Darren Irwin

and 16 more

Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these regions can result from the accumulation of mutational differences in low-recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce a method to identify large well-differentiated haploblock regions (LHBRs), based on the variance in standardized heterozygosity (ViSHet) of single nucleotide polymorphism (SNP) genotypes among individuals, calculated across a genomic region (500 SNPs in our case). We apply this method to the greenish warbler (Phylloscopus trochiloides) ring species, using a newly assembled reference genome and genotypes at more than 1 million SNPs among 257 individuals. Most chromosomes carry a single distinctive LHBR, containing 4-6 distinct haplotypes that are associated with geography, enabling detection of hybridization events and transition zones between taxa. LHBRs have exceptionally low within-haplotype nucleotide variation and moderately low between-haplotype nucleotide distance, suggesting their establishment through recurrent selective sweeps at varying geographic scales. Meiotic drive is potentially a powerful mechanism of producing such selective sweeps, and the LHBRs are likely to often represent centromeric regions where recombination is restricted. Links between populations enable introgression of favored haplotypes and we identify one haploblock showing a highly discordant distribution compared to the rest of the genome, being present in two distantly separated geographic regions that are at similar latitudes in both east and west Asia. Our results set the stage for detailed studies of haploblocks, including their genomic location, gene content, and contribution to reproductive isolation.

Kexin Peng

and 9 more

Winter, the most challenging season for animals, is usually accompanied by extremely cold temperatures and limited food resources. Harsh winter conditions force birds to develop behavioral and physiological adaptations to reduce mortality. Birds might select for sexual segregation to reduce conflict between different social hierarchies at the population level. They can also adjust their body conditioning via fat reserve to balance the trade-off between starvation and predation at the individual level. Using mist-netting surveys and bird banding, we traced 61 orange-flanked bush-robin (Tarsiger cyanurus), an abundant and easily-observed long-distance migratory bird exhibiting delayed plumage maturation, to better understand the winter adaptation of these songbirds. We found that the number of 2yr+ adult males with bright-blue plumage was significantly lower than the number of males with olive-brown plumage. However, the sex-ratio was only slightly skewed to males with olive-brown plumage, suggesting that habitat-type influences sexual segregation. This robin tends to become heavier and store more fat over the course of winter, as they can fine-tune their fat reserve in response to changes in weather (including temperature, humidity, and snowfall) and food abundance. Interestingly, capturing the birds may also have a significant positive effect on their fat reserve. Overall, these results improved our understanding of the flexibility in adaptation of small passerine birds wintering in a subtropical forest and provided vision for considering the inevitable influence by ornithology field methods.