lameduck
12-05-2019, 01:33 PM
link
https://www.nature.com/articles/s41586-019-1793-z
full paper pdf
https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-019-1793-z/MediaObjects/41586_2019_1793_MOESM1_ESM.pdf
https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41586-019-1793-z/MediaObjects/41586_2019_1793_Fig1_HTML.png?as=webp
Summary:
Haplogroups
One hundred and nineteen Y-chromosomal haplogroups were identified
(Supplementary Table S3d) across the 956 male samples (representing 54
populations; includes 142 individuals for whom the gender was assigned based on Y chr
data) that were analyzed. In general Y-chromosomal variability in Asian GAsP samples
follows the same geographic patterns that were found in previous studies (Qamar et al.
2002; Sengupta et al., 2006; Xue et al. 2006). Haplogroups of Western Eurasian origin
(R1a1, R1b, J) predominate in Pakistan and North-Western India, while in Southern and
Eastern India the majority of male lineages belong to sub-clades of haplogroup H (15
50
sub-clades) and L1a. Eastern Eurasian haplogroups O1b and O2 (32 sub-clades in
total) are the major Y chromosomal variants in East and South-East Asia. In New
Guinea M and K2b1 are two predominant haplogroups.
Very specific compositions of haplogroups and low Y-chromosomal withinpopulation diversity was found in isolated island populations – Philippine Negritos,
Flores islanders and Andamanese. The Aeta and Ati, two Philippine Negrito
populations, are characterized by very different male lineages. The major haplogroup in
the Aeta (K2b1c) is closely related to K2b1, found in some Papuan populations, while
the Ati share the majority of their Y-chromosomal variants with Austronesians. All male
Flores islanders have Y haplogroups that belong to the very rare C1b1a2 sub-clade,
while the Y chromosomes of all Andamanese males belong to the D1 haplogroup. The
Y-chromosomal population structure corresponds well to population relationships
inferred from autosomal genome variants by PCA, MSMC and Admixture analysis
(supplementary section S3 and S4).
Denisovan admixture
Our estimates of Denisovan admixture across populations also recapitulate the
broad-scale results of previous studies. However, the larger number of samples and
populations in our study allows us to obtain a more nuanced understanding of the global
patterns of Denisovan admixture. We reexamined the pattern of greater Denisovan
admixture than expected in South Asian populations, first noted by Sankararaman et al.
(2016). For this analysis, we subdivided the South Asian samples into four groups,
consisting of Pakistani samples, high caste individuals, other caste individuals and
Tribal (Adivasi) individuals. We further subdivided each group into Indo-European
language speakers and non-Indo-European language speakers. Our analysis excluded
Tibeto-Burman speakers from Northeast India since they cluster genetically with
Southeast Asian populations. They also excluded enigmatic non-indo-European
Pakistani groups (Burusho and Brahui).
https://www.nature.com/articles/s41586-019-1793-z
full paper pdf
https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-019-1793-z/MediaObjects/41586_2019_1793_MOESM1_ESM.pdf
https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41586-019-1793-z/MediaObjects/41586_2019_1793_Fig1_HTML.png?as=webp
Summary:
Haplogroups
One hundred and nineteen Y-chromosomal haplogroups were identified
(Supplementary Table S3d) across the 956 male samples (representing 54
populations; includes 142 individuals for whom the gender was assigned based on Y chr
data) that were analyzed. In general Y-chromosomal variability in Asian GAsP samples
follows the same geographic patterns that were found in previous studies (Qamar et al.
2002; Sengupta et al., 2006; Xue et al. 2006). Haplogroups of Western Eurasian origin
(R1a1, R1b, J) predominate in Pakistan and North-Western India, while in Southern and
Eastern India the majority of male lineages belong to sub-clades of haplogroup H (15
50
sub-clades) and L1a. Eastern Eurasian haplogroups O1b and O2 (32 sub-clades in
total) are the major Y chromosomal variants in East and South-East Asia. In New
Guinea M and K2b1 are two predominant haplogroups.
Very specific compositions of haplogroups and low Y-chromosomal withinpopulation diversity was found in isolated island populations – Philippine Negritos,
Flores islanders and Andamanese. The Aeta and Ati, two Philippine Negrito
populations, are characterized by very different male lineages. The major haplogroup in
the Aeta (K2b1c) is closely related to K2b1, found in some Papuan populations, while
the Ati share the majority of their Y-chromosomal variants with Austronesians. All male
Flores islanders have Y haplogroups that belong to the very rare C1b1a2 sub-clade,
while the Y chromosomes of all Andamanese males belong to the D1 haplogroup. The
Y-chromosomal population structure corresponds well to population relationships
inferred from autosomal genome variants by PCA, MSMC and Admixture analysis
(supplementary section S3 and S4).
Denisovan admixture
Our estimates of Denisovan admixture across populations also recapitulate the
broad-scale results of previous studies. However, the larger number of samples and
populations in our study allows us to obtain a more nuanced understanding of the global
patterns of Denisovan admixture. We reexamined the pattern of greater Denisovan
admixture than expected in South Asian populations, first noted by Sankararaman et al.
(2016). For this analysis, we subdivided the South Asian samples into four groups,
consisting of Pakistani samples, high caste individuals, other caste individuals and
Tribal (Adivasi) individuals. We further subdivided each group into Indo-European
language speakers and non-Indo-European language speakers. Our analysis excluded
Tibeto-Burman speakers from Northeast India since they cluster genetically with
Southeast Asian populations. They also excluded enigmatic non-indo-European
Pakistani groups (Burusho and Brahui).