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

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.

Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell’s and Gray-Cheeked Thrushes (Aves:Catharus bicknelliandCatharus minimus)

“…In general, our estimates of nucleotide diversity for the three Catharus thrushes for which we sequenced multiple individuals were low compared with what we know about intraspecific genomic diversity in birds ( Wang et al 2021 ). The relative magnitudes of diversity for C. ustulatus compared with C. minimus was similar to that found for allozyme diversity assayed by Avise et al (1980) , who estimated heterozygosity in C. ustulatus to be over twice as high as that in C. minimus .…”

Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards

“…For instance, observed data from isolated gorilla populations provided direct evidence of the purging of strongly deleterious alleles in mountain gorillas and eastern lowland gorillas ( Xue et al 2015 ). In contrast, studies on island foxes ( Robinson et al 2016 ), ancient wooly mammoths ( Rogers and Slatkin 2017 ), and brown-eared pheasants ( Wang et al 2021 ) reported inefficiency of purging in small isolated populations. This between-species discrepancy in purging effectiveness implies that the purging of deleterious alleles during population contraction in endangered species may be more complicated than expected, and therefore merits further research.…”

“…Recent research has used genomic data to address the purging of deleterious alleles in some mammals and birds. However, there have been conflicting results on the purging effect in small wild populations ( Xue et al 2015 ; Robinson et al 2016 , 2018 ; Rogers and Slatkin 2017 ; Grossen et al 2020 ; Wang et al 2021 ). For instance, observed data from isolated gorilla populations provided direct evidence of the purging of strongly deleterious alleles in mountain gorillas and eastern lowland gorillas ( Xue et al 2015 ).…”

Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

“…With the population size decreasing, inbreeding accumulated during the evolutionary history of Père David’s deer ( Zhu et al, 2018 ). The LD pattern is a useful indicator for estimating inbreeding at the individual level, and generally LD rapidly decays to very low levels in populations with low inbreeding level ( Wang et al, 2021 ). Père David’s deer exhibited extremely high LD ( Figure 4 ), which implied that a prolonged population decline might have caused an increased overall burden of inbreeding.…”