One of the smallest dinosaur skulls ever discovered has been identified and described by a team of scientists from London, Cambridge and Chicago. The skull would have been only 45 millimeters (less than two inches) in length. It belonged to a very young Heterodontosaurus, an early dinosaur. This juvenile weighed about 200 grams, less than two sticks of butter.

In the Fall issue of the Journal of Vertebrate Paleontology, the researchers describe important findings from this skull that suggest how and when the ornithischians, the family of herbivorous dinosaurs that includes Heterodontosaurus, made the transition from eating meat to eating plants.

“It’s likely that all dinosaurs evolved from carnivorous ancestors,” said study co-author Laura Porro, a post-doctoral student at the University of Chicago. “Since heterodontosaurs are among the earliest dinosaurs adapted to eating plants, they may represent a transition phase between meat-eating ancestors and more sophisticated, fully-herbivorous descendents.”

“This juvenile skull,” she added, “indicates that these dinosaurs were still in the midst of that transition.”

Heterodontosaurus lived during the Early Jurassic period (about 190 million years ago) of South Africa. Adult Heterodontosaurs were turkey-sized animals, reaching just over three feet in length and weighing around five to six pounds.

Because their fossils are very rare, Heterodontosaurus and its relatives (the heterodontosaurs) are poorly understood compared to later and larger groups of dinosaurs.

“There were only two known fossils of Heterodontosaurus, both in South Africa and both adults,” said Porro, who is completing her doctoral dissertation on feeding in Heterodontosaurus under the supervision of David Norman, researcher at the University of Cambridge and co-author of the study. “There were rumors of a juvenile heterodontosaur skull in the collection of the South African Museum,” she said, “but no one had ever described it.”

As part of her research, Porro visited the Iziko South African Museum, Cape Town, to examine the adult fossils. When she was there, she got permission to “poke around” in the Museum’s collections. While going through drawers of material found during excavations in the 1960s, she found two more heterodontosaur fossils, including the partial juvenile skull.

“I didn’t recognize it as a dinosaur at first,” she said, “but when I turned it over and saw the eye looking straight at me, I knew exactly what it was.”

“This discovery is important because for the first time we can examine how Heterodontosaurus changed as it grew,” said the study’s lead author, Richard Butler of the Natural History Museum, in London. “The juvenile Heterodontosaurus had relatively large eyes and a short snout when compared to an adult,” he said, “similar to the differences we see between puppies and fully-grown dogs.”

A specialist on the mechanics of feeding, Porro was particularly interested in the new fossil’s teeth. Heterodontosaurs, which means “different-toothed lizards,” have an unusual combination of teeth, with large fang-like canines at the front of their jaws and worn, molar-like grinding teeth at the back. In contrast, most reptiles have teeth which change little in shape along the length of the jaw.

This bizarre suite of teeth has led to debate over what heterodontosaurs ate. Some scientists think heterodontosaurs were omnivores who used their differently-shaped teeth to eat both plants and small animals. Others contend that heterodontosaurs were herbivores who ate only plants and that the canines were sexually dimorphic–present only in males, as in living warthogs. In that scenario, the canines could have been used as weapons by rival males in disputes over mates and territories.

Porro and colleagues found that the juvenile already had a fully-developed set of canines.

“The fact that canines are present at such an early stage of growth strongly suggests that this is not a sexually dimorphic character because such characters tend to appear later in life,” said Butler.

Instead, the researchers suspect that the canines were used as defensive weapons against predators, or for adding occasional small animals such as insects, small mammals and reptiles to a diet composed mainly of plants–what the authors refers to as “occasional omnivory.”

The study created a new mystery, however. With the aid of X-rays and CT scans, Porro found a complete lack of replacement teeth in the adult and juvenile skulls.

Most reptiles, including living crocodiles and lizards, replace their teeth constantly throughout their lives, so that sharp, unworn teeth are always available. The same was true for dinosaurs. Most mammals, on the other hand, replace their teeth only once during their lives, allowing the upper and lower teeth to develop a tight, precise fit.

