Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.

Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central Am...

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Autores principales:	Sergio Hernández-León, David S Gernandt, Jorge A Pérez de la Rosa, Lev Jardón-Barbolla
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9db9db70d1bd4f0ab2c4beaeb2392659
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spelling	oai:doaj.org-article:9db9db70d1bd4f0ab2c4beaeb23926592021-11-18T09:01:57ZPhylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.1932-620310.1371/journal.pone.0070501https://doaj.org/article/9db9db70d1bd4f0ab2c4beaeb23926592013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23936218/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities.Sergio Hernández-LeónDavid S GernandtJorge A Pérez de la RosaLev Jardón-BarbollaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e70501 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sergio Hernández-León David S Gernandt Jorge A Pérez de la Rosa Lev Jardón-Barbolla Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.
description	Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities.
format	article
author	Sergio Hernández-León David S Gernandt Jorge A Pérez de la Rosa Lev Jardón-Barbolla
author_facet	Sergio Hernández-León David S Gernandt Jorge A Pérez de la Rosa Lev Jardón-Barbolla
author_sort	Sergio Hernández-León
title	Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.
title_short	Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.
title_full	Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.
title_fullStr	Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.
title_full_unstemmed	Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.
title_sort	phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid dna.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9db9db70d1bd4f0ab2c4beaeb2392659
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Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA.

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