A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach
- Autores
- Cappa, Eduardo Pablo; Muñoz, Facundo; Sanchez, Leopoldo; Cantet, Rodolfo Juan Carlos
- Año de publicación
- 2015
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Negative correlation caused by competition among individuals and positive spatial correlation due to environmental heterogeneity may lead to biases in estimating genetic parameters and predicting breeding values (BVs) from forest genetic trials. Former models dealing with competition and environmental heterogeneity did not account for the additive relationships among trees or for the full spatial covariance. This paper extends an individual-tree mixed model with direct additive genetic, genetic, and environmental competition effects, by incorporating a two-dimensional smoothing surface to account for complex patterns of environmental heterogeneity (competition + spatial model (CSM)). We illustrate the proposed model using simulated and real data from a loblolly pine progeny trial. The CSM was compared with three reduced individual-tree mixed models using a real dataset, while simulations comprised only CSM versus true-parameters comparisons. Dispersion parameters were estimated using Bayesian techniques via Gibbs sampling. Simulation results showed that the CSM yielded posterior mean estimates of variance components with slight or negligible biases in the studied scenarios, except for the permanent environment variance. The worst performance of the simulated CSM was under a scenario with weak competition effects and small-scale environmental heterogeneity. When analyzing real data, the CSM yielded a lower value of the deviance information criterion than the reduced models. Moreover, although correlations between predicted BVs calculated from CSM and from a standard model with block effects and direct genetic effects only were high, the ranking among the top 5 % ranked individuals showed differences which indicated that the two models will have quite different genotype selections for the next cycle of breeding.
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Muñoz, Facundo. Institut National de la Recherche Agronomique; Francia
Fil: Sanchez, Leopoldo. Institut National de la Recherche Agronomique; Francia
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina - Materia
-
Individual-Tree Mixed Model
Genetic And Environmental Competition Effects
Environmental Heterogeneity
Two-Dimensional Smoothing Surface - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/19005
Ver los metadatos del registro completo
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oai:ri.conicet.gov.ar:11336/19005 |
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network_name_str |
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spelling |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approachCappa, Eduardo PabloMuñoz, FacundoSanchez, LeopoldoCantet, Rodolfo Juan CarlosIndividual-Tree Mixed ModelGenetic And Environmental Competition EffectsEnvironmental HeterogeneityTwo-Dimensional Smoothing Surfacehttps://purl.org/becyt/ford/4.1https://purl.org/becyt/ford/4Negative correlation caused by competition among individuals and positive spatial correlation due to environmental heterogeneity may lead to biases in estimating genetic parameters and predicting breeding values (BVs) from forest genetic trials. Former models dealing with competition and environmental heterogeneity did not account for the additive relationships among trees or for the full spatial covariance. This paper extends an individual-tree mixed model with direct additive genetic, genetic, and environmental competition effects, by incorporating a two-dimensional smoothing surface to account for complex patterns of environmental heterogeneity (competition + spatial model (CSM)). We illustrate the proposed model using simulated and real data from a loblolly pine progeny trial. The CSM was compared with three reduced individual-tree mixed models using a real dataset, while simulations comprised only CSM versus true-parameters comparisons. Dispersion parameters were estimated using Bayesian techniques via Gibbs sampling. Simulation results showed that the CSM yielded posterior mean estimates of variance components with slight or negligible biases in the studied scenarios, except for the permanent environment variance. The worst performance of the simulated CSM was under a scenario with weak competition effects and small-scale environmental heterogeneity. When analyzing real data, the CSM yielded a lower value of the deviance information criterion than the reduced models. Moreover, although correlations between predicted BVs calculated from CSM and from a standard model with block effects and direct genetic effects only were high, the ranking among the top 5 % ranked individuals showed differences which indicated that the two models will have quite different genotype selections for the next cycle of breeding.Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Muñoz, Facundo. Institut National de la Recherche Agronomique; FranciaFil: Sanchez, Leopoldo. Institut National de la Recherche Agronomique; FranciaFil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaSpringer Heidelberg2015-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/19005Cappa, Eduardo Pablo; Muñoz, Facundo; Sanchez, Leopoldo; Cantet, Rodolfo Juan Carlos; A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach; Springer Heidelberg; Tree Genetics & Genomes; 11; 12-2015; 120-1351614-29421614-2950CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s11295-015-0917-3info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs11295-015-0917-3info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:06:25Zoai:ri.conicet.gov.ar:11336/19005instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:06:25.554CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
title |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
spellingShingle |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach Cappa, Eduardo Pablo Individual-Tree Mixed Model Genetic And Environmental Competition Effects Environmental Heterogeneity Two-Dimensional Smoothing Surface |
