The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)


Ancient DNA genomics of Madagascar’s extinct subfossil lemurs: Palaeopropithecus ingens genetic diversity

GEORGE PERRY1, LOGAN KISTLER1, CRIS HUGHES2, YINQUI CUI2, AAKROSH RATAN3, BROOKE E. CROWLEY4, LAURIE R. GODFREY5, RUNHUA LEI6, STEPHAN SCHUSTER3, EDWARD LOUIS6, ANNE YODER7,8, RIPAN MALHI2 and WEBB MILLER3.

1Department of Anthropology, Penn State University, 2Department of Anthropology, University of Illinois Urbana-Champaign, 3Center for Comparative Genomics and Bioinformatics, Penn State University, 4Departments of Geology and Anthropology, University of Cincinnati, 5Department of Anthropology, University of Massachusetts, 6Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, 7Duke Lemur Center, Duke University, 8Departments of Biology and Evolutionary Anthropology, Duke University

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With ~100 extant taxa, lemurs are one of the most diverse faunal groups of Madagascar. Yet lemur diversity was even greater prior to the arrival of humans on the island ~2,300 years before present (ybp). From unmineralized skeletal remains, we know of at least 17 “subfossil” lemur species that went extinct between 2,000 and <500 ybp. All extinct subfossil taxa were larger than any extant lemur; humans probably contributed to their extinction through hunting and habitat changes. We are using ancient DNA techniques and massively parallel sequencing to study subfossil lemur extinction biology by estimating genetic diversity and characterizing temporal changes in effective population size, and by making comparisons to extant lemurs. To date, we have sequenced the complete mtDNA genomes of four Palaeopropithecus ingens individuals from two sites. Surprisingly, our preliminary estimate of P. ingens mtDNA diversity (pi=1.8%; accounting for DNA damage) is relatively high compared to our estimates for the largest-bodied extant lemurs, Indri indri (n=10; pi=0.5%), diademed sifaka (Propithecus diadema; n=10; pi=1.3%), and Milne-Edwards’ sifaka (Propithecus edwardsi; n=10; pi=0.7%), each sampled from multiple sites. This difference cannot readily be explained by temporal variance among the Palaeopropithecus ingens samples, as all individuals were estimated to have lived within ~150 years of each other (1,486-1,330 ybp). While these results are preliminary, they suggest that the female effective population size of this subfossil species may have been higher than that of many extant lemurs. Thus, low historical population size may not be a principal extinction risk factor for lemurs.

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