Publicaciones

@article{nokey,

title = {The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes},

author = {Sofía Zorrilla-Azcué and Antonio González-Rodríguez and Ken Oyama and Mailyn A. González and Hernando Rodríguez-Correa},

doi = {10.1002/ece3.7529},

issn = {20457758},

year  = {2021},

date = {2021-01-01},

journal = {Ecology and Evolution},

volume = {11},

issue = {11},

pages = {6814-6828},

publisher = {John Wiley and Sons Ltd},

abstract = {The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.},

keywords = {genetic diversity and structure, historical connectivity, historical demography, Neotropical trees, Oaks, Phylogeography, Pleistocene, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Association of functional trait variation of Quercus castanea with temperature and water availability gradients at the landscape level},

author = {Libny Ingrid Lara-De La Cruz and Felipe García-Oliva and Ken Oyama and Antonio González-Rodríguez},

doi = {10.17129/BOTSCI.2449},

issn = {20074476},

year  = {2020},

date = {2020-01-01},

journal = {Botanical Sciences},

volume = {98},

issue = {1},

pages = {16-27},

publisher = {Sociedad Botanica de Mexico, A.C},

abstract = {Background: Phenotypic variability of tree species is often associated to environmental factors. Quercus castanea is a Mexican red oak with a wide geographical and altitudinal distribution along contrasting environments. It is the most abundant oak species in the Cuitzeo basin, which is characterized by highly heterogeneous environmental conditions. Hypothesis: We hypothesized that gradients in temperature, precipitation and soil characteristics across the distribution of Q. castanea within the Cuitzeo basin promote variability in functional traits related to the adjustment to differential water availability at a landscape level. Studied species: Quercus castanea Née (Fagaceae). Study site and years of study: Cuitzeo basin in Central Mexico. 2015-2016. Methods: We quantified leaf chlorophyll concentration (CC), leaf area (LA), leaf thickness (LT), leaf mass per area (LMA) and the Huber value (HV) in 10 individuals from 22 populations of Q. castanea throughout the basin. Results: Despite the relatively small geographical area (4,000 km2), our results revealed significant differentiation among populations in the studied functional traits. The strongest variation found was in LT, which was negatively correlated with precipitation seasonality. This pattern is opposite to previous reports on Mediterranean oaks but similar to tropical oaks and suggests that the combination with other traits such as leaf phenology is important in the response to water availability. Conclusions: Significant functional differences exist among populations of Q. castanea separated by a few kilometers in the heterogenous landscape of the Cuitzeo basin. This species shows clearly sclerophyllous leaves, but leaf thickness varies to a considerable degree across populations.},

keywords = {Climate gradient, Leaf economic spectrum, Plant morpho-physiological variation, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Seasonal variation in native hydraulic conductivity between two deciduous oak species},

author = {Dilia Mota-Gutiérrez and Guadalupe Arreola-González and Rafael Aguilar-Romero and Horacio Paz and Jeannine Cavender-Bares and Ken Oyama and Antonio Gonzalez-Rodriguez and Fernando Pineda-García},

doi = {10.1093/JPE/RTZ051},

issn = {1752993X},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Plant Ecology},