Heterodontosaurus was more similar to mammals, not only in the specialized, variable shape of its teeth but also in replacing its teeth slowly, if at all, and developing tight tooth-to-tooth contact. “Tooth replacement must have occurred during growth,” the authors conclude, “however, evidence of continuous tooth replacement appears to be absent, in both adult and juvenile specimens.”

The latest breakthrough in a 120 year-old debate on the evolution of the bird wing was published in the open-access journal PloS ONE, October 3, by Alexander Vargas and colleagues at Yale University, the University of Wisconsin-Madison and Yale Peabody Museum of Natural History.

Bird wings only have three fingers, having evolved from remote ancestors that, like humans and most reptiles, had five fingers.  Biologists have typically used embryology to identify the evolutionary origin (homology) of structures; the three fingers of the bird wing develop from cartilage condensations that are found in the same positions in the embryo as fingers two, three and four of humans (the index, middle and ring fingers).  However, the morphology of the fingers of early birds such as Archaeopteryx corresponds to that of fingers one, two and three in other reptiles (thumb, index and middle finger).  The fossil record clearly shows that fingers four and five (ring and pinky finger) were lost and reduced in the dinosaur ancestors of birds.

Further, the lack of expression of the HoxD-11 gene in the first finger of the wing makes it most similar to finger one (the “thumb”) of the mouse, consistent with comparative morphology.  However, the mouse is only distantly related to birds; crocodilians, in turn, are bird’s closest living relatives.

To see whether the evidence from mouse HoxD-11 expression held up, Vargas and colleagues, working at the lab of Gunter Wagner at Yale, have examined the expression of this gene in alligators; they found the expression to be, as in mice, absent only in finger one (the “thumb”).

Developmental and evolutionary biologists are familiar with the phenomenon of homeotic transformations, in which one structure begins to develop at a different position within the body.  A famous example is the case of the fruitfly mutant antennapaedia, which develops legs on its head instead of antennae.  The new work by Vargas et al.  Rekindles the hypothesis that a “hometic frameshift” occurred in the evolution of the bird wing, such that fingers one, two and three began to develop from the embryological positions of fingers two, three and four.

Although anthropologists and evolutionary biologists are still debating this question, a new study, published in the open-access journal PloS ONE, supports the view that the first egalitarian societies may have appeared tens of thousands of years before the French Revolution, Marx, and Lenin.  These societies emerged rapidly through intense power struggle and their origin had dramatic implications for humanity.  In many mammals living in groups, including hyenas, meerkats, and dolphins, group members form coalitions and alliances that allow them to increase their dominance status and their access to mates and other resources.  Alliances are especially common in great apes, some of whom have very intense social life, where they are constantly engaged in a political maneuvering as vividly described in Frans de Waal’s “Chimpanzee politics”.

In spite of this, the great apes’ societies are very hierarchical with each animal occupying a particular place in the existing dominance hierarchy.  A major function of coalitions in apes is to maintain or change the dominance ranking.  When an alpha male is well established, he usually can intimidate any hostile coalition or the entire community.

In sharp contrast, most known hunter-gatherer societies are egalitarian.  Their weak leaders merely assist a consensus-seeking process when the group needs to make decisions, but otherwise all main political actors behave as equal.  Some anthropologists argue that in egalitarian societies the pyramid of power is turned upside down with potential subordinates being able to express dominance over potential alpha-individuals by creating large, group-wide political alliance.

What were the reasons for such a drastic change in the group’s social organization during the origin of our own “uniquely unique” species?  Some evolutionary biologists theorize that at some point in the Pleistocene, humans reached a level of ecological dominance that dramatically transformed the natural selection landscape.  Instead of traditional “hostile forces of nature”, the competitive interactions among members of the same group became the most dominant evolutionary factor.  According to this still controversial view, known as the “social brain” or “Machiavellian intelligence” hypothesis, more intelligent individuals were able to take advantage of other members of their group, achieve higher social status, and leave more offspring who inherited their parent’s genes for larger brain size and intelligence.  As a result of this runaway process, the average brain size and intelligenc e were increasing across the whole human lineage.

