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Y‑chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese
Mayukh Mondal1 · Anders Bergström2 · Yali Xue2 · Francesc Calafell1 ·
Hafd Laayouni1,3 · Ferran Casals4 · Partha P. Majumder5 · Chris Tyler‑Smith2 ·
Jaume Bertranpetit
Abstract We present 42 new Y-chromosomal sequences
from diverse Indian tribal and non-tribal populations,
including the Jarawa and Onge from the Andaman Islands,
which are analysed within a calibrated Y-chromosomal
phylogeny incorporating South Asian (in total 305 individuals) and
worldwide (in total 1286 individuals) data from
the 1000 Genomes Project. In contrast to the more ancient
ancestry in the South than in the North that has been
claimed, we detected very similar coalescence times within
Northern and Southern non-tribal Indian populations. A
closest neighbour analysis in the phylogeny showed that
Indian populations have an affnity towards Southern European
populations and that the time of divergence from
these populations substantially predated the Indo-European
migration into India, probably refecting ancient shared
ancestry rather than the Indo-European migration, which
had little effect on Indian male lineages. Among the tribal
populations, the Birhor (Austro-Asiatic-speaking) and Irula
(Dravidian-speaking) are the nearest neighbours of South
Asian non-tribal populations, with a common origin in
the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking)
and Andamanese have their nearest neighbour lineages in East Asia. The
Jarawa and Onge shared
haplogroup D lineages with each other within the last
~7000 years, but had diverged from Japanese haplogroup
D Y-chromosomes ~53000 years ago, most likely by a split
from a shared ancestral population. This analysis suggests
that Indian populations have complex ancestry which cannot be explained
by a single expansion model.
* Chris Tyler-Smith
cts@sanger.ac.uk
* Jaume Bertranpetit
jaume.bertranpetit@upf.edu
Introduction
The Y-chromosome is a powerful tool for analysing the
paternal ancestry of human populations (Jobling and
Tyler-Smith 2003). As most of the Y-chromosome does
not recombine, reconstructing haplotypes is straightforward.
Thus, it is possible to build a phylogenetic tree for
all human Y-chromosomal variation that analysed in a
geographic context, allows a phylogeographic approach.
Analysis of the whole sequence of the Y-chromosome will
encompass not only the specific variants that defined the
classical “haplogroups”, but all the nucleotide variation
in the accessible regions of the chromosome. This provides
higher resolution and more reliable time estimates of
lineage divergences (Wei et al. 2013; Hallast et al. 2014;
Karmin et al. 2015; Poznik et al. 2016; Willems et al.
2016).
Indian subcontinental population ancestry is complex
and many attempts have been made to unravel this intricate
history using both uniparental markers, mtDNA and
the Y-chromosome (Kivisild et al. 2003; Cordaux et al.
Mayukh Mondal1 · Anders Bergström2 · Yali Xue2 · Francesc Calafell1 ·
Hafd Laayouni1,3 · Ferran Casals4 · Partha P. Majumder5 · Chris Tyler‑Smith2 ·
Jaume Bertranpetit
Abstract We present 42 new Y-chromosomal sequences
from diverse Indian tribal and non-tribal populations,
including the Jarawa and Onge from the Andaman Islands,
which are analysed within a calibrated Y-chromosomal
phylogeny incorporating South Asian (in total 305 individuals) and
worldwide (in total 1286 individuals) data from
the 1000 Genomes Project. In contrast to the more ancient
ancestry in the South than in the North that has been
claimed, we detected very similar coalescence times within
Northern and Southern non-tribal Indian populations. A
closest neighbour analysis in the phylogeny showed that
Indian populations have an affnity towards Southern European
populations and that the time of divergence from
these populations substantially predated the Indo-European
migration into India, probably refecting ancient shared
ancestry rather than the Indo-European migration, which
had little effect on Indian male lineages. Among the tribal
populations, the Birhor (Austro-Asiatic-speaking) and Irula
(Dravidian-speaking) are the nearest neighbours of South
Asian non-tribal populations, with a common origin in
the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking)
and Andamanese have their nearest neighbour lineages in East Asia. The
Jarawa and Onge shared
haplogroup D lineages with each other within the last
~7000 years, but had diverged from Japanese haplogroup
D Y-chromosomes ~53000 years ago, most likely by a split
from a shared ancestral population. This analysis suggests
that Indian populations have complex ancestry which cannot be explained
by a single expansion model.
* Chris Tyler-Smith
cts@sanger.ac.uk
* Jaume Bertranpetit
jaume.bertranpetit@upf.edu
Introduction
The Y-chromosome is a powerful tool for analysing the
paternal ancestry of human populations (Jobling and
Tyler-Smith 2003). As most of the Y-chromosome does
not recombine, reconstructing haplotypes is straightforward.
Thus, it is possible to build a phylogenetic tree for
all human Y-chromosomal variation that analysed in a
geographic context, allows a phylogeographic approach.
Analysis of the whole sequence of the Y-chromosome will
encompass not only the specific variants that defined the
classical “haplogroups”, but all the nucleotide variation
in the accessible regions of the chromosome. This provides
higher resolution and more reliable time estimates of
lineage divergences (Wei et al. 2013; Hallast et al. 2014;
Karmin et al. 2015; Poznik et al. 2016; Willems et al.
2016).
Indian subcontinental population ancestry is complex
and many attempts have been made to unravel this intricate
history using both uniparental markers, mtDNA and
the Y-chromosome (Kivisild et al. 2003; Cordaux et al.