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RAD Sequencing and ...
RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
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- Humble, Emily (author)
- Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England.
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- Dasmahapatra, Kanchon K. (author)
- Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England.
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- Martínez Barrio, Álvaro, 1977- (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär evolution
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- Gregorio, Ines (author)
- Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.
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- Forcada, Jaume (author)
- British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England.
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- Polikeit, Ann-Christin (author)
- Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.
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- Goldsworthy, Simon D. (author)
- South Australian Res & Dev Inst, 2 Hamra Ave, West Beach, SA 5024, Australia.
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- Goebel, Michael E. (author)
- NOAA, Antarctic Ecosyst Res Div, SWFSC, NMFS, La Jolla, CA 92037 USA.
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- Kalinowski, Jorn (author)
- Univ Bielefeld, CeBiTec, Ctr Biotechnol, Univ Str 27, D-33615 Bielefeld, Germany.
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- Wolf, Jochen B. W. (author)
- Uppsala universitet,Evolutionsbiologi,Science for Life Laboratory, SciLifeLab,Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinstried, Germany.
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- Hoffman, Joseph, I (author)
- Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England.
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Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England. Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England. (creator_code:org_t)
- 2018-08-01
- 2018
- English.
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In: G3. - : GENETICS SOCIETY AMERICA. - 2160-1836. ; 8:8, s. 2709-2722
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Abstract
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- PacBio sequencing
- RAD sequencing
- comparative genomics
- single nucleotide polymorphism (SNP)
- linkage disequilibrium (LD)
- population structure
- genomic inbreeding coefficient
Publication and Content Type
- ref (subject category)
- art (subject category)
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Humble, Emily
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Dasmahapatra, Ka ...
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Martínez Barrio, ...
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Gregorio, Ines
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Forcada, Jaume
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Polikeit, Ann-Ch ...
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Goldsworthy, Sim ...
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Goebel, Michael ...
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Kalinowski, Jorn
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Wolf, Jochen B. ...
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Hoffman, Joseph, ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
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G3
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Uppsala University