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- Song, Kai, 1988-, et al.
(författare)
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Conservation genomics in the boreal forest : Population structure and local adaptation in the sibling species Chinese Grouse and Hazel Grouse
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The climate of the world’s arctic regions, including the poles and the Tibetan plateau region, act as a bellwether for global change. On the Tibetan plateau, there are numerous species well adapted to cold environments. The Chinese Grouse and Hazel Grouse are sibling species distributed in the Eurasian subarctic forests of the Tibetan plateau respectively. Conservation genomics are transforming our understanding of organismal responses in a changing Arctic boreal forest. In this study, we used 29 individuals from the sister species Chinese Grouse and Hazel Grouse from the boreal forest in Eurasia. Our results provide insights into the genetic diversity and differentiation in to different geographic populations of the two species. Full genome sequencing of samples covering the distribution area of grouse species throughout the Eurasian boreal forest has enabled us to provide the first analysis of the population structure and introgression. Through selective sweep analysis, we detected that the Chinese Grouse inhabiting the QTP high altitude environment show evidence of having evolved adaptations to hypobaric hypoxia and high ultraviolet radiation.
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- Song, Kai, 1988-, et al.
(författare)
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Demographics and divergence of the sibling species Chinese Grouse and Hazel Grouse inferred from whole genome sequencing
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To provide insights into the role of recent ice ages in species divergence and population history in southern Eurasian boreal forests, we sequenced the genomes of 32 individuals from the sister species Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of outgroup species from Europe and China. Our results show very different population demographic histories between the sibling species. Using PSMC we show that the peak and bottleneck of effective population size (Ne) occurred at different times; the Hazel Grouse had a peak in the Mid-Pleistocene and a bottleneck during the Last Glacial Period, in contrast to the Chinese Grouse, which peaked with a larger population size after the Hazel Grouse. In addition, the northern population of Chinese Grouse inhabiting the Qilian Mountains became separated from the main population residing in the south and since then consistently showed lower effective population size than the southern population. The Hazel Grouse population in northern China had a higher effective population size at the peak of the Last Glacial Period compared to the European population, which appeared to have gone through a severe bottleneck. As revealed by MSMC modelling, both species have recently decreased and now have low effective population sizes. The results of this study, suggest that differences in the demographic processes that shaped the evolutionary history and distribution for both species, will contribute to the understanding of the biological processes affecting the fauna in boreal forests in Eurasia.
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- Song, Kai, 1988-, et al.
(författare)
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Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: The Quaternary is characterized by marked climatic oscillations between glacial and interglacial periods that had worldwide consequences in forming the contemporary diversity of many populations, species and communities. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouse Tetrastes sewerzowi is a forest-dwelling species endemic to the mountains to the east of the Qinghai–Tibet Plateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. Understanding demographic history is important in placing current population status into a broader ecological and evolutionary context.Results: Analysis of the Chinese Grouse genome reveals fluctuation in effective population size throughout the Pleistocene. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene then followed a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that suitable habitat shift between high altitude regions to low altitude regions were due to a changing climate. The result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period and then a peak and a bottleneck occurring at the LGM. Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and will become highly fragmented if boreal forest cover restricts the ecological niche.Conclusions: The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck happened during the LGM, when the conifer forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support the historical population fluctuation. The distribution of the Chinese Grouse was strongly dependent on the boreal forest cover. To protect the fragmented boreal forest is an essential action to protect the Chinese Grouse.
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- Song, Kai, 1988-, et al.
(författare)
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Purifying selection in Grouse is more efficient in large populations
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Inbreeding depression and purging are recognized as essential factors to be considered in conservation programs. Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals, including humans. Genomic techniques are increasingly used in measuring and understanding inbreeding and inbreeding depression and their importance in evolution and conservation. We use whole genome resequencing data from isolated, bottlenecked, and outbred Tetrastes and Lagopus populations in subarctic Eurasia to quantify inbreeding depression and purifying selection. We found a large range of inbreeding measured as FROH in populations of Chinese Grouse (Tetrastes sewerzowi) and Hazel Grouse (T. bonasia). FROH estimated from genome-wide runs of homozygosity (ROH) ranged from 0.02 to 0.24 among Chinese Grouse populations and 0.01 to 0.44 in Hazel grouse. A population of Chinese Grouse residing in the Qilian mountains and the European populations of Hazel Grouse (including samples from Sweden, Germany and North East Poland) were both highly inbred (FROH ranged from 0.10 to 0.23 and 0.11 to 0.44, respectively). Hazel grouse from northern China and Chinese grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels. In addition, through comparison of the ratio between deleterious missense mutations and synonymous mutations, purifying selection was found to be more efficient in Hazel grouse and ptarmigan populations which hold larger population sizes than Chinese grouse. However, when we compared the ratio between loss-of-function and synonymous mutations, Hazel Grouse had slightly higher levels than Chinese Grouse while Willow Ptarmigan and Rock Ptarmigan had lower levels of genetic load. These results indicate that purifying selection has been more efficient in the wide ranging hazel grouse which thereby can sustain higher levels of inbreeding compared to Chinese grouse. Our study provides the first genetic evidence of inbreeding depression and purging patterns in boreal forest species in Eurasia from the respective sibling species and provide relevant information for future conservation and management of the species.
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