Also increasing were the abilities to keep track of within-group social interactions, to remember friends and their allies and enemies, and to attract and use allies.  At some point, physically weaker members of the group started forming successful and stable large coalitions against strong individuals who otherwise would achieve alpha-status and usurp the majority of the crucial resources.  Eventually, an egalitarian society was established.  Although some of its components are well supported by data, this scenario remains highly controversial.  One reason is its complexity which makes it difficult to interpret the data and to intuit the consequences of interactions between multiple evolutionary, ecological, behavioral, and social factors acting simultaneously.  It is also tricky to evaluate relevant time-scales and figure out possible evolutionary dynamics.

A paper published in PloS ONE today makes steps towards answering these challenges.  The paper is co-authored by Sergey Gavrilets, a theoretical evolutionary biologist, and two computer scientists, Edgar Duenez-Guzman and Michael Vose, all from the University of Tennessee, Knoxville.

The researchers built a complex mathematical model describing the process of alliance formation which they then studied using analytical methods and large-scale numerical simulations.  The model focuses on a group of individuals who vary strongly in their fighting abilities.  If all conflicts were exclusively between pairs of individuals, a hierarchy would emerge with a few strongest individuals getting most of the resource.  However, there is also a tendency (very small initially) for individuals to interfere in an ongoing dyadic conflict thus biasing its outcome one way or another.  Positive outcomes of such interferences increase the affinities between individuals while negative outcomes decrease them.  Naturally, larger coalitions have higher probability of winning a conflict.

Gavrilets and colleagues identified conditions under which alliances can emerge in the group: increasing group size, growing awareness of ongoing conflicts, better abilities in attracting allies and building complex coalitions, and better memories of past events.

Most interestingly, the model shows that the shift from a group with no alliances to one or more alliances typically occurs suddenly, within several generations, in a phase-transition like fashion.  Even more surprisingly, under certain conditions (which include some cultural inheritance of social networks) a single alliance comprising all members of the group can emerge in which resources are divided evenly.  That is, the competition among non-equal individuals can paradoxically result in their eventual equality.

Gavrilets and colleagues argue that such an “egalitarian revolution” could also follow a change in the mating system that would increase father-son social bonds or an increase in fidelity of cultural inheritance of social networks.  Interestingly, the fact that mother-daughter social bonds are often very strong in apes suggests (everything else being the same) that females could more easily achieve egalitarian societies.

The model also highlights the importance of the presence of outsiders (or “scapegoats”) for stability of small alliances.  The researchers suggest that the establishment of a stable group-wide egalitarian alliance should create conditions promoting the origin of conscience, moralistic aggression, altruism, and other cultural norms favoring group interests over those of individuals.  Increasing within-group cohesion should also promote the group efficiency in between-group conflicts and intensify cultural group selection.

“Our language probably emerged to simplify the formation and improve the efficiency of coalitions and alliances,” says Gavrilets.  The scientists caution that one should be careful in applying their model to contemporary humans (whether members of modern societies or hunter-gathers).  In contemporary humans, an individual’s decision to join coalitions is strongly affected by his/her estimates of costs, benefits, and risks associated as well as by cultural beliefs and traditions.  These are the factors explicitly left outside of the modeling framework.

In humans, a secondary transition from egalitarian societies to hierarchical states took place as the first civilizations were emerging.  How can it be understood in terms of the model discussed?  One can speculate that technological and cultural advances made the coalition size much less important in controlling the outcome of a conflict than the individuals’ ability to directly control and use resources (e.g. weapons, information, food) that strongly influence the outcomes of conflicts.

Yale researchers have harnessed the power of 21st century computing to confirm an idea first proposed in 1916 — that plants with rapid reproductive cycles evolve faster.  Their findings appear in the October 3rd edition of Science.

