Biomedical Engineering Reference
In-Depth Information
the genome. The genetic characterization of colonies of
rhesus macaques has led to the identification of genotypes
at particular loci that are optimal in research subjects in the
study of particular diseases. A working group (WG) of the
National Nonhuman Primate Research Consortium,
the Genetics and Genomics WG, was formed in 2008 under
the auspices of the NCRR to develop panels of SNPs and
other genetic resources for the analysis of genetic data for
genetic management and genomic research of captive
colonies of rhesus macaques bred for biomedical research
at the eight National Primate Research Centers in the USA
(
Kanthaswamy et al., 2009
).
SNPs are far more numerous in the genome, provide
closely linked markers for any gene of interest, less
frequently reflect homoplasy, and are easier, and cheaper, to
genotype in large numbers (albeit, exhibiting lower levels
of heterozygosity) than STRs. The higher diversity in
Chinese than in Indian rhesus macaques, recently
confirmed in a study of approximately 1500 SNPs identi-
fied in ENCODE regions (
Hernandez et al., 2007
), is
consistent with additional evidence of a recent expansion of
Chinese rhesus, a recent genetic bottleneck in Indian rhe-
sus, and significantly greater linkage disequilibrium in
Indian than in Chinese macaques reported in that same
study.
Hernandez et al. (2007)
estimated that Indian and
Chinese rhesus macaques diverged from each other
approximately 160 000 ybp, soon after the end of the
penultimate glacial maximum, which might have isolated
the western-most rhesus macaques in a wet-zone refugium
between India and Burma. However, studies of an even
larger number of SNPs, predominantly in noncoding
regions distant from genes and randomly and evenly
distributed (approximately 0.85 Mb) throughout the rhesus
genome, reveal slightly higher levels of genetic diversity in
Indian than in Chinese rhesus macaques and minimal
genetic subdivision between eastern and western Chinese
rhesus macaques as was inferred from mtDNA and STR
loci (
Satkoski et al., 2008b
). It is likely that selection
operating on coding regions of the rhesus genome influ-
enced the study of
Hernandez et al. (2007)
and explains the
conflicting results with the study of
Satkoski et al. (2008b)
that employed predominantly SNPs outside coding regions.
Fewer studies of regional variation among relatively
large samples of populations of longtail macaques have
been done. However, several studies of relatively small
populations indicate a fundamental difference between
insular (e.g. Indonesia) and mainland (e.g. IndoChina)
longtail macaques (
Harihara et al., 1988; Tosi and Coke,
2006; Stevison and Kohn, 2008
), with a barrier at the
Isthmus of Kra (
Tosi et al. (2002)
, in general conformance
to the taxonomic distinctions between M. f. fascicularis and
M. f. aureus. There was a paucity of genetic diversity in
longtail macaques from Mauritius (
Kondo et al., 1993;
Lawler et al., 1995
). More recent studies of mtDNA (
Smith
et al., 2007; Blancher et al., 2008
) and microsatellite
polymorphisms (
Kanthaswamy et al., 2008a
) in a much
larger sample of longtail macaques confirmed these find-
ings and revealed that genetic differences between some
regional populations of longtail macaques exceeded the
degree of genetic difference between Indian and Chinese
rhesus macaques and others were nearly comparable.
Genetic heterogeneity of mtDNA is particularly low in
Mauritian macaques (
Kawamoto et al., 2007; Smith et al.,
2007; Stevison and Kohn, 2008
), whose origins
Tosi and
Coke (2006)
place in Sumatra, and, though less so, the
Philippines (
Smith et al., 2007
), probably due to the loss of
rare alleles resulting from founder effects. Genetic differ-
ences in the DRB genes of the Mhc region between regional
populations of longtail macaques have also been reported
(e.g.
Leuchte et al., 2004
). The genetic homogeneity of
Mhc class I loci in Mauritian longtail macaques (
Krebs
et al., 2005; Weisman et al., 2007; Mee et al., 2009
), as for
Indian (
Smith and McDonough, 2005
) and Nepalese (
Kyes
et al., 2006
) rhesus macaques, should reduce the genetic
component of phenotypic variance in response to experi-
mental infection with infectious diseases making it
a particularly desirable animal model.
The mtDNA of longtail macaques from Indonesia is
more genetically heterogeneous than of those from Indo-
china (e.g. Vietnam) and, like nuclear STR genotypes, that
of both are far more heterogeneous than those from the
Philippines and especially Mauritius (
Smith et al., 2007;
Blancher et al., 2008
). The mtDNA of longtail macaques
from the Philippines and Indochina differ more from each
other than does the mtDNA of Indian and Chinese rhesus
macaques, consistent with their different subspecific
designations (
Fooden, 2006
), but the STR genotypes of the
two regional populations are much more similar to each
other than either is to those of Indonesian longtail
macaques. Recent studies have also reported a remarkably
high level of allele sharing at Mhc (
Doxiadis et al., 2006
),
STR (
Kanthaswamy et al., 2008a
), and SNP (
Street et al.,
2007
) loci between rhesus and longtail macaques and both
share genes in common with the other two species of the
fascicularis group of macaque species (M. fuscata and
M. cyclopis) as well as other cercopithecine primates
including, somewhat surprisingly, African green monkeys
(
Malhi et al., 2011
). mtDNA studies by
Li and Zhang
(2005)
support
Groves' (2001)
placement of stumptail
macaques (M. arctoides) in a species group, together with
longtail macaques, that is separate from a “mulatta” group
comprising rhesus, Japanese, and Taiwanese rhesus
macaques.
Tosi et al. (2000, 2003)
have addressed this
controversial lumping of M. arctoides with M. fascicularis
by arguing that stumptail macaques originated from natural
hybridization between males of
the sinica group of
macaque
species
(M. assamensis/M.
thibetana)
and
M.
fascicularis-like females.
It should be noted that