volume = {13},

issue = {1},

pages = {78-86},

publisher = {Oxford University Press},

abstract = {Aims Mechanisms of plant drought resistance include both tolerance and avoidance. Xylem vulnerability to embolism and turgor loss point are considered traits that confer tolerance, while leaf abscission and deciduousness characterizes the avoidance strategy. While these mechanisms are thought to trade-off expressing a continuum among species, little is known on how variation in the timing and duration of leaf shedding in response to drought affect the relationship between xylem and leaf tolerance. In the present study, we explored the extent to which drought tolerance differs between two oak (Quercus) species that exhibit different leaf shedding behaviours. Particularly, we predicted that Q. deserticola Trel., which loses leaves at the end of the dry season (late-deciduous) and is thus exposed to a greater risk of cavitation, would be more drought tolerant and more conservative in its water use than Q. laeta Liebm., which loses its leaves for only a short period of time in the middle of the dry season (brevideciduous). Methods The study was conducted in central Mexico in a single population of each of the two oak species, separated from each other by a distance of 1.58 km, and by an altitudinal difference of 191 m. Quercus deserticola (late deciduous) is more frequent down slope, while Q. laeta (brevideciduous) tends to occur at higher elevations along the gradient. We assessed seasonal differences (rainy versus dry season) in native stem hydraulic conductivity, and tested for variation in xylem vulnerability to cavitation, leaf water use and leaf turgor loss point between the two species. Important Findings The two oak species did not differ in traits conferring drought tolerance, including xylem vulnerability to embolism, leaf turgor loss point, or stomatal conductance. However, both species had different performance during the dry season; the brevideciduous species had lower negative impact in the xylem function than the late-deciduous species. Overall, seasonal changes in plant physiological performance between the two oak species were determined by a reduction in the canopy leaf area.},

keywords = {Embolisms, Hydraulic conductivity, Leaf phenology, Quercus},

pubstate = {published},

tppubtype = {article}

}

@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{Oyama2018,

title = {High Genetic Diversity and Connectivity Among Populations of Quercus candicans , Quercus crassifolia , and Quercus castanea in a Heterogeneous Landscape in Mexico},

author = {Ken Oyama and Wilfrido Ramírez-Toro and Juan Manuel Peñaloza-Ramírez and Alberto Esteban Pérez Pedraza and César Andrés Torres-Miranda and Eduardo Ruiz-Sánchez and Antonio González-Rodríguez},

doi = {10.1177/1940082918766195},

issn = {1940-0829},

year  = {2018},

date = {2018-01-01},

journal = {Tropical Conservation Science},

volume = {11},

pages = {194008291876619},

abstract = {Oaxaca state is one of the main hotspots of biodiversity in Mexico, containing almost 40% of the Mexican vascular flora, due to its high variability in habitat and climatic conditions coupled with high elevations in mountains and low elevations in valleys. We studied the genetic diversity and population structure of Quercus candicans, Quercus crassifolia, and Quercus castanea across their geographical distribution in Oaxaca state to understand how the heterogeneous physiography had driven the genetic diversity and population differentiation in these three oak species. We found high levels of genetic diversity but ca. 40% of the populations had significant values of Wright’s inbreeding coefficient. The analysis of molecular variance indicated that most of the variation occurred within populations in the three oak species. Resistance analyses showed connectivity among almost all the populations but barrier analysis found genetic breaks that limited gene flow among some populations of the oak species. Even in a heterogeneous environment such as in Oaxaca state, the oak species still have high levels of genetic diversity and landscape connectivity. However, it is necessary to maintain the genetic connectivity through the preservation of natural corridors with forests in good condition, which is necessary to maintain the cohesiveness of the species in the long term. It is also important to protect the centers of species diversity in Oaxaca state located in the subprovinces of Western Oaxacan Mountains and Valleys, Sierra Madre de Oaxaca, and Sierra Madre del Sur because they harbor most of the population genetic diversity and oak species richness, as has been shown in previous studies.},

keywords = {conservation genetics, genetic connectivity, genetic diversity and structure, Mexico, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{Rodriguez-Correa2018,

title = {Contrasting Patterns of Population History and Seed-mediated Gene Flow in Two Endemic Costa Rican Oak Species},

author = {Hernando Rodríguez-Correa and Ken Oyama and Mauricio Quesada and Eric J. Fuchs and Antonio González-Rodríguez},

doi = {10.1093/jhered/esy011},

issn = {14657333},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Heredity},

volume = {109},

issue = {5},

pages = {530-542},

abstract = {Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in 2 partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. The phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.},

keywords = {chloroplast microsatellites, Fagaceae, gene flow, Middle America, Phylogeography, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{Chavez-Vergara2018,

title = {Direct and legacy effects of planttraits control litter decomposition in a deciduous oak forest in Mexico},

