TY - JOUR T1 - Taxonomy and Systematics of Quercus subgenus Cyclobalanopsis JF - International OaksInternational Oaks Y1 - 2013 A1 - Deng, Min A1 - Zhou, Zhekun A1 - Li, Qiansheng SP - 49 EP - 60 VL - 24 ER - TY - JOUR T1 - Molecular and morphological support for a Florida origin of the Cuban oak JF - Journal of BiogeographyJournal of Biogeography Y1 - 2013 A1 - Gugger, Paul F. A1 - Cavender-Bares, Jeannine SP - 632 EP - 645 KW - cpDNA KW - Cuba KW - founder effect KW - morphology KW - nuclear microsatellites KW - over-water dispersal KW - phylogeography KW - Quercus oleoides KW - Quercus sagraeana KW - Quercus virginiana AB - Aim  The origins of the Cuban biota are of long-standing interest in biogeography, and the source of a small live oak (Quercus series Virentes) population on Cuba remains unresolved. Based on morphological evidence, previous authors have hypothesized a Florida origin from either Q. geminata or Q. virginiana or both; a Mexican origin from Q. oleoides; or a hybrid origin from both sources. We use molecular data and taxonomically informative leaf morphology to identify the source species and timing of colonization. Location  Cuba, Central America, Mexico and the south-eastern United States. Methods  We collected representative samples of Cuban oaks and each putative source species and genotyped each sample at 12 nuclear microsatellites and two chloroplast DNA sequences. We estimated population structure using a Bayesian clustering analysis and F-statistics, pairwise migration rates among taxa, and divergence time using an isolation-with-migration model. We measured seven leaf traits and conducted an analysis of similarity (ANOSIM) to determine which putative source species was most similar to Cuban oaks. Results  Cuban oak contains one chloroplast DNA haplotype, which is common in southern Florida. Bayesian clustering analysis of microsatellites revealed that the Cuban oak forms a distinct and pure population cluster, and F-statistics showed that Cuban oaks are differentiated least from Q. virginiana and most from Q. geminata. Migration rates were highest out of Cuba to Q. oleoides. Molecular diversity, the ratio of allelic richness to allele size range, and effective population size of the Cuban oak were relatively low, suggesting a founder effect. Divergence time estimates fell entirely within the Pleistocene (628–6 ka), considering a range of mutation rates and generation times. Cuban oaks were morphologically most similar to Q. virginiana and least similar to Q. geminata. Main conclusions  Molecular and morphological data support a Pleistocene dispersal of Q. virginiana from Florida to Cuba, followed by isolation and divergence, then limited dispersal and introgression from Cuba to Q. oleoides in Central America. Birds could have dispersed acorns to Cuba during a glacial period when sea levels were low. These results highlight the varied origin of the Cuban biota and the possible role of Pleistocene glaciations in the establishment of temperate taxa in the tropics. PB - Blackwell Publishing Ltd VL - 40 SN - 1365-2699 JO - J Biogeogr ER - TY - JOUR T1 - Outlier loci highlight the direction of introgression in oaks JF - Molecular EcologyMolecular Ecology Y1 - 2013 A1 - Guichoux, E. A1 - Garnier-GÉRÉ, P. A1 - Lagache, L. A1 - Lang, T. A1 - Boury, C. A1 - Petit, R. J. SP - 450 EP - 462 KW - asymmetric introgression KW - divergent selection KW - gene flow barriers KW - genetic assignment KW - outlier loci KW - Quercus petraea KW - Quercus robur KW - single nucleotide polymorphism AB - Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late-successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized. VL - 22 SN - 1365-294X JO - Mol Ecol ER - TY - JOUR T1 - Seed-mediated connectivity among fragmented populations of Quercus castanea (Fagaceae) in a Mexican landscape JF - American Journal of BotanyAmerican Journal of Botany Y1 - 2013 A1 - M. Luisa Herrera-Arroyo A1 - Victoria L. Sork A1 - González-Rodríguez, Antonio A1 - Victor Rocha-Ramirez A1 - Ernesto Vega A1 - Ken Oyama SP - 1663 EP - 1671 VL - 100 JO - Am J Bot ER - TY - JOUR T1 - Using phylogenomics to infer the evolutionary history of oaks JF - International Oak JournalInternational Oak Journal Y1 - 2013 A1 - Hipp, Andrew L. A1 - Manos, Paul S. A1 - Cavender-Bares, Jeannine A1 - Eaton, Deren A. R. A1 - Nipper, Rick SP - 61 EP - 71 KW - Phylogenetics KW - Quercus KW - restriction-site associated DNA (RAD) tags KW - systematics AB - One of the most basic questions about oaks has long vexed botanists, systematists, and oak enthusiasts of all stripes: what is the shape and timing of the oak tree of life? In this paper, we present new data from a genomic study of 20 oak individuals representing a broad