Publicaciones

@article{Hipp2019,

title = {Genomic landscape of the global oak phylogeny},

author = {Andrew L. Hipp and Paul S. Manos and Marlene Hahn and Michael Avishai and Cathérine Bodénès and Jeannine Cavender-Bares and Andrew A. Crowl and Min Deng and Thomas Denk and Sorel Fitz-Gibbon and Oliver Gailing and M. Socorro González-Elizondo and Antonio González-Rodríguez and Guido W. Grimm and Xiao Long Jiang and Antoine Kremer and Isabelle Lesur and John D. McVay and Christophe Plomion and Hernando Rodríguez-Correa and Ernst Detlef Schulze and Marco C. Simeone and Victoria L. Sork and Susana Valencia-Avalos},

doi = {10.1111/nph.16162},

issn = {14698137},

year  = {2019},

date = {2019-01-01},

journal = {New Phytologist},

abstract = {The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.},

keywords = {diversification rates, genomic mosaicism, introgression, Oaks, phylogenomics, Quercus, restriction-site associated DNA sequencing (RAD-se, tree diversity},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Geographic structure of genetic and phenotypic variation in the hybrid zone between Quercus affinis and Q. laurina in Mexico},

author = {S. Ramos-Ortiz and K. Oyama and H. Rodríguez-Correa and A. González-Rodríguez},

doi = {10.1111/1442-1984.12109},

issn = {14421984},

year  = {2016},

date = {2016-01-01},

journal = {Plant Species Biology},

volume = {31},

issue = {3},

pages = {219-232},

publisher = {Blackwell Publishing},

abstract = {Analyzing the structure of hybrid zones is important for inferring their origin, dynamics and evolutionary significance. We examined the geographic structure of phenotypic and genetic variation in the contact zone between two Mexican red oaks, Quercus affinis and Q. laurina. A total of 105 individuals from seven populations were sampled along a 600-km latitudinal gradient representing the distribution area of the two species and their contact zone. Individuals were genotyped for nine nuclear and four chloroplast DNA microsatellite loci (ncSSR and cpSSR, respectively), and characterized for several leaf and acorn traits. The cpSSR data revealed extensive haplotype sharing among populations of the two species, while a Bayesian assignment analysis based on ncSSRs identified two main genetic groups, each corresponding to one of the species, and two populations in the contact zone showing evidence of admixture. The proportion of genetic ancestry in the populations was strongly associated with latitude and showed a pattern of variation with the shape of a narrow sigmoidal cline. The variation in three of the seven phenotypic traits was partially congruent with molecular variation, while the other traits did not conform to a geographic cline but instead were correlated with environmental variables. In conclusion, the hybrid zone between the two oak species has some of the characteristics of a tension zone, but heterogeneous variation across traits suggests differential introgression and the action of extrinsic selection.},

keywords = {cline, hybrid zone, introgression, Microsatellites, morphologic variation, Quercus},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{Albarran-Lara2010,

title = {Leaf fluctuating asymmetry increases with hybridization and introgression between quercus magnoliifolia and quercus resinosa (fagaceae) through an altitudinal gradient in Mexico},

author = {Ana Luisa Albarrán-Lara and Luis Mendoza-Cuenca and Susana Valencia-Avalos and Antonio González-Rodríguez and Ken Oyama},

doi = {10.1086/650317},

issn = {10585893},

year  = {2010},

date = {2010-01-01},

journal = {International Journal of Plant Sciences},

volume = {171},

issue = {3},

pages = {310-322},

abstract = {We tested the effects of hybridization and introgression on the levels of leaf fluctuating asymmetry (FA) in a hybrid zone between Quercus magnoliifolia and Quercus resinosa at the Tequila volcano, Jalisco state, Mexico, in which the species are distributed along an altitudinal gradient ranging from 1400 to 2100 m. Bayesian clustering analysis was performed with STRUCTURE on data for eight nuclear microsatellite loci to assign individuals from reference populations and from the hybrid zone to pure or hybrid genotypic classes. To test the performance of the assignment procedure and to determine optimal thresholds for genetic assignment pure, hybrid and backcrossed genotypes were simulated (from the allelic frequencies found in real pure populations of the two species) and reanalyzed with STRUCTURE. Leaf FA and morphological identification of parental and hybrid individuals were obtained using geometric morphometric techniques. We found genetic and morphological evidence of a hybrid zone by secondary contact at the Tequila volcano. The genotypes and phenotypes were significantly correlated with altitude along the mountain, but no correlation between them was found. FA was higher in F1 hybrids and backcrossed genotypes than in pure species. Levels of FA were more correlated with the proportion of genetic ancestry of each individual than with leaf morphology or altitude, supporting the hypothesis that hybridization is associated with development instability potentially caused by disruption of coadapted gene complexes characteristic of each species. © 2010 by The University of Chicago. All rights reserved.},

keywords = {Genetic assignment, Hybridization, introgression, Leaf fluctuating asymmetry, Quercus.},

pubstate = {published},

tppubtype = {article}

}

@article{Penaloza-Ramirez2010,

title = {Interspecific gene flow in a multispecies oak hybrid zone in the Sierra Tarahumara of Mexico.},

author = {Juan Manuel Peñaloza-Ramírez and Antonio González-Rodríguez and Luis Mendoza-Cuenca and Henri Caron and Antoine Kremer and Ken Oyama},

doi = {10.1093/aob/mcp301},

issn = {10958290},

year  = {2010},

date = {2010-01-01},

journal = {Annals of botany},

volume = {105},

issue = {3},

pages = {389-399},

abstract = {BACKGROUND AND AIMS: Interspecific gene flow can occur in many combinations among species within the genus Quercus, but simultaneous hybridization among more than two species has been rarely analysed. The present study addresses the genetic structure and morphological variation in a triple hybrid zone formed by Q. hypoleucoides, Q. scytophylla and Q. sideroxyla in north-western Mexico. METHODS: A total of 247 trees from ten reference and 13 presumed intermediate populations were characterized using leaf shape variation and geometric morphometrics, and seven nuclear microsatellites as genetic markers. Discriminant function analysis was performed for leaf shape variation, and estimates of genetic diversity and structure, and individual Bayesian genetic assignments were obtained. KEY RESULTS: Reference populations formed three completely distinct groups according to discriminant function analysis based on the morphological data, and showed low, but significant, genetic differentiation. Populations from the zone of contact contained individuals morphologically intermediate between pairs of species in different combinations, or even among the three species. The Bayesian admixture analysis found that three main genetic clusters best fitted the data, with good correspondence of reference populations of each species to one of the genetic clusters, but various degrees of admixture evidenced in populations from the contact area. CONCLUSIONS: The three oak species have formed a complex hybrid zone that is geographically structured as a mosaic, and comprising a wide range of genotypes, including hybrids between different species pairs, backcrosses and probable triple hybrids.},

keywords = {altitudinal cline, Hybridization, introgression, leaf shape variation, Mexico, nuclear microsatellites, quercus hypoleucoides, quercus scytophylla, quercus sideroxyla, red oak},

pubstate = {published},

tppubtype = {article}

}