author = {Bruno Chávez-Vergara and Agustín Merino and Antonio González-Rodríguez and Ken Oyama and Felipe García-Oliva},

doi = {10.7717/peerj.5095},

issn = {21678359},

year  = {2018},

date = {2018-01-01},

journal = {PeerJ},

volume = {2018},

issue = {6},

pages = {1-27},

abstract = {Background. Litter decomposition is a key process in the functioning of forest ecosystems, because it strongly controls nutrient recycling and soil fertility maintenance. The interaction between the litter chemical composition and the metabolism of the soil microbial community has been described as the main factor of the decomposition process based on three hypotheses: substrate-matrix interaction (SMI), functional breadth (FB) and home-field advantage (HFA). The objective of the present study was to evaluate the effect of leaf litter quality (as a direct plant effect, SMI hypothesis), the metabolic capacity of the microbial community (as a legacy effect, FB hypothesis), and the coupling between the litter quality and microbial activity (HFA hypothesis) on the litter decomposition of two contiguous deciduous oak species at a local scale. Methods. To accomplish this objective, we performed a litterbag experiment in the field for 270 days to evaluate mass loss, leaf litter quality and microbial activity in a complete factorial design for litter quality and species site. Results. The litter of Quercus deserticola had higher rate of decomposition independently of the site, while the site of Quercus castanea promoted a higher rate of decomposition independently of the litter quality, explained by the specialization of the soil microbial community in the use of recalcitrant organic compounds. The Home- Field Advantage Index was reduced with the decomposition date (22% and 4% for 30 and 270 days, respectively). Discussion. We observed that the importance of the coupling of litter quality and microbial activity depends on decomposition stage. At the early decomposition stage, the home-advantage hypothesis explained the mass loss of litter; however, in the advanced decomposition stage, the litter quality and the metabolic capacity of the microbial community can be the key drivers.},

keywords = {13C NMR, Differential Scaning Calorimetry, Enzymatic activity, Litter decomposition, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{Oyama2018b,

title = {High Genetic Diversity and Connectivity Among Populations of Quercus candicans, Quercus crassifolia, and Quercus castanea in a Heterogeneous Landscape in Mexico},

author = {Ken Oyama and Wilfrido Ramírez-Toro and Juan Manuel Peñaloza-Ramírez and Alberto Esteban Pérez Pedraza and César Andrés Torres-Miranda and Eduardo Ruiz-Sánchez and Antonio González-Rodríguez},

doi = {10.1177/1940082918766195},

issn = {19400829},

year  = {2018},

date = {2018-01-01},

journal = {Tropical Conservation Science},

volume = {11},

publisher = {SAGE Publications Inc.},

abstract = {Oaxaca state is one of the main hotspots of biodiversity in Mexico, containing almost 40% of the Mexican vascular flora, due to its high variability in habitat and climatic conditions coupled with high elevations in mountains and low elevations in valleys. We studied the genetic diversity and population structure of Quercus candicans, Quercus crassifolia, and Quercus castanea across their geographical distribution in Oaxaca state to understand how the heterogeneous physiography had driven the genetic diversity and population differentiation in these three oak species. We found high levels of genetic diversity but ca. 40% of the populations had significant values of Wright’s inbreeding coefficient. The analysis of molecular variance indicated that most of the variation occurred within populations in the three oak species. Resistance analyses showed connectivity among almost all the populations but barrier analysis found genetic breaks that limited gene flow among some populations of the oak species. Even in a heterogeneous environment such as in Oaxaca state, the oak species still have high levels of genetic diversity and landscape connectivity. However, it is necessary to maintain the genetic connectivity through the preservation of natural corridors with forests in good condition, which is necessary to maintain the cohesiveness of the species in the long term. It is also important to protect the centers of species diversity in Oaxaca state located in the subprovinces of Western Oaxacan Mountains and Valleys, Sierra Madre de Oaxaca, and Sierra Madre del Sur because they harbor most of the population genetic diversity and oak species richness, as has been shown in previous studies.},

