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NetNomad
06-29-2019, 01:45 PM
Abstract
Background
Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations.

Results
Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 5416 kya. Eastern and western CRHG lineages diverged by ~ 5031 kya, and the western CRHG lineages diverged by ~ 1812 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations.

Conclusions
We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.

URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1679-2

NetNomad
06-29-2019, 01:50 PM
Anyone here know whether they analyzed the Y-Chromosomes of those new population (see spoiler for the list)?

Aari
Agaw
Amhara
Baka
Bakola
Bedzan
Bulala
Elmolo
Fulani
Hadza
Iraqw
Kaba
Kikuyu
Laka
Mada
Mursi
Ngumba
Ogiek
Rendille
Sandawe
Sengwer
Tikar_South

If so, is it uploadable to yfull?

After some research I got to this link:
https://ega-archive.org/datasets/EGAD00001005019

Thank you in advance.

VytautusofAukstaitija
07-01-2019, 01:39 AM
They dont have most of those ethnic groups in this paper, but those tested here should be in the ydna bam files here: https://reichdata.hms.harvard.edu/pub/datasets/sgdp/

All the samples in this paper are seemingly included.

NetNomad
07-01-2019, 09:50 AM
They dont have most of those ethnic groups in this paper, but those tested here should be in the ydna bam files here: https://reichdata.hms.harvard.edu/pub/datasets/sgdp/

All the samples in this paper are seemingly included.


Have they included those new populations? Because in the paper it seems like they did WGS on those new samples, so I assume new bams should be out there?