560
Chimpanzee Genome
differences exist not only as divergence
between species but also as diversity
within species. In analogy to the use of
divergence to reconstruct a phylogenetic
tree that helps infer the evolutionary
relationships among species, diversity data
can be used to model a within-species tree
representing the relationships of sequence
variants at a given locus in a population.
Such a genealogical tree can help clarify
the demographic history of an individual
species. Following a genealogical tree
backwards in time, the genetic lineages
represented by the individual alleles will
gradually join until only a single lineage
remains. This lineage from which all
extant sequence variants are derived is
termed the
most recent common ancestor
(MRCA). Making an assumption about
the mutation rate and the long-term
population size of the species – diversity
increases
with
an
increase
of
either
parameter – the estimated time point of
the MRCA can be inferred and reflects
the amount of diversity present in the
extant population.
For
chimpanzees and
humans,
the
date of their MRCAs as assessed from
single nucleotide polymorphism data is
1 900 000 years and 500 000 years before
present respectively. Accordingly, contem-
porary chimpanzees are two to fourfold
more diverse compared to contemporary
humans. What can explain the differing
amounts of genetic diversity between both
species? Since there is clear indication
that the mutation rate in chimpanzees
and humans is approximately the same,
a difference in their population history
is proposed as the underlying cause.
Contemporary humans are, presumably,
descendants of a small African population
that subsequently expanded and spread
over the entire world. Owing to the small
size of the founding population, the ma-
jority of DNA sequence variation present
in the ancestral human population has
been lost, and thus, the genetic diversity in
present day humans is low. Chimpanzees,
in contrast, are believed to have not un-
dergone such a substantial population size
decrease. Therefore, a larger proportion of
old genetic lineages could contribute to
their present day diversity.
From the analysis of genetic diversity
in chimpanzees, a second interesting as-
pect emerges. According to the location
of their habitats in Africa, three groups
of chimpanzees are distinguished: west-
ern, central, and eastern chimpanzees.
From the perspective of DNA sequence
variation of the mitochondrial genome
and at a Y chromosomal locus, each of
the three groups appear to be genetically
unique. No shared DNA sequence vari-
ants for these loci have been observed,
which indicate an independent evolution
of the three chimpanzee populations. As
a consequence, they were given the sta-
tus of a subspecies: western chimpanzee
(
Pan troglodytes verus
), central chimpanzee
(
P
.
t
.
troglodytes
) and eastern chimpanzee
(
P
.
t
.
schweinfurthii
). However, no such
genetic uniqueness is seen at autosomal
and X chromosomal loci. This was initially
t
a
k
ena
sanin
d
i
c
a
t
i
onth
a
tth
er
e
s
p
e
c
-
tive chimpanzee populations do not evolve
independently and raised doubts on the
biological signi±cance of their classi±ca-
tion into different subspecies. Recently,
an alternative explanation has been pro-
posed that would be consistent with an
independent evolution of the chimpanzee
populations. Subsequent to the repro-
ductive isolation of populations, shared
ancestral polymorphisms will gradually
become extinct by genetic drift, that is,
the stochastic loss of alleles caused by the
fact that some individuals in a generation
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