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New Genomes Bring Clues to Bat Evolution

NEW YORK (GenomeWeb News) – An international team has sequenced two new bat genomes in the hopes of learning more about the mammal's unique biological features — from its ability to fly to its propensity for carrying potentially pathogenic viruses.

The new draft genomes represent the fruit bat Pteropus alecto, known as the Black flying fox, and the insect-eating Myotis davidii, or "David's Myotis" bat — species selected from distant branches of the bat family tree.

"These wonderfully diverse bats are in a special position in the evolutionary processes, and have some fascinating biological characteristics, including sustained flight, hibernation, echolocation, among others," co-first author Guojie Zhang, a project manager at BGI-Shenzhen who is also affiliated with the University of Copenhagen's Centre for Social Evolution, said in a statement.

Findings from the study, presented online today in Science, not only helped researchers place bats within the mammalian lineage, but also revealed some genetic patterns that may help explain the animals' biology and evolutionary history.

For instance, investigators saw signs that positive selection on certain DNA damage checkpoint genes might have contributed to the advent of flight in bats. Moreover, their results hinted that some of the genetic adaptations that reduce the risk of genetic damage by reactive oxygen species produced through flight-related metabolic processes could also have had secondary effects on bat immunity.

"Concentration of positively selected genes in the DNA damage checkpoint in bats may indicate an important step in the evolution of flight," the team wrote, "while evidence of change in components shared by the DNA damage pathway and the innate immune system raises the interesting possibility that flight-induced adaptations have had inadvertent effects on bat immune function and possibly also life expectancy."

Past studies have suggested that positive selection for metabolic genes in the so-called oxidative phosphorylation, or OXPHOS, pathway contributed to the evolution of bat flight, the researchers said. But less is known about the compensatory changes that could have accompanied this apparent metabolic shift or about ways in which immunity-related bat genes have been molded over time.

"Bats are the only mammals capable of sustained flight," they noted, "and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS)."

For the current study, researchers put together high-quality draft assemblies of the P. alecto and M. davidii bat genomes, estimated to have around two billion bases apiece, by generating about 100-fold average coverage of each genome using DNA from wild bats and Illumina's HiSeq 2000 instrument.

Each of the genomes contained a comparable number of predicted protein-coding genes, the team reported. For the fruit bat, P. alecto, investigators found an estimated 21,392 genes, while the insectivorous M. davidii bat genome apparently houses 21,705 genes.

The investigators' window into bat phylogeny came when they stacked up orthologous nuclear genes found in single copies in the new bat genomes and in the genomes of the human, rhesus macaque, mouse, rat, dog, cat, cattle, and horse.

Using this set of nearly 2,500 mammalian genes, they found evidence that bats belong to a lineage that shared a common ancestor with horses until roughly 88 million years ago.

However, phylogenetic analyses based on mitochondrial sequence data told a slightly different story, placing bats outside of their usual clade — an inconsistency that study authors attributed to especially speedy evolution in the bat mitochondrial genome, perhaps related to the advent of flight in these mammals.

When they narrowed in on genes from pathways with potential ties to the evolution of OXPHOS-dependent flight and/or extensive viral exposure, meanwhile, the researchers uncovered certain genes that seem to have been subjected to positive selective pressures in both bat species. But other genes showed signs of positive selection in only one of the two bat species.

On the flight front, there's evidence that DNA damage checkpoint and DNA repair genes, such as RAD50 and ATM, were subject to positive selection in a shared bat ancestor, they reported, as were certain genes involved in skin elasticity and muscle contraction.

The team's analysis suggested that positive selection for DNA damage response genes may also have helped animals in the bat lineage ward off some of the negative effects of viruses, as did selection for other components of innate and adaptive immune pathways, including genes that interact with the NF-kappa-beta transcription factor family.

On the other hand, both new bat genomes were missing some of the genes tasked with sensing and responding to microbial pathogens in other mammals, consistent with the notion that certain features of bat immunity are distinct from those in other animals.

Differences in immune genes turned up between the bat species, too, as did species-specific patterns involving genes expected to influence the bats' digestion, hibernation, and echolocation capabilities.

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