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Research article - Peer-reviewed, 2020

Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi

Song, Kai; Gao, Bin; Halvarsson, Peter; Fang, Yun; Jiang, Ying-Xin; Sun, Yue-Hua; Hoglund, Jacob

Abstract

Background The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and interglacial periods. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouseTetrastes sewerzowiis a forest-dwelling species endemic to the mountains to the east of the Qinghai-TibetPlateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. It is important to place current population status into a broader ecological and evolutionary context to understand their demographic history. Results Analyses of the Chinese Grouse genome revealed fluctuations throughout the Pleistocene in effective population size. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene which was then followed by a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that a suitable habitat shift between high altitude regions to low altitude regions was due to a changing climate. This 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 (LIG) and then a peak and a bottleneck occurring at the last glacial maximum (LGM). Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and fragmented. It will likely become even more fragmented in the future since coniferous forest cover is threatened in the region of their distribution and the availability of such habitat restricts their 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 occurred during the LGM, when the coniferous forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support historical population fluctuations. The distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. To protect the fragmented coniferous forests is an essential action to protect the Chinese Grouse.

Keywords

Demographic history; MaxEnt; Qinghai-Tibet plateau; Chinese grouse; Tetrastes sewerzowi; Whole genome sequence

Published in

BMC Genomics
2020, volume: 21, number: 1, article number: 581
Publisher: BMC

Authors' information

Song, Kai
Uppsala University
Gao, Bin
Chinese Academy of Sciences
Uppsala University
Fang, Yun
Chinese Academy of Sciences
Jiang, Ying-Xin
Chinese Academy of Sciences
Sun, Yue-Hua
Chinese Academy of Sciences
Hoglund, Jacob
Uppsala University

Sustainable Development Goals

SDG15 Life on land

UKÄ Subject classification

Ecology
Genetics

Publication Identifiers

DOI: https://doi.org/10.1186/s12864-020-06957-5

URI (permanent link to this page)

https://res.slu.se/id/publ/107883