has started to turn up on other islands, including Maui, and a number of scientists believe that it poses a serious threat to a culturally-significant endemic plant - the Wiliwili (Erythrina sandwichensis). The threat is being taken so seriously that scientists have reportedly begun to bank Wiliwlil seeds as a precaution in case the extant population is completely lost.

So what does this have to do with evolution?

Individual species do not evolve in a vacuum. They evolve in an environment, and natural selection favors the preservation of variations that increase the chances for an organism to survive within that environment. This is common knowedge. What people sometimes forget, however, is that when we discuss the "environment" that an organism evolves in, we are talking about much, much more than just the climate. The evolutionary environment also includes every other species of organism that has any sort of effect on it. Species evolve within the ecosystem or ecosystems that they inhabit, and they evolve as a part of those ecosystems.

So what happens when people - either intentionally or inadvertantly - introduce a species to a new habitat? That's a broad question, and one where the answer is obviously going to depend on a lot of things - not least, what the new species is, and where it is being introduced. (Biology can be really annoying that way, with the answers to so many questions depending on specific circumstances.)

Since the broad question isn't really answerable, let's narrow it in a way that is tailored to these specific circumstances: what happens if you introduce a pest species (either parasite or predator) into a new, hospitable environment that contains a species that is closely related to the pest's usual target? That is a very complexly worded question, but it has a simple answer. Nothing good is going to happen.

In the case of the Erythrina gall wasp, this is exactly what happened. The gall wasp is not native to Hawai'i, and it did not evolve here. This means that up until now, it has not been a part of the evolutionary environment for any of the native species. As a result, it should come as no surprise that the native species has no natural defences against the gall wasp. At the same time, the gall wasp has now found itself in an environment where it has lots of access to a number of species that it can use, and which completely lacks any of it's normal predators. In short, it's gall wasp heaven out here - at least until the Erythrina are all gone.

For more on how evolution helps us understand invasive species and vice versa, check out TQA, a new kid on the evolution blogging block.

628: Pleistocene Horses

2005-08-17T20:31:00.000-05:00

Pharyngula::Pleistocene Horses:

Prior hypotheses of the relationship of these three North American groups suggested that, because of their morphology similarity to Asian stock, the stilt-legged horses were related the Asian asses, and had migrated into the Americas by way of the Bering land bridge. Hippidion was so distinctly different from other horses that it was considered to have diverged from the equid lineage about 10 million years ago. These species were thought to have spread into South America during the Great American Biotic Interchange about 2.5 million years ago, when the Isthmus of Panama formed and allowed animals to move north and south between the continents. Two competing models of these relationships, based on morphological analyses, are shown below.

The molecular data revealed a surprise, though. The tree below was constructed by analysis of mtDNA, and it groups the animals very differently. The caballines of America and Europe form a single clade, as expected. The stilt-legged horses and Hippodion, though, cluster together; Hippodion diverged only recently, and the stilt-legged horses are more closely related to the caballines than to the Asian asses. The authors also suggest that many species within the caballines ought to be lumped together, are more likely to represent regional variants than true species.

The figure is a maximum likelihood phylogeny based on mitochondrial DNA. Black numbers above/beside nodes are posterior probabilities and bootstrap values, respectively (only values > 50% are shown). White numbers on black background are divergence times as calculated from the molecular data. Numbers/letters in bold at the beginning of each specimen's name are sample numbers or GenBank accession numbers. Labels of prehistoric specimens are followed by their age, if available, in thousands of years. The outgroup (Rhinoceros and Ceratotherium) is not shown.

Tests of evolutionary hypotheses.

627: The Genetic Origins of Corn on the Cob | Science Blog

2005-08-17T20:23:00.000-05:00

The Genetic Origins of Corn on the Cob | Science Blog:

In 1909, while harvesting a typical corn crop (Zea mays) in Illinois, a field worker noticed a plant so unusual that it was initially believed to be a new species. Its "peculiarly shaped ear" was "laid aside as a curiosity" and the specimen was designated Zea ramosa (from the Latin ramosus, "having many branches"). Due to the alteration of a single gene, later named ramosa1, both the ear and the tassel of the plant were more highly branched than usual, leading to loose, crooked kernel rows and to a tassel that was far bushier than the tops of normal corn plants.

Now, researchers at Cold Spring Harbor Laboratory in New York have isolated the ramosa1 gene and shown how it controls the arrangement and length of flower-bearing branches in corn, related cereal crops, and ornamental grasses. The study indicates that during the domestication of corn from its wild ancestor (teosinte), early farmers selected plants with special versions of the ramosa1 gene that suppressed branching in the ear, leading to the straight rows of kernels and the compact ears of modern-day corn on the cob (see photo). The findings are described in the July 24 advance online edition of the journal Nature.

" We've shown that corn and related grasses have either none, some, or a lot of ramosa1 gene activity, and that these different levels of activity have a big impact on the architecture of the plants," says Dr. Robert Martienssen of Cold Spring Harbor Laboratory, who led the study. "The ramosa1 gene appears to be a key player in the domestication of corn, and we've shown that it acts by signaling cells to form short rather than long branches," says Martienssen, who was joined in the study by lead author Dr. Erik Vollbrecht, now at Iowa State University.

Says Vollbrecht, "We solved this enduring puzzle by combining classical and modern molecular genetics. The former included our use of transposable elements or 'jumping genes'--discovered at Cold Spring Harbor by [Nobel laureate] Barbara McClintock--to 'tag' the ramosa1 gene. That enabled us to isolate the gene and determine its DNA sequence for a variety of other experiments."

" As corn was being domesticated, farmers selected a larger and larger ear with more and more rows of kernels, based on the activity of genes other than ramosa1. But we suspect that as the ear got larger, it needed special alleles of ramosa1 to prevent the extra rows from forming branches instead of kernels," says Martienssen. "There may have been other reasons for selecting an unbranched ear, including the interaction with other genes that were subsequently lost during domestication, but we don't yet know if this is the case."

The evolution of grasses, selection, and good biology.

" We also looked at a popular ornamental grass that grows outside my office and found the same result. It has a spiky top like corn, so we were delighted to find that they have similar profiles of ramosa1 activity," says Martienssen.

That's common descent.

626: Genetics links whale to two different ocean basins | Science Blog

2005-08-17T20:11:00.000-05:00

Genetics links whale to two different ocean basins | Science Blog:

For the first time ever, a genetic study has followed a single humpback whale from one ocean basin to another, adding to traditional notions of the migratory patterns of these majestic marine mammals in the process, according to researchers from the Wildlife Conservation Society (WCS), the American Museum of Natural History (AMNH), and New York University. In the most recent Royal Society's Biology Letters, a male humpback whale that was first sighted in Madagascar's Antongil Bay in 2000 was found in 2002 swimming off the coast of Loango National Park in Gabon--on the other side of the African continent.

This is gene flow, one of the 4 evolutionary mechanisms, along with genetic drift, mutation, and natural selection. Understanding gene flow in whales improves conservation, and helps us understand how whales have evolved. It's known that there are a number of distinct genetic populations of humpbacks, and how often and by what means they exchange genetic information is crucial to conservation.

625: Generating right-left asymmetries

2005-08-17T20:07:00.000-05:00

Pharyngula::Generating right-left asymmetries:

We're only sorta bilaterally symmetric: superficially, our left and right halves are very similar, but dig down a little deeper, and all kinds of interesting differences appear. Our hearts are larger on the left than the right, our appendix is on the right side, even our brains have significant differences, with the speech centers typically on the left side. That there is asymmetry isn't entirely surprising—if you've got this long coil of guts with a little appendix near one end, it's got to flop to one side or the other—but what has puzzled scientists for a long time is how things so consistently flop over in the same direction in individual after individual. There has to be some deep-seated mechanism that biases developmental events to favor one direction over the other. We know many of the genes involved in asymmetry, but what is the first step that skews development to make consistent asymmetrical choices?

In mammals, we're getting close to the answer. And it looks to be beautifully elegant—it's a simple trick to convert an anterior-posterior difference into a left-right one.

Nonaka et al. have examined the node of the mouse embryo. At the time of gastrulation, the mouse embryo (and the human embryo as well) is essentially a flat, two-layered sheet, with a groove in the middle called the primitive streak, and a dimple at the anterior end called Henson's node.

…

Zooming in on that area of the node in C, you can see the tops of the epithelial cells looking vaguely like cobblestones, with white strings scattered around. These are ciliated cells, and the strings the whip-like cilia that would be swinging around in a clockwise rotation if the cells were alive. You can watch a QuickTime movie of node cilia to see it in action.

When you watch those cilia spin around, here's the subtle but important thing to look for: their paths don't form perfect circles, which would indicate that they are pointing straight up at you, but are instead deformed to varying degrees, showing that they are tilted at an angle…and they are all tilted in the same direction, towards the posterior end of the embryo.

That tilt is what generates the left-right asymmetry. The tilt isn't asymmetric—all of the cilia are aimed just a little bit posteriorly, rather than straight up—but because the cilia are also rotating in a clockwise direction, it generates unequal lateral forces.

Why does the same mechanism operate in all mammals? Common descent.

624: Mutant mice helping cure diseases - Aug 10, 2005

2005-08-15T16:13:00.000-05:00

CNN.com - Mutant mice helping cure diseases - Aug 10, 2005:

Researchers first genetically engineered a mouse in 1980. But until recently, such creations were mostly scientific novelties.

That changed drastically after President Clinton announced the mapping of the human genome in 2000. That's because mice and men are nearly genetically identical, each possessing just a few hundred different genes out of a possible 25,000 or so. Cancer in mice is a lot like human cancer, for instance. Mice have become powerful, living research tools.

The number of mutant research mice has grown so dramatically in recent years that companies are now profiting by housing and breeding scientists' creations.

Common descent explains that similarity, and evolutionary biology is bringing us closer and closer to cures for cancer, Parkinson's and diabetes, among other things.

623: The rise of the hominids as an adaptive shift in fallback foods: Plant underground storage organs (USOs) and australopith origins

2005-08-15T00:31:00.000-05:00

ScienceDirect - Journal of Human Evolution : The rise of the hominids as an adaptive shift in fallback foods: Plant underground storage organs (USOs) and australopith origins:

We propose that a key change in the evolution of hominids from the last common ancestor shared with chimpanzees was the substitution of plant underground storage organs (USOs) for herbaceous vegetation as fallback foods. Four kinds of evidence support this hypothesis: (1) dental and masticatory adaptations of hominids in comparison with the African apes; (2) changes in australopith dentition in the fossil record; (3) paleoecological evidence for the expansion of USO-rich habitats in the late Miocene; and (4) the co-occurrence of hominid fossils with root-eating rodents. We suggest that some of the patterning in the early hominid fossil record, such as the existence of gracile and robust australopiths, may be understood in reference to this adaptive shift in the use of fallback foods. Our hypothesis implicates fallback foods as a critical limiting factor with far-reaching evolutionary effects. This complements the more common focus on adaptations to preferred foods, such as fruit and meat, in hominid evolution.

Carl Zimmer discusses some of the implications and background of the research.

622: Model Gives Clearer Idea Of How Oxygen Came To Dominate Earth's Atmosphere

2005-08-14T12:29:00.000-05:00

Thanks to afarensis, Model Gives Clearer Idea Of How Oxygen Came To Dominate Earth's Atmosphere:

A number of hypotheses have been used to explain how free oxygen first accumulated in Earth's atmosphere some 2.4 billion years ago, but a full understanding has proven elusive. Now a new model offers plausible scenarios for how oxygen came to dominate the atmosphere, and why it took at least 300 million years after bacterial photosynthesis started producing oxygen in large quantities.

