A collaboration of more than 100 researchers from 10 countries announce the results of an unprecedented scientific study that resolves the history of the evolution of insects.

The results are published in Science, the world’s leading peer-reviewed research journal, and include answers to many long held questions about the evolutionary history of the world’s largest and most diverse group of organisms.

The results, published by scientists from the 1KITE project (1,000 Insect Transcriptome Evolution, www.1kite.org), are essential to understanding the millions of living insect species that shape our terrestrial living space and both support and threaten our natural resources.

“Insects are the most species rich organisms on earth. They are of immense ecological, economic and medical importance and affect our daily lives, from pollinating our crops to vectoring diseases,” says Dr. Bernhard Misof, Professor from Research Museum Alexander Koenig – Leibniz Institute for Animal Biodiversity (ZFMK) in Bonn, Germany, one of those who led the research effort. “We can only start to understand the enormous species richness and ecological importance of insects with a reliable reconstruction of how they are related.”

Using a dataset consisting of 144 carefully chosen species, 1KITE scientists present reliable estimates on the dates of origin and relationships of all major insect groups based on the enormous molecular dataset they collected. They show that insects originated at the same time as the earliest terrestrial plants about 480 million years ago. Their analyses therefore suggest that insects and plants shaped the earliest terrestrial ecosystems together, with insects developing wings to fly 400 million years ago, long before any other animal could do so, and at nearly the same time that land plants first grew substantially upwards to form forests.

“Phylogeny forms the foundation for telling us the who?, what?, when?, and why? of life,” says Dr. Karl Kjer, (Rutgers – State University of New Jersey, USA). “Many previously intractable questions are now resolved, while many of the “revolutions” brought about by previous analyses of smaller molecular datasets have contained errors that are now being corrected”.

The new reconstruction of the insect tree of life was only possible by a cooperation of more than 100 experts in molecular biology, insect morphology, paleontology, insect taxonomy, evolution, embryology bioinformatics and scientific computing. The consortium was led by Prof. Dr. Karl Kjer (Rutgers – State University of New Jersey, USA), Dr. Xin Zhou (Deputy Director of the China National GeneBank, BGI-Shenzhen), and Prof. Dr. Bernhard Misof from the ZFMK.

“We wanted to promote research on the little-studied genetic diversity of insects,” says Dr. Xin Zhou, Deputy Director of the China National GeneBank, BGI-Shenzhen in China, who initiated the project. “For applied research, it will become possible to comparatively analyze metabolic pathways of different insects and use this information to more specifically target pest species or insects that affect our resources. The genomic data we studied (the transcriptome – all of the expressed genes) gives us a very detailed and precise view into the genetic constitution and evolution of the species studied.”

However, the goal to analyze more than 1,000 insect transcriptomes, a set of all RNA molecules,  posed a major challenge to the bioinformatics and scientific computing team within 1KITE. “During the planning phase of the project it became clear that the available software would not be able to handle the enormous amount of data,” relates Prof. Dr. Alexandros Stamatakis, head of the research group „Scientific Computing“ at the Heidelberg Institute for Theoretical Studies (HITS) and Professor for High Performance Computing at the life sciences of the Karlsruhe Institute for Technology (KIT). “The development of novel software and algorithms to handle “big data” such as these, is another notable accomplishment of the 1KITE team, and lays a theoretical foundation for future analyses of other very large phylogenomic data sets.”

The 1KITE team’s diverse strengths and strong international cooperation, including museum repositories for vouchering of specimens, results, and meta data, is a blueprint for international excellence in research.

Zoologisches Forschungsmuseum Alexander Koenig – Leibniz-Institut für Biodiversität der Tiere

Header Image : Gold Wasp (Hedychrum nobile), Copyright: Dr. Oliver Niehuis, ZFMK, Bonn

Eight percent of your genome derives from retroviruses that inserted themselves into human sex cells millions of years ago. Right now the koala retrovirus (KoRV) is invading koala genomes, a process that can help us understand our own viral lineage and make decisions about managing this vulnerable species.

