PUB - Publikationen an der Universität Bielefeld

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

AUTHOR UNKNOWN, 2009

Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus.
Arca M, Hinsinger DD, Cruaud C, Tillier A, Bousquet J, Frascaria-Lacoste N., PLoS ONE 7(3), 2012
PMID: 22479532

Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA., PLoS ONE 3(10), 2008
PMID: 18852878

Identification of SNP and SSR markers in eggplant using RAD tag sequencing.
Barchi L, Lanteri S, Portis E, Acquadro A, Vale G, Toppino L, Rotino GL., BMC Genomics 12(), 2011
PMID: 21663628

AUTHOR UNKNOWN, 2012

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex).
Burgarella C, Lorenzo Z, Jabbour-Zahab R, Lumaret R, Guichoux E, Petit RJ, Soto A, Gil L., Heredity (Edinb) 102(5), 2009
PMID: 19240752

The species concept in Quercus
AUTHOR UNKNOWN, 1975

Stacks: building and genotyping Loci de novo from short-read sequences.
Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH., G3 (Bethesda) 1(3), 2011
PMID: 22384329

Stacks: an analysis tool set for population genomics.
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA., Mol. Ecol. 22(11), 2013
PMID: 23701397

Diversity, distribution and ecosystem services of the North American Oaks
AUTHOR UNKNOWN, 2016

Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach.
Cavender-Bares J, Gonzalez-Rodriguez A, Eaton DA, Hipp AA, Beulke A, Manos PS., Mol. Ecol. 24(14), 2015
PMID: 26095958

A high density genetic map of maritime pine based on AFLPs
AUTHOR UNKNOWN, 2002

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.
Chancerel E, Lepoittevin C, Le Provost G, Lin YC, Jaramillo-Correa JP, Eckert AJ, Wegrzyn JL, Zelenika D, Boland A, Frigerio JM, Chaumeil P, Garnier-Gere P, Boury C, Grivet D, Gonzalez-Martinez SC, Rouze P, Van de Peer Y, Neale DB, Cervera MT, Kremer A, Plomion C., BMC Genomics 12(), 2011
PMID: 21767361

A novel set of single‐copy nuclear gene markers in white oak and implications for species delimitation
AUTHOR UNKNOWN, 2017

Realized gene flow within mixed stands of Quercus robur L. and Q. petraea (Matt.) L. revealed at the stage of naturally established seedling.
Chybicki IJ, Burczyk J., Mol. Ecol. 19(10), 2010
PMID: 20550635

Population differentiation among three species of white oak in northeastern Illinois
AUTHOR UNKNOWN, 2006

Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community.
Curtu AL, Gailing O, Finkeldey R., BMC Evol. Biol. 7(), 2007
PMID: 17996115

RADSeq: next-generation population genetics.
Davey JW, Davey JL, Blaxter ML, Blaxter MW., Brief Funct Genomics 9(5-6), 2010
PMID: 21266344

The oaks of western Eurasia: Traditional classifications and evidence from two nuclear markers
AUTHOR UNKNOWN, 2010

Phylogeny.fr: robust phylogenetic analysis for the non-specialist.
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18424797

Selection and dispersal in a multispecies oak hybrid zone.
Dodd RS, Afzal-Rafii Z., Evolution 58(2), 2004
PMID: 15068344

Phylogeographic structure of white oaks throughout the European continent.
Dumolin-Lapegue S, Demesure B, Fineschi S, Le Corre V, Petit RJ., Genetics 146(4), 1997
PMID: 9258689

ARE CHLOROPLAST AND MITOCHONDRIAL DNA VARIATION SPECIES INDEPENDENT IN OAKS?
Dumolin-Lapegue S, Kremer A, Petit RJ., Evolution 53(5), 1999
PMID: 28565571

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.
Durand J, Bodenes C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herran A, Ikaran Z, Cabane C, Ueno S, Alberto F, Dumoulin PY, Guichoux E, de Daruvar A, Kremer A, Plomion C., BMC Genomics 11(), 2010
PMID: 20950475

