Runs of homozygosity in killer whale genomes provide a global record of demographic histories ...

• Main Authors: Foote, Andrew D., Hooper, Rebecca, Alexander, Alana, Baird, Robin W., Baker, Charles Scott, Ballance, Lisa, Barlow, Jay, Brownlow, Andrew, Collins, Tim, Constantine, Rochelle, Dalla Rosa, Luciano, Davison, Nicholas J., Durban, John W., Esteban, Ruth, Excoffier, Laurent, Fordyce Martin, Sarah L., Forney, Karin A., Gerrodette, Tim, Gilbert, M. Thomas P., Guinet, Christophe, Hanson, M. Bradley, Li, Songhai, Martin, Michael D., Robertson, Kelly M., Samarra, Filipa I. P., de Stephanis, Renaud, Tavares, Sara B., Tixier, Paul, Totterdell, John A., Wade, Paul, Wolf, Jochen B. W., Fan, Guangyi, Zhang, Yaolei, Morin, Phillip A.
• Format: Text
• Language: unknown
• Published: Wiley-Blackwell 2021
• Subjects: 570 Life sciences; biology; Pacific; Killer Whale; Orca; Orcinus orca; Killer whale
• Online Access: https://dx.doi.org/10.48350/160433; https://boris.unibe.ch/160433/

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population ...