03248nas 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/15301189nas 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/15602764nas a2200265   4500008004100000245008000041210006900121300001100190490000600201520194800207653003402155653001302189653003102202653001802233653002202251653001202273653003602285100002102321700002402342700002902366700002202395700001702417700002002434856004402454       2014                        eng d00aA framework phylogeny of the American oak clade based on sequenced RAD data0 aframework phylogeny of the American oak clade based on sequenced  ae939750 v93 aOaks (Quercus, Fagaceae) are notorious in plant systematics for the problems they pose at the species level and for higher-level phylogenetics. Previous studies based on nuclear and chloroplast DNA sequences have failed to resolve the backbone phylogeny of the genus with strong support. In this study, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.39E06 aligned nucleotides, constituting 27,727 sequence clusters or ‘loci.’ We reran a subset of seven individuals as technical replicates and found that RAD-Seq data are readily combined across runs, with no difference in phylogenetic placement between replicates, despite the fact that a change in sequencing platforms between replicate runs resulted in data overlap between technical replicates of only 43–64%. 17% (4,715) of the loci we analyzed could be matched with high confidence (BLASTN E-value < 1E–15) to one or more expressed sequence tags (ESTs) in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as same-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. The phylogeny we recover provides a robust estimate of the framework phylogeny for the American oak clade and demonstrates the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old vascular plant clade.10aExpressed sequence tags (EST)10aFagaceae10anext-generation sequencing10aphylogenomics10aplant systematics10aQuercus10arestriction-site associated DNA1 aHipp, Andrew, L.1 aEaton, Deren, A. R.1 aCavender-Bares, Jeannine1 aFitzek, Elisabeth1 aNipper, Rick1 aManos, Paul, S.  uhttps://quercus.myspecies.info/node/16100412nas a2200145   4500008004500000020002200045245001200067210001200079260004300091300001100134100002500145700002900170700002300199856004400222       2011                        Engldsh    a978-3-642-21249-900aQuercus0 aQuercus  bSpringer Berlin Heidelbergc2011/01/01  a89-1291 aAldrich, Preston, R.1 aCavender-Bares, Jeannine1 aKole, Chittaranjan  uhttps://quercus.myspecies.info/node/13303959nas a2200277   4500008004100000245014000041210006900181490000700250520301000257653002003267653003003287653002003317653002303337653002003360653001903380653002803399653003103427653004403458653001403502100002903516700003203545700002103577700001803598700002103616856004403637       2011                        eng d00aPhylogeography and climatic niche evolution in live oaks (<i>Quercus </i>series <i>Virentes</i>) from the tropics to the temperate zone0 aPhylogeography and climatic niche evolution in live oaks iQuercu0 v383 aAim: We investigated the phylogeography, geographic variation in leaf morphology, freezingtolerance and climatic niches of two widespread evergreen sister oak species (Quercus) in theseries Virentes to gain insight into 1) the historical biogeographic explanations for populationgenetic structure and leaf morphological variation, and 2) the influence of genetically-basedvariation in freezing tolerance within and between species on climatic range limits and geneflow, and 3) to examine the evidence for contrasting impacts of Pleistocene glacial cycles ongenetic structure and diversity in tropical and temperate regions.Location: Southeastern U.S., Mexico and Central AmericaMethods: Nuclear microsatellites, non-recombining nuclear sequences within ITS and NIA-i3and chloroplast DNA sequences were obtained from samples collected throughout the range oftwo sister lineages of live oaks, represented by Quercus virginiana in the temperate zone andQuercus oleoides in the tropics. Divergence times were estimated for the two major geographicand genetic breaks. Differentiation in leaf morphology, analyzed from field specimens, wascompared to the molecular data. Freezing sensitivities of Q. virginiana and Q. oleoidespopulations were assessed in a common garden under controlled tropical and temperate climatesand compared to minimum temperature climatic niches for each species.Results: The geographic break between Q. virginiana and Q. oleoides was associated withstrong genetic differentiation of possible Miocene origin and with differentiation in freezingsensitivity, climatic envelopes and leaf morphology. A second important geographic and geneticbreak within Q. oleoides between Costa Rica and the rest of Central America showed aPleistocene divergence time and no differentiation in leaf morphology. Population geneticdifferentiation was greater but genetic diversity was lower within temperate Q. virginianacompared to tropical Q. oleoides, and genetic breaks largely corresponded to breaks in leafmorphology.Main Conclusions: Two major breaks, one between Mexico and the U.S. at the speciesboundary, and a more recent one within Q. oleoides between Honduras and Costa Rica implicateclimatic changes as potential causes. The latter break may be associated with formation of theCordillera Guanacaste followed by seasonal changes in precipitation. In the former case, an “outof the tropics” scenario is hypothesized, in which acquisition of freezing tolerance in Q.virginiana permitted colonization of and expansion in the temperate zone while differences inclimatic tolerances between the species limited secondary contact. More pronounced Pleistocenechanges in climate and sea level in the southeastern U.S. relative to Central America may explainthe greater population differentiation within temperate Q. virginiana and greater genetic diversityin tropical Q. oleoides. These patterns are predicted to hold for other taxa that span temperateand tropical zones of North and Middle America10aCentral America10achloroplast DNA sequences10aclimatic niches10afreezing tolerance10aleaf morphology10aNIA-i3 and ITS10anuclear microsatellites10aPleistocene glacial cycles10arise, unglaciated eastern North America10asea level1 aCavender-Bares, Jeannine1 aGonzalez-Rodriguez, Antonio1 aPahlich, Annette1 aKoehler, Kari1 aDeacon, Nicholas  uhttps://quercus.myspecies.info/node/13502231nas a2200229   4500008004100000020001400041245014400055210007100199260002900270300001000299520145500309653002301764653001601787653001401803653002801817653001401845653003201859100001801891700001901909700002901928856004401957       2011                        eng d  a1469-813700aEvidence for a freezing tolerance–growth rate trade-off in the live oaks (Quercus series Virentes) across the tropical–temperate divide0 aEvidence for a freezing tolerance–growth rate tradeoff in the li  bBlackwell Publishing Ltd  ano-no3 a* •It has long been hypothesized that species are limited to the north by minimum temperature and to the south by competition, resulting in a trade-off between freezing tolerance and growth rate. We investigated the extent to which the climatic origins of populations from four live oak species (Quercus series Virentes) were associated with freezing tolerance and growth rate, and whether species fitted a model of locally adapted populations, each with narrow climatic tolerances, or of broadly adapted populations with wide climatic tolerances. * •Acorns from populations of four species across a tropical–temperate gradient were grown under common tropical and temperate conditions. Growth rate, seed mass, and leaf and stem freezing traits were compared with source minimum temperatures. * •Maximum growth rates under tropical conditions were negatively correlated with freezing tolerance under temperate conditions. The minimum source temperature predicted the freezing tolerance of populations under temperate conditions. The tropical species Q. oleoides was differentiated from the three temperate species, and variation among species was greater than among populations. * •The trade-off between freezing tolerance and growth rate supports the range limit hypothesis. Limited variation within species indicates that the distributions of species may be driven more strongly by broad climatic factors than by highly local conditions.10afreezing tolerance10agrowth rate10alive oaks10aQuercus series Virentes10atrade-off10atropical–temperate divide1 aKoehler, Kari1 aCenter, Alyson1 aCavender-Bares, Jeannine  uhttps://quercus.myspecies.info/node/137