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Bayesian inference of ancient human demography from individual genome sequences
This work used a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times and migration rates from inferred genealogies at many neutrally evolving loci across the genome.
Genome Sequencing Highlights the Dynamic Early History of Dogs
It is found that none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade, suggesting that a re-evaluation of past hypotheses regarding dog origins is necessary.
Genome-Wide Inference of Ancestral Recombination Graphs
A new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes and which converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations.
Ancient gene flow from early modern humans into Eastern Neanderthals
It is concluded that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Optimal implementations of UPGMA and other common clustering algorithms
Worldwide patterns of genomic variation and admixture in gray wolves.
No single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population, and extensive admixture between dogs and wolves is found, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry.
Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf
Genome admixture in two endemic North American wolf species. Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most…
Probabilities of Fitness Consequences for Point Mutations Across the Human Genome
A novel computational method for estimating the probability that a point mutation at each position in a genome will influence fitness is described, which indicates that recent evolutionary turnover has had limited impact on the functional content of the genome.
Genome-wide inference of natural selection on human transcription factor binding sites
It is found that, on average, transcription factor binding sites have experienced somewhat weaker selection than protein-coding genes, however, the binding sites of several transcription factors show clear evidence of adaptation.
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence.
- Ilan Gronau, Leonardo Arbiza, Jaaved Mohammed, A. Siepel
- BiologyMolecular biology and evolution
- 29 September 2011
A new computational method, called Inference of Natural Selection from Interspersed Genomically CoHerent ElemenTs (INSIGHT), for measuring the influence of natural selection on small noncoding elements and significantly improves on methods based on summary statistics describing polymorphism and divergence.