The big reason for the long delay was that processes such as volcanic gas production acted as sinks to consume free oxygen before it reached levels high enough to take over the atmosphere, said Mark Claire, a University of Washington doctoral student in astronomy and astrobiology. Free oxygen would combine with gases in a volcanic plume to form new compounds, and that process proved to be a significant oxygen sink, he said.

Another sink was iron delivered to the Earth's outer crust by bombardment from space. Free oxygen was consumed as it oxidized, or rusted, the metal.

But Claire said that just changing the model to reflect different iron content in the outer crust makes a huge difference in when the model shows free oxygen filling the atmosphere. Increasing the actual iron content fivefold would have delayed oxygenation by more than 1 billion years, while cutting iron to one-fifth the actual level would have allowed oxygenation to happen more than 1 billion years earlier.

…

The work is funded by NASA's Astrobiology Institute and the National Science Foundation's Integrative Graduate Education and Research Traineeship program, both of which foster research to understand life in the universe by examining the limits of life on Earth.

"There is interest in this work not just to know how an oxygen atmosphere came about on Earth but to look for oxygen signatures for other Earth-like planets," Claire said.

Research inspired by evolutionary biology.

621: Structural Basis for the Activation of Cholera Toxin by Human ARF6-GTP -- O'Neal et al. 309 (5737): 1093 -- Science

2005-08-12T11:58:00.000-05:00

Structural Basis for the Activation of Cholera Toxin by Human ARF6-GTP -- O'Neal et al. 309 (5737): 1093 -- Science:

The Vibrio cholerae bacterium causes cholera, a serious diarrheal disease that claims thousands of victims in third-world, war-torn, and disaster-stricken nations each year (1). V. cholerae secretes its major virulence factor, cholera toxin (CT), when colonizing the mucosa of the human small intestine. CT is composed of a globular A subunit and a pentamer of B subunits (2, 3). Heat-labile enterotoxin (LT) produced by enterotoxigenic Escherichia coli, which is responsible for hundreds of thousands of children's deaths from diarrheal diseases annually (4), shares more than 80% sequence identity with CT. In both toxins, proteolytic cleavage of the A subunit and reduction of the Cys187-Cys199 disulfide bond covalently separate the A1 and A2 domains, formed by residues 1 to 192 and 193 to 240, respectively (5). A1 is solely responsible for the toxin's enzymatic activity; however, in vivo delivery of the A1 enzyme to its target requires the nonenzymatic B pentamer and A2 peptide, which testifies to an extensive coevolution of the diarrheal pathogens with their human hosts (6, 7).

Co-evolution and common descent explain why we get sick.

618-620: PLANT SCIENCE: Enhanced: The Right Time and Place for Making Flowers -- Blázquez 309 (5737): 1024 -- Science

2005-08-12T11:47:00.000-05:00

PLANT SCIENCE: Enhanced: The Right Time and Place for Making Flowers -- Blázquez 309 (5737): 1024 -- Science:

Reproductive success in plants depends on the synchronization of flowering within a given species. Many plants have developed a highly complex signaling network that monitors environmental conditions, such as day length, temperature, or nutrient availability, and determines the appropriate timing for flowering (1, 2). This is the case for the model plant Arabidopsis thaliana and the pea that both flower in spring when day length and ambient temperature increase, or certain rice varieties and soybean that flower early in the fall when days get shorter. The initiation of flowering requires an additional developmental program to specify the floral identity of the new structures that continuously arise at the shoot apex (3). For instance, during the long vegetative phase in Arabidopsis, every primordium, the groups of cells poised to differentiate, forms a leaf. However, once the decision to flower has been made, all newly emerging primordia follow a developmental program that culminates in the formation of flowers rather than leaves. Thus, constructing a flower requires both temporal and spatial information that restricts the initiation of flowering to specific locations. But how this information is integrated has not been clear. Three studies now reveal the molecular mechanism by which this integration is achieved. In this issue, Abe et al. on page 1052 (4) and Wigge et al. on page 1056 (5) report that interaction between Flowering Locus T (FT), a protein encoded by a gene that is expressed in leaves, and FD, a bZIP transcription factor that is present only in the shoot apex, triggers the expression of floral identity genes in the new primordia. The third paper by Huang et al. in this week's Science Express (6) reports how the two factors meet--FT transcript travels from leaf to shoot via the plant vascular tissue.

Common descent reveals the way flowers form.

617: Plant pollen records ozone holes - Fossil measurements might reveals causes of mass extinction.

2005-08-12T11:08:00.000-05:00

news @ nature.com - Plant pollen records ozone holes - Fossil measurements might reveals causes of mass extinction.:

There are many ideas about the Permian extinction, when almost 90% of all species died. "So far, no-one's come up with a definitive mechanism," says Andrew Saunders, a geochemist from the University of Leicester who has researched the event.

Some scientists think a comet or meteorite struck the Earth. Others link the event to an enormous volcanic eruption that left a large mass of lava in Siberia.

This eruption would have released dust, sulphur and halogen compounds, disrupting the chemistry of the atmosphere and possibly eating a hole in the ozone layer.

Spores from the time show severe mutations, which may have been caused by ultraviolet radiation let through by a thinner ozone layer1. But at the moment there's no conclusive evidence of an ozone loss at that time, says Barry Lomax, part of the Sheffield team, who presented the team's results on 10 August at the Earth System Processes conference in Calgary, Canada.

"We hope this method will be the first independent test of ozone levels from that period," says Wellman. There is an excellent fossil record of pollen spores, and although the para-coumaric acids break down over time, they leave signature chemicals that should remain in fossils that have not been heated, he says.

"If it works, we should see a massive increase in pigments during the Permian," says Wellman. With a thinner ozone layer, more ultraviolet radiation would hit plants, forcing them to slather on more sunscreen.

The evolutionary response to an ozone hole tells us about the climate 252 million years ago, and about the causes of the extinction of 90% of the species alive at the time.

616: A cure for HIV?

2005-08-12T11:05:00.000-05:00

Hitting HIV Where It Hides -- Cohen 2005 (811): 1 -- sciencenow:

One of the most effective defensive tools used by the AIDS virus is its ability to hide out in some of the body's cells. This has prevented even the most powerful drug regimens from completely eradicating HIV in patients. Now, scientists report a strategy that flushes the virus from its hideout, and they claim that it paves the way for a cure.

In 1996, early enthusiasm about the power of new anti-HIV drug cocktails led to a proposition that totally eradicating the virus from the body might take only 2 to 3 years of treatment. But the concept lost currency when it became clear that HIV hides out in reservoirs of "resting" CD4+ white blood cells from which it is very hard to dislodge.

The new study takes an unusually precise approach to dislodging the latent pool. Using evidence that an enzyme called histone deacetylase 1 (HDAC1) plays a crucial role in keeping CD4+ cells in a latent state, virologist David Margolis of the University of North Carolina in Chapel Hill and colleagues gave AIDS patients valproic acid, an HDAC1 inhibitor that's licensed to treat epileptic seizures. Active CD4+ cells evict HIV from its hiding place, and the team administered a new drug, T-20, to help mop up bursts of the virus after the cells spat it out. After 4 months, the amount of infectious HIV in each patient's pool of latent cells declined an average of 75% in three of the four patients studied, the investigators report 13 August in The Lancet.

The resistance of HIV to treatment is a result of selection throughout its history, selection strengthened by treatment with the cocktails. This research is based on those evolutionary insights.

615: Guppy See, Guppy Do -- Mason 2005 (811): 4 -- sciencenow

2005-08-12T10:59:00.000-05:00

Guppy See, Guppy Do -- Mason 2005 (811): 4 -- sciencenow:

in some species, generation after generation, animals still seem to copy each other's behaviors, leaving scientists to wonder if the copying habit itself can be inherited.

To test the idea, biologist Lee Dugatkin of the University of Louisville in Kentucky examined female guppies, which mimic the mate choices of their peers. After a group of female fish gave birth, Dugatkin watched the moms to see how likely they were to copy another female's mate choice. Each mom was put in a tank alone with two males in adjacent tanks on either side. Another female was placed in a tank next to one of the males, and the mom was able to watch the courtship unfold. The courting female was then removed, leaving the mom alone to make a selection. If she spent more of her time near the male "chosen" by the other female, she was a considered a copier. About 85% of the females proved to be copiers, Dugatkin found.

Once the offspring of the copiers were ready to mate, Dugatkin put them through the same tests and found that they also were more likely to be copiers than were the offspring of the 15% of moms with an independent streak. This suggests that the tendency to copy another's mate choice preference is a heritable trait, says Dugatkin, who presented his results here 9 August at a meeting of the Animal Behavior Society.

The evolution of imitation. Very cool.

614: Canada the cradle of life, eh?

2005-08-11T10:59:00.000-05:00

Via Majikthise, Canada the cradle of life, eh?:

A study of the Haughton Impact Crater on Devon Island in the Canadian Arctic by the Canadian Space Agency has revealed the presence of a number of features associated with the emergence of microscopic life forms. These include hydrothermal systems and fissures and cracks in rocks created by the blast.

While further study will be necessary, the findings could prod scientists to begin to examine the search for life on this planet or Mars slightly differently.

Evolutionary hypotheses.

613: Molecular mechanism of feather formation found | Science Blog

2005-08-11T10:58:00.000-05:00

Molecular mechanism of feather formation found | Science Blog:

The results suggested that a simple interaction between Shh and Bmp2 is sufficient to model the creation and patterning of barbs in feather development. The team then tested whether such interactions truly exist in the developing feather. In the first steps of feather development, cells exposed to essentially the same levels of Bmp2 and Shh grow from a small bud to form a uniform ring. Shh then is expressed in specific spots along the ring, giving rise to bumps, seen microscopically as longitudinal stripes demarcating the edges of ridges in the developing barb.

"Each barb ridge grows in length by recruiting new cells, which proliferate at the growing base of the feather germ, to join the base of that barb ridge," Harris says. "The variations in the initial number of barb ridges will directly affect the shape, and consequent function, of the feather."

To test the activator-inhibitor model, Harris injected retroviruses to force the expression of either Shh or Bmp2 into the skin of six-day-old chick embryos. The virus infected only small patches of cells and allowed Harris to locally examine the effects of the treatment on barb patterning during feather development.

To assess the specific role of Bmp2 in regulating Shh expression, Harris tricked the cells into believing that Bmp2 was signaling them continuously by altering receptors in the cells. The over-expression of Bmp2 signaling via the altered receptors led to ongoing down-regulation of normal Shh expression needed to form the barbs.

Harris and colleagues used a similar experiment to test whether Shh could up-regulate its own expression during barb formation, and found that it could. Similarly, they found that regional expression of Shh led to detectable up-regulation of Bmp2 in feather buds as they first grew.

The underlying assumptions of the model were found to be true in developing feathers. These findings suggest that simple relationships between developmental genes can provide the basis for the formation of complex forms.

The researchers predict that a more complicated version of the model can be applied to the formation of more complex feathers. Termed pennaceous, these feathers occur in the duck and other birds, including adult chickens, and are not characterized as downy. The more primitive young chicken feathers, which are downy, are called plumalaceous.

"We don't have empirical evidence for this yet, but mathematical analyses lead us to believe that the addition of a third signaling factor leads to the development of the more complex pennaceous feather," Fallon says. " Our model supports paleontologic evidence that pennaceous feathers are more advanced than plumalaceous feathers."

Evolutionary hypotheses generated from a combination of fossils and molecular biology.

