title: Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulans.
abstract: Commensal plants and animals have long been used to track human migrations, with Rattus exulans (the Pacific rat) a common organism for reconstructing Polynesian dispersal in the Pacific. However, with no knowledge of the homeland of R. exulans, the place of origin of this human-commensal relationship is unknown. We conducted a mitochondrial DNA phylogeographic survey of R. exulans diversity across the potential natural range in mainland and Island Southeast Asia in order to establish the origin of this human-commensal dyad. We also conducted allozyme electrophoresis on samples from ISEA to obtain a perspective on patterns of genetic diversity in this critical region. Finally, we compared molecular genetic evidence with knowledge of prehistoric rodent faunas in mainland and ISEA. We find that ISEA populations of R. exulans contain the highest mtDNA lineage diversity including significant haplotype diversity not represented elsewhere in the species range. Within ISEA, the island of Flores in the Lesser Sunda group contains the highest diversity in ISEA (across all loci) and also has a deep fossil record of small mammals that appears to include R. exulans. Therefore, in addition to Flores harboring unusual diversity in the form of Homo floresiensis, dwarfed stegodons and giant rats, this island appears to be the homeland of R. exulans.
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Vicki
authors.initials: V
authors.lastname: Thomson
authors.affiliation: Division of Mammals, United States National Museum, Smithsonian Institution, Washington D.C., United States of America, and Department of Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory, Australia.
authors.forename: Ken P
authors.initials: KP
authors.lastname: Aplin
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
authors.affiliation: Austin Academic Centre, The University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Susan
authors.initials: S
authors.lastname: Hisheh
authors.affiliation: Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: Zoology Division, Research Centre for Biology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia.
authors.forename: Ibnu
authors.initials: I
authors.lastname: Maryanto
authors.affiliation: Environmental Health Institute, National Environment Agency, Singapore, Singapore.
authors.forename: Grace
authors.initials: G
authors.lastname: Yap
authors.affiliation: South Australian Museum, Adelaide, South Australia, Australia, and Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Donnellan
mesh_terms: D000818:Animals; D045303:Cytochromes b / Q000235:genetics; D066264:Datasets as Topic; D019143:Evolution, Molecular; D005828:Genetics, Population; D006239:Haplotypes; D007527:Isoenzymes; D008969:Molecular Sequence Data; D009115:Muridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
chemical_list: D007527:Isoenzymes; D045303:Cytochromes b