keywords = {conservation genetics, genetic connectivity, genetic diversity and structure, Mexico, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{Martins2018,

title = {Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa},

author = {Karina Martins and Paul F. Gugger and Jesus Llanderal-Mendoza and Antonio González-Rodríguez and Sorel T. Fitz-Gibbon and Jian Li Zhao and Hernando Rodríguez-Correa and Ken Oyama and Victoria L. Sork},

doi = {10.1111/eva.12684},

issn = {17524571},

year  = {2018},

date = {2018-01-01},

journal = {Evolutionary Applications},

volume = {11},

issue = {10},

pages = {1842-1858},

publisher = {Wiley-Blackwell},

abstract = {Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to non-native habitat and results in species-wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under future climate as a tool for forest restoration or management of the widely distributed high-elevation oak species Quercus rugosa in Mexico. Using genotyping by sequencing, we identified 5,354 single nucleotide polymorphisms (SNPs) genotyped from 103 individuals across 17 sites in the Trans-Mexican Volcanic Belt, and, after controlling for neutral genetic structure, we detected 74 FST outlier SNPs and 97 SNPs associated with climate variation. Then, we deployed a nonlinear multivariate model, Gradient Forests, to map turnover in allele frequencies along environmental gradients and predict areas most sensitive to climate change. We found that spatial patterns of genetic variation were most strongly associated with precipitation seasonality and geographic distance. We identified regions of contemporary genetic and climatic similarities and predicted regions where future populations of Q. rugosa might be at risk due to high expected rate of climate change. Our findings provide preliminary details for future management strategies of Q. rugosa in Mexico and also illustrate how a landscape genomic approach can provide a useful tool for conservation and resource management strategies.},

keywords = {assisted gene flow, climate change, genotyping by sequencing, landscape genomics, natural selection, Quercus, restoration, Trans-Mexican Volcanic Belt},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Patterns of herbivory and leaf morphology in two Mexican hybrid oak complexes: Importance of fluctuating asymmetry as indicator of environmental stress in hybrid plants},

author = {Pablo Cuevas-Reyes and Armando Canché-Delgado and Yurixhi Maldonado-López and G. Wilson Fernandes and Ken Oyama and Antonio González-Rodríguez},

doi = {10.1016/j.ecolind.2018.03.009},

issn = {1470160X},

year  = {2018},

date = {2018-01-01},

journal = {Ecological Indicators},

volume = {90},

pages = {164-170},

publisher = {Elsevier B.V.},

abstract = {Interspecific hybridization is a prevalent process in plant species that may have different ecological and evolutionary consequences. Interactions with herbivorous insects may be altered because of hybridization among host plants. These changes result from the morphological, physiological and chemical traits expressed in hybrid individuals. Therefore, it is of interest to document the changes in traits such as leaf morphology and their consequences on patterns of herbivory by insects in hybrid complexes of plants. Another useful indicator that may serve to evaluate developmental instability resulting from genetic or environmental stress in hybrid plants is fluctuating asymmetry. In this study, we used two previously genetically characterized complexes of hybridizing Mexican oaks as models to compare and understand the relationships between leaf morphology, fluctuating asymmetry and herbivory levels in parental and hybrid individuals. Results indicated that in the Quercus affinis × Q. laurina complex, hybrid individuals show a distinct morphology in relation to the parental species, while in the Q. magnoliifolia × Q. resinosa complex, hybrids were similar to Q. resinosa. In both hybrid complexes, our results show that hybrid individuals have higher levels of fluctuating asymmetry and herbivory levels, which may reflect higher levels of genetic or environmental stress in comparison to the parental species. These results might help explain why oak species usually remain distinct despite the high frequency of hybridization characteristic of the genus.},

keywords = {Environmental stress, Fluctuating asymmetry, Herbivory, Hybrid complexes, Leaf morphology, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{Hipp2018,

