Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulans

PLoS One. 2014 Mar 17;9(3):e91356. doi: 10.1371/journal.pone.0091356. eCollection 2014.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cytochromes b / genetics
  • Datasets as Topic
  • Evolution, Molecular
  • Genetics, Population
  • Haplotypes
  • Isoenzymes
  • Molecular Sequence Data
  • Muridae / classification
  • Muridae / genetics*
  • Phylogeny


  • Isoenzymes
  • Cytochromes b

Associated data

  • GENBANK/KJ155750
  • GENBANK/KJ155751
  • GENBANK/KJ155752
  • GENBANK/KJ155753
  • GENBANK/KJ155754
  • GENBANK/KJ155755
  • GENBANK/KJ155756
  • GENBANK/KJ155757
  • GENBANK/KJ155758
  • GENBANK/KJ155759
  • GENBANK/KJ155760
  • GENBANK/KJ155761
  • GENBANK/KJ155762
  • GENBANK/KJ155763
  • GENBANK/KJ155764
  • GENBANK/KJ155765
  • GENBANK/KJ155766
  • GENBANK/KJ155767
  • GENBANK/KJ155768
  • GENBANK/KJ155769
  • GENBANK/KJ155770
  • GENBANK/KJ155771
  • GENBANK/KJ155772
  • GENBANK/KJ155773
  • GENBANK/KJ155774
  • GENBANK/KJ155775
  • GENBANK/KJ155776
  • GENBANK/KJ155777
  • GENBANK/KJ155778
  • GENBANK/KJ155779
  • GENBANK/KJ155780
  • GENBANK/KJ155781
  • GENBANK/KJ155782
  • GENBANK/KJ155783

Grant support

A National Geographic Society Exploration Grant provided funding for the vertebrate fauna survey in eastern Indonesia, and the Australian Centre for International Agricultural Research and AUSAid provided funding for fieldwork in the agricultural landscapes of Southeast Asia. The study was partially funded from Australian Research Council grant DP0988863 to SCD and KPA. VT was supported by an Australian post-graduate award. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.