title_short |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
title_full |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
title_fullStr |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
title_full_unstemmed |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
title_sort |
A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach |
dc.creator.none.fl_str_mv |
Cappa, Eduardo Pablo Muñoz, Facundo Sanchez, Leopoldo Cantet, Rodolfo Juan Carlos |
author |
Cappa, Eduardo Pablo |
author_facet |
Cappa, Eduardo Pablo Muñoz, Facundo Sanchez, Leopoldo Cantet, Rodolfo Juan Carlos |
author_role |
author |
author2 |
Muñoz, Facundo Sanchez, Leopoldo Cantet, Rodolfo Juan Carlos |
author2_role |
author author author |
dc.subject.none.fl_str_mv |
Individual-Tree Mixed Model Genetic And Environmental Competition Effects Environmental Heterogeneity Two-Dimensional Smoothing Surface |
topic |
Individual-Tree Mixed Model Genetic And Environmental Competition Effects Environmental Heterogeneity Two-Dimensional Smoothing Surface |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/4.1 https://purl.org/becyt/ford/4 |
dc.description.none.fl_txt_mv |
Negative correlation caused by competition among individuals and positive spatial correlation due to environmental heterogeneity may lead to biases in estimating genetic parameters and predicting breeding values (BVs) from forest genetic trials. Former models dealing with competition and environmental heterogeneity did not account for the additive relationships among trees or for the full spatial covariance. This paper extends an individual-tree mixed model with direct additive genetic, genetic, and environmental competition effects, by incorporating a two-dimensional smoothing surface to account for complex patterns of environmental heterogeneity (competition + spatial model (CSM)). We illustrate the proposed model using simulated and real data from a loblolly pine progeny trial. The CSM was compared with three reduced individual-tree mixed models using a real dataset, while simulations comprised only CSM versus true-parameters comparisons. Dispersion parameters were estimated using Bayesian techniques via Gibbs sampling. Simulation results showed that the CSM yielded posterior mean estimates of variance components with slight or negligible biases in the studied scenarios, except for the permanent environment variance. The worst performance of the simulated CSM was under a scenario with weak competition effects and small-scale environmental heterogeneity. When analyzing real data, the CSM yielded a lower value of the deviance information criterion than the reduced models. Moreover, although correlations between predicted BVs calculated from CSM and from a standard model with block effects and direct genetic effects only were high, the ranking among the top 5 % ranked individuals showed differences which indicated that the two models will have quite different genotype selections for the next cycle of breeding. Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Muñoz, Facundo. Institut National de la Recherche Agronomique; Francia Fil: Sanchez, Leopoldo. Institut National de la Recherche Agronomique; Francia Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina |
description |
Negative correlation caused by competition among individuals and positive spatial correlation due to environmental heterogeneity may lead to biases in estimating genetic parameters and predicting breeding values (BVs) from forest genetic trials. Former models dealing with competition and environmental heterogeneity did not account for the additive relationships among trees or for the full spatial covariance. This paper extends an individual-tree mixed model with direct additive genetic, genetic, and environmental competition effects, by incorporating a two-dimensional smoothing surface to account for complex patterns of environmental heterogeneity (competition + spatial model (CSM)). We illustrate the proposed model using simulated and real data from a loblolly pine progeny trial. The CSM was compared with three reduced individual-tree mixed models using a real dataset, while simulations comprised only CSM versus true-parameters comparisons. Dispersion parameters were estimated using Bayesian techniques via Gibbs sampling. Simulation results showed that the CSM yielded posterior mean estimates of variance components with slight or negligible biases in the studied scenarios, except for the permanent environment variance. The worst performance of the simulated CSM was under a scenario with weak competition effects and small-scale environmental heterogeneity. When analyzing real data, the CSM yielded a lower value of the deviance information criterion than the reduced models. Moreover, although correlations between predicted BVs calculated from CSM and from a standard model with block effects and direct genetic effects only were high, the ranking among the top 5 % ranked individuals showed differences which indicated that the two models will have quite different genotype selections for the next cycle of breeding. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-12 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/19005 Cappa, Eduardo Pablo; Muñoz, Facundo; Sanchez, Leopoldo; Cantet, Rodolfo Juan Carlos; A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach; Springer Heidelberg; Tree Genetics & Genomes; 11; 12-2015; 120-135 1614-2942 1614-2950 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/19005 |
identifier_str_mv |
Cappa, Eduardo Pablo; Muñoz, Facundo; Sanchez, Leopoldo; Cantet, Rodolfo Juan Carlos; A novel individual-tree mixed model to account for competition and environmental heterogeneity: a Bayesian approach; Springer Heidelberg; Tree Genetics & Genomes; 11; 12-2015; 120-135 1614-2942 1614-2950 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1007/s11295-015-0917-3 info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs11295-015-0917-3 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Springer Heidelberg |
publisher.none.fl_str_mv |
Springer Heidelberg |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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1844613912930025472 |
score |
13.070432 |