swath of the oaks of the Americas. The paper explains how we are using next-generation sequencing methods to analyze millions of base pairs of DNA data for all individuals studied, and what we have learned to date from this work about the oak tree of life. VL - 24 ER - TY - JOUR T1 - New Approaches to the Biogeography and Areas of Endemism of Red Oaks (Quercus L., Section Lobatae) JF - Systematic BiologySystematic Biology Y1 - 2013 A1 - Torres-Miranda, Andres A1 - Luna-Vega, Isolda A1 - Oyama, Ken SP - 555 EP - 573 AB - An area of endemism is defined by the spatial congruence among two or more species with distributions that are limited by barriers. In this study, we explored and discussed the use of the network analysis method (NAM) and neighbor-joining (NJ) to analyze the areas of endemism of Quercus sect. Lobatae (red oak species) in Mexico and Central America. We compared the NAM and NJ with other methods commonly used in biogeographic studies to show the advantages of these new approaches and to identify the shortcomings of other approaches. The NAM used in this study is based on notions of centrality measures, such as betweenness. We incorporated the strength of the ties within the internal networks through p-cores and aggregate constraints in iterative analyses. The NAM based on betweenness is ideal for recognizing completely allopatric areas of endemism. The iterative NAMs increase the number of possible areas of endemism because they minimize the effect of minimal overlap, and the p-core is efficient at identifying the closest relationships among species in the cases in which betweenness is not informative. The number of areas of endemism increases when the sympatry matrix minimizes the dispersal effect and the sample effort is maximized, allowing the identification of the greatest number of these areas. The NJ method supports the idea that areas diverge among themselves in a differential way; the long branches correspond to zones with high speciation rates and complex histories (biotic and tectonic), and the short branches correspond to zones with low speciation rates and simple histories. In a classification scheme, NJ was capable of identifying the areas that are considered biotically complex because of their high speciation rates. The results obtained with the NAM and NJ showed that the physiographic regions of Mexico are not natural units and that many of them are composed of at least two different biotic components. [Areas of endemism; biogeographic patterns; Mexico and Central America; neighbor-joining; net-like methods; network analysis; Quercus; reticulate evolution; tree-like methods.] VL - 62 JO - Syst Biol ER - TY - JOUR T1 - Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications JF - Botanical Journal of the Linnean SocietyBotanical Journal of the Linnean Society Y1 - 2013 A1 - Simeone, Marco C. A1 - Piredda, Roberta A1 - Papini, Alessio A1 - Vessella, Federico A1 - Schirone, Bartolomeo SP - n/a EP - n/a KW - cerris KW - ecology KW - ilex KW - phylogeny KW - regional sampling AB - DNA barcoding, a species identification system based on sequences from a short, standardized DNA region, has emerged recently as a new tool for taxonomists. We investigated the discriminatory power of a subset of highly variable proposed plant barcoding loci (matK, trnH-psbA, ITS2) in Quercus, a taxonomically complex tree genus of global importance. The research included all currently recognized species and some major variants of the Mediterranean region and Europe (32 taxa) and 17 East Asian and North American species used for comparison. Based on sequence character state, we assigned unique plastid haplotypes to 40.8% of the investigated species; ITS2 increased the resolution up to 87.8% of total taxa. Nevertheless, unsuccessful genetic distance-based discrimination questioned the potential efficiency of correct species identification for future studies. Most species appeared to be nonmonophyletic in parallel phylogenetic tests. Three subgeneric groups were outlined, with different rates of within-group variability and geographical differentiation. Members of one of these groups (corresponding to the Eurasian Group Ilex) were paraphyletic to Group Quercus from the New and Old World and the Eurasian Group Cerris. The data gathered indicate that barcoding markers may help to identify closely related species clusters and contribute to the inference of major diversification and evolutionary patterns in oaks, but the methodology per se appears to be of limited efficacy in defining species limits, unless we make a profound revision of traditional Quercus taxonomic categories. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 00, 000–000. SN - 1095-8339 JO - Bot J Linn Soc ER -