Cargando…

Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian

Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval li...

Descripción completa

Detalles Bibliográficos
Autores principales: O'Connell, Kyle A., Mulder, Kevin P., Maldonado, Jose, Currie, Kathleen L., Ferraro, Dennis M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434569/
https://www.ncbi.nlm.nih.gov/pubmed/30962914
http://dx.doi.org/10.1002/ece3.4994
_version_ 1783406499475750912
author O'Connell, Kyle A.
Mulder, Kevin P.
Maldonado, Jose
Currie, Kathleen L.
Ferraro, Dennis M.
author_facet O'Connell, Kyle A.
Mulder, Kevin P.
Maldonado, Jose
Currie, Kathleen L.
Ferraro, Dennis M.
author_sort O'Connell, Kyle A.
collection PubMed
description Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within‐pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.
format Online
Article
Text
id pubmed-6434569
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-64345692019-04-08 Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian O'Connell, Kyle A. Mulder, Kevin P. Maldonado, Jose Currie, Kathleen L. Ferraro, Dennis M. Ecol Evol Original Research Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within‐pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes. John Wiley and Sons Inc. 2019-03-06 /pmc/articles/PMC6434569/ /pubmed/30962914 http://dx.doi.org/10.1002/ece3.4994 Text en © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
O'Connell, Kyle A.
Mulder, Kevin P.
Maldonado, Jose
Currie, Kathleen L.
Ferraro, Dennis M.
Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
title Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
title_full Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
title_fullStr Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
title_full_unstemmed Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
title_short Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
title_sort sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434569/
https://www.ncbi.nlm.nih.gov/pubmed/30962914
http://dx.doi.org/10.1002/ece3.4994
work_keys_str_mv AT oconnellkylea samplingrelatedindividualswithinpondsbiasesestimatesofpopulationstructureinapondbreedingamphibian
AT mulderkevinp samplingrelatedindividualswithinpondsbiasesestimatesofpopulationstructureinapondbreedingamphibian
AT maldonadojose samplingrelatedindividualswithinpondsbiasesestimatesofpopulationstructureinapondbreedingamphibian
AT curriekathleenl samplingrelatedindividualswithinpondsbiasesestimatesofpopulationstructureinapondbreedingamphibian
AT ferrarodennism samplingrelatedindividualswithinpondsbiasesestimatesofpopulationstructureinapondbreedingamphibian