Reconstructing an African haploid genome from the 18th century

@article{Jagadeesan2017ReconstructingAA,
  title={Reconstructing an African haploid genome from the 18th century},
  author={Anuradha Jagadeesan and Ellen Dr{\"o}fn Gunnarsd{\'o}ttir and Sigr{\'i}ður Sunna Ebenesersd{\'o}ttir and Vald{\'i}s B. Guðmundsd{\'o}ttir and Elisabet Linda Thordardottir and Margr{\'e}t Einarsd{\'o}ttir and H{\'a}kon J{\'o}nsson and Jean Michel Dugoujon and Cesar A. Fortes-Lima and Florence Migot-Nabias and Achille Massougbodji and Gil Bellis and Lu{\'i}sa Pereira and G{\'i}sli M{\'a}sson and Augustine Kong and K{\'a}ri Stef{\'a}nsson and Agnar Helgason},
  journal={Nature Genetics},
  year={2017},
  volume={50},
  pages={199-205}
}
A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ’s… 
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Aging is an adaptation that selects in animals against disruption of homeostasis.
  • A. Muller
  • Medicine, Biology
    Medical hypotheses
  • 2018
TLDR
Generalize, motivated by the parallels between cancer and aging, the purifying selection posited for cancer to aging, and says that by lessening the offspring's survival by proxy through diminishing parental care, they can still contribute to the selection.
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References

SHOWING 1-10 OF 30 REFERENCES
Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
TLDR
Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification, and illustrated the importance of African genomic diversity in understanding human evolutionary history.
Large-scale whole-genome sequencing of the Icelandic population
TLDR
The insights gained from sequencing the whole genomes of Icelanders to a median depth of 20× provide a study design that can be used to determine how variation in the sequence of the human genome gives rise to human diversity.
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.
TLDR
Major changes in the topology of the parsimony tree are described and names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002 are provided.
The Genetic Structure and History of Africans and African Americans
TLDR
A detailed genetic analysis of most major groups of African populations is provided, suggesting that Africans represent 14 ancestral populations that correlate with self-described ethnicity and shared cultural and/or linguistic properties.
Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool.
TLDR
The principal route for the expansion out of Africa ~60 kya remains unresolved, and linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.
The African Genome Variation Project shapes medical genetics in Africa
TLDR
It is shown that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa.
The landscape of recombination in African Americans
TLDR
This work builds a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans, and identifies about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans.
Admixture into and within sub-Saharan Africa
TLDR
It is shown that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions.
Genome-wide patterns of population structure and admixture in West Africans and African Americans
Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale.
A high-resolution recombination map of the human genome
TLDR
Recombination rates are significantly correlated with both cytogenetic structures and sequence and paternal chromosomes show many differences in locations of recombination maxima, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.
...
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3
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