Human Genomic Diversity and Disease Research Unit
Research highlights
Prehistory
of southern African populations: Y chromosome evidence
Archaeological,
linguistic, historical, cultural and genetic data demonstrate that the patterns
of genetic variation in southern African populations are complex due to varying
degrees of admixture between Khoisan people, migrating Bantu-speakers and
immigrants from western Europe, India and the Malay Archipelago.
We have used Y chromosome
markers (YAP, DYS393, DYS19, DYS390 and DYS391) to construct haplotypes that
were used to examine the male contribution to the gene pool of southern African
populations.
By examining the relationship
of Y chromosome haplotypes on a network using the step-wise mutation model,
we were able to examine:
- The effect of the
Bantu-expansion on the peopling of southern Africa;
- The relationship between
Khoisan and Bantu-speaking populations;
- Date-specific clusters
of Y chromosome haplotypes.
One haplotype (YAP-ECHC),
found in all three major population groups of Africa, has been identified
as the most likely ancestral Y haplotype in Africa. The frequencies and distribution
of another haplotype (YAP-ECHC) appear to be associated with the Bantu expansion.
Although linguistic and
archaeological data show that different migrations were associated with the
spread of southeastern and southwestern Bantu-speakers, Y chromosome data
support a common ancestry for both groups.
Differences are also detected
between them, however, presumably due to varying degrees of gene admixture
with populations they encountered en-route to southern Africa.
The Khoisan and Caucasoid
groups also have distinct haplotype distribution patterns. Differences in
the Y chromosome haplotypes among the various southern African populations
is further supported by their patterns of association in phylogenetic trees
and PC-plots.
The
genetic affinities of Biaka pygmies from the Central African Republic
The genetic
relationship between Biaka Pygmies from the Central African Republic (C.A.R.)
and Mbuti Pygmies from the Democratic Republic of Congo is unresolved.
Haploid DNA markers, including
mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome,
are frequently used to study the affinities of human populations.
We have used both mtDNA
and Y chromosome DNA to examine the genetic affinities between Biaka and Mbuti
Pygmies, and to examine the relationships of the Biaka population with other
sub-Saharan African populations.
Comparisons of mtDNA control
region sequences and Y chromosome haplotypes, found in both groups of Pygmies,
with those of other sub-Saharan Africans revealed that the Biaka have certain
unique polymorphisms. No mtDNA types were shared by the Biaka and Mbuti. Biaka
and Mbuti mtDNA types were, however, closely associated in an NJ-tree suggesting
that they share more recent female ancestry with each other than with other
African populations.
While the Biaka had unique
mtDNA types, those found in the Mbuti also showed close associations with
some mtDNA types from other sub-Saharan African populations.
Nuclear gene markers have
indicated that non-Pygmy populations have contributed to the gene pool of
the Biaka, but the low level of mtDNA type-sharing between the Biaka and non-Pygmy
populations from the C.A.R. indicates that this was not through female contributions.
Y chromosome data, on the other hand, suggest that males from non-Pygmy groups
have contributed to the gene pool of the Biaka.
African
and Asian origins of Malagasy Y chromosomes
Linguistic and
historic data have led to consensus that the proto-Malagasy comprise a people
of both Austronesian and African origin. The role played by Polynesians and
Indians in the peopling of Madagascar is still, however, uncertain.
Earlier genetic studies
on blood groups and serogenetic markers have shown support for both Asian
and African contributions to the Malagasy, but these studies have been limited
to relatively small sample sizes.
More recently, genetic
data from autosomal and X-linked markers have provided strong support for
contributions from Bantu-speakers from central and east Africa to the Malagasy
gene pool.
Observations made by historians,
as well as a study based on anthropometric measures, suggest that there were
several differences in physical features which distinguished populations living
in the highland regions of Madagascar from those living in the lowlands.
We used five Y chromosome
markers consisting of a Y Alu insertion polymorphism (YAP) and four short
tandem repeat (STR) loci (DYS393, DYS19, DYS390 and DYS391) to construct Y
chromosome haplotypes in approximately 550 males representing 11 of the eighteen
major ethnic groups in Madagascar.
These data were compared
with African, SE Asian and Indian data to assess their respective genetic
contributions to the Malagasy.
YAP is a useful marker
in tracing the contribution of African males to the Malagasy and 50% or more
of Y chromosomes in the Malagasy ethnic groups have the insertion (YAP+ chromosomes),
establishing that the gene pool of present-day Malagasy is derived from a
major African contribution.
A comparison of the five
site haplotypes constructed with the above markers shows that a number of
haplotypes are shared both by the different Malagasy ethnic groups as well
as the African populations. Neither is there any evidence supporting a decreased
African contribution to highland populations.
To resolve the ancestry
of YAP- chromosomes, we used M9, a marker useful for identifying non-African
YAP- chromosomes. Using this Y chromosome data, we show that African- and
non-African-derived Y chromosomes are found throughout the island.
The similarity of the
gene pools of the eleven ethnic groups examined from different regions of
the island may be due to their recent common ancestry, or to a high level
of gene flow between all the ethnic groups. Unfortunately, the data from the
present study cannot resolve whether the proto-Malagasy were an admixed African/Indonesian
population prior to colonisation, or whether admixture between these groups
occurred following their independent arrivals in Madagascar. |
