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Population genetics of wild Macaca fascicularis with low‐coverage shotgun sequencing of museum specimens


Yao, Lu; Witt, Kelsey; Li, Hongjie; Rice, Jonathan; Salinas, Nelson R; Martin, Robert D; Huerta‐Sánchez, Emilia; Malhi, Ripan S (2020). Population genetics of wild Macaca fascicularis with low‐coverage shotgun sequencing of museum specimens. American Journal of Physical Anthropology, 173(1):21-33.

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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Institute of Evolutionary Medicine
Dewey Decimal Classification:610 Medicine & health
Scopus Subject Areas:Health Sciences > Anatomy
Social Sciences & Humanities > Anthropology
Uncontrolled Keywords:Anatomy, Anthropology
Language:English
Date:1 September 2020
Deposited On:26 Nov 2020 16:43
Last Modified:27 Nov 2020 21:01
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:0002-9483
OA Status:Closed
Publisher DOI:https://doi.org/10.1002/ajpa.24099
PubMed ID:32643146

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