@article{5a266dec4ed54d24896a560fe56b1dff,
title = "Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens",
abstract = "Objectives: Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. Methods: We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. Results: We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. Conclusions: Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.",
keywords = "Macaca, Southeast Asia, long-tailed macaque, next-generation sequencing, nuclear DNA, phylogeography",
author = "Lu Yao and Kelsey Witt and Hongjie Li and Jonathan Rice and Salinas, {Nelson R.} and Martin, {Robert D.} and Emilia Huerta-S{\'a}nchez and Malhi, {Ripan S.}",
note = "Funding Information: We are thankful for the kind cooperation from the following individuals for providing access to their respective museum collections for dried tissues: the late William Stanley and Dr. Lawrence Heaney at The Field Museum of Natural History (FMNH), Eileen Westwig and Neil Duncan at the American Museum of Natural History (AMNH), Darrin P. Lunde at the Smithsonian Institution National Museum of Natural History (NMNH) and Pepijn Kamminga and Steven van der Mije at the Naturalis Biodiversity Center (Leiden, Netherlands). We would also like to acknowledge the reviewers for their efforts in revising this article. Data collection, sample preparation, and sequencing were previously supported by the NSF DDIG DEB-1501733 to Robert D. Martin and Lu Yao, grants to Lu Yao (NSF GRFP 100152161, The Field Museum Women-in-Science Graduate Fellowship, Arts and Science Fund from the Arts, Science and Culture Initiative at University of Chicago, and Hinds Fund Award, Field Museum Pritzker Lab Award, and Travel Award from the Committee on Evolutionary Biology at University of Chicago), research funding from The Field Museum to Robert D. Martin and research funds from the University of Illinois Urbana-Champaign to Ripan S. Malhi. The remainder of this research was supported by the Gerstner Postdoctoral Fellowship at the American Museum of Natural History to Lu Yao. Kelsey E. Witt and Emilia Huerta-Sanchez were funded by NSF award #1557151 and NIH award #1R35GM128946-01. Funding Information: We are thankful for the kind cooperation from the following individuals for providing access to their respective museum collections for dried tissues: the late William Stanley and Dr. Lawrence Heaney at The Field Museum of Natural History (FMNH), Eileen Westwig and Neil Duncan at the American Museum of Natural History (AMNH), Darrin P. Lunde at the Smithsonian Institution National Museum of Natural History (NMNH) and Pepijn Kamminga and Steven van der Mije at the Naturalis Biodiversity Center (Leiden, Netherlands). We would also like to acknowledge the reviewers for their efforts in revising this article. Data collection, sample preparation, and sequencing were previously supported by the NSF DDIG DEB‐1501733 to Robert D. Martin and Lu Yao, grants to Lu Yao (NSF GRFP 100152161, The Field Museum Women‐in‐Science Graduate Fellowship, Arts and Science Fund from the Arts, Science and Culture Initiative at University of Chicago, and Hinds Fund Award, Field Museum Pritzker Lab Award, and Travel Award from the Committee on Evolutionary Biology at University of Chicago), research funding from The Field Museum to Robert D. Martin and research funds from the University of Illinois Urbana‐Champaign to Ripan S. Malhi. The remainder of this research was supported by the Gerstner Postdoctoral Fellowship at the American Museum of Natural History to Lu Yao. Kelsey E. Witt and Emilia Huerta‐Sanchez were funded by NSF award #1557151 and NIH award #1R35GM128946‐01. Funding Information: American Museum of Natural History, Grant/Award Number: Gerstner Postdoctoral Fellowship; Field Museum, Grant/Award Numbers: Pritzker Lab Award, Women‐in‐Science Graduate Fellowship; Foundation for the National Institutes of Health, Grant/Award Number: 1R35GM128946‐01; National Science Foundation, Grant/Award Numbers: DEB‐1557151, DDIG DEB‐1501733, GRFP 100152161; University of Chicago, Grant/Award Numbers: Arts and Science Fund from the Arts, Hinds Fund Award, Travel Award from the Committee on Evolutionary Biology Funding information Publisher Copyright: {\textcopyright} 2020 Wiley Periodicals LLC",
year = "2020",
month = sep,
day = "1",
doi = "10.1002/ajpa.24099",
language = "English (US)",
volume = "173",
pages = "21--33",
journal = "American journal of physical anthropology",
issn = "0002-9483",
publisher = "Wiley-Liss Inc.",
number = "1",
}