Using genomic data to better understand how demographic history, inbreeding, and selection shape mutation load in whales

The reduced genetic diversity and inbreeding associated with declining populations can drive the accumulation and expression of deleterious mutations that can then lead to extinction. In other instances, however, purifying selection coupled with inbreeding purges declining populations of deleterious mutations. The patterns of inbreeding, demographic history, and selective regimes that support population recovery over extinction remain largely unresolved in nature. To understand the dynamics of declining populations, I estimated mutation load and inbreeding, and I inferred demographic history and the strength of selection from the genomes of 11 populations of whale. To this end, I quantified and characterized the mutation load of four critically endangered populations: the North Atlantic right whale (Eubalaena glacialis [NARW]), the St. Lawrence beluga whale (Delphinapterus leucus [SLE]), the Gulf of California fin whale (Balaenoptera physalus [GOC]), and the Southern resident killer whale (Orcinus orca [SRKW]). I found that endangered populations tend to be marked by low genetic diversity, small population size, inbreeding, and high mutation load. Still, I found evidence that genetic purging reduced mutation load in NARW and SRKW, but not in the SLE or GOC. Because the degree of inbreeding and the strength of bottlenecks are greater in NARW and SRKW than in all other populations, my results suggest that genetic purging depends on the timing and degree of population bottlenecks and inbreeding. Moreover, I identified two suites of deleterious genetic mutations that were 1) linked to congenital defects in nulliparous NARW and 2) to cellular responses to arsenic in beluga whale neonate mortalities in the St. Lawrence estuary. My results also indicate that balancing selection is unlikely to harbor high impact deleterious mutations, even though genetic purging in bottlenecked populations can erode signal of balancing selection. Collectively, my doctoral thesis highlights the population dynamics that underpin genetic purging in nature.