It is demonstrated that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data.
SMC++ is presented, a new statistical tool capable of analyzing orders of magnitude more samples than existing methods while requiring only unphased genomes and employing a novel spline regularization scheme that greatly reduces estimation error.
It is found that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases and suggesting a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences.
This report of independent genome sequences of two natural populations of Drosophila melanogaster provides unique insight into forces shaping genomic polymorphism and divergence, suggesting many targets of directional selection are shared between these species.
Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome.
The results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders.
It is shown that both dark and light pigmentation alleles arose before the origin of modern humans and that both light and dark pigmented skin has continued to evolve throughout hominid history.
This work generalizes the recently developed sequentially Markov conditional sampling distribution framework, which provides an accurate approximation of the probability of observing a newly sampled haplotype given a set of previously sampled haplotypes.
Analysis of the oldest genomes suggests that there was an early split within Beringian populations, giving rise to the Northern and Southern lineages, and that the early population spread widely and rapidly suggests that their access to large portions of the hemisphere was essentially unrestricted, yet there are genomic and archaeological hints of an earlier human presence.