David S Gernandt1, Xitlali Aguirre Dugua1, Alejandra Vázquez-Lobo2, Ann Willyard3, Alejandra Moreno Letelier4, Jorge A Pérez de la Rosa5, Daniel Piñero6, Aaron Liston7. 1. Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico. 2. Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Col. Chamilpa, Cuernavaca, Morelos, 62209, Mexico. 3. Biology Department, Hendrix College, Conway, Arkansas, 72032, USA. 4. Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico. 5. Centro Universitario de Ciencias Biológicas y Agropecuarias, Instituto de Botánica, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, 45510, Mexico. 6. Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico. 7. Department of Botany and Plant Pathology, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA.
Abstract
PREMISE OF THE STUDY: Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers. METHODS: We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation. KEY RESULTS: Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal. CONCLUSIONS: Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.
PREMISE OF THE STUDY: Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers. METHODS: We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation. KEY RESULTS: Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal. CONCLUSIONS: Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.
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Authors: Christian Wehenkel; Samantha Del Rocío Mariscal-Lucero; M Socorro González-Elizondo; Víctor A Aguirre-Galindo; Matthias Fladung; Carlos A López-Sánchez Journal: PeerJ Date: 2020-02-26 Impact factor: 2.984