In a recent study, published in Molecular Biology and Evolution, scientists from the University of Illinois discovered that 39 different KoRVs in a koala’s genome were all endogenous, which means passed down to the koala from one parent or the other; one of the KoRVs was found in both parents.

Koalas are the only known organisms where a retrovirus is transitioning from exogenous to endogenous. An exogenous retrovirus infects a host, inserts its genetic information into the cell’s DNA, and uses the host cell’s machinery to manufacture more viruses. When an exogenous retrovirus infects an egg or sperm cell and the viral genetic information is then passed down to the host’s offspring, the virus becomes an endogenous retrovirus (ERV).

Becoming part of the koala genome

Like humans, koalas have evolutionary defenses against endogenization.

“During the early stages of endogenization, there are huge numbers of retroviruses. KoRVs are present all across koalas’ genomes, with many thousands or tens of thousands of KoRVs in the population,” said Alfred Roca, a Professor of Animal Sciences and member of the Institute for Genomic Biology at the University of Illinois at Urbana-Champaign. “Over time most of them will disappear because these copies of the virus may be present in as few as one individual chromosome. If that one individual happens to not reproduce, or if it reproduces and the other chromosome is passed down, then that ERV will disappear.”

In order to end up with 100 ERVs in an organism, the species may have to start with 10,000 ERVs in its ancestors, Roca said. It takes retroviruses, like KoRV, many thousands of years to become a fixed part of the koala genome, like the eight percent of retroviral DNA that all humans share.

The ERVs that are successfully passed down are protected by the koala’s DNA repair mechanisms so that their rate of mutation is extremely low. Based on the dearth of mutations in the endogenous koala retroviruses, Roca’s team was able to estimate that the KoRVs integrated into the host germ line less than 50,000 years ago. “This is quite recent compared with other ERVs that are millions of years old and have accumulated mutations,” said first author Yasuko Ishida, a research specialist in Roca’s lab.

Overcoming retroviral fitness effects

In koalas, KoRV has been linked to leukemia, lymphoma, and immune suppression, which can lead to increased susceptibility to chlamydia.

“It seems likely that for thousands of years since this virus integrated, the koala host has suffered fitness effects,” Roca said. “It is possible that across species, when a host lineage has been invaded by ERVs, it had to go through this process of adaptation between host and virus, which is a very sad finding. It may be a very long, slow, painful process for the host species, one which human ancestors have gone through and overcome many times in the distant past.”

In mammals, retroviral DNA is associated with placental development and has been found to protect hosts from harmful exogenous retroviruses.

“But once retroviruses become part of the host, they begin to help the host because that is how they survive,” Roca said. “They will be better off if they evolve to protect the host. Over time, the detrimental effects go down and the beneficial effects go up.”

Conserving koala populations

In the 1900s, koalas were extensively hunted for their fur. In an effort to preserve koalas, a few individuals were moved to an island off the coast of Australia. Years later, the inbred island population was reintroduced to southern Australia. Today some of the southern koalas remain uninfected while almost all northern koalas have dozens of KoRVs in their genomes.

“Which is the lesser of two evils?” Roca said. “Do you try to conserve genetic diversity, which is present in the northern populations along with the retrovirus or do you conserve southern populations that don’t have the retrovirus but are horribly inbred?”

Roca’s research team included research specialist Yasuko Ishida, graduate student Kai Zhao, and scientific collaborator Alex Greenwood of the Leibnitz Institute in Berlin. Their work was supported by the National Institute of General Medical Sciences. The San Diego Zoo, Columbus Zoo, San Francisco Zoo, and Riverbanks Zoo provided the koala samples.

University of Illinois College of Agricultural, Consumer and Environmental Sciences (ACES)

A new study suggests that the flightless birds named moa were completely extinct by the time New Zealand’s human population had grown to two and half thousand people at most.

The new findings, which appear in the prestigious journal Nature Communications, incorporate results of research by international teams involved in two major projects led by Professor Richard Holdaway (Palaecol Research Ltd and University of Canterbury) and Mr Chris Jacomb (University of Otago), respectively.

The researchers calculate that the Polynesians whose activities caused moa extinction in little more than a century had amongst the lowest human population densities on record. They found that during the peak period of moa hunting, there were fewer than 1500 Polynesian settlers in New Zealand, or about 1 person per 100 square kilometres, one of the lowest population densities recorded for any pre-industrial society.