title = {Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity},

author = {Andrew L. Hipp and Paul S. Manos and Antonio González-Rodríguez and Marlene Hahn and Matthew Kaproth and John D. McVay and Susana Valencia Avalos and Jeannine Cavender-Bares},

doi = {10.1111/nph.14773},

issn = {14698137},

year  = {2018},

date = {2018-01-01},

journal = {New Phytologist},

volume = {217},

issue = {1},

pages = {439-452},

publisher = {Blackwell Publishing Ltd},

abstract = {Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.},

keywords = {American oaks, convergence, niche evolution, phylogeny, Quercus, restriction site-associated DNA sequencing (RAD-seq), sympatric parallel diversification, woody plants},

pubstate = {published},

tppubtype = {article}

}

@article{Hipp2018b,

title = {Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity},

author = {Andrew L. Hipp and Paul S. Manos and Antonio González-Rodríguez and Marlene Hahn and Matthew Kaproth and John D. McVay and Susana Valencia Avalos and Jeannine Cavender-Bares},

doi = {10.1111/nph.14773},

issn = {14698137},

year  = {2018},

date = {2018-01-01},

journal = {New Phytologist},

volume = {217},

issue = {1},

pages = {439-452},

publisher = {Blackwell Publishing Ltd},

abstract = {Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.},

keywords = {American oaks, convergence, niche evolution, phylogeny, Quercus, restriction site-associated DNA sequencing (RAD-seq), sympatric parallel diversification, woody plants},

pubstate = {published},

tppubtype = {article}

}

@article{Ramirez-Toro2017,

title = {A Multicriteria Analysis for Prioritizing Areas for Conservation of Oaks (Fagaceae: Quercus) in Oaxaca, Southern Mexico},

author = {Wilfrido Ramírez-Toro and Andrés Torres-Miranda and Antonio González-Rodríguez and Eduardo Ruiz-Sanchez and Isolda Luna-Vega and Ken Oyama},

doi = {10.1177/1940082917714227},

issn = {19400829},

year  = {2017},

date = {2017-01-01},

journal = {Tropical Conservation Science},

volume = {10},

abstract = {Mexico has the fifth place among megadiverse countries, and the southern part of the country belongs to the Mesoamerican hotspot, where Oaxaca state has a very rich flora, related to its intricate topography. In this study, a multicriteria analysis (species richness, rareness, irreplaceability, turnover, and vulnerability) was used to prioritize conservation areas in Oaxaca, using as model system the genus Quercus (oaks), due to its high diversity and ecological importance. Our results indicate that the Sierra Madre de Oaxaca (SMOax) is the physiographic subprovince with the highest richness (38 species), rareness and irreplaceability of Quercus species, followed by the Montañas y Valles del Occidente (MVO; 29 species), the Sierra Madre del Sur (SMS; 25 species), and the Montañas y Valles del Centro (20 species). Areas that have retained most primary vegetation cover from 2000 to 2010 are mainly in the SMOax, in the Ixtlán district, and in the SMS, in the Miahuatlán district. On the other hand, MVO is the area with greater habitat disturbance, mainly in the Juxtlahuaca-Tlaxiaco districts. Oaxaca has numerous areas without official protection, named Indigenous Conservation and Community Areas, which play a central role as an alternative for conservation for 11 oak species. In conclusion, the priority conservation areas for the genus are mainly located in the SMOax and in the SMS. For white oaks, the semiarid area of Coixtlahuaca-Teposcolula-Nochitlán is important, while for the red oaks, the most important regions are the humid areas of Teotitlán, Sola de Vega, and Miahuatlán.},

keywords = {irreplaceability, Oaxaca, Quercus, rareness, species richness, turnover, vulnerability},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Differentiation in the water-use strategies among oak species from central Mexico},

author = {Rafael Aguilar-Romero and Fernando Pineda-Garcia and Horacio Paz and Antonio González-Rodríguez and Ken Oyama},