612: Drunken flies and fish

2005-08-11T10:54:00.000-05:00

Drunken flies and fish:

Scholz et al. screened mutagenized flies, looking for mutants that never learned to hold their liquor. They found one, called hangover (hang). Flies mutant for hangover have significantly reduced tolerance, and similar doses of alcohol knock them out over and over again. They have some capacity for tolerance, but it's greatly reduced. There is also a second molecular pathway, the octopaminergic pathway (octopamine is a neurotransmitter used in the fly's brain), and mutating that in addition reduces the animal's tolerance still further.

Why would animals have a gene to help them cope with alcohol? Alcohol exposure is ubiquitous in the environment, especially if you have to share your diet with yeast, which spew the stuff all over. The interesting thing, though, is that alcohol tolerance is coupled to an animal's general ability to handle stress, such as heat and oxidants. Flies with the hangover mutation are also more sensitive to heat shock and reactive oxygen species, and tend to have a shorter life span. It's more than just an alcohol tolerance gene—it's a general stressor response gene.

What makes this relevant to us in a utilitarian way is that our response to alcohol is a generic property of many animals: flies, fish, mice, and people can all get drunk and exhibit similar symptoms and cope with similar molecular mechanisms. It's universal!

In summary, the development of ethanol tolerance in Drosophila engages two systems that function in parallel, one involving a cellular stress pathway defined by the hang gene and the other involving octopaminergic systems. Octopamine has recently been implicated in the formation of appetitive (sugar-reinforced) memories in Drosophila. The contribution of learned behaviours and stress, at both the cellular and systemic levels, to drug- and addiction-related behaviours in mammals is being increasingly recognized. Our studies in Drosophila suggest that these pathways are conserved, allowing further analysis in this genetically tractable model organism.

And that's why I'm thinking of trying a few pilot experiments to get my fish drunk. There are tools and techniques out there that will allow us to probe the details of these processes in our experimental animal, and they are applicable to lots of other beasties as well…this evolution idea is the glue that brings many ideas together.

Ah, common descent.

611: Chirality in Snails

2005-08-09T21:50:00.000-05:00

Pharyngula::Chirality in Euhadra:

There are 22 species in the group, and 5 of them are sinistral, with the rest dextral. The question is whether speciation events can reasonably be traced back to changes in a single gene, whether this diverse assemblage can be explained by occasional mutations in chirality that split off new reproductively isolated groups.

To make a long and somewhat mathematical story short, the answer is no. There have to be other isolating mechanisms present to help out.

One observation is that if you are a newborn dextral snail in a population of sinistrals, you're going to have a much harder time finding a mate than your sinistral cousins. The more common your morphology, the more likely you are to find a compatible mate. This competitive advantage for the most common form will typically drive the population towards a single chirality.

There are, however, conditions under which it is good to be a weirdo. When two species of the same chirality overlap, it will be common for individuals of those two species to mate—which may be fun, but it's fruitless. If one species has a subpopulation with a different chirality, though, they may have an advantage. While they are only able to mate with conspecifics of the same handedness, they won't be wasting time and gametes on members of the other species. This is a phenomenon called character displacement, and could be an additional force for speciation.

In the simpler case where a single population has two chiral variants, though, chirality is insufficient in itself to isolate the two forms. With mathematical modeling, the authors showed that the separation will be incomplete because of gene flow, so the two types will reach an equilibrium, but outside of chance variations, one will not replace the other. The catch is the way maternal effects are delayed in the expression of their phenotype by a generation. That means that a sinistral snail can mate with a sinistral snail, and their progeny may be dextral, and able to breed with the dextral population. Similarly, some of those dextral snails will mate with other dextral snails, and produce progeny which are sinistral. Gene flow is slowed between the two subgroups, but it would require other phenomena, such as geographic separation, to complete the process.

Chirality is how the snail shell twists. Sinistral is to the left, dextral to the right. This is a speciation being studied, evolutionary hypotheses tested, and new ones being generated.

610: Convergent Evolution in Poison Frogs - Yahoo! News

2005-08-09T10:42:00.000-05:00

Convergent Evolution in Poison Frogs - Yahoo! News:

Scientists have discovered one of the most intricate examples of convergent evolution with the help of South American "poison" frogs and ants and their cousins in Madagascar.

Poison frogs can't make their own poison--they steal it from ants. Poison frogs secrete a variety of chemicals called alkaloids to create a poisonous defense against predators. Since they can't produce alkaloids on their own, these frogs maintain a steady diet of specific alkaloid-rich ants to keep up their defense.

Now, Valerie Clark of Cornell University and her colleagues have detailed two instances of convergent evolution--the process in which organisms not closely related independently acquire similar characteristics while evolving in separate ecosystems--between frogs and ants on two continents.

Convergent evolution and a test of evolutionary hypotheses.

609: Big game hunters, not climate change, killed off sloths | Science Blog

2005-08-09T01:42:00.000-05:00

Big game hunters, not climate change, killed off sloths | Science Blog:

“If climate were the major factor driving the extinction of ground sloths, you would expect the extinctions to occur at about the same time on both the islands and the continent since climate change is a global event,” Steadman said.

Gary Haynes, anthropology professor at the University of Nevada, Reno, said Steadman’s study “clearly shows that ground sloth extinctions in the New World didn’t happen after serious changes in climate or vegetation – and that the first appearance of humans must have been the decisive factor.”

The fossil record shows the people who arrived in North America were making sophisticated tools out of stone, bone and ivory, Steadman said. These “big-game hunters” had a traumatic effect on the animals living there, he said.

More than three-fourths of the large species of mammals that roamed the North American landscape became extinct within a few thousand years, which, besides ground sloths, included mammoths, mastodons, saber-toothed tigers and giant bears, Steadman said.

…

While the largest of the prehistoric ground sloths grew to the size of a modern elephant and fed on bushes and the leaves of lower branches of trees, today’s only surviving descendants are several small tree sloths whose range extends from southern Mexico to southern Brazil, he said.

…

The only reason the living species of sloths survive is that they live high up in trees, where their green-algae-colored fur camouflages them, Steadman said. “God save the sloth that comes down to the ground because usually somebody is there to kill it,” he said.

Interfacing human evolution and the evolution of the sloths. An evolutionary hypothesis tested.

608: Manipulative Malaria Parasite Makes You More Attractive (to Mosquitoes) - New York Times

2005-08-09T00:12:00.000-05:00

Manipulative Malaria Parasite Makes You More Attractive (to Mosquitoes) - New York Times:

Malaria is a staggeringly devastating disease, striking an estimated 300 million to 500 million people a year and killing more than a million of them. Scientists have long wondered how the parasite that causes malaria - a single-cell creature, plasmodium, carried by mosquitoes - manages to be so successful.

New research has shown an unexpected source of its success. The parasite makes infected humans smell more attractive to mosquitoes.

The research, published on Monday in the journal Public Library of Science Biology, was carried out by a team of French and Kenyan scientists led by Jacob Koella, an evolutionary biologist at Pierre and Marie Curie University in Paris. Dr. Koella is a leading expert on the ways in which parasites manipulate their hosts.

…

Many parasites that need to live inside two different hosts during their life cycles also manipulate their hosts. A single-celled parasite called toxoplasma lives inside cats and then inside their prey, like rats. Research shows that infection with toxoplasma makes rats lose their fear of the odor of cats. Tapeworms that live in fish can turn them white and make them jump around near the surface of the water, where the fish are more likely to be eaten by birds, which the tapeworms make their new host. "It's amazing how much manipulation is going on in parasites," Dr. Koella said. "It would be hard to find a case where there wasn't some manipulation."

Scientists consider most of these examples as products of natural selection. A parasite's reproductive success depends on its ability to be transmitted toa new host. "And manipulation appears to be an obvious way to do it," Dr. Koella said.

The evolution of malaria. Hypotheses tested.

607: The Riddle of the Appendix - New York Times

2005-08-09T00:09:00.000-05:00

The Riddle of the Appendix - New York Times:

Still, I wondered how such a dangerous and disposable organ could survive over evolutionary time. "We consider it maladaptive because we want to live to a very old age," Dr. Fisher said. "But from a strictly Darwinian view, it might not be."

Imagine a trait that helps an animal survive to adulthood, but that also has side effects that can cause trouble later in life. If, on balance, animals produce more offspring with the trait than without it, natural selection will favor it.

Perhaps the appendix lifted the odds that our ancestors could resist childhood diseases and live to childbearing years. Even if it also caused deaths by appendicitis, the appendix might have been a net plus. (It's also possible that appendicitis wasn't such a big problem in the past. Some scientists have argued that modern Western life has made appendicitis more common, either as a result of a change in hygiene or in the foods we eat.)

Dr. Fisher's "net-plus" hypothesis is one of several possible explanations. But they all remain speculation, she said, until scientists learn a lot more about the appendix. "It seems basic, but it's also very hard," she said.

Evolutionary hypotheses guide the search for an explanation of appendicitis, summarized in Carl Zimmer's explanation.

606: Very Old Eggs Reveal A Fast, Changing Path Through Evolution

2005-08-07T02:12:00.000-05:00

Philosophy of Biology: Very Old Eggs Reveal A Fast, Changing Path Through Evolution:

BIOLOGISTS STUDYING how species change over the eons have always been hampered by the little problem of previous generations of a species being, well, dead. Sure, you can infer something about what a creature was like from fossils, but fossils generally fail to preserve much except bone. As a result, some of an animal's most interesting features vanish into the dust of time.

But these days, not even death is forever. A few years ago, biologist W. Charles Kerfoot was examining "cores" -- basically, muck deposited decades earlier -- in a Michigan lake. Lo and behold, he and his colleagues discovered eggs, and not just any eggs. They had been laid long ago by tiny creatures (mostly insects and crustaceans) that no longer lived in the lake. Even better, there was still life in the eggs. Under the right conditions, they would hatch.

Testing evolutionary hypotheses.

605: EVOLUTION: Sumptuous Survey of Hexapod History -- Jarzembowski 309 (5736): 880 -- Science

2005-08-04T23:55:00.000-05:00

EVOLUTION: Sumptuous Survey of Hexapod History -- Jarzembowski 309 (5736): 880 -- Science:

If the number of described species is a measure of success, then insects (with nearly 1 million) are the most successful group of all time. And if the number of families known from the fossil record is a proxy for past biodiversity, then insects (with more than 1200) are also the most diverse paleo group. Insects have only existed for 11% of the duration of life on Earth. Yet in that time, they have pervaded all terrestrial ecosystems and evolved social organization several times. They conquered the air long before any flying vertebrate and have outlasted trilobites and dinosaurs. They pollinate our crops and arguably gave us our greatest laboratory animal, Drosophila. Love them or hate them, we have evolved alongside them.

There are a number of good entomology books on the market. Few, however, have integrated the living and fossil record as seamlessly as David Grimaldi and Michael Engel's Evolution of the Insects. None, moreover, has combined this integration with so much student-friendly text and such a wealth of illustrations (more than 900). The book shows that lavish photography and lucidity need not be the prerogative of popular entomology and that segregation of entomology and paleoentomology is tantamount to intellectual apartheid. While looking good, Evolution is no coffee-table adornment. Weighing in at 2.92 kg, it is the western challenger to History of Insects (1), a multiauthored, English-language account by Russian paleoentomologists. That work, which highlighted the fossil insect riches of Asia, is unashamedly phylistic; its approach to evolutionary relationships combines cladogenesis and evolutionary divergence. Evolution offers a cladistic treatment rooted in the Hennigian tradition--as one would expect from the previous contributions of Grimaldi (a curator of invertebrate zoology at the American Museum of Natural History) and Engel (a paleoentomologist at the University of Kansas). This methodological difference influences the interpretation of the evolutionary history of insects (e.g., the longevity of groups like caddisflies and cockroaches).

