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.”

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.

Scientists funded by the Biotechnology and Biological Sciences Research Council (BBSRC) have discovered how evolution may have lumbered humans with allergy problems. The team from the Randall Division of Cell & Molecular Biophysics, King’s College London are working on a molecule vital to a chicken’s immune system which represents the evolutionary ancestor of the human antibodies that cause allergic reactions. Crucially, they have discovered that the chicken molecule behaves quite differently from its human counterpart, which throws light on the origin and cause of allergic reactions in humans and gives hope for new strategies for treatment. The work is published today (13 June) in The Journal of Biological Chemistry.

Researcher, Dr Alex Taylor said: “This molecule is like a living fossil – finding out that it has an ancient past is like turning up a coelacanth in your garden pond. By studying this molecule, we can track the evolution of allergic reactions back to at least 160 million years ago and by looking at the differences between the ancient and the modern antibodies we can begin to understand how to design better drugs to stop allergic reactions in their tracks.”

The chicken molecule, an antibody called IgY, looks remarkably similar to the human antibody IgE. IgE is known to be involved in allergic reactions and humans also have a counterpart antibody called IgG that helps to destroy invading viruses and bacteria. Scientists know that both IgE and IgG were present in mammals around 160 million years ago because the corresponding genes are found in the recently published platypus genome. However, in chickens there is no equivalent to IgG and so IgY performs both functions.

Lead researcher, Dr. Rosy Calvert said: “Although these antibodies all started from a common ancestor, for some reason humans have ended up with two rather specialised antibodies, whereas chickens only have one that has a much more general function.

“We know that part of the problem with IgE in humans is that it binds extremely tightly to white blood cells causing an over-reaction of the immune system and so we wanted to find out whether IgY does the same thing.”

By examining how tightly IgY binds to white blood cells the researchers have found that it behaves in a much more similar way to the human IgG, which is not involved in allergic reactions and binds much less tightly.

Professor Brian Sutton, head of the laboratory where the work was done said: “It might be that there was a nasty bug or parasite around at the time that meant that humans needed a really dramatic immune response and so there was pressure to evolve a tight binding antibody like IgE. The problem is that now we’ve ended up with an antibody that can tend to be a little over enthusiastic and causes us problems with apparently innocuous substances like pollen and peanuts, which can cause life-threatening allergic conditions.”

The next stage of the work is to examine in very fine detail the interaction between the antibodies and the surface of the white blood cell. This is with a view to designing drugs that could alter this interaction and therefore ‘loosen’ the binding of IgE, making it more like its chicken counterpart.

Nautiloids are the sole surviving family of externally-shelled cephalopods that thrived in the tropical oceans 450–150 million years ago. However, in the intervening years their modern soft bodied relatives dumped the shell and developed complex central nervous systems; which makes Nautilus ideally suited to discover the ‘evolutionary pathways that led to the development of the complex coleoid [soft bodied cephalopod] brains’ say Robyn Crook and Jennifer Basil. Knowing that the simple Nautilus brain lacks the structures required for memory in more sophisticated cephalopods, Crook and Basil decided to test the living fossil’s memory.

Training Nautilus pompilus to associate the smell of food with a blue light, the cephalopods eventually learned to respond to a flash of blue light by extending their tentacles. Then the scientists tested the cephalopods memories with a flash of light 3min, 30min, 1h, 6h, 12h and 24h after training. Amazingly, Nautilus remembered their training for up to an hour before the memory was lost, but then the memory returned 6h later, lasting up to 24h. Nautilus has both short and long term memory, just like modern cephalopods, despite lacking the same brain structures.

Crook and Basil are optimistic that the unsophisticated Nautilus brain could teach us how modern cephalopod brains evolved.