Biology subjects

Arnason, E.

Publications and source records attributed to Arnason, E..

3 recordsLinked to original sources

bioRxiv2023

Widespread but spotty: Atlantic cod is a complex of five species through ecological speciation.

Withdrawal StatementThe authors have withdrawn their manuscript because they have discovered errors in the alignment of parts of the data. Miscommunication with the sequencing center led to a misunderstanding of the pooling design and incorrect merging of sequencing read files from different individuals into single bam files. Thus bam alignments for each individual sample of four out of 12 batches are based on a majority of reads from that individual but also on reads from one or two other individuals. Individuals in eight other batches were not affected by this. However, for this paper, the entire data was jointly genotyped to produce vcf files, and the joint genotyping may thus indirectly affect samples of other batches. Revising the paper by teasing apart the affected and non-affected parts of the data is not an option, and they, therefore, withdraw the preprint. They are reanalyzing the dataset. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

evolutionary biology↗

bioRxiv2022

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.

evolutionary biology↗

bioRxiv2018

Identifying loci under positive selection in complex population histories

Detailed modeling of a species history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method--called Graph-aware Retrieval of Selective Sweeps (GRoSS)--has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.

evolutionary biology↗