Evolution of the Insects by David Grimaldi, Michael S. Engel

Sounds like a good book.

604: Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel -- Long et al. 309 (5736): 897 -- Science

2005-08-04T23:49:00.000-05:00

Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel -- Long et al. 309 (5736): 897 -- Science:

Most of our knowledge of Kv channel function comes from studies of the Shaker K+ channel from Drosophila melanogaster and its family members from mammalian cells (2). Shaker family channels have been extensively studied with electrophysiology, because they can easily be expressed in Xenopus laevis oocytes and in other cells. In contrast, nearly all of our knowledge of K+ channel structure is based on studies of prokaryotic K+ channels, because they are more easily expressed at high levels in Escherichia coli. Such studies have taught us much about their pores, selectivity filters, and gates (3).

Eukaryotic Kv channels in many respects are very similar to their prokaryotic counterparts. The selectivity filter sequence is so conserved that we expect its structure to be essentially the same in all K+ channels. The pore's "inverted teepee" arrangement of inner helices, which holds the selectivity filter in its wider half near the extracellular surface, is also expected to be a conserved feature (4). However, beyond their conserved pore and certain domains that regulate the opening of the pore's gate, eukaryotic Kv channels have certain unique features.

Evolutionarily conserved structures with various derived changes? Evolution at work.

603: Antagonistic Control of Disease Resistance Protein Stability in the Plant Immune System -- Holt et al. 309 (5736): 929 -- Science

2005-08-04T23:41:00.000-05:00

Antagonistic Control of Disease Resistance Protein Stability in the Plant Immune System -- Holt et al. 309 (5736): 929 -- Science:

Pathogen recognition by the plant immune system is governed by structurally related, polymorphic products of disease resistance (R) genes. RAR1 and/or SGT1b mediate the function of many R proteins. RAR1 controls preactivation R protein accumulation by an unknown mechanism. We demonstrate that Arabidopsis SGT1b has two distinct, genetically separable functions in the plant immune system: SGT1b antagonizes RAR1 to negatively regulate R protein accumulation before infection, and SGT1b has a RAR1-independent function that regulates programmed cell death during infection. The balanced activities of RAR1 and SGT1, in concert with cytosolic HSP90, modulate preactivation R protein accumulation and signaling competence.

Understanding the Arabidopsis immune system reveals information about other plants because of common descent.

602: Stem Cell Depletion Through Epidermal Deletion of Rac1 -- Benitah et al. 309 (5736): 933 -- Science

2005-08-04T23:38:00.000-05:00

Stem Cell Depletion Through Epidermal Deletion of Rac1 -- Benitah et al. 309 (5736): 933 -- Science:

Mammalian epidermis is maintained by self-renewal of stem cells, but the underlying mechanisms are unknown. Deletion of Rac1, a Rho guanosine triphosphatase, in adult mouse epidermis stimulated stem cells to divide and undergo terminal differentiation, leading to failure to maintain the interfollicular epidermis, hair follicles, and sebaceous glands. Rac1 exerts its effects in the epidermis by negatively regulating c-Myc through p21-activated kinase 2 (PAK2) phosphorylation. We conclude that a pleiotropic regulator of cell adhesion and the cytoskeleton plays a critical role in controlling exit from the stem cell niche and propose that Rac and Myc represent a global stem cell regulatory axis.

Research in mice teaches us about the regulation of stem cells in humans. Common descent!

601: Regulation of Blood Glucose by Hypothalamic Pyruvate Metabolism -- Lam et al. 309 (5736): 943 -- Science

2005-08-04T23:36:00.000-05:00

Regulation of Blood Glucose by Hypothalamic Pyruvate Metabolism -- Lam et al. 309 (5736): 943 -- Science:

The brain keenly depends on glucose for energy, and mammalians have redundant systems to control glucose production. An increase in circulating glucose inhibits glucose production in the liver, but this negative feedback is impaired in type 2 diabetes. Here we report that a primary increase in hypothalamic glucose levels lowers blood glucose through inhibition of glucose production in rats. The effect of glucose requires its conversion to lactate followed by stimulation of pyruvate metabolism, which leads to activation of adenosine triphosphate (ATP)–sensitive potassium channels. Thus, interventions designed to enhance the hypothalamic sensing of glucose may improve glucose homeostasis in diabetes.

Understanding an evolutionarily conserved pathway (common descent) may help treat diabetes.

600: Export-Mediated Assembly of Mycobacterial Glycoproteins Parallels Eukaryotic Pathways -- VanderVen et al. 309 (5736): 941 -- Science

2005-08-04T23:33:00.000-05:00

Export-Mediated Assembly of Mycobacterial Glycoproteins Parallels Eukaryotic Pathways -- VanderVen et al. 309 (5736): 941 -- Science:

Protein O-mannosylation is an essential and evolutionarily conserved post-translational modification among eukaryotes. This form of protein modification is also described in Mycobacterium tuberculosis; however, the mechanism of mannoprotein assembly remains unclear. Evaluation of differentially translocated chimeric proteins and mass spectrometry to monitor glycosylation demonstrated that specific translocation processes were required for protein O-mannosylation in M. tuberculosis. Additionally, Rv1002c, a M. tuberculosis membrane protein homolog of eukaryotic protein mannosyltransferases, was shown to catalyze the initial step of protein mannosylation. Thus, the process of protein mannosylation is conserved between M. tuberculosis and eukaryotic organisms.

A widely evolutionarily conserved biochemical pathway discovered thanks to an evolutionary hypothesis.

599: No oceans on Titan from the absence of a near-infrared specular reflection : Nature

2005-08-04T23:26:00.000-05:00

No oceans on Titan from the absence of a near-infrared specular reflection : Nature:

With its substantial atmosphere of nitrogen, hydrocarbons and nitriles, Saturn's moon Titan is a unique planetary satellite. Photochemical processing of the gaseous constituents produces an extended haze that obscures the surface. Soon after the Voyager fly-bys in 1980 and 1981 photochemical models1, 2, 3 led to the conclusion that there should be enough liquid methane/ethane/nitrogen to cover the surface to a depth of several hundred metres. Recent Earth-based radar echoes imply that surface liquid may be present at a significant fraction of the locations sampled4. Here we present ground-based observations (at near-infrared wavelengths) and calculations showing that there is no evidence thus far for surface liquid5. Combined with the specular signatures from radar observations, we infer mechanisms that produce very flat solid surfaces, involving a substance that was liquid in the past but is not in liquid form at the locations we studied.

The presence of liquid hydrocarbon oceans was an idea that had exobiologists salivating. This doesn't necessarily eliminate speculation about life on Titan, but it changes the possible dynamics.

598: Dental microwear texture analysis shows within-species diet variability in fossil hominins : Nature

2005-08-04T23:23:00.000-05:00

Dental microwear texture analysis shows within-species diet variability in fossil hominins : Nature:

Reconstructing the diets of extinct hominins is essential to understanding the paleobiology and evolutionary history of our lineage. Dental microwear, the study of microscopic tooth-wear resulting from use1, 2, 3, 4, provides direct evidence of what an individual ate in the past. Unfortunately, established methods5, 6, 7, 8, 9, 10 of studying microwear are plagued with low repeatability and high observer error11. Here we apply an objective, repeatable approach for studying three-dimensional microwear surface texture to extinct South African hominins. Scanning confocal microscopy12, 13 together with scale-sensitive fractal analysis14, 15, 16, 17, 18, 19 are used to characterize the complexity and anisotropy of microwear. Results for living primates show that this approach can distinguish among diets characterized by different fracture properties. When applied to hominins20, microwear texture analysis indicates that Australopithecus africanus microwear is more anisotropic, but also more variable in anisotropy than Paranthropus robustus. This latter species has more complex microwear textures, but is also more variable in complexity than A. africanus. This suggests that A. africanus ate more tough foods and P. robustus consumed more hard and brittle items, but that both had variable and overlapping diets.

Understanding the teeth of our ancestors tells us about our evolution.

597: Refractory periods and climate forcing in cholera dynamics : Nature

2005-08-04T23:21:00.000-05:00

Refractory periods and climate forcing in cholera dynamics : Nature:

Outbreaks of many infectious diseases, including cholera, malaria and dengue, vary over characteristic periods longer than 1 year1, 2. Evidence that climate variability drives these interannual cycles has been highly controversial, chiefly because it is difficult to isolate the contribution of environmental forcing while taking into account nonlinear epidemiological dynamics generated by mechanisms such as host immunity2, 3, 4. Here we show that a critical interplay of environmental forcing, specifically climate variability, and temporary immunity explains the interannual disease cycles present in a four-decade cholera time series from Matlab, Bangladesh. We reconstruct the transmission rate, the key epidemiological parameter affected by extrinsic forcing, over time for the predominant strain (El Tor) with a nonlinear population model that permits a contributing effect of intrinsic immunity. Transmission shows clear interannual variability with a strong correspondence to climate patterns at long periods (over 7 years, for monsoon rains and Brahmaputra river discharge) and at shorter periods (under 7 years, for flood extent in Bangladesh, sea surface temperatures in the Bay of Bengal and the El Niño−Southern Oscillation). The importance of the interplay between extrinsic and intrinsic factors in determining disease dynamics is illustrated during refractory periods, when population susceptibility levels are low as the result of immunity and the size of cholera outbreaks only weakly reflects climate forcing.

Understanding the dynamics of disease means understanding the evolution of the infectious agent.

596: Licensing of natural killer cells by host major histocompatibility complex class I molecules : Nature

2005-08-04T23:15:00.000-05:00

Licensing of natural killer cells by host major histocompatibility complex class I molecules : Nature:

Self versus non-self discrimination is a central theme in biology from plants1 to vertebrates, and is particularly relevant for lymphocytes that express receptors capable of recognizing self-tissues and foreign invaders. Comprising the third largest lymphocyte population, natural killer (NK) cells recognize and kill cellular targets and produce pro-inflammatory cytokines. These potentially self-destructive effector functions can be controlled by inhibitory receptors for the polymorphic major histocompatibility complex (MHC) class I molecules that are ubiquitously expressed on target cells2, 3, 4. However, inhibitory receptors are not uniformly expressed on NK cells, and are germline-encoded by a set of polymorphic genes that segregate independently from MHC genes5, 6. Therefore, how NK-cell self-tolerance arises in vivo is poorly understood. Here we demonstrate that NK cells acquire functional competence through 'licensing' by self-MHC molecules. Licensing involves a positive role for MHC-specific inhibitory receptors and requires the cytoplasmic inhibitory motif originally identified in effector responses. This process results in two types of self-tolerant NK cells—licensed or unlicensed—and may provide new insights for exploiting NK cells in immunotherapy. This self-tolerance mechanism may be more broadly applicable within the vertebrate immune system because related germline-encoded inhibitory receptors are widely expressed on other immune cells.

Common descent.

595: Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin : Nature

2005-08-04T17:57:00.000-05:00

Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin : Nature:

Transcription of eukaryotic genes is performed by three nuclear RNA polymerases, of which RNA polymerase II is thought to be solely responsible for the synthesis of messenger RNAs1. Here we show that transcription of some mRNAs in humans and rodents is mediated by a previously unknown single-polypeptide nuclear RNA polymerase (spRNAP-IV). spRNAP-IV is expressed from an alternative transcript of the mitochondrial RNA polymerase gene (POLRMT). The spRNAP-IV lacks 262 amino-terminal amino acids of mitochondrial RNA polymerase, including the mitochondrial-targeting signal, and localizes to the nucleus. Transcription by spRNAP-IV is resistant to the RNA polymease II inhibitor alpha-amanitin but is sensitive to short interfering RNA specific for the POLRMT gene. The promoters for spRNAP-IV differ substantially from those used by RNA polymerase II, do not respond to transcriptional enhancers and contain a common functional sequence motif.

