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...
Published in: | G3 Genes|Genomes|Genetics |
---|---|
Main Authors: | , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Ludwig-Maximilians-Universität München
2018
|
Subjects: | |
Online Access: | https://epub.ub.uni-muenchen.de/67728/1/2709.full.pdf https://epub.ub.uni-muenchen.de/67728/ http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-67728-9 https://doi.org/10.1534/g3.118.200171 |
id |
ftmuenchenepub:oai:epub.ub.uni-muenchen.de:67728 |
---|---|
record_format |
openpolar |
spelling |
ftmuenchenepub:oai:epub.ub.uni-muenchen.de:67728 2023-05-15T13:55:00+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 Gregorio, Ines Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Göbel, Michael E. Kalinowski, Jorn Wolf, Jochen B. W. Hoffman, Joseph 2018-01-01 application/pdf https://epub.ub.uni-muenchen.de/67728/1/2709.full.pdf https://epub.ub.uni-muenchen.de/67728/ http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-67728-9 https://doi.org/10.1534/g3.118.200171 eng eng Ludwig-Maximilians-Universität München Humble, Emily; Dasmahapatra, Kanchon K.; Martinez-Barrio, Alvaro; Gregorio, Ines; Forcada, Jaume; Polikeit, Ann-Christin; Goldsworthy, Simon D.; Göbel, Michael E.; Kalinowski, Jorn; Wolf, Jochen B. W.; Hoffman, Joseph (2018): RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. In: G3-Genes Genomes Genetics, Vol. 8, Nr. 8: S. 2709-2722 [PDF, 1MB] https://epub.ub.uni-muenchen.de/67728/1/2709.full.pdf http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-67728-9 https://epub.ub.uni-muenchen.de/67728/ doi:10.1534/g3.118.200171 G3-Genes Genomes Genetics Department Biologie II ddc:570 doc-type:article Zeitschriftenartikel NonPeerReviewed 2018 ftmuenchenepub https://doi.org/10.1534/g3.118.200171 2022-04-25T12:49:44Z 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 Open Access LMU (Ludwig-Maximilians-University Munich) Antarctic G3 Genes|Genomes|Genetics 8 8 2709 2722 |
institution |
Open Polar |
collection |
Open Access LMU (Ludwig-Maximilians-University Munich) |
op_collection_id |
ftmuenchenepub |
language |
English |
topic |
Department Biologie II ddc:570 |
spellingShingle |
Department Biologie II ddc:570 Humble, Emily Dasmahapatra, Kanchon K. Martinez-Barrio, Alvaro Gregorio, Ines Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Göbel, Michael E. Kalinowski, Jorn Wolf, Jochen B. W. Hoffman, Joseph RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding |
topic_facet |
Department Biologie II ddc:570 |
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 Gregorio, Ines Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Göbel, Michael E. Kalinowski, Jorn Wolf, Jochen B. W. Hoffman, Joseph |
author_facet |
Humble, Emily Dasmahapatra, Kanchon K. Martinez-Barrio, Alvaro Gregorio, Ines Forcada, Jaume Polikeit, Ann-Christin Goldsworthy, Simon D. Göbel, Michael E. Kalinowski, Jorn Wolf, Jochen B. W. Hoffman, Joseph |
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 |
Ludwig-Maximilians-Universität München |
publishDate |
2018 |
url |
https://epub.ub.uni-muenchen.de/67728/1/2709.full.pdf https://epub.ub.uni-muenchen.de/67728/ http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-67728-9 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_source |
G3-Genes Genomes Genetics |
op_relation |
Humble, Emily; Dasmahapatra, Kanchon K.; Martinez-Barrio, Alvaro; Gregorio, Ines; Forcada, Jaume; Polikeit, Ann-Christin; Goldsworthy, Simon D.; Göbel, Michael E.; Kalinowski, Jorn; Wolf, Jochen B. W.; Hoffman, Joseph (2018): RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. In: G3-Genes Genomes Genetics, Vol. 8, Nr. 8: S. 2709-2722 [PDF, 1MB] https://epub.ub.uni-muenchen.de/67728/1/2709.full.pdf http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-67728-9 https://epub.ub.uni-muenchen.de/67728/ doi:10.1534/g3.118.200171 |
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_ |
1766261228853788672 |