“Our study has profound consequence for the understanding of evolution made possible by the critical role of the computer in revealing major evolutionary patterns,” said senior author Michael Donoghue, the G. Evelyn Hutchinson Professor of Ecology & Evolutionary Biology and Curator of Botany at Yale’s Peabody Museum of Natural History

Long involved with the Tree of Life Web Project, which is attempting to reconstruct the “tree” representing the genealogical relationships of all species on Earth, Donoghue has spearheaded the study of flowering plant evolution.  In animals, the variation in rate of molecular evolution has been ascribed to differences in generation time, metabolic rate, DNA repair, and body size; in plants, the differences have been more difficult to determine.

The current analysis evaluated DNA sequence data for five major evolutionary lineages within the flowering plants, comparing genetic markers in their chloroplast, nuclear, and mitochondrial genomes.  The authors also employed new methods for making some of the largest phylogenetic trees ever built.

A clear pattern emerged.  Plants with a shorter generation time — from the time they germinate to the time that a seed they produce germinates — generally show more rapid rates of molecular evolution.  Longer-lived trees and shrubs, by contrast, evolve more slowly and show less variability in their rates of evolution.  The study also showed that the difference in rate seen between herbs and woody plants has been maintained through evolutionary time.

“To give an idea of the scope of the data managed in this study, the largest data set contained over 4500 species, while typical tests of such hypotheses are based on less than 50 species in total,” said Yale graduate student and lead author Stephen Smith.

For each branch on each limb of the “tree,” the researchers calculated the rate of molecular evolution by determining the number of DNA nucleotide substitutions per site per million years.

Their analyses highlight the difficulty in using molecular data to infer the timing of evolutionary events, and suggest that new strategies may be necessary in using DNA sequence “barcodes” to identify plant species, and in setting conservation priorities.

“Our data indicate that some kinds of plants will be easy to ID and others will be much more difficult,” said Smith.  “The slower a plant species evolves, the harder it is to differentiate it from related plants.  But our analyses point in a good new direction.”

T. rex and Triceratops: In the popular imagination, dinosaurs are extraordinary reptiles that ruled the world for over 160 million years. But Steve Brusatte, a doctoral student at Columbia University who is an affiliate of the American Museum of Natural History, and colleagues are challenging this idea with new fossil data and math. By comparing early dinosaurs to their competitors, the crurotarsan ancestors to crocodiles, they have found that dinosaurs were not “superior,” as has long been thought. Rather, crurotarsans were the more successful group during the 30 million years they overlapped until the devastating mass extinction 200 million years ago, an event that dinosaurs weathered successfully.

“For a long time it was thought that there was something special about dinosaurs that helped them become more successful during the Triassic, the first 30 million years of their history, but this isn’t true,” says Brusatte. “If any of us were standing by during the Triassic and asked which group would rule the world for the next 130 million years, we would have identified the crurotarsans, not dinosaurs.”

Both dinosaurs and crurotarsans evolved and filled some of the same niches after a massive extinction event that occurred at the end of the Permian (250 million years ago). Of the crurotarsan group, crocodilians are the only living members. But in the Triassic, crurotarsans were amazingly diverse—from giant carnivorous rauisuchians to long–snouted, flesh eating phytosaurs to herbivorous armored aetosaurs—and they have often been mistaken for dinosaurs in the fossil record, the animals that they probably competed with for the same resources. Both groups survived an extinction event 228 million years ago, but only a few crurotarsans—the crocodiles—squeaked through a period of rapid global warming at the end of the Triassic 200 million years ago. Dinosaurs faired better during the latter extinction: most types of dinosaurs survived until an asteroid ended their dominance 65 million years ago. It is because of this stroke of luck that dinosaurs were assumed to be the better competitors.

Brusatte and colleagues tested this assumption by measuring the evolution in both competing groups. Based on a database of 437 features of the skeletons of 64 species of dinosaurs and crurotarsans, as well as a new phylogenetic tree of these groups, they performed two calculations to look at the evolutionary pattern. The first measurement is of the disparity, or the known range of different body plans, of the two groups. Disparity is a reliable indicator of the different lifestyles, diets, and habitats of a group of animals. Remarkably, Brusatte and colleagues found that crurotarsans had twice the disparity of dinosaurs: They were exploring twice the range of body plans as early dinosaurs. “With this information, it’s difficult to argue that dinosaurs were ’superior’ during the Triassic. They just lucked out when the crurotarsans were hit hard at the end Triassic extinction,” says Brusatte.

