@article{9723fab7e2d444aea22b0cd70323ab07,
title = "Not out of the woods yet: Signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re-expanding wader, the black-faced spoonbill Platalea minor",
abstract = "The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) after its rapid population recovery. Our data suggest that the bird's effective population size, Ne, had been relatively stable (7500–9000) since 22,000 years ago; however, a recent brief yet severe bottleneck (Ne = 20) which we here estimated to occur around the 1940s wiped out >99% of its historical Ne in roughly three generations. Despite a >15-fold population recovery since 1988, we found that black-faced spoonbill population has higher levels of inbreeding (7.4 times more runs of homozygosity) than its sister species, the royal spoonbill (P. regia), which is not thought to have undergone a marked population contraction. Although the two spoonbills have similar levels of genome-wide genetic diversity, our results suggest that selection on more genes was relaxed in the black-faced spoonbill; moreover individual black-faced spoonbills carry more putatively deleterious mutations (Grantham's score > 50), and may therefore express more deleterious phenotypic effects than royal spoonbills. Here we demonstrate the value of using genomic indices to monitor levels of genetic erosion, inbreeding and mutation load in species with conservation concerns. To mitigate the prolonged negative genetic effect of a population bottleneck, we recommend that all possible measures should be employed to maintain population growth of a threatened species.",
author = "Li, {Shou Hsien} and Yang Liu and Yeh, {Chia Fen} and Yuchen Fu and Yeung, {Carol K.L.} and Lee, {Chun Cheng} and Chiu, {Chi Cheng} and Kuo, {Tung Hui} and Chan, {Fang Tse} and Chen, {Yu Chia} and Ko, {Wen Ya} and Yao, {Cheng Te}",
note = "Funding Information: We thank Terry Chesser and the Commonwealth Scientific and Industrial Research Organization of Australia for providing samples of the royal spoonbills and Carrie K.W. Ma for providing samplings of black‐faced spoonbills from Hong Kong. We are grateful for the valuable help and comments by Chih‐Ming Hong, Wei Liang, Teng‐Chiu Lin, and Benyang Liao. We thank Dr Josephine Pemberton and three anonymous reviewers providing numerous insightful and valuable comments to our earlier version of manuscript. We are in debt to Alan Watson who has greatly improved the readability of this manuscript. This work was supported by grants to C.‐ T. Yao from the Taiwan Endemic Species Research Institute and to S.‐H. Li from the Ministry of Science and Technology, Taiwan, R.O.C., and Y. Liu by Forestry Administration of Guangdong Province, China (DFGP Project of Fauna of Guangdong‐202115). It was also kindly supported by endorsement from Mr. Y.‐C. Chen. Funding Information: We thank Terry Chesser and the Commonwealth Scientific and Industrial Research Organization of Australia for providing samples of the royal spoonbills and Carrie K.W. Ma for providing samplings of black-faced spoonbills from Hong Kong. We are grateful for the valuable help and comments by Chih-Ming Hong, Wei Liang, Teng-Chiu Lin, and Benyang Liao. We thank Dr Josephine Pemberton and three anonymous reviewers providing numerous insightful and valuable comments to our earlier version of manuscript. We are in debt to Alan Watson who has greatly improved the readability of this manuscript. This work was supported by grants to C.- T. Yao from the Taiwan Endemic Species Research Institute and to S.-H. Li from the Ministry of Science and Technology, Taiwan, R.O.C., and Y. Liu by Forestry Administration of Guangdong Province, China (DFGP Project of Fauna of Guangdong-202115). It was also kindly supported by endorsement from Mr. Y.-C. Chen. Publisher Copyright: {\textcopyright} 2021 John Wiley & Sons Ltd",
year = "2022",
month = jan,
doi = "10.1111/mec.16260",
language = "English",
volume = "31",
pages = "529--545",
journal = "Molecular Ecology",
issn = "0962-1083",
publisher = "Wiley-Blackwell",
number = "2",
}