title: Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis).
abstract: BACKGROUND
  Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon's range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.
  
  
  RESULTS
  Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.
  
  
  CONCLUSIONS
  Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.
authors.affiliation: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. rliedigk@gmx.de.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Liedigk
authors.affiliation: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. j.kolleck@gmx.net.
authors.forename: Jakob
authors.initials: J
authors.lastname: Kolleck
authors.affiliation: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. KBoeker@dpz.eu.|Junior Research Group Medical RNA Biology, Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. KBoeker@dpz.eu.
authors.forename: Kai O
authors.initials: KO
authors.lastname: Böker
authors.affiliation: Borneo Futures Project, People & Nature Consulting International, Country Woods house 306, JL. WR Supratman, Pondok Ranji, Ciputat, 15412, Jakarta, Indonesia. emeijaard@gmail.com.|School of Archaeology & Anthropology, Building 14, Australian National University, Canberra, ACT 0200, Australia. emeijaard@gmail.com.|School of Biological Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia. emeijaard@gmail.com.
authors.forename: Erik
authors.initials: E
authors.lastname: Meijaard
authors.affiliation: School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. abgbadd1966@yahoo.com.
authors.forename: Badrul Munir
authors.initials: BM
authors.lastname: Md-Zain
authors.affiliation: School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. abdullatiff12@yahoo.com.
authors.forename: Muhammad Abu Bakar
authors.initials: MA
authors.lastname: Abdul-Latiff
authors.affiliation: Sarawak Forest Department Hq, Wisma Sumber Alam Jalan Stadium, 93660, Petra Jaya Kuching, Sarawak, Malaysia. ahmada@sarawak.gov.my.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Ampeng
authors.affiliation: Sabah Parks, Research and Education Division, PO Box 10626, 88806, Kota Kinabalu, Sabah, Malaysia. maklarinlakim@gmail.com.
authors.forename: Maklarin
authors.initials: M
authors.lastname: Lakim
authors.affiliation: Department of Wildlife and National Parks, Km 10, Jalan Cheras, 50664, Kuala Lumpur, Malaysia. fadzilns9@gmail.com.
authors.forename: Pazil
authors.initials: P
authors.lastname: Abdul-Patah
authors.affiliation: Department of Anthropology, Kent State University, 238 Lowry Hall, Kent, OH, 44242, USA. atosi@kent.edu.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Tosi
authors.affiliation: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. brameier@dpz.eu.
authors.forename: Markus
authors.initials: M
authors.lastname: Brameier
authors.affiliation: Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. dzinner@gwdg.de.
authors.forename: Dietmar
authors.initials: D
authors.lastname: Zinner
authors.affiliation: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. croos@dpz.eu.|Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. croos@dpz.eu.
authors.forename: Christian
authors.initials: C
authors.lastname: Roos
mesh_terms: D000818:Animals; D001208:Asia; D001210:Asia, Southeastern; D054629:Genome, Mitochondrial; D008252:Macaca fascicularis / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA