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New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.
- T. Karafet, F. Mendez, Monica B. Meilerman, P. Underhill, S. Zegura, M. Hammer
- BiologyGenome research
- 1 May 2008
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.
Genetic evidence for archaic admixture in Africa
- M. Hammer, August E. Woerner, F. Mendez, Joseph Watkins, J. Wall
- BiologyProceedings of the National Academy of Sciences
- 30 August 2011
DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations are used to test models of African archaic admixture and suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
A calibrated phylogenetic tree is constructed on the basis of binary single-nucleotide variants and the more complex variants onto it, estimating the number of mutations for each class and shows bursts of extreme expansion in male numbers that have occurred independently among the five continental superpopulations examined.
A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
A study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples, infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky, and hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity
Factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability.
An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data.
Substantial support is found for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non- Pygmy NKs group ∼110 thousand years ago over a model incorporating a proto-' proto-KhoeSan-pygmy hunter-gatherer divergence from the ancestors of non- pygmyNKs.
An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree.
Gibbon genome and the fast karyotype evolution of small apes
The assembly and analysis of a northern white-cheeked gibbon genome is presented and the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site is described, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage.
A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea.
A novel DNA sequence database for analyzing human demographic history.
- J. Wall, M. Cox, F. Mendez, August E. Woerner, T. Severson, M. Hammer
- BiologyGenome research
- 1 August 2008
Key differences in patterns of variability are identified in the database compared with other large public databases, including higher levels of nucleotide diversity within populations, greater levels of differentiation between populations, and significant differences in the frequency spectrum.