Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

GigaScience
Zhijin LiuMing Li

Abstract

The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species' natural distribution. Populations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125.8 to 51.3 thousand years ago, but feature recent gene flow. Consistent with the expectation of a larger body size in colder climates and smaller body size in warmer climates (Bergman's rule), the northernmost RM lineage (M. m. tcheliensis), possessing the largest body size of all Chinese RMs, and the southernmost lineage (M. m. brevicaudus), with the smallest body size of all Chinese RMs, feature positively selected genes responsible for skeletal development. Further, two candidate selected genes (Fbp1, Fbp2) found in M. m. tcheliensis are involved in gluconeogenesis, potentially maintaining stable blood glucose levels during starvation when food resources are scarce in winter. The tropical subspecies M. m. brevicaudus showed positively selected ...Continue Reading

References

Feb 15, 2001·Genesis : the Journal of Genetics and Development·A RuvinskyF Costantini
Apr 12, 2002·Biochemical and Biophysical Research Communications·Ko-ichi MorimotoTakuji Shirasawa
Aug 5, 2003·Evolution; International Journal of Organic Evolution·Anthony J TosiDon J Melnick
Aug 7, 2004·Bioinformatics·J C BarrettM J Daly
Mar 17, 2006·Current Psychiatry Reports·Danielle M Dick, Laura J Bierut
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Aug 30, 2008·Physiological Genomics·Robert E DrewBarrie D Robison
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 3, 2009·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Shannon FlynnDavid Glenn Smith
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Oct 21, 2010·Cellular Signalling·Beth BragdonAnja Nohe
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jan 10, 2012·Experimental Physiology·José González-Alonso
Apr 19, 2012·American Journal of Primatology·H Michael KubischDonald E Franke
Aug 30, 2012·Proceedings of the National Academy of Sciences of the United States of America·Sen SongShaoyuan Wu
Jul 5, 2013·Nature·Javier Prado-MartinezTomas Marques-Bonet
Nov 10, 2013·PLoS Genetics·Laurent ExcoffierMatthieu Foll
Jun 24, 2014·Trends in Genetics : TIG·Tanja HausChristian Roos
Jul 9, 2014·Annual Review of Genomics and Human Genetics·Laure SégurelMolly Przeworski
Aug 12, 2014·Bioinformatics·Julia Chifman, Laura Kubatko
Dec 3, 2014·Trends in Genetics : TIG·Qi Zhou
Jun 13, 2015·Nature·Morten E AllentoftEske Willerslev

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA345528

Methods Mentioned

BETA
PCA

Key Resources (RRID) Mentioned

SCR_010910
SCR_002105
SCR_006525
SCR_001876
SCR_012821
SCR_004965
SCR_014931
SCR_001235
SCR_001881

Software Mentioned

PSMC
FigTree
SAMtools
SAM
ClinVar
smartPCA
HGMD
liftOver
Sequence Alignment / Map
fastsimcoal2

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.