"Humans and rodents" says common descent.

594: A cytokinesis furrow is positioned by two consecutive signals : Nature

2005-08-04T17:47:00.000-05:00

A cytokinesis furrow is positioned by two consecutive signals : Nature:

The position of the cytokinesis furrow in a cell determines the relative sizes of its two daughter cells as well as the distribution of their contents. In animal cells, the position of the cytokinesis furrow is specified by the position of the mitotic spindle1. The cytokinesis furrow bisects the spindle midway between the microtubule asters, at the site of the microtubule-based midzone, producing two daughter cells. Experiments in some cell types have suggested that the midzone positions the furrow2, 3, but experiments in other cells have suggested that the asters position the furrow4, 5. One possibility is that different organisms and cell types use different mechanisms to position the cytokinesis furrow. An alternative possibility is that both asters and the midzone contribute to furrow positioning6, 7. Recent work in C. elegans has suggested that centrosome separation and the midzone are implicated in cytokinesis8. Here we examine the relative contributions of different parts of the mitotic spindle to positioning of the cytokinesis furrow in the C. elegans zygote. By spatially separating the spindle midzone from one of the asters using an ultraviolet laser, we show that the cytokinesis furrow is first positioned by a signal determined by microtubule asters, and then by a second signal that is derived from the spindle midzone. Thus, the position of the cytokinesis furrow is specified by two consecutive furrowing activities.

Common descent at work.

593: Common mechanisms of nerve and blood vessel wiring : Nature

2005-08-04T17:29:00.000-05:00

Common mechanisms of nerve and blood vessel wiring : Nature:

Blood vessels and nerve fibres course throughout the body in an orderly pattern, often alongside one another. Although superficially distinct, the mechanisms involved in wiring neural and vascular networks seem to share some deep similarities. The discovery of key axon guidance molecules over the past decade has shown that axons are guided to their targets by finely tuned codes of attractive and repulsive cues, and recent studies reveal that these cues also help blood vessels to navigate to their targets. Parallels have also emerged between the actions of growth factors that direct angiogenic sprouting and those that regulate axon terminal arborization.

During evolution, organisms have come to perform more specialized tasks, requiring an increased degree of information processing by neurons and supply of nutrients by blood vessels. Wiring of neuronal axons and blood vessels into functional circuits is therefore of utmost importance. The complexity of this task is underscored by the high degree of orderly patterning of the neural and vascular networks. The choreographed morphogenesis of both networks suggests that they are directed by genetically programmed mechanisms. Five centuries ago, Andreas Vesalius illustrated the parallels in the stereotyped branching patterns of vessels and nerves (Fig. 1a, b). Today, evidence is emerging that blood vessels, which arose later in evolution than nerves, co-opted several of the organizational principles and molecular mechanisms that evolved to wire up the nervous system. In this review, we highlight these common morphogenetic signals and mechanisms, and illustrate how intricately the navigational mechanisms for both systems are intertwined.

Co-opting of existing pathways is a common occurrence in evolution. This is all about testing evolutionary hypotheses.

592: Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development : Nature

2005-08-04T16:55:00.000-05:00

Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development : Nature:

The vertebrate limb initially develops as a bud of mesenchymal cells that subsequently aggregate in a proximal to distal (P−D) sequence to give rise to cartilage condensations that prefigure all limb skeletal components1. Of the three cardinal limb axes, the mechanisms that lead to establishment and patterning of skeletal elements along the P−D axis are the least understood. Here we identify a genetic interaction between Gli3 (GLI-Kruppel family member 3) and Plzf (promyelocytic leukaemia zinc finger, also known as Zbtb16 and Zfp145), which is required specifically at very early stages of limb development for all proximal cartilage condensations in the hindlimb (femur, tibia, fibula). Notably, distal condensations comprising the foot are relatively unperturbed in Gli3-/-;Plzf-/- mouse embryos. We demonstrate that the cooperative activity of Gli3 and Plzf establishes the correct temporal and spatial distribution of chondrocyte progenitors in the proximal limb-bud independently of known P−D patterning markers and overall limb-bud size. Moreover, the limb defects in Gli3-/-;Plzf-/- embryos correlate with the transient death of a specific subset of proximal mesenchymal cells that express bone morphogenetic protein receptor, type 1B (Bmpr1b) at the onset of limb development. These findings suggest that the development of proximal and distal skeletal elements is distinctly regulated early during limb-bud formation. The initial division of the vertebrate limb into two distinct molecular domains is consistent with fossil evidence indicating that the upper and lower extremities of the limb have different evolutionary origins2.

A developmental pathway common to the vertebrates. Evolutionary hypotheses tested, new hypotheses generated.

591: Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs : Nature

2005-08-04T16:54:00.000-05:00

Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs : Nature:

Birds are unique among living vertebrates in possessing pneumaticity of the postcranial skeleton, with invasion of bone by the pulmonary air-sac system1, 2, 3, 4. The avian respiratory system includes high-compliance air sacs that ventilate a dorsally fixed, non-expanding parabronchial lung2, 3, 5, 6. Caudally positioned abdominal and thoracic air sacs are critical components of the avian aspiration pump, facilitating flow-through ventilation of the lung and near-constant airflow during both inspiration and expiration, highlighting a design optimized for efficient gas exchange2, 5, 6, 7, 8. Postcranial skeletal pneumaticity has also been reported in numerous extinct archosaurs including non-avian theropod dinosaurs and Archaeopteryx9, 10, 11, 12. However, the relationship between osseous pneumaticity and the evolution of the avian respiratory apparatus has long remained ambiguous. Here we report, on the basis of a comparative analysis of region-specific pneumaticity with extant birds, evidence for cervical and abdominal air-sac systems in non-avian theropods, along with thoracic skeletal prerequisites of an avian-style aspiration pump. The early acquisition of this system among theropods is demonstrated by examination of an exceptional new specimen of Majungatholus atopus, documenting these features in a taxon only distantly related to birds. Taken together, these specializations imply the existence of the basic avian pulmonary Bauplan in basal neotheropods, indicating that flow-through ventilation of the lung is not restricted to birds but is probably a general theropod characteristic.

Fossilized evidence that birds' lungs are structured like dinosaur lungs, further strengthening the hypothesis that birds descended from dinosaurs.

590: An Arabidopsis hAT-like transposase is essential for plant development : Nature

2005-08-04T16:52:00.000-05:00

An Arabidopsis hAT-like transposase is essential for plant development : Nature:

A significant proportion of the genomes of higher plants and vertebrates consists of transposable elements and their derivatives. Autonomous DNA type transposons encode a transposase that enables them to mobilize to a new chromosomal position in the host genome by a cut-and-paste mechanism. As this is potentially mutagenic, the host limits transposition through epigenetic gene silencing and heterochromatin formation. Here we show that a transposase from Arabidopsis thaliana that we named DAYSLEEPER is essential for normal plant growth; it shares several characteristics with the hAT (hobo, Activator, Tam3) family of transposases1. DAYSLEEPER was isolated as a factor binding to a motif (Kubox1) present in the upstream region of the Arabidopsis DNA repair gene Ku70 (refs 2, 3). This motif is also present in the upstream regions of many other plant genes. Plants lacking DAYSLEEPER or strongly overexpressing this gene do not develop in a normal manner. Furthermore, DAYSLEEPER overexpression results in the altered expression of many genes. Our data indicate that transposase-like genes can be essential for plant development and can also regulate global gene expression. Thus, transposases can become domesticated by the host to fulfil important cellular functions.

Yeast and plants reveal a developmental regulator shared across the plant kingdom. Understanding this regulatory gene reveals a path to phenotypic variation in plants.

589: A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response : Nature

2005-08-04T16:50:00.000-05:00

A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response : Nature:

DNA breaks are extremely harmful lesions that need to be repaired efficiently throughout the genome. However, the packaging of DNA into nucleosomes is a significant barrier to DNA repair, and the mechanisms of repair in the context of chromatin are poorly understood1. Here we show that lysine 56 (K56) acetylation is an abundant modification of newly synthesized histone H3 molecules that are incorporated into chromosomes during S phase. Defects in the acetylation of K56 in histone H3 result in sensitivity to genotoxic agents that cause DNA strand breaks during replication. In the absence of DNA damage, the acetylation of histone H3 K56 largely disappears in G2. In contrast, cells with DNA breaks maintain high levels of acetylation, and the persistence of the modification is dependent on DNA damage checkpoint proteins. We suggest that the acetylation of histone H3 K56 creates a favourable chromatin environment for DNA repair and that a key component of the DNA damage response is to preserve this acetylation.

A potentially important evolutionary mechanism investigated in yeast.

588: The Lyme disease agent exploits a tick protein to infect the mammalian host : Nature

2005-08-04T16:25:00.000-05:00

The Lyme disease agent exploits a tick protein to infect the mammalian host : Nature:

The Lyme disease agent, Borrelia burgdorferi, is maintained in a tick−mouse cycle1, 2. Here we show that B. burgdorferi usurps a tick salivary protein, Salp15 (ref. 3), to facilitate the infection of mice. The level of salp15 expression was selectively enhanced by the presence of B. burgdorferi in Ixodes scapularis, first indicating that spirochaetes might use Salp15 during transmission. Salp15 was then shown to adhere to the spirochaete, both in vitro and in vivo, and specifically interacted with B. burgdorferi outer surface protein C. The binding of Salp15 protected B. burgdorferi from antibody-mediated killing in vitro and provided spirochaetes with a marked advantage when they were inoculated into naive mice or animals previously infected with B. burgdorferi. Moreover, RNA interference-mediated repression of salp15 in I. scapularis drastically reduced the capacity of tick-borne spirochaetes to infect mice. These results show the capacity of a pathogen to use a secreted arthropod protein to help it colonize the mammalian host.

Co-evolution of the Lyme disease parasite and one of its hosts. Very cool.

587: Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis : Nature

2005-08-04T16:22:00.000-05:00

Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis : Nature:

Mycobacterium tuberculosis infection is a continuing global health crisis that kills 2 million people each year1. Although the structurally diverse lipids of the M. tuberculosis cell envelope each have non-redundant roles in virulence or persistence2, 3, 4, 5, 6, 7, the molecular mechanisms regulating cell envelope composition in M. tuberculosis are undefined. In higher eukaryotes, membrane composition is controlled by site two protease (S2P)-mediated cleavage of sterol regulatory element binding proteins8, 9, membrane-bound transcription factors that control lipid biosynthesis. S2P is the founding member of a widely distributed family of membrane metalloproteases10, 11 that cleave substrate proteins within transmembrane segments12. Here we show that a previously uncharacterized M. tuberculosis S2P homologue (Rv2869c) regulates M. tuberculosis cell envelope composition, growth in vivo and persistence in vivo. These results establish that regulated intramembrane proteolysis is a conserved mechanism controlling membrane composition in prokaryotes and show that this proteolysis is a proximal regulator of cell envelope virulence determinants in M. tuberculosis.

A protein which occurs homologously in prokaryotes and eukaryotes has been co-opted into various processes in the cell. Understanding its operation in an infectious agent may lead to a better treatment for TB, and a better understanding of lipid metabolism in eukaryotes (like you and me).

586: Parasitology Triple genome triumph : Nature

2005-08-04T16:20:00.000-05:00

Parasitology Triple genome triumph : Nature:

There is welcome news for scientists working on sleeping sickness, Chagas' disease and visceral leishmaniasis: the genomes of the three trypanosome parasites responsible for these devastating illnesses have now been cracked. The sequences from Trypanosoma brucei, Trypanosoma cruzi and Leishmania major were published in last week's Science by an array of international research teams (Science 309, 416−422, 409−415, 436−442; 2005).

