Effects of inbreeding, drift, and selection on mutation load in the Florida scrub-jay
Authors: Mitchell G Lokey 1; Tram N Nguyen 2,3; Elissa J Cosgrove 1; Felix EG Beaudry 4; Nancy Chen 4; Reed Bowman 5; John W Fitzpatrick 2,3; Philipp W Messer 1,2,6; Andrew G Clark 1,2,6
Affiliations: 1) Department of Molecular Biology & Genetics, Cornell University, Ithaca, New York, USA; 2) Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA; 3) Lab of Ornithology, Cornell University, Ithaca, New York, USA; 4) Department of Biology, University of Rochester, Rochester, New York, USA; 5) Archbold Biological Station, Venus, FL 33960, USA; 6) Department of Computational Biology, Cornell University, Ithaca, New York, USA
Keywords: Ecological & conservation genetics
Recent human activity has driven population decline for thousands of species around the world. Population genetic theory predicts that as populations decline, genetic drift can result in deleterious variants attaining higher allele frequencies. The aggregate increase of deleterious variants in a population leads to a larger genetic load in small and declining populations relative to large equilibrium populations. Furthermore, if inbreeding is increased due to population decline, the homozygosity of deleterious variants will also increase, thereby raising the homozygous load. Recent studies have claimed, however, that these genetic consequences of a population crash can be impacted by past demographic processes. In particular, ancestral bottlenecks may result in the loss of substantial amounts of recessive deleterious variation, as a consequence of both genetic drift and the increased efficacy of selection on homozygous recessive deleterious variants due to inbreeding, i.e. purging. The intertwined effects of demography, inbreeding, drift, and selection on mutation load has thus become an area of great interest for conservation genetics. In particular, the role of purging relative to random genetic drift in the loss of recessive deleterious variants during a bottleneck has been little studied. Here we explore the interplay of these processes using simulations, and relate these results to whole-genome sequences of 295 individuals from five meta-populations of the charismatic Florida scrub-jay (Aphelocoma coerulescens; FSJ). The FSJ is a well-studied bird with decades of demographic and environmental data collected from multiple conservation sites. Importantly, the FSJ has undergone several recent population bottlenecks, and, due to its non-migratory nature and human development, is currently living in fragmented meta-populations across the Florida peninsula. Using both gene prediction and synteny-based approaches, we identify putatively deleterious variants in whole-genome sequencing data for both historic and contemporary birds from five meta-populations. Comparing load across meta-populations and time in the population sequencing data and in forward genetic simulations, we explore the link between genetic load and the population genetic processes of inbreeding, genetic drift, and purifying selection.