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A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in...

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Autores principales: Mohr, David W., Gaughran, Stephen J., Paschall, Justin, Naguib, Ahmed, Pang, Andy Wing Chun, Dudchenko, Olga, Aiden, Erez Lieberman, Church, Deanna M., Scott, Alan F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9323584/
https://www.ncbi.nlm.nih.gov/pubmed/35886053
http://dx.doi.org/10.3390/genes13071270
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author Mohr, David W.
Gaughran, Stephen J.
Paschall, Justin
Naguib, Ahmed
Pang, Andy Wing Chun
Dudchenko, Olga
Aiden, Erez Lieberman
Church, Deanna M.
Scott, Alan F.
author_facet Mohr, David W.
Gaughran, Stephen J.
Paschall, Justin
Naguib, Ahmed
Pang, Andy Wing Chun
Dudchenko, Olga
Aiden, Erez Lieberman
Church, Deanna M.
Scott, Alan F.
author_sort Mohr, David W.
collection PubMed
description The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.
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spelling pubmed-93235842022-07-27 A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability Mohr, David W. Gaughran, Stephen J. Paschall, Justin Naguib, Ahmed Pang, Andy Wing Chun Dudchenko, Olga Aiden, Erez Lieberman Church, Deanna M. Scott, Alan F. Genes (Basel) Article The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species. MDPI 2022-07-18 /pmc/articles/PMC9323584/ /pubmed/35886053 http://dx.doi.org/10.3390/genes13071270 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Mohr, David W.
Gaughran, Stephen J.
Paschall, Justin
Naguib, Ahmed
Pang, Andy Wing Chun
Dudchenko, Olga
Aiden, Erez Lieberman
Church, Deanna M.
Scott, Alan F.
A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
title A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
title_full A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
title_fullStr A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
title_full_unstemmed A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
title_short A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
title_sort chromosome-length assembly of the hawaiian monk seal (neomonachus schauinslandi): a history of “genetic purging” and genomic stability
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9323584/
https://www.ncbi.nlm.nih.gov/pubmed/35886053
http://dx.doi.org/10.3390/genes13071270
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