Quantifying inbreeding depression in wild bird populations using genomic methods

Abstract

Inbreeding depression can have major negative effects on both individual fitness and population performance. Complex environmental and genetic factors make explicitly disentangling processes contributing to inbreeding depression challenging, particularly in natural open populations where necessary fitness and inbreeding data are only rarely available. As such, studies of inbreeding effects in the wild have been largely limited to insular populations with historical bottlenecks or remnant small population sizes, where population dynamics likely increase the presence and impact of inbreeding load. Consequently, the effect of inbreeding depression over lifetime fitness in large and open populations remains poorly understood. Genomic estimates of realised inbreeding are becoming more accessible, and are able to quantify inbreeding in both immigrants and founders; however, such studies remain limited by the difficulties of quantifying lifetime fitness in the wild.

In this thesis, I present three studies on the genomic basis of inbreeding depression in two wild populations of iconic Australian birds, superb fairy-wrens (Malurus cyaneus), and purple-crowned fairy-wrens (Malurus coronatus coronatus). In Chapter 1, I assess the effect of genomic inbreeding over the full life-history of superb fairy-wrens. While genomic methods were able to recover previous pedigree-based findings of inbreeding depression in early nestling condition, inbreeding effects were not carried through fledgling or juvenile mortality. The only lifetime fitness trait affected, male extra-pair paternity, is highly variable and under strong sexual selection. My findings suggest that natural populations experiencing high effective population sizes and regular immigration and emigration might be affected by inbreeding depression less than previously assumed. In Chapter 2, I examine the effect of genomic inbreeding over the full life-history of purple-crowned fairy-wrens and show that inbreeding has cumulative effects over individual lifetime, as well as additional sex-specific effects on male reproductive success. Finally, in Chapter 3, I further explore a possible somatic explanation for these lifetime inbreeding effects in purple-crowned fairy-wrens by testing for inbreeding depression in nestling telomere length, an early-life indicator of lifespan. My results indicate no direct early somatic costs of inbreeding even under adverse hot and dry conditions, but suggest cryptic intergenerational effects via maternal age and inbreeding.

This thesis provides a detailed breakdown of the somatic and lifetime costs of genomic inbreeding in two iconic Australian species. Moreover, it suggests that natural populations experiencing high effective population sizes and regular dispersal might be affected by inbreeding depression less than previously assumed, or via cryptic intergenerational pathways. Show more