The team also measured the rate of evolution in both dinosaurs and crurotarsans to see if dinosaurs were diversifying into new species at higher rates, as may be expected if they had special abilities or were outcompeting their rivals. But the comparison showed that the two groups were evolving at the same rate over the 30 million years that they overlapped.

“Many people like to think that evolution is progressive: mammals are better than dinosaurs because they came later. This is like progressive improvements in car technology—a Ford Taurus is demonstrably better than a Model T,” says coauthor Michael Benton, a paleontologist at the University of Bristol in the United Kingdom. “So it may be hard for us to accept that dinosaurs achieved their dominant position on earth largely by chance, just as mammals did when the dinosaurs were later wiped out by a meteorite strike.”

When the world’s land was congealed in one supercontinent 240 million years ago, Antarctica wasn’t the forbiddingly icy place it is now. But paleontologists have found a previously unknown amphibious predator species that probably still made it less than hospitable.

The species, named Kryostega collinsoni, is a temnospondyl, a prehistoric amphibian distantly related to modern salamanders and frogs. K. collinsoni resembled a modern crocodile, and probably was about 15 feet in length with a long and wide skull even flatter than a crocodile’s.

In addition to large upper and lower teeth at the edge of the mouth, temnospondyls often had tiny teeth on the roof of the palate. However, fossil evidence shows the teeth on the roof of the mouth of the newly found species were probably as large as those at the edge of the mouth.

“Its teeth, compared to other amphibians, were just enormous. It leads us to believe this animal was a predator taking down large prey,” said Christian Sidor, a University of Washington associate professor of biology and curator of vertebrate paleontology at the Burke Museum of Natural History and Culture at the UW.

Sidor is lead author of a paper describing the new species published in the September issue of the Journal of Vertebrate Paleontology. Co-authors are Ross Damiani of Staatliches Museum für Naturkunde Stuttgart in Germany and William Hammer of Augustana College in Rock Island, Ill. The work was funded in part by the National Science Foundation and the Alexander von Humboldt Foundation.

The scientists worked from a fossilized piece of the snout of K. collinsoni, analyzing structures present in more complete skulls for other temnospondyl species that had similar size characteristics.

“The anatomy of the snout tells us what major group of amphibian this fossil belonged to,” Sidor said.

Teeth at the edge of the mouth, as well as on the palate roof, were clearly visible, and the presence of structures similar to those that allow fish and amphibians to sense changes in water pressure led the researchers to conclude that the species was aquatic.

The fossilized piece of snout also contains a nostril, which aided the scientists in judging proportions of the head when comparing it to other fossils. They estimated the skull was about 2.75 feet long and perhaps 2 feet across at its widest point.

“Kryostega was the largest animal in Antarctica during the Triassic,” Sidor said.

The term “Kryostega” translates to ‘frozen’ and ‘roof,’ which refer to the top of the skull. The scientists named the species for James Collinson, a professor emeritus of Earth sciences at Ohio State University who made important contributions to the study of Antarctic geology.

Hammer collected the fossil in 1986 from an Antarctic geological layer called the Fremouw Formation. He has studied a number of other Antarctic fossils, including dinosaurs, collected at about the same time, and so the temnospondyl fossil was not closely examined until the last couple of years.

At the time K. collinsoni was living, all the world’s land was massed into a giant continent called Pangea. The area of Antarctica where the fossil was found was near what is now the Karoo Basin of South Africa, one of the richest fossil depositories on Earth.

Sidor noted that in the early Triassic period, from about 245 million to 251 million years ago, just before the period that produced the K. collinsoni fossil, it appears that Antarctica and South Africa were populated by largely the same species. While Antarctica was still colder than much of the world, it was substantially warmer than it is today, though it still spent significant periods in complete darkness.

By the middle of the Triassic period perhaps only half the species were the same, he said, and in the early Jurassic period, around 190 million years ago, unique early dinosaur species were appearing in Antarctica.