doi = {10.1093/treephys/tpx033},

issn = {17584469},

year  = {2017},

date = {2017-01-01},

journal = {Tree Physiology},

volume = {37},

issue = {7},

pages = {915-925},

publisher = {Oxford University Press},

abstract = {Oak species (Fagaceae: Quercus) differ in their distribution at the landscape scale, specializing to a certain portion of environmental gradients. This suggests that functional differentiation favors habitat partitioning among closely related species. To elucidate the mechanisms of species coexistence in oak forests, we explored patterns of interspecific variation in functional traits involved in water-use strategies. We tested the hypothesis that oak species segregate along key trade-offs between xylem hydraulic efficiency and safety, and between hydraulic safety and drought avoidance capacity, leading to species niche partitioning across a gradient of aridity. To do so, we quantified biophysical and physiological traits in four red and five white oak species (sections Lobatae and Quercus, respectively) across an aridity gradient in central Mexico. We also explored the trade-offs guiding species differentiation, particularly between the drought tolerance versus water acquisition capacity, and determined whether the water-use strategy was associated with the portion of the environmental gradient that the species occupy. In a trait-by-trait analysis, we detected differences between white and red oak species. However, a larger part of the variation was explained at the species rather than at the section level. We detected two primary axes of trait covariation. The first exhibited differences between species with dense tissues and species with soft tissues (the tissue construction cost axis); however, the oak sections did not constitute separate groups, while the second suggested a trade-off between xylem resistance to cavitation and tree deciduousness. As expected, the water-use strategies of the species were related to the environment; oak species from arid areas had more deciduousness and a higher instantaneous water-use efficiency. In contrast, their humid counterparts had less deciduousness and had a xylem that was more resistant to embolisms. Altogether, these results suggest that aridity filters closely related species, resulting in habitat partitioning and niche divergence.},

keywords = {Aridity gradients, Biophysical traits, Functional trade-offs, Quercus, Water-use strategy},

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{Chavez-Vergara2015,

title = {Foliar nutrient resorption constrains soil nutrient transformations under two native oak species in a temperate deciduous forest in Mexico},

author = {Bruno M. Chávez-Vergara and Antonio González-Rodríguez and Jorge D. Etchevers and Ken Oyama and Felipe García-Oliva},

doi = {10.1007/s10342-015-0891-1},

issn = {16124669},

year  = {2015},

date = {2015-01-01},

journal = {European Journal of Forest Research},

volume = {134},

issue = {5},

pages = {803-817},

abstract = {Foliar nutrient resorption (FNR) is a key process in the dynamics of nutrients in a forest ecosystem. Along with other factors, FNR regulates the chemical composition of the forest floor and, consequently, the rates of organic matter decomposition and soil nutrient availability. The main objective of the present study was to examine the effect of FNR of two deciduous oak species (Quercus castanea and Q. deserticola) in the litter and soil nutrient dynamics, in addition to analyze whether the interaction between two species was positive (synergistic) or negative (antagonistic) through the mixed litter from two species. For this purpose, the nutrient concentration of green leaves, litterfall, litter and soil was measured, as well as soil microbial activity. These measurements were taken in isolated stands with the presence of one of the oak species and stands with the two oak species mixed. Quercus deserticola, with lower FNR, produced litter with a higher N concentration, which apparently enhancing microbial activity in the forest floor litter and increased nutrient transformations and soil fertility. In contrast, Q. castanea has a higher FNR and produced litter with a lower nutrient concentration. The microbial soil community associated with Q. castanea must therefore invest more energy in metabolic processes at the expense of biomass growth. However, forest floor nutrient transformations were more intense and soil fertility increased in areas where both species intermix; in this case, the latter species received the rich-nutrient litterfall of Q. deserticola. These results suggest a strong footprint of species traits on microbial activities and soil nutrient transformations.},

keywords = {Biogeochemistry, Functional interactions, Microbial transformations, Quercus, Species footprint, Temperate deciduous forest},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{Rodriguez-Correa2015,

title = {How are oaks distributed in the neotropics? A perspective from species turnover, areas of endemism, and climatic niches},

