Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus)
Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, hal...
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Online Access: | https://hal.archives-ouvertes.fr/hal-01447439 https://doi.org/10.1016/j.aquaculture.2007.10.036 |
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ftccsdartic:oai:HAL:hal-01447439v1 2023-05-15T18:15:42+02:00 Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) Rodríguez-Ramilo, Silvia Teresa Martínez, Paulino Castro, Jaime Bouza, Carmen Fernández, Jesús Dept Mejora Genet Anim Inst Nacl Invest & Tecnol Agraria & Alimentaria I Universidade de Santiago 2007 https://hal.archives-ouvertes.fr/hal-01447439 https://doi.org/10.1016/j.aquaculture.2007.10.036 en eng HAL CCSD Elsevier info:eu-repo/semantics/altIdentifier/doi/10.1016/j.aquaculture.2007.10.036 hal-01447439 https://hal.archives-ouvertes.fr/hal-01447439 doi:10.1016/j.aquaculture.2007.10.036 PRODINRA: 372773 WOS: 000252299300007 ISSN: 0044-8486 Aquaculture https://hal.archives-ouvertes.fr/hal-01447439 Aquaculture, Elsevier, 2007, 273 (4), pp.434-442. ⟨10.1016/j.aquaculture.2007.10.036⟩ microsatellite molecular marker pairwise pedigree reconstruction coancestry estimator scophthalmus maximus [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2007 ftccsdartic https://doi.org/10.1016/j.aquaculture.2007.10.036 2021-07-24T23:49:02Z Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, half-sibs and unrelated) if there is a previous knowledge of the population structure. Transformations are usually based on arbitrary thresholds, but the possibility of correcting the coancestry estimates via explicit pedigree reconstruction methods has been suggested. Using molecular data for ten highly polymorphic microsatellite loci on a population of turbot (Scophthalmus maximus) with a known genealogy, the behaviour of four pairwise marker-based coancestry estimators and the molecular coancestry has been evaluated. The population consisted on 138 families with 4 full-sib individuals each and one family with 8 full-sib individuals (up to 15 half-sib families were also present due to the sharing of parents between some of the full-sibs families). Our results suggested that transforming the pairwise estimators and the molecular coancestry to family relationships through the establishment of thresholds performs slightly better than the explicit pedigree reconstruction method, when accuracy is measured in a pairwise basis. However, if joint relationships between more than two individuals were tested at a time, the threshold methods led to a high percentage of incongruous triads of full-sib individuals, with Mendelian incompatibilities appearing in congruous full-sib families (more than 70% and 60% in our study, respectively)., The explicit pedigree reconstruction approach, due to its nature, is free from such problems. Therefore, the pedigree reconstruction approach seems to be a valuable tool to provide a congruent and compatible pedigree when the pairwise marker-based coancestry matrices or the molecular coancestry need to be transformed. (C) 2007 Elsevier B.V. All rights reserved. Article in Journal/Newspaper Scophthalmus maximus Turbot Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Aquaculture 273 4 434 442 |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
microsatellite molecular marker pairwise pedigree reconstruction coancestry estimator scophthalmus maximus [SDV]Life Sciences [q-bio] |
spellingShingle |
microsatellite molecular marker pairwise pedigree reconstruction coancestry estimator scophthalmus maximus [SDV]Life Sciences [q-bio] Rodríguez-Ramilo, Silvia Teresa Martínez, Paulino Castro, Jaime Bouza, Carmen Fernández, Jesús Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) |
topic_facet |
microsatellite molecular marker pairwise pedigree reconstruction coancestry estimator scophthalmus maximus [SDV]Life Sciences [q-bio] |
description |
Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, half-sibs and unrelated) if there is a previous knowledge of the population structure. Transformations are usually based on arbitrary thresholds, but the possibility of correcting the coancestry estimates via explicit pedigree reconstruction methods has been suggested. Using molecular data for ten highly polymorphic microsatellite loci on a population of turbot (Scophthalmus maximus) with a known genealogy, the behaviour of four pairwise marker-based coancestry estimators and the molecular coancestry has been evaluated. The population consisted on 138 families with 4 full-sib individuals each and one family with 8 full-sib individuals (up to 15 half-sib families were also present due to the sharing of parents between some of the full-sibs families). Our results suggested that transforming the pairwise estimators and the molecular coancestry to family relationships through the establishment of thresholds performs slightly better than the explicit pedigree reconstruction method, when accuracy is measured in a pairwise basis. However, if joint relationships between more than two individuals were tested at a time, the threshold methods led to a high percentage of incongruous triads of full-sib individuals, with Mendelian incompatibilities appearing in congruous full-sib families (more than 70% and 60% in our study, respectively)., The explicit pedigree reconstruction approach, due to its nature, is free from such problems. Therefore, the pedigree reconstruction approach seems to be a valuable tool to provide a congruent and compatible pedigree when the pairwise marker-based coancestry matrices or the molecular coancestry need to be transformed. (C) 2007 Elsevier B.V. All rights reserved. |
author2 |
Dept Mejora Genet Anim Inst Nacl Invest & Tecnol Agraria & Alimentaria I Universidade de Santiago |
format |
Article in Journal/Newspaper |
author |
Rodríguez-Ramilo, Silvia Teresa Martínez, Paulino Castro, Jaime Bouza, Carmen Fernández, Jesús |
author_facet |
Rodríguez-Ramilo, Silvia Teresa Martínez, Paulino Castro, Jaime Bouza, Carmen Fernández, Jesús |
author_sort |
Rodríguez-Ramilo, Silvia Teresa |
title |
Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) |
title_short |
Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) |
title_full |
Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) |
title_fullStr |
Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) |
title_full_unstemmed |
Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus) |
title_sort |
accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (scophthalmus maximus) |
publisher |
HAL CCSD |
publishDate |
2007 |
url |
https://hal.archives-ouvertes.fr/hal-01447439 https://doi.org/10.1016/j.aquaculture.2007.10.036 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
ISSN: 0044-8486 Aquaculture https://hal.archives-ouvertes.fr/hal-01447439 Aquaculture, Elsevier, 2007, 273 (4), pp.434-442. ⟨10.1016/j.aquaculture.2007.10.036⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.aquaculture.2007.10.036 hal-01447439 https://hal.archives-ouvertes.fr/hal-01447439 doi:10.1016/j.aquaculture.2007.10.036 PRODINRA: 372773 WOS: 000252299300007 |
op_doi |
https://doi.org/10.1016/j.aquaculture.2007.10.036 |
container_title |
Aquaculture |
container_volume |
273 |
container_issue |
4 |
container_start_page |
434 |
op_container_end_page |
442 |
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1766188894207868928 |