Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering
Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering...
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ftdoajarticles:oai:doaj.org/article:6315a1012ad74cbcb75ccafb545d419c 2023-05-15T17:52:25+02:00 Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering Suresh A. Sethi Daniel Linden John Wenburg Cara Lewis Patrick Lemons Angela Fuller Matthew P. Hare 2016-01-01T00:00:00Z https://doi.org/10.1098/rsos.160457 https://doaj.org/article/6315a1012ad74cbcb75ccafb545d419c EN eng The Royal Society https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.160457 https://doaj.org/toc/2054-5703 2054-5703 doi:10.1098/rsos.160457 https://doaj.org/article/6315a1012ad74cbcb75ccafb545d419c Royal Society Open Science, Vol 3, Iss 12 (2016) sample matching genotyping error inference non-invasive capture–recapture Science Q article 2016 ftdoajarticles https://doi.org/10.1098/rsos.160457 2022-12-31T08:21:59Z Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark–recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark–recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus (Odobenus rosmarus divergens) and fishers (Pekania pennanti). A novel two-stage clustering approach is demonstrated for genetic mark–recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark–recapture studies. Moderately sized SNP (64+) and MSAT (10–15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding. Article in Journal/Newspaper Odobenus rosmarus walrus* Directory of Open Access Journals: DOAJ Articles Pacific Royal Society Open Science 3 12 160457 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
sample matching genotyping error inference non-invasive capture–recapture Science Q |
spellingShingle |
sample matching genotyping error inference non-invasive capture–recapture Science Q Suresh A. Sethi Daniel Linden John Wenburg Cara Lewis Patrick Lemons Angela Fuller Matthew P. Hare Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
topic_facet |
sample matching genotyping error inference non-invasive capture–recapture Science Q |
description |
Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark–recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark–recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus (Odobenus rosmarus divergens) and fishers (Pekania pennanti). A novel two-stage clustering approach is demonstrated for genetic mark–recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark–recapture studies. Moderately sized SNP (64+) and MSAT (10–15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding. |
format |
Article in Journal/Newspaper |
author |
Suresh A. Sethi Daniel Linden John Wenburg Cara Lewis Patrick Lemons Angela Fuller Matthew P. Hare |
author_facet |
Suresh A. Sethi Daniel Linden John Wenburg Cara Lewis Patrick Lemons Angela Fuller Matthew P. Hare |
author_sort |
Suresh A. Sethi |
title |
Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
title_short |
Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
title_full |
Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
title_fullStr |
Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
title_full_unstemmed |
Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
title_sort |
accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering |
publisher |
The Royal Society |
publishDate |
2016 |
url |
https://doi.org/10.1098/rsos.160457 https://doaj.org/article/6315a1012ad74cbcb75ccafb545d419c |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Odobenus rosmarus walrus* |
genre_facet |
Odobenus rosmarus walrus* |
op_source |
Royal Society Open Science, Vol 3, Iss 12 (2016) |
op_relation |
https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.160457 https://doaj.org/toc/2054-5703 2054-5703 doi:10.1098/rsos.160457 https://doaj.org/article/6315a1012ad74cbcb75ccafb545d419c |
op_doi |
https://doi.org/10.1098/rsos.160457 |
container_title |
Royal Society Open Science |
container_volume |
3 |
container_issue |
12 |
container_start_page |
160457 |
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1766159831734943744 |