“It could be that these animals were adjusting to their local environment by then, and we are seeing the results of speciation occurring at high latitude,” Sidor said. “Here we have really good evidence that Antarctic climate wasn’t always the way it is today. During the Triassic, it was warmer than it is today – it was warmer globally, not just in Antarctica.”

In a paper published today in Science, Steve Brusatte and Professor Mike Benton challenge the general consensus among scientists that there must have been something special about dinosaurs that helped them rise to prominence.

Dinosaurs epitomize both success and failure.  Failure because they went extinct suddenly 65 million years ago; success because they dominated terrestrial ecosystems for well over 100 million years evolving into a wide array of species that reached tremendous sizes.

But why were the dinosaurs able to become so successful, so diverse, so large?  Many scientists argue that they must have had some feature or characteristic that helped them out-compete other vertebrate groups, including crocodiles and close crocodile cousins.

Mr Brusatte and Professor Benton are the first to look at the overall picture of the evolution of dinosaurs and their closest competitors during the Triassic period (251 to 199 million years ago).  First, they identified the most likely ‘competitors’ to early dinosaurs: the crurotarsan archosaurs, a large group of animals that are closely related to crocodiles, which form one half of the group Archosauria, the other half being dinosaurs (and their descendants, the birds).

Unlike today’s crocodiles, Triassic crurotarsans were amazingly diverse.  There were enormous quadrupedal predators, slender bipedal predators, swift bipedal omnivores, fish-eaters, root-grubbers, and low-to-mid-browsing herbivores.  Many of these crurotarsans look nothing like crocodiles, but instead are eerily similar to dinosaurs and, in fact, have been mistaken for dinosaur ancestors, or even true dinosaurs, in the past.

Crurotarsans and dinosaurs clearly shared many niches in the Late Triassic, looked very similar, and were thus very likely to be competing for similar resources.

The researchers examined the evolutionary pattern of dinosaurs and crurotarsans in the Late Triassic.  Using a very large dataset of anatomical characters – nearly 500 features of the skeleton – and a new family tree of the entire archosaur group, they measured evolutionary rates and morphological disparity (a measurement of the range of different body plans and lifestyles that a group has).

They found no difference in the rates at which dinosaurs and crurotarsans were evolving.  This was surprising as, if dinosaurs were truly ’superior’ or ‘out-competing’ crurotarsans in the Triassic, they should be expected to evolve faster.  Instead, crurotarsans were keeping pace.

The results for the second measure, morphological disparity, were even more remarkable.  Crurotarsans had a much higher disparity than dinosaurs in the Triassic.  In other words, crurotarsans were exploring a larger range of body types, diets, and lifestyles.  This greatly contrasts with the classic image of dinosaur superiority since their greatest competitors, the crurotarsans, were doing so much more.

To these surprising results can be added two other, previously known, findings: crurotarsans were more abundant (more individuals, more fossils, more species) than dinosaurs in many Triassic ecosystems, and crurotarsans were in some cases more diverse (greater number of species).  Putting all this together, it is very difficult to argue that dinosaurs were ’superior’ to crurotarsans, or that they were out-competing crurotarsans.

Steve Brusatte, who conducted the research while an Msc student in Bristol University’s Department of Earth Sciences, said: “If we were standing in the Late Triassic, 210 million years ago or so, and had to bet on which group would eventually dominate ecosystems, all reasonable gamblers would go with the crurotarsans.  There was no sign that dinosaurs were eventually going to succeed so why did they?  The answer is two mass extinction events: the dinosaurs not only got lucky, but they got lucky twice.

“They first weathered the storm during the Carnian-Norian event 228 million years ago, but so did the crurotarsans.  In contrast, many other potential competitor groups went extinct.  Then dinosaurs weathered a second, much bigger, storm 200 million years ago.  This was the end Triassic extinction event, which was a sudden and catastrophic extinction caused by rapid climate change, possibly facilitated by an asteroid impact.  Strangely, and suddenly, all crurotarsans except for a few lineages of crocodiles went extinct.  On the other hand, the dinosaurs did not.  They survived and then radiated in the Early Jurassic, and very quickly established themselves as the dominant vertebrate group on land across the world.