They found that the human population could have reached about 2500 by the time moa went extinct. For several decades before then moa would have been rare luxuries.

Estimates of the human population during the moa hunting period are more sensitive to how long it took to exterminate the birds through hunting and habitat destruction than to the size of the founding population.

To better define the critical period of moa hunting, the research was aimed at “book-ending” the moa hunter period with new estimates for when people started eating moa, and when there were no more moa to eat.

Starting with the latest estimate for a founding population of about 400 people (including 170-230 women), and applying population growth rates in the range achieved by past and present populations, the researchers modelled the human population size through the moa hunter period and beyond. When moa and seals were still available, the better diet enjoyed by the settlers likely fuelled higher population growth, and the analyses took this into account.

The first “book-end” – first evidence for moa hunting – was set by statistical analyses of 93 new high-precision radiocarbon dates on genetically identified moa eggshell pieces. These had been excavated from first settlement era archaeological sites in the eastern South Island, and showed that moa were still breeding nearby.

Chris Jacomb explains: “The analyses showed that the sites were all first occupied – and the people began eating moa – after the major Kaharoa eruption of Mt Tarawera of about 1314 CE.”

Ash from this eruption is an important time marker because no uncontested archaeological evidence for settlement has ever been found beneath it, Mr Jacomb says.

The other “book-end” was derived from statistical analyses of 270 high-precision radiocarbon dates on moa from non-archaeological sites. Analysis of 210 of the ages showed that moa were exterminated first in the more accessible eastern lowlands of the South Island, at the end of the 14th century, just 70-80 years after the first evidence for moa consumption.

Analysis of all 270 dates, on all South Island moa species from throughout the South Island, showed that moa survived for only about another 20 years after that.

Their total extinction most probably occurred within a decade either side of 1425 CE, barely a century after the earliest well-dated site, at Wairau Bar near Blenheim, was settled by people from tropical East Polynesia. The last known birds lived in the mountains of north-west Nelson. Professor Holdaway adds that “the results provide further support for the rapid extinction model for moa that Chris Jacomb and I published 14 years ago in [the US journal] Science.”

The researchers note that it is often suggested that people could not have caused the extinction of megafauna such as the mammoths and giant sloths of North America and the giant marsupials of Australia, because the human populations when the extinctions happened were too small.

Prof Holdaway and Mr Jacomb say that the extinction of the New Zealand terrestrial megafauna of moa, giant eagle, and giant geese, accomplished by the direct and indirect activities of a very low-density human population, shows that population size can no longer be used as an argument against human involvement in extinctions elsewhere.

University of Otago

Many large charismatic mammals went extinct at the end of the Ice Age (approx 11,000 years ago), including the Steppe bison, Bison priscus. A recent find in Eastern Siberia has uncovered one of these bison, literally, frozen in time.

The most complete frozen mummy of the Steppe bison yet known, dated to 9,300 years before present, was recently uncovered in the Yana-Indigirka Lowland and a necropsy was performed to learn about how this animal lived and died at the end of the Ice Age. The Yukagir bison mummy, as it is named, has a complete brain, heart, blood vessels and digestive system, although some organs have shrunk significantly over time. The necropsy of this unique mummy showed a relatively normal anatomy with no obvious cause of death. However, the lack of fat around abdomen of the animal makes researchers think that the animal may have died from starvation.

This project is being led by Dr. Natalia Serduk of the Russian Academy of Sciences in Moscow, Russia with contributions from a large group of scientists mainly from Yakutsk and Moscow, Russia. But one project scientist, Olga Potapova, is from the Mammoth Site of Hot Springs in South Dakota, USA, she tells us, “The Yukagir bison mummy became the third find out of four now known complete mummies of this species discovered in the world, and one out of two adult specimens that are being kept preserved with internal organs and stored in frozen conditions”, making this find one of high importance.

Dr. Evgeny Maschenko, another project scientist, from the Paleontological Institute in Moscow (Russia), comments, “The exclusively good preservation of the Yukagir bison mummy allows direct anatomical comparisons with modern species of Bison and cattle, as well as with extinct species of bison that were gone at the Pleistocene-Holocene boundary.”

