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International Team Uses Phylogenomic Approach to Explain the When and How of Insect Evolution

NEW YORK (GenomeWeb) – A new phylogenomic study has provided the most comprehensive picture of the insect family tree to date, pinning down when and how insect species diverged from one another.

Using genomic techniques, along with novel bioinformatics methods, scientists led by Bernhard Misof of the University of Bonn in Germany, Xin Zhou of the Beijing Genomics Institute, and Karl Kjer from Rutgers University put together a comprehensive account of insect evolution, which was published this week in Science. What they found corroborated many existing hypotheses including when insects first appeared and when they first evolved the ability to fly.

A phylogenomic approach posed challenges right away. Sequencing transcriptomes meant that the scientists couldn't use museum samples and had to collect fresh ones, Misof said. Sequencing was done with standard techniques, but analyzing the data required several innovations in bioinformatics.

"Virtually every step in the pipeline was completely redesigned in order to efficiently handle data of this size, which had never been seen before," Kjer said.

For example, the Chinese group, led by Zhou, completely redesigned the assembly process, writing new software to account for gene isoforms. The German group, led by Misof, developed innovative ways of analyzing protein domains as subdivisions of the data, rather than genes. And the RAxML phylogenetics software — the only program that could load the data without crashing — had to be extensively modified.

The international collaboration, called the 1,000 Insect Transcriptome Evolution project, used Illumina paired end sequencing to analyze more than 2.5 gigabases of cDNA in 1,478 protein-coding genes from the transcriptomes of 144 different species representing all the extant orders of insects.

The genes represent only a fraction of insect genomes, "but it's an interesting fraction, the fraction you can really compare among all species," Misof told GenomeWeb.

The researchers found that approximately 98 percent of the genes analyzed in the study were found in the transcriptomes of all 144 sample species, indicating that they are housekeeping genes that determine cellular function, conserved throughout insect evolutionary history.

By analyzing the genetic drift in these housekeeping genes, the researchers put together a robust phylogenetic tree showing the diversity of insects—over 1 million named insect species with likely millions still undiscovered. Then, using BEAST dating software, the scientists were able to assign dates to the divergences that led to that diversity with greater precision than ever before.

According to the publication, insects first emerged around 479 million years ago, during the Early Ordovician period, around the time that plants began to colonize land. It was at this time that insects diverged from their next closest cousins, crustaceans.

A milestone event for insects was the development of winged flight. Today, the vast majority of insect species have wings. The fossil record shows clear evidence of winged insects by 324 million years ago, but some entomologists have speculated, on the basis of an incomplete fossil showing only a mandible, that winged insects were around as early as 412 million years ago. The new phylogenomic analysis corroborates this earlier date, Misof said, placing the emergence of winged insects around 400 to 420 million years ago.

"Most of what our study tells us is that the morphologists of the 1960s and 70s, like Hennig and Kristensen, got it right. This is not so much a revolution, as a confirmation, and that is a testament to the skill of morphologists before us," Kjer, a professor of entomology at Rutgers and an author on the paper, said in an email to GenomeWeb. "Phylogenetics done right often confirms previous good work."

He added, "The methods we all developed should set the stage for the way 'big data' is handled," in evolutionary biology.