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"1KITE" project to unravel the evolution of insects

The large international “1K Insect Transcriptome Evolution” research project aims to construct a robust phylogenetic tree of insects, which is the most species-rich group of organisms. The project aims to study the transcriptomes of 1000 (1K) insect species. The Heidelberg-based Institute for Theoretical Studies provides the software for producing the phylogenetic trees.

Researchers from eight countries – Germany, China, USA, Austria, Japan, Australia, New Zealand and Mexico – have joined forces in a unique interdisciplinary project that aims to unravel the evolution of insects, which is the most species-rich group of organisms. Using next-generation sequencing technologies and new computer programmes, the 1KITE researchers are studying the transcriptomes, i.e. the entirety of expressed genes, by producing so-called ESTs (expressed sequence tags) for each of the 1000 species under investigation. Gene sequences as well as data gathered in the fields of morphology, embryology, molecular biology, taxonomy and palaeontology will be used to determine the phylogenetic relationship of the insect species.

Prof. Dr. Bernhard Misof, head of the Centre for Molecular Biodiversity Research at the Alexander Koenig Zoological Research Museum (ZFMK) in Bonn, is one of three spokespersons for the interdisciplinary project. The 1KITE secretarial office is also located in the ZFMK from where the collection and selection of the insect groups to be investigated is coordinated. The other two spokespersons are Prof. Dr. Karl Kjer, entomologist at Rutgers University in New Brunswick, NJ, USA, and Prof. Xin Zhou from the Beijing Genomics Institute in Shenzhen, China who is in charge of sequencing the insect transcriptomes. Renowned experts at the fifteen research institutions involved in 1KITE deal with specific systematic groups and phylogenetic issues.

Dr. Alexandros (Alexis) Stamatakis in the HITS garden © HITS

The “Scientific Computing” research group led by Dr. Alexandros Stamatakis at the Heidelberg Institute for Theoretical Studies (HITS) will calculate the phylogenesis of the 1000 insect species using high-performance computers and software developed by group members. As one of the coordinators of the 1KITE project, Stamatakis is also responsible for the development of new bioinformatic methods. He points out that “the production of new data has gained such an enormous speed recently, that the analysis and storage of the data will become the real challenge in the near future.”

Attempting to unravel the secrets of the evolutionary history of insects

Head of a male damselfly (Coenagrion) with huge eyes. © Johannes Dambach, ZFMK

Nobody really knows how many insect species exist. At the International Entomologist Congress in Brazil in 2000, a survey was carried out among the leading insect researchers (entomologists) asking them to estimate the number of insect species on earth. The majority of entomologists estimated the number of insect species at between eight and fifteen million. They also believed that the vast majority of insect species, i.e. at least 90 per cent, are not yet known. Asked to estimate the number of known species, the scientists came up with figures of between 800,000 and 1.2 million. However, this difference is not due to an inability to count or chaos in the archives. Instead, it is down to the increasing lack of experts who have the knowledge required to manage insect collections, distinguish known from unknown species and determine whether a species has been described twice. In addition, the few scientists who are capable of doing all this are confronted with the constantly growing flood of alleged new discoveries from which they have to identify and describe the species that really are new. 

Computers are an absolute prerequisite for calculating phylogenetic relationships between large systematic groups, and a broad range of phylogenetic software programmes is available to produce phylogenetic trees. The criteria according to which phylogenetic trees are produced have been a matter of controversial debate, but discussions have become less polemic as the methods used are continuously being optimized. Stamatakis and his group of researchers, for example, use the maximum likelihood method for producing phylogenetic trees. The maximum likelihood method evaluates a specific hypothesis about the evolutionary history of a group of species in terms of the probability of the proposed model giving rise to the observed data set. Stamatakis has named the Scientific Computing group’s laboratory at the HITS “Exelixis”, which is Greek for evolution. According to Stamatakis, his group of researchers is trying to “close the gap (ed. note: he calls this the “bio-gap”) between the world of systematics and the world of high-performance computing.”

How phylogenetic trees are produced

Sminthurae spec. (springtails of the Collembola order) are wingless insects around 1 mm in size. © Discoverlife.org

Genome sequences are excellently suited for producing phylogenetic trees as they are distinct quantifiable features. The sequences or genome arrangements used for the production of phylogenetic trees need to be long enough for an accidental agreement (convergence) to be excluded as far as possible. The 1KITE project predominantly uses sequences of modern (i.e. living) species for analyzing the phylogenetic relationship of the insects, but also needs to include fossils in the calculations in order to be able to produce the actual or most probable phylogenetic tree and determine the time frame in which evolution has taken place. Palaeontological evidence is also used to calibrate “molecular clocks”. The molecular clock is a technique that uses rates of molecular change (mutations) to deduce the time in geologic history when two species/taxa diverged.

