Divergence, selection, demographic history and conservation genomics of sibling bird species in boreal forest in Northern Eurasia and the Qinghai-Tibetan Plateau

Sammanfattning: I used two pairs of sibling boreal forest bird species to study divergence, selection, demographics, and conservation in northern Eurasia and the Qinghai-Tibetan Plateau at the microsatellite level (chapter 1) and whole genome level (chapters 2, 3, 4 and 5). In chapter 1, which is the first study to describe genetic diversity of the Sichuan Jay, I used microsatellite markers to estimate genetic differentiation in Sichuan Jay and Siberian Jay populations. The results showed similar levels of genetic variability, strong population structure, and high genetic differentiation between the two species and among different populations. In chapter 2, I used demographic analyses, and found that the Chinese Grouse has experienced substantial changes in population size from the beginning of the last interglacial, with a peak just before the last glacial maximum. The results inferred from the whole genome sequencing and species distribution models support a history of population size fluctuations. In chapter 3 to 5, I used population genomic methods to explore genomic variation, demographic divergence, local adaptation, and inbreeding from 29 whole genome re-sequenced individuals of Chinese Grouse and Hazel Grouse. I found strong evidence for population structure, changing demographic histories, and varying inbreeding levels and genetic load within both species. In Chinese Grouse, an isolated population in the northern part of the species range showed the lowest genetic diversity, high pairwise FST, high LD decay, higher inbreeding and genetic load compared to two other populations. In Hazel Grouse, there were strong population differences and inbreeding levels among the three populations, especially among the Swedish and German populations. The Swedish population likely lost genetic diversity during the re-colonization of the boreal forests in Scandinavia after the last glaciation. Analyses of genetic load showed that purifying selection of mildly deleterious mutations has been more efficient in Hazel Grouse, a species with a larger population size and range compared to Chinese Grouse. However, when I compared the genetic load as the ratio between highly deleterious loss-of-function mutations and synonymous mutations for Chinese Grouse and Hazel Grouse, purifying selection did not seem to have a large effect. My findings show that small, isolated and fragmented populations of forests birds loose genetic variation and may thereby become vulnerable to future challenges and also that populations may track past habitat changes and adapt to local conditions.