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Gliding Mammal Genome Reveals Primate Sister Group


NEW YORK (GenomeWeb) – A study appearing online today in Science Advances suggests that a group of gliding mammals from Southeast Asia are part of a primate sister group.

Researchers from Texas A&M University, the National Museum of Natural History's Smithsonian Institution, and elsewhere put together a draft genome assembly for a colugo representative from West Java, in an effort to resolve the creature's place in the animal family tree.

In the past, there has been a debate over whether the two known colugo species are more closely related to bats, treeshrews, primates, or other animal groups. With this genome sequence, and targeted sequencing on samples from dozens of colugo museum specimens, the team concluded that colugos are primates' closest living relatives, despite their physical resemblance to treeshrews.

"Our results imply that any morphological similarities shared by colugos and treeshrews are due to convergent evolution or represent primitive characters lost in the primate ancestor," co-corresponding author William Murphy, a genetics researcher at Texas A&M, and his colleagues wrote.

There are two known colugo species: the Sunda colugo, Galeopterus variegatus, and the Philippine colugo, Cynocephalus volans. Sometimes called flying lemurs, they are the only living representatives of the Dermoptera order. Beyond that, however, the tree-dwelling, gliding mammals have been tricky to classify taxonomically, in part due to the lack of captive colugos.

"[E]volutionary questions surrounding dermopteran origins and taxonomic diversity remain unresolved, despite their importance to the interpretation of early primate origins and evolution, and to developing effective conservation strategies, respectively," the study's authors wrote.

The researchers used Illumina instruments to sequence DNA from a male Sunda colugo from West Java, covering the genome to an average 55-fold coverage. With these reads, they put together a 3.2 billion-base draft genome assembly for the colugo, annotated with the help of colugo RNA sequences from a sequence read archive. The team identified 23,081 predicted protein-coding genes in the genome, which they compared to sequences from several other mammals and to a lower-coverage genome assembly for a male Philippine colugo.

A phylogenetic analysis based on data for species from eight eutherian mammal orders suggested that colugos fall into a primate sister group, with treeshrews in an outgroup, while the researchers' comparative genomic analyses offered hints about specific adaptations in the colugo lineage.

For example, the team saw signs of positive selection affecting genes related to vision and hearing in the colugos, which are nocturnal. Using the colugo for comparison, on the other hand, the researchers picked up brain-related genes that have undergone positive selection in the primate lineage since the split from the colugo group.

To untangle the population history of the colugos, meanwhile, the investigators relied on targeted autosomal, Y chromosome, and mitochondrial DNA sequencing on 66 museum specimens from colugos collected anywhere from 28 to 121 years ago. Along with insights into colugo differentiation in relationship to past changes to biogeography in Southeast Asia, the analysis suggested that there may be multiple colugo species within the Sundaic and Philippine lineages.

The results "have far-reaching implications for the conservation of Sunda and Philippine colugos," the authors wrote. "[W]e present concordant mitochondrial and nuclear genetic evidence for seven to eight colugo lineages that should be recognized as evolutionarily significant units or even distinct species deserving a conservation management strategy."