In the terminology of global public health, these diseases don't even fall into the category of 'neglected diseases' such as malaria and tuberculosis. Rather, they are classed as 'most neglected diseases' — which nonetheless kill millions. But those affected have little means of paying for treatment, making drug development unprofitable. Consequently, there are no vaccines, and medicines are few, expensive and usually toxic.

…

The three parasites share around 6,200 'core' genes, so the proteins these encode might provide targets for drugs that are effective against all three. The parasites make a large and diverse set of kinase and phosphatase enzymes. This means that there could well be regulatory and other processes used by the organisms that could be vulnerable to disruption by drugs.

Many species-specific genes were also identified in the genome sequences, providing potential species- and stage-specific targets. Although the three parasites share many subcellular structures, such as kinetoplasts and glycosomes, the organisms are very different. They are spread by different insects, attack different tissues and cause different pathologies. The specimens of L. major pictured are in the form that is transmitted to humans by sand flies.

Each parasite also has its own mechanism for evading the human immune system: T. brucei does not enter its victim's cells, and evades the immune system by constantly changing its main surface proteins; T. cruzi holes up inside cells, but uses a similar strategy to hide from the immune system; and L. major infects certain immune cells and interferes with their function.

Understanding the evolution of these parasites reveals new paths to immunization and treatment.

585: Neural crest origins of the neck and shoulder : Nature

2005-08-04T16:17:00.000-05:00

Neural crest origins of the neck and shoulder : Nature:

The neck and shoulder region of vertebrates has undergone a complex evolutionary history. To identify its underlying mechanisms we map the destinations of embryonic neural crest and mesodermal stem cells using Cre-recombinase-mediated transgenesis. The single-cell resolution of this genetic labelling reveals cryptic cell boundaries traversing the seemingly homogeneous skeleton of the neck and shoulders. Within this assembly of bones and muscles we discern a precise code of connectivity that mesenchymal stem cells of both neural crest and mesodermal origin obey as they form muscle scaffolds. The neural crest anchors the head onto the anterior lining of the shoulder girdle, while a Hox-gene-controlled mesoderm links trunk muscles to the posterior neck and shoulder skeleton. The skeleton that we identify as neural crest-derived is specifically affected in human Klippel−Feil syndrome, Sprengel's deformity and Arnold−Chiari I/II malformation, providing insights into their likely aetiology. We identify genes involved in the cellular modularity of the neck and shoulder skeleton and propose a new method for determining skeletal homologies that is based on muscle attachments. This has allowed us to trace the whereabouts of the cleithrum, the major shoulder bone of extinct land vertebrate ancestors, which seems to survive as the scapular spine in living mammals.

Evolutionary hypotheses lead to this research, which reveals new information on the evolution of the vertebrates, and yields new hypotheses, and new insight into genetic disorders.

584: Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour : Nature

2005-08-04T16:16:00.000-05:00

Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour : Nature:

Robust innate behaviours are attractive systems for genetically dissecting how environmental cues are perceived and integrated to generate complex behaviours. During courtship, Drosophila males engage in a series of innate, stereotyped behaviours that are coordinated by specific sensory cues. However, little is known about the specific neural substrates mediating this complex behavioural programme1. Genetic, developmental and behavioural studies have shown that the fruitless (fru) gene encodes a set of male-specific transcription factors (FruM) that act to establish the potential for courtship in Drosophila2. FruM proteins are expressed in approx2% of central nervous system neurons, at least one subset of which coordinates the component behaviours of courtship3, 4. Here we have inserted the yeast GAL4 gene into the fru locus by homologous recombination and show that (1) FruM is expressed in subsets of all peripheral sensory systems previously implicated in courtship, (2) inhibition of FruM function in olfactory system components reduces olfactory-dependent changes in courtship behaviour, (3) transient inactivation of all FruM-expressing neurons abolishes courtship behaviour, with no other gross changes in general behaviour, and (4) 'masculinization' of FruM-expressing neurons in females is largely sufficient to confer male courtship behaviour. Together, these data demonstrate that FruM proteins specify the neural substrates of male courtship.

Understanding the operation of this protein in other insects and animals will give insight into the evolution of gender and mating behavior.

583: Deep sub-seafloor prokaryotes stimulated at interfaces over geological time : Nature

2005-08-04T16:02:00.000-05:00

Deep sub-seafloor prokaryotes stimulated at interfaces over geological time : Nature:

The sub-seafloor biosphere is the largest prokaryotic habitat on Earth1 but also a habitat with the lowest metabolic rates2. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism2. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales.

Life keeps turning up in unexpected places, evolving and adapting to unusual conditions.

582: Genomic Sequencing of Pleistocene Cave Bears -- Noonan et al. 309 (5734): 597 -- Science

2005-08-04T15:59:00.000-05:00

Genomic Sequencing of Pleistocene Cave Bears -- Noonan et al. 309 (5734): 597 -- Science:

Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of ~1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.

Direct comparison of modern bear DNA and DNA from bears roughly 42-45,000 years old reveals that Brown bear (grizzly) and polar bear both split off from a common ancestor more recent than the cave bear lineage. The cave bears are not necessarily that common ancestor, and the common ancestor may be older than 45,000 years old.

581: Genome-Scale Identification of Nucleosome Positions in S. cerevisiae -- Yuan et al. 309 (5734): 626 -- Science

2005-08-04T15:09:00.000-05:00

Genome-Scale Identification of Nucleosome Positions in S. cerevisiae -- Yuan et al. 309 (5734): 626 -- Science:

The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. We developed a tiled microarray approach to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions. The majority of the nucleosomes identified were well-positioned. We found a stereotyped chromatin organization at Pol II promoters consisting of a nucleosome-free region ~200 base pairs upstream of the start codon flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved and were enriched in poly-deoxyadenosine or poly-deoxythymidine sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.

Testing evolutionary hypotheses.

580: Extreme Reversed Sexual Dichromatism in a Bird Without Sex Role Reversal -- Heinsohn et al. 309 (5734): 617 -- Science

2005-08-04T15:07:00.000-05:00

Extreme Reversed Sexual Dichromatism in a Bird Without Sex Role Reversal -- Heinsohn et al. 309 (5734): 617 -- Science:

Brilliant plumage is typical of male birds, reflecting differential enhancement of male traits when females are the limiting sex. Brighter females are thought to evolve exclusively in response to sex role reversal. The striking reversed plumage dichromatism of Eclectus roratus parrots does not fit this pattern. We quantify plumage color in this species and show that very different selection pressures are acting on males and females. Male plumage reflects a compromise between the conflicting requirements for camouflage from predators while foraging and conspicuousness during display. Females are liberated from the need for camouflage but compete for rare nest hollows.

Evolutionary hypotheses tested.

579: Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps -- Murphy et al. 309 (5734): 613 -- Science

2005-08-04T15:03:00.000-05:00

Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps -- Murphy et al. 309 (5734): 613 -- Science:

The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.

Evolutionary hypothesis testing, macroevolution, and common descent.

578: Web-Spinning Caterpillar Stalks Snails -- Rubinoff and Haines 309 (5734): 575 -- Science

2005-08-04T14:55:00.000-05:00

Web-Spinning Caterpillar Stalks Snails -- Rubinoff and Haines 309 (5734): 575 -- Science:

Moths and butterflies compose one of the most diverse insect orders, but they are overwhelmingly herbivorous. Less than 0.2% are specialized predators, indicating that lepidopteran feeding habits are highly constrained. We report a Hawaiian caterpillar that specializes on snails, a unique food source requiring an unusual feeding strategy. The caterpillar uses silk to restrain live prey. All caterpillars have silk glands, but none are known to use silk in this spiderlike fashion. Considering the canalization of caterpillar diets, evolution to attack and feed on snails is an anomaly. Hawaii's isolation and consequently disharmonic biota likely promote evolutionary experiments that occur nowhere else.

An important principle of evolution is that you work with what you've got. In a low diversity area, normal traits get co-opted to unexpected uses.

577: EVOLUTION: Of Whale Knuckles and Placental Trees -- de Muizon 309 (5734): 559 -- Science

2005-08-04T14:53:00.000-05:00

EVOLUTION: Of Whale Knuckles and Placental Trees -- de Muizon 309 (5734): 559 -- Science:

Cetaceans are probably the most extraordinary mammals. They are highly adapted to life in water and strictly dependent on their aquatic environment. As a consequence, their anatomy and physiology have been strongly modified and do not resemble those of other mammals. Because cetaceans are so drastically transformed from their terrestrial ancestors, their affinities with other mammals have long been debated. Although researchers agreed that cetaceans had their origin in some group of land mammals that lived during the early Tertiary, there was no consensus on the identity of the group that subsequently evolved into whales and dolphins. Whales have been seen as closely related to seals, creodonts (hyaenodonts), ungulates, and mesonychid condylarths (large carnivorous to omnivorous archaic ungulates). In the absence of a better candidate, the mesonychids were on the verge of becoming accepted when molecular biologists claimed that cetaceans were most closely related to artiodactyls (even-toed ungulates)--specifically to hippos. A few years later, paleontologists discovered postcranial remains of early Eocene cetaceans that demonstrated the presence of a double-pulleyed astragalus (like the sheep ankle bones that the Romans used to play at knucklebones), a characteristic of all artiodactyls and exclusively found in that order. This discovery, among the most important paleontological finds of the past hundred years, led to an immediate consensus on cetacean ancestry. It also demonstrated a remarkable complementarity of two different approaches to the study of the evolution and phylogeny of mammals.

This from a review of

The Rise of Placental Mammals : Origins and Relationships of the Major Extant Clades by Kenneth D. Rose, J. David Archibald

Sounds like a good book.

576: Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system : Nature

2005-08-04T14:43:00.000-05:00

Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system : Nature:

Transposons have provided important genetic tools for functional genomic screens in lower eukaryotes but have proven less useful in higher eukaryotes because of their low transposition frequency. Here we show that Sleeping Beauty (SB), a member of the Tc1/mariner class of transposons, can be mobilized in mouse somatic cells at frequencies high enough to induce embryonic death and cancer in wild-type mice. Tumours are aggressive, with some animals developing two or even three different types of cancer within a few months of birth. The tumours result from SB insertional mutagenesis of cancer genes, thus facilitating the identification of genes and pathways that induce disease. SB transposition can easily be controlled to mutagenize any target tissue and can therefore, in principle, be used to induce many of the cancers affecting humans, including those for which little is known about the aetiology. The uses of SB are also not restricted to the mouse and could potentially be used for forward genetic screens in any higher eukaryote in which transgenesis is possible.

Common descent and an evolutionary hypothesis to test. Excellent.

575: Evolutionary biologyRelativity for molecular clocks : Nature

2005-08-04T14:42:00.000-05:00

Evolutionary biologyRelativity for molecular clocks : Nature:

The relative constancy of the rate at which DNA sequences evolve has been a treasured icon of molecular evolution for nearly 40 years. The occurrence of such a stochastic 'molecular clock' was initially quite unexpected, and was explained by Motoo Kimura1 by assuming that most changes to amino-acid and nucleotide sequences were neutral — "neither beneficial nor injurious", in Charles Darwin's prescient phrase.

However, there have been several inklings2, 3, 4 that the rate of molecular evolution accelerates when measured over evolutionarily short timescales. As they report in Molecular Biology and Evolution, Ho and colleagues5 have now put the evidence together. Their analyses of primate and bird data sets reveal that there is indeed a decided acceleration of molecular evolution on short timescales. This is an effect that demands explanation; moreover, estimates for the timing of recent events in population biology will need to be reconsidered.

