Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis
Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigre...
Published in: | BMC Evolutionary Biology |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BioMed Central Ltd.
2014
|
Subjects: | |
Online Access: | http://hdl.handle.net/10468/2234 https://doi.org/10.1186/1471-2148-14-68 |
id |
ftunivcollcork:oai:cora.ucc.ie:10468/2234 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
University College Cork, Ireland: Cork Open Research Archive (CORA) |
op_collection_id |
ftunivcollcork |
language |
English |
topic |
Atlantic salmon Heritability Incomplete sampling MasterBayes Parentage assignment Power analysis Reproductive success |
spellingShingle |
Atlantic salmon Heritability Incomplete sampling MasterBayes Parentage assignment Power analysis Reproductive success Aykanat, Tutku Johnston, Susan E. Cotter, Deirdre Cross, Thomas F. Poole, Russell Prodhl, Paulo A. Reed, Thomas E. Rogan, Ger McGinnity, Philip Primmer, Craig R. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis |
topic_facet |
Atlantic salmon Heritability Incomplete sampling MasterBayes Parentage assignment Power analysis Reproductive success |
description |
Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of ... |
format |
Article in Journal/Newspaper |
author |
Aykanat, Tutku Johnston, Susan E. Cotter, Deirdre Cross, Thomas F. Poole, Russell Prodhl, Paulo A. Reed, Thomas E. Rogan, Ger McGinnity, Philip Primmer, Craig R. |
author_facet |
Aykanat, Tutku Johnston, Susan E. Cotter, Deirdre Cross, Thomas F. Poole, Russell Prodhl, Paulo A. Reed, Thomas E. Rogan, Ger McGinnity, Philip Primmer, Craig R. |
author_sort |
Aykanat, Tutku |
title |
Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis |
title_short |
Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis |
title_full |
Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis |
title_fullStr |
Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis |
title_full_unstemmed |
Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis |
title_sort |
molecular pedigree reconstruction and estimation of evolutionary parameters in a wild atlantic salmon river system with incomplete sampling: a power analysis |
publisher |
BioMed Central Ltd. |
publishDate |
2014 |
url |
http://hdl.handle.net/10468/2234 https://doi.org/10.1186/1471-2148-14-68 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
68 AYKANAT, T., JOHNSTON, S. E., COTTER, D., CROSS, T. F., POOLE, R., PRODŐHL, P. A., REED, T., ROGAN, G., MCGINNITY, P. & PRIMMER, C. R. 2014. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evolutionary Biology, 14:68, 1-17. http://dx.doi.org/10.1186/1471-2148-14-68 doi:10.1186/1471-2148-14-68 17 1471-2148 BMC Evolutionary Biology 1 http://hdl.handle.net/10468/2234 14 |
op_rights |
© Aykanat et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. http://creativecommons.org/licenses/by/2.0 |
op_doi |
https://doi.org/10.1186/1471-2148-14-68 |
container_title |
BMC Evolutionary Biology |
container_volume |
14 |
container_issue |
1 |
container_start_page |
68 |
_version_ |
1810432358828998656 |
spelling |
ftunivcollcork:oai:cora.ucc.ie:10468/2234 2024-09-15T17:56:09+00:00 Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis Aykanat, Tutku Johnston, Susan E. Cotter, Deirdre Cross, Thomas F. Poole, Russell Prodhl, Paulo A. Reed, Thomas E. Rogan, Ger McGinnity, Philip Primmer, Craig R. 2014-03-31 application/pdf application/vnd.openxmlformats-officedocument.wordprocessingml.document http://hdl.handle.net/10468/2234 https://doi.org/10.1186/1471-2148-14-68 en eng BioMed Central Ltd. 68 AYKANAT, T., JOHNSTON, S. E., COTTER, D., CROSS, T. F., POOLE, R., PRODŐHL, P. A., REED, T., ROGAN, G., MCGINNITY, P. & PRIMMER, C. R. 2014. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evolutionary Biology, 14:68, 1-17. http://dx.doi.org/10.1186/1471-2148-14-68 doi:10.1186/1471-2148-14-68 17 1471-2148 BMC Evolutionary Biology 1 http://hdl.handle.net/10468/2234 14 © Aykanat et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. http://creativecommons.org/licenses/by/2.0 Atlantic salmon Heritability Incomplete sampling MasterBayes Parentage assignment Power analysis Reproductive success Article (peer-reviewed) 2014 ftunivcollcork https://doi.org/10.1186/1471-2148-14-68 2024-07-29T03:06:03Z Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of ... Article in Journal/Newspaper Atlantic salmon Salmo salar University College Cork, Ireland: Cork Open Research Archive (CORA) BMC Evolutionary Biology 14 1 68 |