00433nas a2200133 4500008004100000245007900041210006900120300001000189490000700199100001400206700001700220700001800237856004400255 2013 eng d00aTaxonomy and Systematics of Quercus subgenus Cyclobalanopsis0 aTaxonomy and Systematics of iQuercus isubgenus iCyclobalanopsisi a49-600 v241 aDeng, Min1 aZhou, Zhekun1 aLi, Qiansheng uhttps://quercus.myspecies.info/node/15203248nas a2200277 4500008004100000020001400041245007800055210006900133260002900202300001200231490000700243520243500250653001002685653000902695653001902704653001502723653002802738653002502766653001902791653002102810653002202831653002302853100002102876700002902897856004402926 2013 eng d a1365-269900aMolecular and morphological support for a Florida origin of the Cuban oak0 aMolecular and morphological support for a Florida origin of the  bBlackwell Publishing Ltd a632-6450 v403 aAim  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.10acpDNA10aCuba10afounder effect10amorphology10anuclear microsatellites10aover-water dispersal10aphylogeography10aQuercus oleoides10aQuercus sagraeana10aQuercus virginiana1 aGugger, Paul, F.1 aCavender-Bares, Jeannine uhttps://quercus.myspecies.info/node/15302459nas a2200289 4500008004100000020001400041245006600055210006600121300001200187490000700199520162900206653002901835653002401864653002301888653002301911653001701934653002001951653001801971653003501989100001702024700002302041700001602064700001302080700001402093700001802107856004402125 2013 eng d a1365-294X00aOutlier loci highlight the direction of introgression in oaks0 aOutlier loci highlight the direction of introgression in oaks a450-4620 v223 aLoci 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.10aasymmetric introgression10adivergent selection10agene flow barriers10agenetic assignment10aoutlier loci10aQuercus petraea10aQuercus robur10asingle nucleotide polymorphism1 aGuichoux, E.1 aGarnier-GÉRÉ, P.1 aLagache, L.1 aLang, T.1 aBoury, C.1 aPetit, R., J. uhttps://quercus.myspecies.info/node/15400609nas a2200169 4500008004100000245012100041210006900162300001400231490000800245100002600253700002300279700003400302700002600336700001800362700001500380856004400395 2013 eng d00aSeed-mediated connectivity among fragmented populations of Quercus castanea (Fagaceae) in a Mexican landscape0 aSeedmediated connectivity among fragmented populations of iQuerc a1663-16710 v1001 aHerrera-Arroyo, Luisa1 aSork, Victoria, L.1 aGonzález-Rodríguez, Antonio1 aRocha-Ramirez, Victor1 aVega, Ernesto1 aOyama, Ken uhttps://quercus.myspecies.info/node/15501189nas a2200217 4500008004100000245006600041210006600107300001000173490000700183520053300190653001800723653001200741653004700753653001600800100002100816700002000837700002900857700002400886700001700910856004400927 2013 eng d00aUsing phylogenomics to infer the evolutionary history of oaks0 aUsing phylogenomics to infer the evolutionary history of oaks a61-710 v243 aOne 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.10aPhylogenetics10aQuercus10arestriction-site associated DNA (RAD) tags10asystematics1 aHipp, Andrew, L.1 aManos, Paul, S.1 aCavender-Bares, Jeannine1 aEaton, Deren, A. R.1 aNipper, Rick uhttps://quercus.myspecies.info/node/15602645nas a2200157 4500008004100000245010300041210006900144260001700213300001200230490000700242520213000249100002702379700002202406700001502428856004402443 2013 eng d00aNew Approaches to the Biogeography and Areas of Endemism of Red Oaks (Quercus L., Section Lobatae)0 aNew Approaches to the Biogeography and Areas of Endemism of Red  cJuly 1, 2013 a555-5730 v623 aAn 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.]1 aTorres-Miranda, Andres1 aLuna-Vega, Isolda1 aOyama, Ken uhttps://quercus.myspecies.info/node/15802458nas a2200229 4500008004100000020001400041245016200055210006900217300001200286520170600298653001102004653001202015653000902027653001402036653002202050100002302072700002102095700002002116700002302136700002502159856004402184 2013 eng d a1095-833900aApplication of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications0 aApplication of plastid and nuclear markers to DNA barcoding of E an/a-n/a3 aDNA 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, 000–000.10acerris10aecology10ailex10aphylogeny10aregional sampling1 aSimeone, Marco, C.1 aPiredda, Roberta1 aPapini, Alessio1 aVessella, Federico1 aSchirone, Bartolomeo uhttps://quercus.myspecies.info/node/157