Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

Pengcheng Wang, John T. Burley, Yang Liu, Jiang Chang, De Chen, Qi Lu, Shou Hsien Li, Xuming Zhou, Scott Edwards, Zhengwang Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.

Original languageEnglish
Pages (from-to)263-273
Number of pages11
JournalMolecular Biology and Evolution
Volume38
Issue number1
DOIs
Publication statusPublished - 2021 Jan 1

Keywords

  • conservation genetics
  • deleterious alleles
  • genetic diversity
  • inbreeding depression
  • pheasant
  • purifying selection

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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