RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the lev...
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Genetics Society of America
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Online Access: | http://nora.nerc.ac.uk/id/eprint/520762/ https://nora.nerc.ac.uk/id/eprint/520762/1/Humble.pdf https://doi.org/10.1534/g3.118.200171 |
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ftnerc:oai:nora.nerc.ac.uk:520762 2023-05-15T13:49:35+02:00 RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding Humble, Emily Dasmahapatra, Kanchon K. Martinez-Barrio, Alvaro Gregório, Inês Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Goebel, Michael E. Kalinowski, Jörn Wolf, Jochen B. W. Hoffman, Joseph I. 2018-08 text http://nora.nerc.ac.uk/id/eprint/520762/ https://nora.nerc.ac.uk/id/eprint/520762/1/Humble.pdf https://doi.org/10.1534/g3.118.200171 en eng Genetics Society of America https://nora.nerc.ac.uk/id/eprint/520762/1/Humble.pdf Humble, Emily; Dasmahapatra, Kanchon K.; Martinez-Barrio, Alvaro; Gregório, Inês; Forcada, Jaume orcid:0000-0002-2115-0150 Polikeit, Ann-Christin; Goldsworthy, Simon D.; Goebel, Michael E.; Kalinowski, Jörn; Wolf, Jochen B. W.; Hoffman, Joseph I. 2018 RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding. Genes, Genomes, Genetics, 8 (8). 2709-2722. https://doi.org/10.1534/g3.118.200171 <https://doi.org/10.1534/g3.118.200171> cc_by_4 CC-BY Publication - Article PeerReviewed 2018 ftnerc https://doi.org/10.1534/g3.118.200171 2023-02-04T19:46:58Z Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Canis lupus Natural Environment Research Council: NERC Open Research Archive Antarctic G3 Genes|Genomes|Genetics 8 8 2709 2722 |
institution |
Open Polar |
collection |
Natural Environment Research Council: NERC Open Research Archive |
op_collection_id |
ftnerc |
language |
English |
description |
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization. |
format |
Article in Journal/Newspaper |
author |
Humble, Emily Dasmahapatra, Kanchon K. Martinez-Barrio, Alvaro Gregório, Inês Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Goebel, Michael E. Kalinowski, Jörn Wolf, Jochen B. W. Hoffman, Joseph I. |
spellingShingle |
Humble, Emily Dasmahapatra, Kanchon K. Martinez-Barrio, Alvaro Gregório, Inês Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Goebel, Michael E. Kalinowski, Jörn Wolf, Jochen B. W. Hoffman, Joseph I. RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
author_facet |
Humble, Emily Dasmahapatra, Kanchon K. Martinez-Barrio, Alvaro Gregório, Inês Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Goebel, Michael E. Kalinowski, Jörn Wolf, Jochen B. W. Hoffman, Joseph I. |
author_sort |
Humble, Emily |
title |
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
title_short |
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
title_full |
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
title_fullStr |
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
title_full_unstemmed |
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
title_sort |
rad sequencing and a hybrid antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding |
publisher |
Genetics Society of America |
publishDate |
2018 |
url |
http://nora.nerc.ac.uk/id/eprint/520762/ https://nora.nerc.ac.uk/id/eprint/520762/1/Humble.pdf https://doi.org/10.1534/g3.118.200171 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Canis lupus |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Canis lupus |
op_relation |
https://nora.nerc.ac.uk/id/eprint/520762/1/Humble.pdf Humble, Emily; Dasmahapatra, Kanchon K.; Martinez-Barrio, Alvaro; Gregório, Inês; Forcada, Jaume orcid:0000-0002-2115-0150 Polikeit, Ann-Christin; Goldsworthy, Simon D.; Goebel, Michael E.; Kalinowski, Jörn; Wolf, Jochen B. W.; Hoffman, Joseph I. 2018 RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding. Genes, Genomes, Genetics, 8 (8). 2709-2722. https://doi.org/10.1534/g3.118.200171 <https://doi.org/10.1534/g3.118.200171> |
op_rights |
cc_by_4 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.118.200171 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
8 |
container_issue |
8 |
container_start_page |
2709 |
op_container_end_page |
2722 |
_version_ |
1766251802759528448 |