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.
Eaton DA., Bioinformatics 30(13), 2014
PMID: 24603985

Historical introgression among the American live oaks and the comparative nature of tests for introgression.
Eaton DA, Hipp AL, Gonzalez-Rodriguez A, Cavender-Bares J., Evolution 69(10), 2015
PMID: 26299374

Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691

Natural hybridization and hybrid zones between Quercus crassifolia and Quercus crassipes (Fagaceae) in Mexico: morphological and molecular evidence.
Tovar-Sanchez E, Oyama K., Am. J. Bot. 91(9), 2004
PMID: 21652368

Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
Evanno G, Regnaut S, Goudet J., Mol. Ecol. 14(8), 2005
PMID: 15969739

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus).
Fitz-Gibbon S, Hipp AL, Pham KK, Manos PS, Sork VL., Genome 60(9), 2017
PMID: 28355490

High rates of gene flow by pollen and seed in oak populations across Europe.
Gerber S, Chadœuf J, Gugerli F, Lascoux M, Buiteveld J, Cottrell J, Dounavi A, Fineschi S, Forrest LL, Fogelqvist J, Goicoechea PG, Jensen JS, Salvini D, Vendramin GG, Kremer A., PLoS ONE 9(1), 2014
PMID: 24454802

AUTHOR UNKNOWN, 2013

Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.).
Guichoux E, Lagache L, Wagner S, Leger P, Petit RJ., Mol Ecol Resour 11(3), 2011
PMID: 21481218

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O., Syst. Biol. 59(3), 2010
PMID: 20525638

Hybridization and introgression in Quercus alba
AUTHOR UNKNOWN, 1975

Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species.
Hasselman DJ, Argo EE, McBride MC, Bentzen P, Schultz TF, Perez-Umphrey AA, Palkovacs EP., Mol. Ecol. 23(5), 2014
PMID: 24450302

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio.
Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ, Hiscock SJ., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 363(1506), 2008
PMID: 18579474

Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.
Heslot N, Rutkoski J, Poland J, Jannink JL, Sorrells ME., PLoS ONE 8(9), 2013
PMID: 24040295

Should hybridization make us skeptical of the oak phylogeny ?
AUTHOR UNKNOWN, 2015

A framework phylogeny of the American oak clade based on sequenced RAD data.
Hipp AL, Eaton DA, Cavender-Bares J, Fitzek E, Nipper R, Manos PS., PLoS ONE 9(4), 2014
PMID: 24705617

Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity.
Hipp AL, Manos PS, Gonzalez-Rodriguez A, Hahn M, Kaproth M, McVay JD, Avalos SV, Cavender-Bares J., New Phytol. 217(1), 2017
PMID: 28921530

Taxonomy of Hill's Oak (Quercus ellipsoidalis: Fagaceae): evidence from AFLP data.
Hipp AL, Weber JA., Syst. Bot. 33(1), 2008
PMID: IND44028912

Human-impacted landscapes facilitate hybridization between a native and an introduced tree.
Hoban SM, McCleary TS, Schlarbaum SE, Anagnostakis SL, Romero-Severson J., Evol Appl 5(7), 2012
PMID: 23144658

Choosing and using a plant DNA barcode.
Hollingsworth PM, Graham SW, Little DP., PLoS ONE 6(5), 2011
PMID: 21637336

Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus
AUTHOR UNKNOWN, 2014

Resolving whether botanic gardens are on the road to conservation or a pathway for plant invasions.
Hulme PE., Conserv. Biol. 29(3), 2014
PMID: 25439324

Review. Hybrid trait speciation and Heliconius butterflies.
Jiggins CD, Salazar C, Linares M, Mavarez J., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 363(1506), 2008
PMID: 18579480

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A., Bioinformatics 28(12), 2012
PMID: 22543367

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama
AUTHOR UNKNOWN, 2009

DNA barcodes for ecology, evolution, and conservation.
Kress WJ, Garcia-Robledo C, Uriarte M, Erickson DL., Trends Ecol. Evol. (Amst.) 30(1), 2014
PMID: 25468359