…

Much more remains to be done. There is the challenge of formulating a single theory that operates smoothly over disparate timescales, from current heterozygosity to the long-term rate of evolution. In addition, a single mutation rate (mu) does not really exist. Even for nucleotides there are many 'mutation rates', at least one between each pair of nucleotides, and these can be estimated separately using three-dimensional matrices12. The J-shaped curve cannot rest until a single theory holds for it: we live in interesting times.

An unsolved problem in molecular biology identified through phylogenetic analyses. What implications this has for evolution is unclear until a mechanism is developed. Is this variation an effect of evolution and natural selection on long time scales? Or a strange statistical artifact? We don't yet know, and that's what makes science fascinating.

574: Wolbachia variability and host effects on crossing type in Culex mosquitoes : Nature

2005-08-04T14:36:00.000-05:00

Wolbachia variability and host effects on crossing type in Culex mosquitoes : Nature:

Wolbachia is a common maternally inherited bacterial symbiont able to induce crossing sterilities known as cytoplasmic incompatibility (CI) in insects1, 2. Wolbachia-modified sperm are unable to complete fertilization of uninfected ova, but a rescue function allows infected eggs to develop normally. By providing a reproductive advantage to infected females, Wolbachia can rapidly invade uninfected populations3, and this could provide a mechanism for driving transgenes through pest populations4, 5. CI can also occur between Wolbachia-infected populations and is usually associated with the presence of different Wolbachia strains1. In the Culex pipiens mosquito group (including the filariasis vector C. quinquefasciatus) a very unusual degree of complexity of Wolbachia-induced crossing-types has been reported, with partial or complete CI that can be unidirectional or bidirectional6, 7, 8, 9, 10, 11, yet no Wolbachia strain variation was found11. Here we show variation between incompatible Culex strains in two Wolbachia ankyrin repeat-encoding genes associated with a prophage region, one of which is sex-specifically expressed in some strains, and also a direct effect of the host nuclear genome on CI rescue.

The evolution of cytoplasmic incompatibility is a coevolution between the parasite and its host. Evolution at work, hypotheses tested.

573: Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis : Nature

2005-08-04T14:34:00.000-05:00

Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis : Nature:

Gradients of signalling and transcription factors govern many aspects of embryogenesis, highlighting the need for spatiotemporal control of regulatory protein levels. MicroRNAs are phylogenetically conserved small RNAs that regulate the translation of target messenger RNAs, providing a mechanism for protein dose regulation. Here we show that microRNA-1-1 (miR-1-1) and miR-1-2 are specifically expressed in cardiac and skeletal muscle precursor cells. We found that the miR-1 genes are direct transcriptional targets of muscle differentiation regulators including serum response factor, MyoD and Mef2. Correspondingly, excess miR-1 in the developing heart leads to a decreased pool of proliferating ventricular cardiomyocytes. Using a new algorithm for microRNA target identification that incorporates features of RNA structure and target accessibility, we show that Hand2, a transcription factor that promotes ventricular cardiomyocyte expansion, is a target of miR-1. This work suggests that miR-1 genes titrate the effects of critical cardiac regulatory proteins to control the balance between differentiation and proliferation during cardiogenesis.

The development of mouse hearts teaches us about human hearts. Common descent. Tracing these genes will yield more evolutionary hypotheses.

572: MICROBIOLOGY: What's in a Name? -- Chin 309 (5734): 536d -- Science

2005-08-04T14:24:00.000-05:00

MICROBIOLOGY: What's in a Name? -- Chin 309 (5734): 536d -- Science:

The human pathogen Staphylococcus aureus exhibits a golden hue, which comes from a carotenoid that is made by joining two molecules of farnesyl pyrophosphate, a reaction that is catalyzed by dehydrosqualene synthase (encoded by the gene crtM). Liu et al.have looked closely at this bacterium and find that its pigment is in fact a defensive weapon. Deleting crtM changed S. aureus color from gold to pale yellow and increased its sensitivity to being killed by reactive oxygen species (ROS). Conversely, adding this gene to another human pathogen, Streptococcus pyogenes, enhanced its color as well as its resistance to singlet oxygen. Survival of crtM-deleted S. aureus when challenged by human neutrophils or by whole blood from mice and humans was much lower than for wild-type bacteria. Protection could be conferred by an inhibitor of NADPH oxidase, which generates ROS; this was consistent with no difference in the survival of mutant and wild-type bacteria when cocultured with blood from a patient with chronic granulomatous disease (CGD; caused by NADPH oxidase deficiency) or from a mouse model of human CGD. Taken together, these results suggest that inhibition of carotenoid synthesis may render S. aureus more susceptible to host immune defenses.

The evolution of infectious agents has obvious importance.

571: Independent Codes for Spatial and Episodic Memory in Hippocampal Neuronal Ensembles -- Leutgeb et al. 309 (5734): 619 -- Science

2005-08-04T14:23:00.000-05:00

Independent Codes for Spatial and Episodic Memory in Hippocampal Neuronal Ensembles -- Leutgeb et al. 309 (5734): 619 -- Science:

Hippocampal neurons were recorded under conditions in which the recording chamber was varied but its location remained unchanged versus conditions in which an identical chamber was encountered in different places. Two forms of neuronal pattern separation occurred. In the variable cue-constant place condition, the firing rates of active cells varied, often over more than an order of magnitude, whereas the location of firing remained constant. In the variable place-constant cue condition, both location and rates changed, so that population vectors for a given location in the chamber were statistically independent. These independent encoding schemes may enable simultaneous representation of spatial and episodic memory information.

How rat brains work tells us how human brains work. That's common descent, and it means evolution at work.

570: Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants : Nature

2005-08-04T13:35:00.000-05:00

Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants : Nature:

Caenorhabditis elegans homologues of the retinoblastoma (Rb) tumour suppressor complex specify cell lineage during development1, 2. Here we show that mutations in Rb pathway components enhance RNA interference (RNAi) and cause somatic cells to express genes and elaborate perinuclear structures normally limited to germline-specific P granules. Furthermore, particular gene inactivations that disrupt RNAi reverse the cell lineage transformations of Rb pathway mutants. These findings suggest that mutations in Rb pathway components cause cells to revert to patterns of gene expression normally restricted to germ cells. Rb may act by a similar mechanism to transform mammalian cells.

Why in mammalian cells? Common descent. That's an evolutionary hypothesis waiting to be tested.

569: Somatic control of germline sexual development is mediated by the JAK/STAT pathway : Nature

2005-08-04T13:33:00.000-05:00

Somatic control of germline sexual development is mediated by the JAK/STAT pathway : Nature:

Germ cells must develop along distinct male or female paths to produce the sperm or eggs required for sexual reproduction. In both mouse and Drosophila, the sexual identity of germ cells is influenced by the sex of the surrounding somatic tissue (for example, refs 1, 2, reviewed in refs 3, 4); however, little is known about how the soma controls germline sex determination. Here we show that the janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway provides a sex-specific signal from the soma to the germ line in Drosophila embryonic gonads. The somatic gonad expresses a JAK/STAT ligand, unpaired (upd), in a male-specific manner, and activates the JAK/STAT pathway in male germ cells at the time of gonad formation. Furthermore, the JAK/STAT pathway is necessary for male-specific germ cell behaviour during early gonad development, and is sufficient to activate aspects of male germ cell behaviour in female germ cells. Our findings provide direct evidence that the JAK/STAT pathway mediates a key signal from the somatic gonad that regulates male germline sexual development.

The fact that this pathway is common to mice and flies indicates common ancestry, and tells us about the evolution of gender in the animal kingdom.

568: Robust habit learning in the absence of awareness and independent of the medial temporal lobe : Nature

2005-08-04T13:32:00.000-05:00

Robust habit learning in the absence of awareness and independent of the medial temporal lobe : Nature:

In contrast to the findings from humans, monkeys learned the same concurrent discrimination task gradually in several hundred trials, and after hippocampal lesions they learned this task (or a related version) at a normal rate7, 12, 13. A standard interpretation of the monkey data is that monkeys acquire the concurrent discrimination task by trial-and-error (habit) learning with the support of the basal ganglia1, 13, 14. That is, they acquire a disposition to respond appropriately to each object pair. Habit memory is proposed to involve slowly acquired associations between stimuli and responses that develop outside awareness and are rigidly organized, with the result that what is learned is not readily expressed except when the task is presented just as it was during training.

One possibility is that habit learning is only weakly developed in humans, and some amount of declarative memory must be available to guide the learning. Indeed, successful learning of habit-like tasks has been reported only for moderately impaired amnesic patients who retain a considerable capacity for declarative memory15, 16. Moreover, some amnesic patients do not learn such tasks17. A related view is that the concept of an independent habit system is unnecessary, because habit learning and other kinds of learning depend on similar mechanisms18. Alternatively, if the capacity for habit learning is as well developed in humans as it appears to be, for example, in the monkey, then patients with large medial temporal lobe lesions and no capacity for declarative memory should be able to acquire the concurrent learning task gradually and to a high level of proficiency in the same manner that monkeys learn the task.

Evolutionary hypothesis tested.

567: Trail geometry gives polarity to ant foraging networks : Nature

2005-08-04T13:31:00.000-05:00

Trail geometry gives polarity to ant foraging networks : Nature:

Pheromone trails are used by many ants to guide foragers between nest and food1, 2, 3, 4. But how does a forager that has become displaced from a trail know which way to go on rejoining the trail? A laden forager, for example, should walk towards the nest. Polarized trails would enable ants to choose the appropriate direction, thereby saving time and reducing predation risk. However, previous research has found no evidence that ants can detect polarity from the pheromone trail alone3, 5, 6, 7. Pharaoh's ants (Monomorium pharaonis) produce elaborate trail networks throughout their foraging environment8. Here we show that by using information from the geometry of trail bifurcations within this network, foragers joining a trail can adaptively reorientate themselves if they initially walk in the wrong direction. The frequency of correct reorientations is maximized when the trail bifurcation angle is approximately 60 degrees, as found in natural networks. These are the first data to demonstrate how ant trails can themselves provide polarity information. They also demonstrate previously unsuspected sophistication in the organization and information content of networks in insect societies.

Evolution solves a problem even Richard Feynmann couldn't work out.

566: Optimality and evolutionary tuning of the expression level of a protein : Nature

2005-08-04T13:28:00.000-05:00

Optimality and evolutionary tuning of the expression level of a protein : Nature:

Different proteins have different expression levels. It is unclear to what extent these expression levels are optimized to their environment. Evolutionary theories suggest that protein expression levels maximize fitness1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, but the fitness as a function of protein level has seldom been directly measured. To address this, we studied the lac system of Escherichia coli, which allows the cell to use the sugar lactose for growth12. We experimentally measured the growth burden13, 14 due to production and maintenance of the Lac proteins (cost), as well as the growth advantage (benefit) conferred by the Lac proteins when lactose is present. The fitness function, given by the difference between the benefit and the cost, predicts that for each lactose environment there exists an optimal Lac expression level that maximizes growth rate. We then performed serial dilution evolution experiments at different lactose concentrations. In a few hundred generations, cells evolved to reach the predicted optimal expression levels. Thus, protein expression from the lac operon seems to be a solution of a cost−benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments.

A beautiful test of an evolutionary hypothesis. Elegant as all get out.

