Biology subjects

Thomas Mailund

Publications and source records attributed to Thomas Mailund.

3 recordsLinked to original sources

bioRxiv2016

Ohana, a tool set for population genetic analyses of admixture components

MotivationStructure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components.\n\nContributionWe introduce a new optimization algorithm of the classical Structure model in a maximum likelihood framework. Using analyses of real data we show that the new optimization algorithm finds higher likelihood values than the state-of-the-art method in the same computational time. We also present a new method for estimating population trees from ancestry components using a Gaussian approximation. Using coalescence simulations modeling populations evolving in a tree-like fashion, we explore the adequacy of the Structure model and the Gaussian assumption for identifying ancestry components correctly and for inferring the correct tree. In most cases, ancestry components are inferred correctly, although sample sizes and times since admixture can influence the inferences. Similarly, the popular Gaussian approximation tends to perform poorly when branch lengths are long, although the tree topology is correctly inferred in all scenarios explored. The new methods are implemented together with appropriate visualization tools in the computer package Ohana.\n\nAvailabilityOhana is publicly available at https://github.com/jade-cheng/ohana. Besides its source code and installation instructions, we also provide example workflows in the project wiki site.\n\nContactjade.cheng@birc.au.dk

Bioinformatics↗

bioRxiv2016

Genome-wide evidence for a hybrid origin of modern polar bears

Interspecific hybridization is recognized as a widespread phenomenon but measuring its extent, directionality, and adaptive importance in the evolution of species remain challenging. Polar bears possess unique adaptations to life on the Arctic sea ice, whereas their closest relatives -brown bears - are boreal and subarctic generalists. Despite largely non-overlapping modern distributions, genomic evidence demonstrates ancient admixture between these species. Here, we analyze new genomes from contemporary zones of species overlap as well as a previously sequenced 120,000-year old polar bear subfossil. We use explicit statistical fitting of data to admixture graphs to provide a framework for testing alternative scenarios of population relationships and gene flow directionality. Our analyses favor a single, parsimonious introgression event from relatives of extant Southeast Alaskan coastal brown bears into the ancestor of extant polar bears, which inverts the current paradigm of unidirectional gene flow from polar into brown bear. This conclusion has clear implications for our understanding of the impact of climate change: a specialist Arctic lineage may have been the recipient of generalist, boreal genetic variants at crucial times during critical phases of Northern Hemisphere glacial oscillations.

Evolutionary Biology↗

bioRxiv2014

Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence

The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence. This has led to a controversial hypothesis proposing a unique role of the X chromosome in human-chimpanzee speciation. We study incomplete lineage sorting patterns between humans, chimpanzees and gorillas to show that this low divergence is entirely due to megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced. Background selection can explain 10% of this reduction at most. Instead, we show that several strong selective sweeps in the ancestral species can explain this reduction of diversity in the ancestor. We also report evidence of population specific sweeps in extant humans that overlap the regions of low diversity in the ancestral species. These regions further correspond to chromosomal sections shown to be devoid of Neanderthal introgression into modern humans. This suggests that the same X-linked regions that undergo selective sweeps are among the first to form reproductive barriers between diverging species. We hypothesize that meiotic drive is the underlying mechanism causing these two observations.\n\nAuthors' SummaryBecause the speciation events that leads to human, chimpanzee and gorilla were close in time, their genetic relationship of these species varies along the genome. While human and chimpanzee species are most closely related, 15% of the human genome is more closely related to the gorilla genome than the chimpanzee genome, a phenomenon called incomplete lineage sorting (ILS). The amount and distribution of ILS can be predicted using population genetics theory, and is affected by demography and selection in the ancestral populations. It was previously reported that the X chromosome, in contrast to autosomes, is deprived of ILS, and this givies rise to controversial theories about the speciation event that splits humans and chimpanzees. Using a full genome alignment of the X chromosome, we show that this deprivation of ILS affects only one third of the chromosome. These regions also show reduced diversity in the extant populations of human and great apes, and coincide with regions devoid of Neanderthal introgression. We propose that these regions are targets of selection and that they played a role in the formation of reproductive barriers.

Evolutionary Biology↗