Genomics of population decline

Abstract: With human populations forecasted to grow in the next decades, many mammals face increasing anthropogenic threats. The consequential population declines are a precursor to extinctions, as small populations are not only more sensitive to stochastic events, but reduction in population size is generally also followed by a decrease in genetic diversity, which in turn reduces adaptive potential and fitness of the population. By using molecular methods I aimed to estimate the magnitude of the genomic consequences as a result of rapid population declines with a focus on the endangered eastern gorillas. First, I genotyped Grauer’s gorilla (Gorilla beringei graueri) faecal samples, which revealed lower genetic diversity and high differentiation in the peripheral compared to the central populations, indicating a strong effect of genetic drift and limited gene flow among the small, isolated forest fragments (Chapter 1). Next, by using a target capture approach I obtained complete mitochondrial genomes from degraded Grauer’s and mountain (Gorilla beringei beringei) gorilla faecal and museum samples (Chapter 2) which showed a loss of mitochondrial diversity within the last century in Grauer’s gorillas, mainly driven by the extinction of peripheral populations (Chapter 3). Genome-wide sequence data from historical samples suggests that this loss has also affected the nuclear genome, as modern Grauer’s gorillas carry on average more genetic variants with putatively negative fitness consequences than historically. No significant temporal changes were observed in the closely related mountain gorillas, which might be due to their contrasting demographic history (Chapter 4). I then switched study species to the endangered Dryas monkey and find that, despite its possible small population size, the current Dryas monkey population is genetically diverse with low levels of inbreeding and as such likely viable in the long-term if appropriate conservation measures are taken (Chapter 5). Finally, I aimed to estimate the strength of genetic purging across a range of mammalian species. This revealed that although genetic purging might be common among endangered species, it mainly acts on long evolutionary time scales with limited strength during the rapid population declines as experienced by many species today (Chapter 6).