“Why did crurotarsans go extinct and not dinosaurs?  We don’t know the answer to that, but we suspect that it was nothing more than luck, plain and simple.”

A new study suggests that although humans may have developed complex thought processes that can help to regulate their emotions, these processes are linked with evolutionarily older mechanisms that are common across species.  The research, published by Cell Press in the September 11th issue of the journal Neuron, provides new insight into way the brain manages fear and may guide exploration of novel pharmacological and therapeutic treatments for anxiety disorders.

“The ability to eliminate, control or diminish negative emotional responses is important for adaptive function and critical in the treatment of psychopathology,” says study author, Dr. Mauricio Delgado from Rutgers University.  “Recent research examining the neural mechanisms for diminishing fears has focused on two techniques: extinction, which has been explored across species, and cognitive emotion regulation strategies, which are unique to humans.”  Previous work in rodents and humans has implicated activity in the amygdala and ventral medial prefrontal cortex (vmPFC) in extinction.  In contrast, neural circuits underlying cognitive strategies to regulate emotions are not as well understood.

Dr. Delgado, Dr. Elizabeth A. Phelps from New York University, and their colleagues were interested in examining the similarities and differences of diminishing fear through both techniques.  They used similar experimental paradigms with different means of controlling fear to directly compare the neural mechanisms that mediate extinction and emotional regulation.  A typical fear conditioning method was paired with a measurement of physiological arousal to examine extinction, while a cognitive emotion regulation strategy was also implemented.  Functional magnetic resonance imaging (fMRI) was used to compare the neural activation patterns of extinction and emotional regulation.

The researchers observed that the lateral prefrontal cortex regions engaged by cognitive emotion regulation strategies influenced the amygdala and diminished fear through similar vmPFC connections that are thought to inhibit the amygdala during extinction.  Taken together, the findings indicate that there is overlap in the neural circuitry of diminishing learned fears through emotion regulation and extinction and that vmPFC may play a general regulatory role in diminishing fear across a range of paradigms.

“Our results suggest that even though humans may have developed unique capabilities for using complex cognitive strategies to control emotion, these strategies may influence the amygdala through phylogenetically shared mechanisms of extinction,” explains Dr. Phelps.  “Extinction and cognitive emotion regulation may be, in part, complementary in that they rely on a common neural circuitry and, perhaps, similar neurophysiological and neurochemical mechanisms.”

Researchers have determined that there are hundreds of biological differences between the sexes when it comes to gene expression in the cerebral cortex of humans and other primates.  These findings, published June 20th in the open-access journal PloS Genetics, indicate that some of these differences arose a very long time ago and have been preserved through evolution.  These conserved differences constitute a signature of sex differences in the brain.

Many more obvious gender differences have been preserved throughout primate evolution; examples include average body size and weight, and genitalia design.  This study, believed to be the first of its kind, focuses on gene expression within the cerebral cortex.  The cerebral cortex is involved in many of the more complex functions in both humans and other primates, including memory, attentiveness, thought processes and language.

The researchers measured gene expression in the brains of male and female primates from three species: humans, macaques, and marmosets.  To measure activity of specific genes, the products of genes (RNA) obtained from the brain of each animal were hybridized to microarrays containing thousands of DNA clones coding for thousands of genes.  The authors also investigated DNA sequence differences among primates for genes showing different levels of expression between the sexes.

“Knowledge about gender differences is important for many reasons.  For example, this information may be used in the future to calculate medical dosages, as well as for other treatments of diseases or damage to the brain,” says team leader Professor Elena Jazin, at Uppsala University, Sweden.

In addition to the results mentioned above, the researchers also report on evolutionary speeds in genes that have been identified as male or female-oriented.  This could provide clues about the power of natural selection processes during the evolution of primates.

Lead author Björn Reinius notes that the study does not determine whether these differences in gene expression are in any way functionally significant.  Such questions remain to be answered by future studies.

