Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data
Summary: This protocol demonstrates how a fragmented reference genome and low-coverage sequencing data can be efficiently utilized for population genetic analyses of a species with highly reduced genetic diversity. Focusing on endangered Saimaa ringed seals, we detail the steps for data preparation...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723005348 |
| _version_ | 1797676567046914048 |
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| author | Emmi Olkkonen Ari Löytynoja |
| author_facet | Emmi Olkkonen Ari Löytynoja |
| author_sort | Emmi Olkkonen |
| collection | DOAJ |
| description | Summary: This protocol demonstrates how a fragmented reference genome and low-coverage sequencing data can be efficiently utilized for population genetic analyses of a species with highly reduced genetic diversity. Focusing on endangered Saimaa ringed seals, we detail the steps for data preparation and conventional analyses and then extend the latter by combining genomic and geospatial data. In addition, we introduce coancestry as a measure of genetic identity and describe accessible tools for the quantification of across-genome variation in genetic diversity.For complete details on the use and execution of this protocol, please refer to Löytynoja et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-11T22:31:05Z |
| format | Article |
| id | doaj.art-98a05e98a29e4c2098a6c53b09a3c172 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-11T22:31:05Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-98a05e98a29e4c2098a6c53b09a3c1722023-09-23T05:12:41ZengElsevierSTAR Protocols2666-16672023-12-0144102567Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence dataEmmi Olkkonen0Ari Löytynoja1Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Corresponding authorInstitute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, FinlandSummary: This protocol demonstrates how a fragmented reference genome and low-coverage sequencing data can be efficiently utilized for population genetic analyses of a species with highly reduced genetic diversity. Focusing on endangered Saimaa ringed seals, we detail the steps for data preparation and conventional analyses and then extend the latter by combining genomic and geospatial data. In addition, we introduce coancestry as a measure of genetic identity and describe accessible tools for the quantification of across-genome variation in genetic diversity.For complete details on the use and execution of this protocol, please refer to Löytynoja et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723005348Sequence AnalysisGenomicsEvolutionary Biology |
| spellingShingle | Emmi Olkkonen Ari Löytynoja Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data STAR Protocols Sequence Analysis Genomics Evolutionary Biology |
| title | Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data |
| title_full | Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data |
| title_fullStr | Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data |
| title_full_unstemmed | Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data |
| title_short | Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data |
| title_sort | analysis of population structure and genetic diversity in low variance saimaa ringed seals using low coverage whole genome sequence data |
| topic | Sequence Analysis Genomics Evolutionary Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723005348 |
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