RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding

Humble E, Dasmahapatra KK, Martinez-Barrio A, Gregório I, Forcada J, Polikeit A-C, Goldsworthy SD, Goebel ME, Kalinowski J, Wolf JBW, Hoffman J (2018)
G3: Genes|Genomes|Genetics 8(8): 2709-2722.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
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.
Stichworte
PacBio sequencing; RAD sequencing; comparative genomics; single nucleotide polymorphism (SNP); linkage disequilibrium (LD); population structure; genomic inbreeding coefficient
Erscheinungsjahr
2018
Zeitschriftentitel
G3: Genes|Genomes|Genetics
Band
8
Ausgabe
8
Seite(n)
2709-2722
eISSN
2160-1836
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
Page URI
https://pub.uni-bielefeld.de/record/2930693

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Humble E, Dasmahapatra KK, Martinez-Barrio A, et al. RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3: Genes|Genomes|Genetics. 2018;8(8):2709-2722.
Humble, E., Dasmahapatra, K. K., Martinez-Barrio, A., Gregório, I., Forcada, J., Polikeit, A. - C., Goldsworthy, S. D., et al. (2018). RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3: Genes|Genomes|Genetics, 8(8), 2709-2722. doi:10.1534/g3.118.200171
Humble, E., Dasmahapatra, K. K., Martinez-Barrio, A., Gregório, I., Forcada, J., Polikeit, A. - C., Goldsworthy, S. D., Goebel, M. E., Kalinowski, J., Wolf, J. B. W., et al. (2018). RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3: Genes|Genomes|Genetics 8, 2709-2722.
Humble, E., et al., 2018. RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3: Genes|Genomes|Genetics, 8(8), p 2709-2722.
E. Humble, et al., “RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding”, G3: Genes|Genomes|Genetics, vol. 8, 2018, pp. 2709-2722.
Humble, E., Dasmahapatra, K.K., Martinez-Barrio, A., Gregório, I., Forcada, J., Polikeit, A.-C., Goldsworthy, S.D., Goebel, M.E., Kalinowski, J., Wolf, J.B.W., Hoffman, J.: RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3: Genes|Genomes|Genetics. 8, 2709-2722 (2018).
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., and Hoffman, Joseph. “RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding”. G3: Genes|Genomes|Genetics 8.8 (2018): 2709-2722.
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