Frozen bison and mammoth mummies are changing the way we think about paleontology because of the large amount of information that can be ascertained from each specimen, with new scientific methods and approaches that became available within the last decade. Potapova adds,

“The next steps to be done include further examination of the bison’s gross anatomy, and other detailed studies on its histology, parasites, and bones and teeth. We expect that the results of these studies will reveal not only the cause of death of this particular specimen, but also might shed light on the species behavior and causes of its extinction.”

Society of Vertebrate Paleontology

Virtually all organisms in the living world compete with members of their own species.

However, individuals differ strongly in how much they invest into their competitive ability. Some individuals are highly competitive and eager to get access to high-quality resources, while others seem to avoid competition, instead making prudent use of the lower-quality resources that are left over for them.

Moreover, the degree of competitiveness in animal and human societies seems to fluctuate considerably over time. A theoretical study published in “Nature Communications” this week sheds some new light on these findings. The authors demonstrate that the evolution of competitiveness has a strong tendency towards diversification. When competitiveness is externally favoured, it can destabilize animal and human societies and in extreme cases even threaten their survival.

To analyse the evolution of competitiveness, a team of scientists from the Universities of Bonn (Germany), Bielefeld (Germany) and Groningen (Netherlands) developed a model that reflects the idea that competitiveness comes at a price. In the model, individuals that invest a lot into being competitive gain access to high-quality resources, but the features making them competitive hamper them in making maximal use of these resources. “In many organisms, some individuals invest a lot into being successful in the competition with their conspecifics”, says Sebastian Baldauf from the University of Bonn, first author of the study. “They grow, for example, weaponry like horns or antlers and do hardly feed in order to be able to conquer and defend large territories. This may secure them many matings, but they might get more fitness out of each mating when they would spend their energy on other activities, like paternal care.”

The simple assumption that individuals with highest competitive ability are not able to make maximal use of the acquired resources suffices to explain the diversity in competitiveness observed in nature. If not too much is at stake, that is, if high-competitive individuals acquire only slightly better resources than low-competitive individuals, evolution leads to the stable coexistence of two types of individuals: one type does not invest into competition at all and is content with lower-quality resources, and a second type that invest an appreciable (but not maximal) part of their energy into being competitive. If much is at stake, such coexistence does not occur.

Instead, the model predicts cyclical changes in competitive ability over time. For large periods, there is an arm’s race to the top, leading to an ever-increasing degree of competitiveness in the population. This process continues until the costs of competitiveness become too high: competitiveness crashes to zero, but once there the whole rat race starts again. “Hence, the same model explains the coexistence of alternative strategies and the change of competitiveness in time”, Baldauf says. “Moreover, the model can explain the variation in competitiveness across populations of the same species.”

Heating up the fire

The study also considers how the evolution of competitiveness is affected by external factors. As an example, the authors considered the joint evolution of competitiveness in males and the evolution of preferences in females for either high- or low-competitive males. “We were interested in the question whether females evolve preferences for males with high-quality resources but little energy left for paternal care or for males that are content with low-quality resources but able to compensate by providing much care,” says Leif Engqvist, co-author of the study. It turned out that females almost always evolved preferences for highly competitive males, even if mating with uncompetitive but caring males would have resulted in more offspring. These preferences, in turn, fuelled the males’ arm’s race towards higher and higher levels of competitiveness. Engqvist: “In stressful times, like periods of food shortage, this process can even lead to population extinction, since the investment in competition exceeds the value of the resources.”

“Extreme care is required when transferring insights from a simple evolutionary model to humans“, says Franjo Weissing from the University of Groningen. “Our article therefore does not say too much about competitiveness in humans. However, also in humans there is huge diversity in competitiveness, and individuals with highest competitive ability often seem least prudent in the exploitation of their resources. It is therefore tempting to speculate that the external stimulation of competitiveness by societal pressure, which is analogous to the stimulation of competitiveness by the female preferences in our model, can lead to such a wastage of resources that our future survival is threatened.”

Universität Bonn