author = {Hernando Rodríguez-Correa and Ken Oyama and Ian Macgregor-Fors and Antonio González-Rodríguez},

doi = {10.1086/679904},

issn = {10585893},

year  = {2015},

date = {2015-01-01},

journal = {International Journal of Plant Sciences},

volume = {176},

issue = {3},

pages = {222-231},

abstract = {Premise of research. The most important diversity hot spot of genus Quercus (Fagaceae) in America is situated in southern Mexico. From this area down to the Colombian Andes, oak species diversity decreases considerably, but the pattern of species distribution and turnover has not been analyzed. This study aimed at determining geographical patterns of species turnover, species distribution, and endemism for Neotropical Quercus species. Methodology. Occurrence records for 58 oak species belonging to the Quercus and Lobatae sections were obtained. Patterns of species turnover were determined by comparing species composition among latitudinal/ longitudinal units. Areas of endemism were determined using weighted networks. The potential distribution of oak species was determined using ecological niche models. Finally, a principal component analysis was used to identify changes in the oak species’ ecological niche across areas. Pivotal results. The species composition analysis indicated that the Tehuantepec Isthmus, the Nicaraguan Depression, and the Panamanian Isthmus represent species turnover points. Nine areas of endemism were recovered, distributed through mountainous ranges from Mexico to Costa Rica. Most of these areas were delimited by the species turnover points detected. Ecological niche modeling indicated that the turnover points represent areas with low climatic suitability for most oak species and represent discontinuities in the distribution of Quercus. Niche comparisons suggest niche differentiation among species distributed in different areas of endemism or on opposite sides of turnover points. Conclusions. The results indicate that the Tehuantepec Isthmus, the Nicaraguan Depression, and the Panamanian Isthmus have acted as important barriers to the dispersal of oak species, influencing species diversity, biogeographic patterns, and niche divergence.},

keywords = {biogeography, Distribution, Diversity, Neotropical trees, Quercus},

pubstate = {published},

tppubtype = {article}

}

@article{Scareli-Santos2007,

title = {Comparative analysis of micromorphological characters in two distantly related Mexican oaks, Quercus conzattii and Q. eduardii (Fagaceae), and their hybrids},

author = {Claudia Scareli-Santos and María Luisa Herrera-Arroyo and María L. Sánchez-Mondragón and Antonio González-Rodríguez and Jeffrey Bacon and Ken Oyama},

doi = {10.1663/0007-196X(2007)59[37:CAOMCI]2.0.CO;2},

issn = {0007196X},

year  = {2007},

date = {2007-01-01},

journal = {Brittonia},

volume = {59},

issue = {1},

pages = {37-48},

abstract = {Interspecific hybridization occurs with high frequency in the genus Quercus, but few studies have analyzed and compared micromorphological characters in putative parental species and their hybrids, Quercus eduardii and Q. conzattii are two Mexican black oak species that, although distantly related, have formed at least one population of hybrid origin, where individuals with intermediate macromorphology are present. The purpose of this investigation was to analyze the degree of differentiation in micromorphological characters between the two species and to assess the expression of these characters in individuals with intermediate macromorphology. Foliar trichomes, epicuticular waxes, stomata, and pollen grains, were examined using scanning electron microscopy (SEM) in the three types of individuals (Q. conzattii, Q. eduardii, and intermediates). Trichome density was quantified with light microscopy. Types of trichomes present, length of trichome arms, types of epicuticular wax on the leaf surfaces, and the position of stomata with respect to the foliar surface were characters useful to differentiate between Q. conzattii and Q. eduardii. Plants with intermediate macromorphology displayed a pattern of micromorphological characters that were identical to one parental species (Q. conzattii), or extreme or novel relative to both species. © 2007, by The New York Botanical Garden Press.},

keywords = {Epicuticular wax, Hybridization, Micromorphology, Pollen, Quercus, SEM, Trichomes},

