2015
Cavender-Bares, Jeannine; González-Rodríguez, Antonio; Eaton, Deren A. R.; Hipp, Andrew A. L.; Beulke, Anne; Manos, Paul S.
Phylogeny and biogeography of the american live oaks (Quercus subsection Virentes): A genomic and population genetics approach Artículo de revista
En: Molecular Ecology, vol. 24, iss. 14, pp. 3668-3687, 2015, ISSN: 1365294X.
Resumen | Enlaces | Etiquetas: Conservation, Ecological and climatic niches, Fossil calibration, Genomic data, introgression, Phylogeography, RADseq, Sea of Cortés, Virentes
@article{Cavender-Bares2015,
title = {Phylogeny and biogeography of the american live oaks (Quercus subsection Virentes): A genomic and population genetics approach},
author = {Jeannine Cavender-Bares and Antonio González-Rodríguez and Deren A. R. Eaton and Andrew A. L. Hipp and Anne Beulke and Paul S. Manos},
doi = {10.1111/mec.13269},
issn = {1365294X},
year = {2015},
date = {2015-01-01},
journal = {Molecular Ecology},
volume = {24},
issue = {14},
pages = {3668-3687},
abstract = {The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA-i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cortes in a speciation event ~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical-temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co-occurrence may thus influence which niche axis plants diverge along.},
keywords = {Conservation, Ecological and climatic niches, Fossil calibration, Genomic data, introgression, Phylogeography, RADseq, Sea of Cortés, Virentes},
pubstate = {published},
tppubtype = {article}
}
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA-i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cortes in a speciation event ~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical-temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co-occurrence may thus influence which niche axis plants diverge along.
Eaton, Deren A. R.; Hipp, Andrew L.; González-Rodríguez, Antonio; Cavender-Bares, Jeannine
Historical introgression among the American live oaks and the comparative nature of tests for introgression Artículo de revista
En: Evolution, vol. 69, iss. 10, pp. 2587-2601, 2015, ISSN: 15585646.
Resumen | Enlaces | Etiquetas: Admixture, Cuba, Hybridization, phylogeny, Quercus, RADseq
@article{Eaton2015,
title = {Historical introgression among the American live oaks and the comparative nature of tests for introgression},
author = {Deren A. R. Eaton and Andrew L. Hipp and Antonio González-Rodríguez and Jeannine Cavender-Bares},
doi = {10.1111/evo.12758},
issn = {15585646},
year = {2015},
date = {2015-01-01},
journal = {Evolution},
volume = {69},
issue = {10},
pages = {2587-2601},
abstract = {Introgressive hybridization challenges the concepts we use to define species and infer phylogenetic relationships. Methods for inferring historical introgression from the genomes of extant species, such as ABBA-BABA tests, are widely used, however, their results can be easily misinterpreted. Because these tests are inherently comparative, they are sensitive to the effects of missing data (unsampled species) and nonindependence (hierarchical relationships among species). We demonstrate this using genomic RADseq data sampled from all extant species in the American live oaks (Quercus series Virentes), a group notorious for hybridization. By considering all species and their phylogenetic relationships, we were able to distinguish true hybridizing lineages from those that falsely appear admixed. Six of seven species show evidence of admixture, often with multiple other species, but which is explained by introgression among a few related lineages occurring in close proximity. We identify the Cuban oak as the most admixed lineage and test alternative scenarios for its origin. The live oaks form a continuous ring-like distribution around the Gulf of Mexico, connected in Cuba, across which they could effectively exchange alleles. However, introgression appears highly localized, suggesting that oak species boundaries and their geographic ranges have remained relatively stable over evolutionary time.},
keywords = {Admixture, Cuba, Hybridization, phylogeny, Quercus, RADseq},
pubstate = {published},
tppubtype = {article}
}
Introgressive hybridization challenges the concepts we use to define species and infer phylogenetic relationships. Methods for inferring historical introgression from the genomes of extant species, such as ABBA-BABA tests, are widely used, however, their results can be easily misinterpreted. Because these tests are inherently comparative, they are sensitive to the effects of missing data (unsampled species) and nonindependence (hierarchical relationships among species). We demonstrate this using genomic RADseq data sampled from all extant species in the American live oaks (Quercus series Virentes), a group notorious for hybridization. By considering all species and their phylogenetic relationships, we were able to distinguish true hybridizing lineages from those that falsely appear admixed. Six of seven species show evidence of admixture, often with multiple other species, but which is explained by introgression among a few related lineages occurring in close proximity. We identify the Cuban oak as the most admixed lineage and test alternative scenarios for its origin. The live oaks form a continuous ring-like distribution around the Gulf of Mexico, connected in Cuba, across which they could effectively exchange alleles. However, introgression appears highly localized, suggesting that oak species boundaries and their geographic ranges have remained relatively stable over evolutionary time.