scholarly journals The Recombination Landscape of the Khoe-San - the Upper Limits of Recombination Divergence in Humans

2021 ◽  
Author(s):  
Gerald van Eeden ◽  
Caitlin Uren ◽  
Evlyn Pless ◽  
Mira Mastoras ◽  
Gian van der Spuy ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Southern Africa ◽  
Demographic History ◽  
African Ancestry ◽  
West African ◽  
Population Divergence ◽  
Whole Genome ◽  
Fine Scale ◽  
Upper Limits ◽  
West African Ancestry

Recombination maps are important resources for epidemiological and evolutionary analyses, however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We inferred the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derived a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesized that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. We showed that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we used selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans.

scholarly journals Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry

PLoS ONE ◽  
2017 ◽  
Vol 12 (6) ◽  
pp. e0179021 ◽  
Author(s):  
Gordon L. Spangler ◽  
Benjamin D. Rosen ◽  
Moses Babatunde Ilori ◽  
Olivier Hanotte ◽  
Eui-Soo Kim ◽  
...  
Keyword(s):  
Structural Analysis ◽  
African Ancestry ◽  
West African ◽  
Whole Genome ◽  
Hair Sheep ◽  
West African Ancestry

Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises

2021 ◽  
Author(s):  
Evelyn L. Jensen ◽  
Stephen J. Gaughran ◽  
Ryan C. Garrick ◽  
Michael A. Russello ◽  
Adalgisa Caccone
Keyword(s):  
Molecular Evolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Demographic History ◽  
Whole Genome

scholarly journals Prevalence of HIV/hepatitis B and HIV/hepatitis C coinfection among people of East, South, Central and West African ancestry in the United Kingdom

AIDS ◽  
2021 ◽  
Vol Publish Ahead of Print ◽  
Author(s):  
Rachel Hung ◽  
Nisha Patel ◽  
Julie Fox ◽  
Catherine Cosgrove ◽  
Sarah L. Pett ◽  
...  
Keyword(s):  
United Kingdom ◽  
Hepatitis C ◽  
Hepatitis B ◽  
African Ancestry ◽  
West African ◽  
The United Kingdom ◽  
South Central ◽  
West African Ancestry

Abstract 3516: Commercial gene expression tests for prostate cancer outcome risk in men of West African ancestry

2020 ◽  
Author(s):  
Sandra M. Gaston ◽  
Rick A. Kittles ◽  
Radka Stoyanova ◽  
Teresa M. Giret ◽  
Saba A. Ansari ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
African Ancestry ◽  
West African ◽  
Cancer Outcome ◽  
West African Ancestry

scholarly journals Insights into platypus population structure and history from whole-genome sequencing

2017 ◽  
Author(s):  
Hilary C. Martin ◽  
Elizabeth M. Batty ◽  
Julie Hussin ◽  
Portia Westall ◽  
Tasman Daish ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Demographic History ◽  
Population Decline ◽  
Egg Laying ◽  
Whole Genome ◽  
Data Set ◽  
Important Species

AbstractThe platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly-improved reference genome, we called over 6.7M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative amongst other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0×10−9/bp/generation (95% CI 4.1×10−9 − 1.2×10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

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