565: Insect defences Taste alteration and endoparasites : Nature

2005-08-04T13:27:00.000-05:00

Insect defences Taste alteration and endoparasites : Nature:

Taste sensation and food selection by animals can change adaptively in response to experience, for example to redress specific nutrient deficiencies1. We show here, in two species of caterpillar, that infection by lethal parasites alters the taste of specific phytochemicals for the larvae. Given that these compounds are toxic to the parasites and are found in plants eaten by the caterpillars, their changed taste may encourage parasitized caterpillars to increase consumption of plants that provide a biochemical defence against the invaders.

Speaking of taste, here's a study showing how neural responses changed with the environment, an evolved response to parasitism.

Host shift to an invasive plant triggers rapid animal hybrid speciation : Nature

2005-08-04T13:24:00.000-05:00

Host shift to an invasive plant triggers rapid animal hybrid speciation : Nature:

Speciation in animals is almost always envisioned as the split of an existing lineage into an ancestral and a derived species. An alternative speciation route is homoploid hybrid speciation1 in which two ancestral taxa give rise to a third, derived, species by hybridization without a change in chromosome number. Although theoretically possible it has been regarded as rare1 and hence of little importance in animals. On the basis of molecular and chromosomal evidence, hybridization is the best explanation for the origin of a handful of extant diploid bisexual animal taxa2, 3, 4, 5, 6. Here we report the first case in which hybridization between two host-specific animals (tephritid fruitflies) is clearly associated with the shift to a new resource. Such a hybrid host shift presents an ecologically robust scenario for animal hybrid speciation because it offers a potential mechanism for reproductive isolation through differential adaptation to a new ecological niche7. The necessary conditions for this mechanism of speciation7 are common in parasitic animals, which represent much of animal diversity8. The frequency of homoploid hybrid speciation in animals may therefore be higher than previously assumed.

This is a test of an evolutionary hypothesis, and it reveals new hypotheses.

Plus, it's another case of natural speciation.

Oops, already did this.

564: Genes that mediate breast cancer metastasis to lung : Nature

2005-08-04T13:23:00.000-05:00

Genes that mediate breast cancer metastasis to lung : Nature:

By means of in vivo selection, transcriptomic analysis, functional verification and clinical validation, here we identify a set of genes that marks and mediates breast cancer metastasis to the lungs. Some of these genes serve dual functions, providing growth advantages both in the primary tumour and in the lung microenvironment. Others contribute to aggressive growth selectively in the lung. Many encode extracellular proteins and are of previously unknown relevance to cancer metastasis.

Using mice to study breast cancer metastasis? Common descent.

563: Functional coordination of intraflagellar transport motors : Nature

2005-08-04T13:21:00.000-05:00

Functional coordination of intraflagellar transport motors : Nature:

Cilia have diverse roles in motility and sensory reception, and defects in cilia function contribute to ciliary diseases such as Bardet−Biedl syndrome (BBS). Intraflagellar transport (IFT) motors assemble and maintain cilia by transporting ciliary precursors, bound to protein complexes called IFT particles, from the base of the cilium to their site of incorporation at the distal tip1, 2, 3. In Caenorhabditis elegans, this is accomplished by two IFT motors, kinesin-II and osmotic avoidance defective (OSM)-3 kinesin, which cooperate to form two sequential anterograde IFT pathways that build distinct parts of cilia4, 5, 6, 7. By observing the movement of fluorescent IFT motors and IFT particles along the cilia of numerous ciliary mutants, we identified three genes whose protein products mediate the functional coordination of these motors. The BBS proteins BBS-7 and BBS-8 are required to stabilize complexes of IFT particles containing both of the IFT motors, because IFT particles in bbs-7 and bbs-8 mutants break down into two subcomplexes, IFT-A and IFT-B, which are moved separately by kinesin-II and OSM-3 kinesin, respectively. A conserved ciliary protein, DYF-1, is specifically required for OSM-3 kinesin to dock onto and move IFT particles, because OSM-3 kinesin is inactive and intact IFT particles are moved by kinesin-II alone in dyf-1 mutants. These findings implicate BBS ciliary disease proteins and an OSM-3 kinesin activator in the formation of two IFT pathways that build functional cilia.

I don't know what all that means, but I do know what this is all about:

Notably, phylogenetic analysis identified 14 homologues of DYF-1 (Supplementary Fig. S1) and revealed that, similar to BBS-7, BBS-8 and the kinesin-2 motors8, 17, it is highly conserved among ciliated organisms but is not found in organisms lacking cilia. The functions of these DYF-1 proteins are unknown.

Common descent lets these researchers test an evolutionary hypothesis.

562: Evidence for magmatic evolution and diversity on Mars from infrared observations : Nature

2005-08-04T13:17:00.000-05:00

Evidence for magmatic evolution and diversity on Mars from infrared observations : Nature:

Compositional mapping of Mars at the 100-metre scale with the Mars Odyssey Thermal Emission Imaging System (THEMIS) has revealed a wide diversity of igneous materials. Volcanic evolution produced compositions from low-silica basalts to high-silica dacite in the Syrtis Major caldera. The existence of dacite demonstrates that highly evolved lavas have been produced, at least locally, by magma evolution through fractional crystallization. Olivine basalts are observed on crater floors and in layers exposed in canyon walls up to 4.5 km beneath the surface. This vertical distribution suggests that olivine-rich lavas were emplaced at various times throughout the formation of the upper crust, with their growing inventory suggesting that such ultramafic (picritic) basalts may be relatively common. Quartz-bearing granitoid rocks have also been discovered, demonstrating that extreme differentiation has occurred. These observations show that the martian crust, while dominated by basalt, contains a diversity of igneous materials whose range in composition from picritic basalts to granitoids rivals that found on the Earth.

Understanding the geology of Mars helps predict where water is and was, and where life might be, if it evolved on Mars.

Volcanos also play an important role in some theories of the origins of terrestrial life, and understanding Martian volcanos may help us understand the origin of life here and there, as well as teaching us more about the Earth's formation.

557-561: Animal personalities

2005-08-04T13:12:00.000-05:00

ANIMAL BEHAVIOR: Strong Personalities Can Pose Problems in the Mating Game -- Pennisi 309 (5735): 694 -- Science:

Many researchers credit Sih for bringing to prominence the idea that animal personalities carry survival risks. The notion plays off a proposal made 25 years ago by the late paleontologist Steven J. Gould and geneticist Richard Lewontin, both from Harvard. At that time, the two stirred up the evolutionary biology community by arguing that maladaptive traits could persist if they were linked with beneficial ones in an often-precarious balancing act. For example, guppies living around predators reproduce as early as possible so as to pass on their genes before being eaten. But the eggs slow gravid females down, making them easier prey earlier in life, a finding that lent credibility to Gould and Lewontin's idea.

Several researchers have shown how "personality" traits involved in such evolutionary tradeoffs. Evolutionary hypotheses tested.

556: The Role of Social Groups in the Persistence of Learned Fear -- Olsson et al. 309 (5735): 785 -- Science

2005-08-04T13:09:00.000-05:00

The Role of Social Groups in the Persistence of Learned Fear -- Olsson et al. 309 (5735): 785 -- Science:

Classical fear conditioning investigates how animals learn to associate environmental stimuli with an aversive event. We examined how the mechanisms of fear conditioning apply when humans learn to associate social ingroup and outgroup members with a fearful event, with the goal of advancing our understanding of basic learning theory and social group interaction. Primates more readily associate stimuli from certain fear-relevant natural categories, such as snakes, with a negative outcome relative to stimuli from fear-irrelevant categories, such as birds. We assessed whether this bias in fear conditioning extends to social groups defined by race. Our results indicate that individuals from a racial group other than one's own are more readily associated with an aversive stimulus than individuals of one's own race, among both white and black Americans. This prepared fear response might be reduced by close, positive interracial contact.

Evidence of an evolved xenophobia. Evolutionary psychology, especially results like these, are best taken with a grain of salt, but look how evolutionary comparisons play a key role.

555: Regulation of X-Chromosome Counting by Tsix and Xite Sequences -- Lee 309 (5735): 768 -- Science

2005-08-04T13:08:00.000-05:00

Regulation of X-Chromosome Counting by Tsix and Xite Sequences -- Lee 309 (5735): 768 -- Science:

In mammals, X-inactivation establishes X-chromosome dosage parity between males and females. How X-chromosome counting regulates this process remains elusive, because neither the hypothesized inactivation "blocking factor" nor the required cis-elements have been defined. Here, a mouse knockout and transgenic analysis identified DNA sequences within the noncoding Tsix and Xite genes as numerators. Homozygous deficiency of Tsix resulted in "chaotic choice" and a variable number of inactive X's, whereas overdosage of Tsix/Xite inhibited X-inactivation. Thus, counting was affected by specific Tsix/Xite mutations, suggesting that counting is genetically separable from but molecularly coupled to choice. The mutations affect XX and XY cells differently, demonstrating that counting and choice are regulated not by one "blocking factor," but by both a "blocking" and a "competence" factor.

A pattern common to all mammals? Common descent, plus insight into the evolution of sex determination in mammals.

554: Recognition of Host Immune Activation by Pseudomonas aeruginosa -- Wu et al. 309 (5735): 774 -- Science

2005-08-04T13:06:00.000-05:00

Recognition of Host Immune Activation by Pseudomonas aeruginosa -- Wu et al. 309 (5735): 774 -- Science:

It is generally reasoned that lethal infections caused by opportunistic pathogens develop permissively by invading a host that is both physiologically stressed and immunologically compromised. However, an alternative hypothesis might be that opportunistic pathogens actively sense alterations in host immune function and respond by enhancing their virulence phenotype. We demonstrate that interferon-{gamma} binds to an outer membrane protein in Pseudomonas aeruginosa, OprF, resulting in the expression of a quorum-sensing dependent virulence determinant, the PA-I lectin. These observations provide details of the mechanisms by which prokaryotic organisms are directly signaled by immune activation in their eukaryotic host.

Evolution of parasites.

553: Pesticide Resistance via Transposition-Mediated Adaptive Gene Truncation in Drosophila -- Aminetzach et al. 309 (5735): 764 -- Science

2005-08-04T13:05:00.000-05:00

Pesticide Resistance via Transposition-Mediated Adaptive Gene Truncation in Drosophila -- Aminetzach et al. 309 (5735): 764 -- Science:

To study adaptation, it is essential to identify multiple adaptive mutations and to characterize their molecular, phenotypic, selective, and ecological consequences. Here we describe a genomic screen for adaptive insertions of transposable elements in Drosophila. Using a pilot application of this screen, we have identified an adaptive transposable element insertion, which truncates a gene and apparently generates a functional protein in the process. The insertion of this transposable element confers increased resistance to an organophosphate pesticide and has spread in D. melanogaster recently.

One mechanism behind the evolution of pesticide resistance. Drosophila are not just a great lab organism, they can be agricultural pests.

551-552: Tasting

2005-08-04T13:03:00.000-05:00

Genetic Tracing Shows Segregation of Taste Neuronal Circuitries for Bitter and Sweet -- Sugita and Shiba 309 (5735): 781 -- Science:

The recent discovery of mammalian bitter, sweet, and umami taste receptors indicates how the different taste qualities are encoded at the periphery. However, taste representations in the brain remain elusive. We used a genetic approach to visualize the neuronal circuitries of bitter and sweet tastes in mice to gain insight into how taste recognition is accomplished in the brain. By selectively expressing a transsynaptic tracer in either bitter- or sweet and/or umami-responsive taste receptor cells, and by comparing the locations of the tracer-labeled neurons in the brain, our data revealed the potential neuronal bases that underlie discrimination of bitter versus sweet.

Combine this with the recent discovery that cats can't taste "sweet" and we have more data on the evolution of taste.