Biomedical Engineering Reference
In-Depth Information
polymorphic in members of three different species of genus
Saimiri (S. boliviensis from Bolivia, S. sciureus sciureus
from Guyana, and S. s. collins from Brazil) housed at the
Cayenne (French Guiana) breeding colony of the Pasteur
Institute. The three species/subspecies were found to be
reciprocally monophyletic for mtDNA with each of the
three saimiri taxa being approximately equally distant from
each other. The S. boliviensis samples exhibited several
private STR alleles and could be easily distinguished from
the two subspecies of S. sciureus, but the latter two
subspecies were paraphyletic with respect to each other.
The numbers of alleles per STR locus ranged from nine to
14 and the expected level of heterozygosity ranged from
0.51 to 0.75. While the two subspecies of S. sciureus could
not be distinguished based on STR alleles, some Bolivian/
Guyane/Brazilian hybrid squirrel monkeys could be
identified. As additional informative STR loci are identified
in particular Platyrrhine species, then tested in others,
more detailed studies designed to clarify the taxonomy
of New World species can be envisioned. However, the
ascertainment bias introduced by the use loci known to
be polymorphic in one species to characterize genetic
heterogeneity in another
conflicting pictures of phylogenetic history and that some
populations, such as those exhibiting high levels of linkage
disequilibrium, require fewer loci for mapping specific
phenotypes to specific regions of the genome. As the coa-
lescence of some genes will predate and that of others will
post-date any speciation event of interest, an average
phylogenetic history should be constructed using multiple
genes, but that reconstruction will reflect sampling error
based on gene selection. A very large number of genes
selected to be representative of the entire genome of the
taxa under study is not presently practical or even possible
for all species but would provide the most accurate illus-
tration of evolutionary history for those species most rele-
vant to biomedical research.
Taxonomy is notoriously conservative and resistant to
revision except where the validity of a species tree based on
morphology is confronted with incontrovertible evidence
of its failure to properly reflect phylogenetic history. The
resistance to revision of taxonomy based on conclusive
evidence that apes do not constitute a monophyletic clade
(i.e. that chimpanzees are more closely related to humans
than to gorillas) is a case in point. Within the next few short
years the draft genome sequences of at least 15 primate
species will have been completed making primates one of
the most completely genetically understood taxon. Some of
these genome sequences have already revealed surprises
such as the emergence of approximately 2000 Alu insertion
elements in the human lineage since sharing a common
ancestor with chimpanzees, far stronger linage disequilib-
rium in Indian rhesus macaques (and non-African humans)
than in Chinese rhesus macaques (and African humans),
and the large number of segmental duplications and copy
number variants that influence gene expression in primates.
These draft sequences will allow the development of SNP
maps for primate species that are representative of their
genomes and provide far stronger evidence of evolutionary
history than species trees based on morphology and should
be relied upon for appropriately revising taxonomy.
species
should always be
considered.
FROM PHYLOGENETICS TO
PHYLOGENOMICS
Taxonomy of primates informs the suitablility of use of
either one or another regional population of a given species
or a species itself as an animal model for the study of
particular human diseases. Taxonomies are often based on
a very limited number of morphological traits, such as, in
the case of macaques, tail length and genital morphology,
and may not reflect “true” phylogenetic history, and the
species trees provided by these traits often conflict with
gene trees. Moreover, because different genes have
different evolutionary histories, a tree based on any given
gene, including mtDNA, the Y-chromosome, or DNA from
the same haplotype block, might or might not exhibit the
same topology as the “true” species tree due to incomplete
lineage sorting (i.e. when the haplotypes from two closely
related species coalesce so deeply that the haplotype of one
of the two species coalesces with the haplotype of a third
more remote species before coalescing with its sister
species;
Siepel, 2009
). This is especially likely to occur
when the ancestral population sizes are large relative to
time of speciation, as with the hominoids. In addition,
introgressive hybridization has been extensive in many
primate taxa leading to extensive paraphyly as well as
linkage disequilibrium (LD), as reflected by some of the
genetic studies discussed above. Thus, it should not trouble
us
ACKNOWLEDGMENT
This study was supported by NIH grants R24RR005090 and
R24RR025871.
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AESOP-Project. (2006). Trends in US primate importation for 11 years
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that different genes provide us with sometimes