pubstate = {published},

tppubtype = {article}

}

@article{Gonzalez-Rodriguez2005,

title = {Genetic variation and differentiation of populations within the Quercus affinis - Quercus laurina (Fagaceae) complex analyzed with RAPD markers},

author = {Antonio González-Rodríguez and Dulce M. Arias and Ken Oyama},

doi = {10.1139/B04-162},

issn = {00084026},

year  = {2005},

date = {2005-01-01},

journal = {Canadian Journal of Botany},

volume = {83},

issue = {2},

pages = {155-162},

abstract = {The population genetics of two hybridizing Mexican red oaks, Quercus affinis Schweid. and Quercus laurina Humb. & Bonpl., was investigated with 54 randomly amplified polymorphic DNA (RAPD) markers scored in 415 individuals from 16 populations representing the distribution area of the two species and a probable secondary hybrid zone. Genetic relationships among populations, depicted in a unweighted pair group method with arithmetic averaging (UPGMA) dendrogram, were largely incongruent with the morphological classification of populations as Q. affinis-like or Q. laurina-like that was obtained in previous studies. In contrast, the two main population clusters in the UPGMA dendrogram corresponded to the location of populations in two distinct geographical areas: southwestern and northeastern. A Mantel test confirmed a significant association between geographic and genetic distances among populations. Analyses of molecular variance (AMOVA) indicated that most genetic variation is contained within populations (84%), while 10.5% (P < 0.0001) is among populations, and 5.1% (P = 0.007) is between the two morphological groups. Differentiation between the southwestern and northeastern geographical groups (as recognized by the UPGMA), was 7.8% (P < 0.0001). The incongruence between genetic and phenotypic patterns suggests that introgression of neutral markers has been considerable between the two species in the hybrid zone, while morphological differentiation has remained comparatively stable. © 2005 NRC.},

keywords = {Hybridization, Population genetics, Quercus, RAPD markers},

pubstate = {published},

tppubtype = {article}

}

@article{Gonzalez-Rodriguez2004,

title = {Chloroplast DNA variation in the Quercus affinis-Q. laurina complex in Mexico: Geographical structure and associations with nuclear and morphological variation},

author = {A. González-Rodríguez and J. F. Bain and J. L. Golden and K. Oyama},

doi = {10.1111/j.1365-294X.2004.02344.x},

issn = {09621083},

year  = {2004},

date = {2004-01-01},

journal = {Molecular Ecology},

volume = {13},

issue = {11},

pages = {3467-3476},

abstract = {The geographical distribution of chloroplast DNA (cpDNA) variation in 39 populations of two hybridizing Mexican red oaks, Quercus affinis and Q. laurina, was investigated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Six haplotypes were identified. Of these, two (H1 and H4), separated by four mutations, had high frequencies (58 and 23% of the individuals, respectively) and were present across the whole geographical range of both species, often co occurring in the same populations. The other four haplotypes were rare, geographically restricted, and are probably derived from the two frequent haplotypes. Latitudinal or other clinal patterns in diversity levels or haplotype composition of populations were not apparent. The pattern of haplotype distribution was characterized by some mosaicism, with contrasting populations often situated in proximity. Average within-population diversity (hS = 0.299) and population differentiation (GST = 0.499) were, respectively, higher and lower than values reported in previous studies of oak species. There was evidence for phylogeographical structure, as indicated by NST (0.566) being significantly higher than GST. Haplotypic variation was largely species-independent, although some very weak associations were detected between haplotypes H1 and H4 and morphological and nuclear molecular variation correspondingly characterizing Q. affinis and Q. laurina. These oaks probably did not experience a marked restriction to one or a few particular subregions of their present range during the last glacial cycle. It is more likely that substantial populations persisted throughout several episodes of climatic change, but experienced recurrent latitudinal and altitudinal migrations which may have caused the widespread distribution of haplotypes H1 and H4 and frequent intermixing of populations.},

keywords = {Chloroplast dna, Geographical structure, Hybridization, Mexico, Population history, Quercus},

pubstate = {published},

tppubtype = {article}

}