What makes a human different from a chimp?  Researchers from the European Molecular Biology Laboratory’s European Bioinformatics Institute [EMBL-EBI] have come one important step closer to answering such evolutionary questions correctly.  In the current issue of Science they uncover systematic errors in existing methods that compare genetic sequences of different species to learn about their evolutionary relationships.  They present a new computational tool that avoids these errors and provides accurate insights into the evolution of DNA and protein sequences.  The results challenge our understanding of how evolution happens and suggest that sequence turnover is much more common than assumed.

“Evolution is happening so slowly that we cannot study it by simply watching it.  That’s why we learn about the relationships between species and the course and mechanism of evolution by comparing genetic sequences,” says Nick Goldman, group leader at EMBL-EBI.

The four letter code that constitutes the DNA of all living things changes over time; for example individual or several letters can be copied incorrectly [substitution], lost [deletion] or gained [insertion].  Such changes can lead to functional and structural changes in genes and proteins and ultimately to the formation of new species.  Reconstructing the history of these mutation events reveals the course of evolution.

A comparison of multiple sequences starts with their alignment.  Characters in different sequences that share common ancestry are matched and gains and losses of characters are marked as gaps.  Since this procedure is computationally heavy, multiple alignments are often built progressively from several pairwise alignments.  It is impossible, however, to judge if a length difference between two sequences is a deletion in one or an insertion in the other sequence.  For correct alignment of multiple sequences, distinguishing between these two events is crucial.  Existing methods, that fail to do that, lead to a flawed understanding of the course of evolution.

“Our new method gets around these errors by taking into account what we already know about evolutionary relationships,” says Ari Löytynoja, who developed the tool in Goldman’s lab.  “Say we are comparing the DNA of human and chimp and can’t tell if a deletion or an insertion happened.  To solve this our tool automatically invokes information about the corresponding sequences in closely related species, such as gorilla or macaque.  If they show the same gap as the chimp, this suggests an insertion in humans.”

Findings achieved with the new technique suggest that insertions are much more common than assumed, while the frequency of deletions has been overestimated by existing methods.  A likely reason for these systematic errors of other techniques is that they were originally developed for structural matching of protein sequences.  The focus of molecular biology is shifting, however, and understanding functional changes in genomes requires specifically designed methods that consider sequences’ histories.  Such approaches will likely reveal further bugs in our understanding of evolution in future and might challenge the conventional picture of sequence evolution.

The immune system of vertebrate animals consists of two components: the innate immune response, a constitutive system ready to respond to a pathogen, and the adaptive immune response, a system of immunological memory that responds to previously encountered pathogens. In a study led by Dr. Anlong Xu of Sun Yat-sen University, scientists searched the amphioxus genome for genes that may be relevant to immunity in order to gain an understanding of what the immune system repertoire of the vertebrate ancestor may have looked like. “Our chordate ancestors had a remarkably elaborate innate immune system, but this system was somehow reduced in the vertebrate lineage, which is unusual to our conventional thinking of the immune system,” explains Xu. Furthermore, Xu notes that this work helps to describe a global picture of innate immunity and uncover the evolutionary footsteps underlying the evolution of human immune pathways.

Genome Research is publishing several papers related to analyses of the amphioxus (Branchiostoma floridae) genome sequence. The amphioxus, or lancelet, is a cephalochordate residing in shallow regions of tropical and temperate seas, bearing resemblance to a small fish, however lacking pairs of eyes, limbs, and ears. A member of the chordata phylum along with tunicates (sea squirts) and vertebrates, amphioxus lacks the backbone or spinal column characteristic of vertebrate animals, yet shares the same basic body plan. Amphioxus is therefore an excellent model for investigating how vertebrates evolved from an invertebrate ancestor. Now, researchers are finding that the amphioxus genome sequence is revealing new insights into vertebrate origins and the evolution of complex biological systems, such as immunity and nervous system development. Primary research reports describing these novel findings will be published online June 19, concurrent with publication of the amphioxus genome sequence report in the journal Nature.