Although computers and powerful phylogenetic software facilitate the search for the correct phylogenetic tree, it is nevertheless difficult and only possible by making numerous assumptions. Professor Dr. Michael Wink from the University of Heidelberg explains in his introduction to molecular evolutionary research (in V. Storch, U. Welsch, M. Wink: Evolutionsbiologie, Springer Verlag 2007): “The sequences of 50 species can theoretically produce 2.8 x 1074 phylogenetic trees, which is much more than the number of atoms found in the universe… As it is so complex, the mathematical procedures have to be simplified and the possible combinations have to be reduced from the very beginning.” Computer simulations are nevertheless the tools of choice for a highly reliable reconstruction of the evolution of the insects, in particular when simplifying assumptions are based on the knowledge and experience of evolutionary experts. 

How did the insect wing develop?

One of the greatest issues 1KITE hopes to clarify relates to the evolution of modern winged insects (Pterygota) from wingless forms. The phylogenetic relationship of five groups of these small, rather inconspicuous “basal hexapods” is not yet well understood. The best-known representatives include springtails, which are frequently found alongside brooks and look like bouncing blackish spots, as well as bristletails that are the unwanted guests in dark corners of kitchens and kitchen cupboards. Springtail and bristletail fossils date back to the Devonian period, and are estimated to have lived around 400 million years ago. Their morphology has barely changed since the time when the plants moved from the water to the land, and can therefore rightly be called “living fossils”.

Nemoptera bipennis is a species of insect in the Neuropteridae famiy (spoonwings); it has butterfly-like wings. © Ekkehard Wachmann, ZFMK

Insects with wings are evolutionarily younger and date back to the Carboniferous (362 to 290 million years ago) period. Representatives include dayflies and dragonfly-like insects as well as insect species that are still found today, including cockroaches, locusts and snakeflies. No transitional insect forms have been found that would have linked wingless with winged insects. It did not come as a surprise that this missing link was promptly picked up by creationists and used as evidence against evolution. Insect researchers have long debated whether insect wings developed from thoracic protrusions or whether they are modifications of movable abdominal gills like those found on aquatic arthropods. Insights into the genetics and embryonic development of primitive flying insects and the discovery of a fossil of a primitive aquatic nymph with wing-like gills in all thoracic segments dating from around 300 years ago have since convinced the majority of scientists of the validity of the “gill theory”. It is expected that further evidence on the origin of insect wings will be obtained from the transcriptome analysis of dragonflies (Odonata), which are regarded as the oldest living member of the Pterygota.

Numerous 1KITE subprojects deal with the phylogenetic relationship within the large Pterygota groups. Until recently, termites were classified as an own taxonomic order related to cockroaches and mantids (insects that develop through incomplete metamorphosis; superorder Dictyoptera), but new research has provided evidence suggesting that termites are a genus of cockroaches. Further unexpected insights into phylogenetic relationships will probably arise when the phylogenetic trees of the individual insect groups have been reconstructed on the basis of the comprehensive datasets available in the 1KITE project.

Biodiversity research

The clarification of the phylogenetic tree and correct classification of the large insect groups are important prerequisites for being able to answer elementary questions related to evolutionary biology, ecology and biodiversity research, which were all identified by the German government as important research priorities in the “International Year of Biodiversity 2010”. The BMBF (German Federal Ministry of Education and Research) and the BMU (German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety) are funding projects on biodiversity research under the “National Strategy on Biodiversity” programme. As part of the so-called Potsdam Initiative, the European Union has commissioned a series of reports on the “Economic significance of the global loss of biological diversity”. The report “The Economics of Ecosystems & Biodiversity” (TEEB) draws attention to the global economic benefits of biodiversity. It also highlights the crucial role of insects for most ecosystems on earth and the need to precisely understand their systematics. Many insect species have a huge economic and medical impact on humans, for example as pollinators of flowering plants, transmitters of diseases, and as pests or predators. It is expected that the 1KITE project will also provide answers to the question as to why insects are so ecologically successful and how their vast species diversity has developed.

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