Fine-scale environmental control of hybridization in oaks.
Lagache L, Klein EK, Guichoux E, Petit RJ., Mol. Ecol. 22(2), 2012
PMID: 23173566

Lengths and correlates of lag phases in upper-Midwest plant invasions
Larkin DJ., Biol. Invasions 14(4), 2012
PMID: IND44692418

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic I, Bork P., Nucleic Acids Res. 44(W1), 2016
PMID: 27095192

Shared alleles in sympatric oaks: recurrent gene flow is a more parsimonious explanation than ancestral polymorphism.
Lexer C, Kremer A, Petit RJ., Mol. Ecol. 15(7), 2006
PMID: 16689915

High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology.
Lijavetzky D, Cabezas JA, Ibanez A, Rodriguez V, Martinez-Zapater JM., BMC Genomics 8(), 2007
PMID: 18021442

Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects.
Lynch M., Mol. Biol. Evol. 25(11), 2008
PMID: 18725384

Hybrid speciation.
Mallet J., Nature 446(7133), 2007
PMID: 17361174

Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America.
McVay JD, Hauser D, Hipp AL, Manos PS., Genome 60(9), 2017
PMID: 28727934

A genetic legacy of introgression confounds phylogeny and biogeography in oaks.
McVay JD, Hipp AL, Manos PS., Proc. Biol. Sci. 284(1854), 2017
PMID: 28515204

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model.
Meng C, Kubatko LS., Theor Popul Biol 75(1), 2008
PMID: 19038278

Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae).
Moran EV, Willis J, Clark JS., Am. J. Bot. 99(1), 2011
PMID: 22174334

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pages H, Gentleman R., Bioinformatics 25(19), 2009
PMID: 19654119

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome.
Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M., BMC Genomics 9(), 2008
PMID: 18590545

Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences
AUTHOR UNKNOWN, 2008

Taxonomic Relationships and Gene Flow in Four North American Quercus Species (Quercus section Lobatae)
Owusu SA, Sullivan AR, Weber JA, Hipp AL, Gailing O., Syst. Bot. 40(2), 2015
PMID: IND604666240

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach.
Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q., BMC Genomics 14(), 2013
PMID: 23947483

Interspecific gene flow in a multispecies oak hybrid zone in the Sierra Tarahumara of Mexico.
Penaloza-Ramirez JM, Gonzalez-Rodriguez A, Mendoza-Cuenca L, Caron H, Kremer A, Oyama K., Ann. Bot. 105(3), 2010
PMID: 20056653

Understanding the spectacular failure of DNA barcoding in willows (Salix): does this result from a trans-specific selective sweep?
Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW., Mol. Ecol. 23(19), 2014
PMID: 24944007

Gene diversity in natural populations of oak species
AUTHOR UNKNOWN, 1993

Hybridization as a mechanism of invasion in oaks
AUTHOR UNKNOWN, 2004

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.
Pham KK, Hipp AL, Manos PS, Cronn RC., Genome 60(9), 2017
PMID: 28445658

Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity.
Piredda R, Simeone MC, Attimonelli M, Bellarosa R, Schirone B., Mol Ecol Resour 11(1), 2010
PMID: 21429102

Exploring tree species colonization potentials using a spatially explicit simulation model: implications for four oaks under climate change.
Prasad AM, Gardiner JD, Iverson LR, Matthews SN, Peters M., Glob Chang Biol 19(7), 2013
PMID: 23526802

Inference of population structure using multilocus genotype data.
Pritchard JK, Stephens M, Donnelly P., Genetics 155(2), 2000
PMID: 10835412

Challenges in analysis and interpretation of microsatellite data for population genetic studies.
Putman AI, Carbone I., Ecol Evol 4(22), 2014
PMID: 25540699

AUTHOR UNKNOWN, 2016

Horticulture as a pathway of invasive plant introductions in the United States
AUTHOR UNKNOWN, 2001

DISTRUCT: A program for the graphical display of population structure
AUTHOR UNKNOWN, 2004

