1Anthropology, Pennsylvania State University, 2Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, 3Anthropology, University of Massachusetts Amherst, 4Biology, Pennsylvania State University, 5Mention Anthropobiologie et Developpement Durable, University of Antananarivo, 6Geology and Anthropology, University of Cincinnati, 7Anatomy, Midwestern University, 8Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 9Anthropology and Animal Biology, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, 10Biology and Evolutionary Anthropology, Duke University, 11Conservation Genetics, Omaha’s Henry Doorly Zoo and Aquarium, 12Anthropology, National Museum of Natural History, Smithsonian Institution, 13Huck Institutes of the Life Sciences, Pennsylvania State University
April 17, 2020 2:15PM, Diamond 3
The extinction of megafauna on Madagascar over the past millennium has substantially impacted the island’s biodiversity, for example with no surviving endemic animals having average body masses >10kg. Morphological and isotopic analyses of ‘subfossil’ skeletal remains have helped reconstruct aspects of the biology and behavioral ecology of some of these extinct taxa; yet much remains unknown and uncertainty lingers over particular phylogenetic relationships. As a complementary information source, we generated a nuclear paleogenome sequence (~2x coverage) from the extinct subfossil lemur Megaladapis edwardsi (~85 kg body mass). To test among the various competing phylogenetic hypotheses for this taxon, we also needed to generate nuclear genome sequences for two additional extant lemurs, Eulemur rufifrons and Lepilemur mustelinus. All of these data were then integrated with published sequences from three other lemurs and 46 non-lemur vertebrates. Our phylogenetic results confirm that M. edwardsi is most closely related to the Lemuridae (represented by E. rufifrons in our analysis); this grouping is supported by 567 out of 771 (74%) gene trees. Meanwhile, our evolutionary analyses identified significant enrichments for convergent amino acid evolution between M. edwardsi and extant folivores and herbivores in genes whose protein products degrade plant toxins (with two-toed sloth for “scavenger receptor activity”, FDR=0.0018; with a colobine monkey for “hydrolase activity”, FDR=0.00535) and absorb nutrients from the breakdown of plant fibers (with horse for “brush border”, FDR=0.00216), respectively. Thus, our paleogenomic results are consistent with inferences from various prior non-genomic analyses in suggesting that M. edwardsi was likely a specialist folivore.
NSF (BCS-1317163, G.P.; BCS-1750598, L.R.G.), Ahmanson Foundation (E.E.L.)