title: Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.
abstract: Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct 'subfossil' lemur species, all of which were substantially larger (body mass ∼11-160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study subfossil lemur extinction biology and update our understanding of extant lemur conservation risk factors by i) reconstructing a comprehensive phylogeny of extinct and extant lemurs, and ii) testing whether low genetic diversity is associated with body size and extinction risk. We recovered complete or near-complete mitochondrial genomes from five subfossil lemur taxa, and generated sequence data from population samples of two extinct and eight extant lemur species. Phylogenetic comparisons resolved prior taxonomic uncertainties and confirmed that the extinct subfossil species did not comprise a single clade. Genetic diversity estimates for the two sampled extinct species were relatively low, suggesting small historical population sizes. Low genetic diversity and small population sizes are both risk factors that would have rendered giant lemurs especially susceptible to extinction. Surprisingly, among the extant lemurs, we did not observe a relationship between body size and genetic diversity. The decoupling of these variables suggests that risk factors other than body size may have as much or more meaning for establishing future lemur conservation priorities.
authors.affiliation: Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Logan
authors.initials: L
authors.lastname: Kistler
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.affiliation: Department of Anthropology, University of Massachusetts, Amherst, MA 01003, USA.
authors.forename: Laurie R
authors.initials: LR
authors.lastname: Godfrey
authors.affiliation: Department of Geology, University of Cincinnati, Cincinnati, OH 45221, USA; Department of Anthropology, University of Cincinnati, Cincinnati, OH 45221, USA.
authors.forename: Brooke E
authors.initials: BE
authors.lastname: Crowley
authors.affiliation: Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Cris E
authors.initials: CE
authors.lastname: Hughes
authors.affiliation: Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA.
authors.forename: Runhua
authors.initials: R
authors.lastname: Lei
authors.affiliation: Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Yinqiu
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA.
authors.forename: Mindy L
authors.initials: ML
authors.lastname: Wood
authors.affiliation: Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ 85308, USA.
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Muldoon
authors.affiliation: Department of Paleontology and Biological Anthropology, University of Antananarivo, Antananarivo, Madagascar.
authors.forename: Haingoson
authors.initials: H
authors.lastname: Andriamialison
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: McGraw
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Lynn P
authors.initials: LP
authors.lastname: Tomsho
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore.
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.affiliation: Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA.
authors.forename: Edward E
authors.initials: EE
authors.lastname: Louis
authors.affiliation: Duke Lemur Center, Duke University, Durham, NC 27705, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
authors.forename: Anne D
authors.initials: AD
authors.lastname: Yoder
authors.affiliation: Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Ripan S
authors.initials: RS
authors.lastname: Malhi
authors.affiliation: Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: ghp3@psu.edu.
authors.forename: George H
authors.initials: GH
authors.lastname: Perry
mesh_terms: D000818:Animals; D049628:Body Size / Q000235:genetics / Q000502:physiology; D004247:DNA / Q000032:analysis / Q000235:genetics; D053476:Extinction, Biological; D005580:Fossils; D023281:Genomics / Q000379:methods*; D007900:Lemur / Q000145:classification / Q000235:genetics / Q000502:physiology; D008270:Madagascar; D010163:Paleontology / Q000379:methods*; D010802:Phylogeny
chemical_list: D004247:DNA
keywords: Conservation genomics; Extinction genomics; Human–environment interactions; Malagasy biodiversity; Paleogenomics