Natural hybridization within the genus Quercus L
AUTHOR UNKNOWN, 1993

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.
Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S., BMC Genomics 13(), 2012
PMID: 22214349

How common is homoploid hybrid speciation?
Schumer M, Rosenthal GG, Andolfatto P., Evolution 68(6), 2014
PMID: 24620775

Speciation reversal and biodiversity dynamics with hybridization in changing environments.
Seehausen O, Takimoto G, Roy D, Jokela J., Mol. Ecol. 17(1), 2007
PMID: 18034800

Application of plastid and nuclear markers to DNA barcoding of Euro‐Mediterranean oaks (Quercus, Fagaceae): Problems, prospects and phylogenetic implications
AUTHOR UNKNOWN, 2013

Leaf morphological evidence of natural hybridization between two oak species (Quercus austrocochinchinensis and Q. kerrii) and its implications for conservation management
AUTHOR UNKNOWN, 2015

A rapid bootstrap algorithm for the RAxML Web servers.
Stamatakis A, Hoover P, Rougemont J., Syst. Biol. 57(5), 2008
PMID: 18853362

The distribution of the genus Quercus in Illinois: An update
AUTHOR UNKNOWN, 2002

Hybridization and divergence in multi‐species oak (Quercus) communities
AUTHOR UNKNOWN, 2016

Megaphylogenetic Specimen-Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for ClassificationThe Global Carex Group
JimA©nez-MejA­as P, Brown Bethany H. , Chouinard Brianna N. , Chung Kyong-Sook , Escudero Marcial , Ford Bruce A. , Ford Kerry A. , Gebauer Sebastian , Gehrke Berit , Hahn Marlene , Hipp Andrew. L. , Hoffmann Matthias H. , Jin Xiao-Feng , Jung Jongduk , Kim Sangtae , LuceA±o Modesto , Lueders Kate , MA­guez MA³nica , Maguilla Enrique , MartA­n-Bravo Santiago , Molina Ana , Naczi Robert F. C. , Pender Jocelyn E. , Reznicek Anton A. , Roalson Eric H. , Starr Julian R. , Villaverde Tamara , Waterway Marcia J. , Wilson Karen L. , Yang Jong-Cheol , Zhang Shuren ., Syst. Bot. 41(3), 2016
PMID: IND605454477

Next-generation hybridization and introgression.
Twyford AD, Ennos RA., Heredity (Edinb) 108(3), 2011
PMID: 21897439

Estimating exotic gene flow into native pine stands: zygotic vs. gametic components.
Unger GM, Vendramin GG, Robledo-Arnuncio JJ., Mol. Ecol. 23(22), 2014
PMID: 25277767

Phylogenetic analysis of the highland papayas ( Vasconcellea) and allied genera (Caricaceae) using PCR-RFLP.
Van Droogenbroeck B, Kyndt T, Maertens I, Romeijn-Peeters E, Scheldeman X, Romero-Motochi JP, Van Damme P, Goetghebeur P, Gheysen G., Theor. Appl. Genet. 108(8), 2004
PMID: 14752605

Ecological species, multispecies, and oaks
AUTHOR UNKNOWN, 1976

Variation in morphological traits in a recent hybrid zone between closely related Quercus liaotungensis and Q. mongolica (Fagaceae)
AUTHOR UNKNOWN, 2015

Interspecific gene flow in sympatric oaks.
Whittemore AT, Schaal BA., Proc. Natl. Acad. Sci. U.S.A. 88(6), 1991
PMID: 11607170

High‐throughput SNP genotyping with the Goldengate assay in Maize
AUTHOR UNKNOWN, 2010

Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes.
Yang J, Vazquez L, Chen X, Li H, Zhang H, Liu Z, Zhao G., Front Plant Sci 8(), 2017
PMID: 28579999

Genetic characterization of hybridization between native and invasive bittersweet vines (Celastrus spp.)
Zaya DN, Leicht-Young SA, Pavlovic NB, Feldheim KA, Ashley MV., Biol. Invasions 17(10), 2015
PMID: IND604393701