title: Genetic, morphological, geographical and ecological approaches reveal phylogenetic relationships in complex groups, an example of recently diverged pinyon pine species (Subsection Cembroides).
abstract: Elucidating phylogenetic relationships and species boundaries within complex taxonomic groups is challenging for intrinsic and extrinsic (i.e., technical) reasons. Mexican pinyon pines are a complex group whose phylogenetic relationships and species boundaries have been widely studied but poorly resolved, partly due to intrinsic ecological and evolutionary features such as low morphological and genetic differentiation caused by recent divergence, hybridization and introgression. Extrinsic factors such as limited sampling and difficulty in selecting informative molecular markers have also impeded progress. Some of the Mexican pinyon pines are of conservation concern but others may remain unprotected because the species boundaries have not been established. In this study we combined approaches to resolve the phylogenetic relationships in this complex group and to establish species boundaries in four recently diverged taxa: P. discolor, P. johannis, P. culminicola and P. cembroides. We performed phylogenetic analyses using the chloroplast markers matK and psbA-trnH as well as complete and partial chloroplast genomes of species of Subsection Cembroides. Additionally, we performed a phylogeographic analysis combining genetic data (18 chloroplast markers), morphological data and geographical data to define species boundaries in four recently diverged taxa. Ecological divergence was supported by differences in climate among localities for distinct genetic lineages. Whereas the phylogenetic analysis inferred with matK and psbA-trnH was unable to resolve the relationships in this complex group, we obtained a resolved phylogeny with the use of the chloroplast genomes. The resolved phylogeny was concordant with a haplotype network obtained using chloroplast markers. In species with potential for recent divergence, hybridization or introgression, nonhierarchical network-based approaches are probably more appropriate to protect against misclassification due to incomplete lineage sorting. The boundaries among genetic lineages were delimited by the inclusion of morphological, geographical and ecological data in the haplotype network. These multiple lines of evidence help to assign species boundaries in this complex group. P. johannis, P. discolor, P. culminicola and P. cembroides are different species based on their genetic, morphological and ecological niche differences. We suggest a reevaluation of the conservation status of these species considering the information generated in this study.
authors.affiliation: Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Coyoacán, DF 04510, Mexico; Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ 86011, USA. Electronic address: lluvia.flores@nau.edu.
authors.forename: Lluvia
authors.initials: L
authors.lastname: Flores-Rentería
authors.forename: Ana
authors.initials: A
authors.lastname: Wegier
authors.forename: Diego
authors.initials: D
authors.lastname: Ortega Del Vecchyo
authors.forename: Alejandra
authors.initials: A
authors.lastname: Ortíz-Medrano
authors.forename: Daniel
authors.initials: D
authors.lastname: Piñero
authors.forename: Amy V
authors.initials: AV
authors.lastname: Whipple
authors.forename: Francisco
authors.initials: F
authors.lastname: Molina-Freaner
authors.forename: César A
authors.initials: CA
authors.lastname: Domínguez
mesh_terms: D001499:Bayes Theorem; D003247:Conservation of Natural Resources; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D054628:Genome, Chloroplast; D006239:Haplotypes; D008800:Mexico; D018895:Microsatellite Repeats; D008957:Models, Genetic; D010802:Phylogeny; D058974:Phylogeography; D028223:Pinus / Q000145:classification* / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant
keywords: Complex taxonomic groups; Cryptic species; Pinus cembroides; Pinus culminicola; Pinus discolor; Pinus johannis