Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus )

Exploring the potential of gametic reconstruction of parental genotypes by F1 hybrids as a bridge for rapid introgression

(2017) Charles H. Cannon et al.   GENOME

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

(2017) Sorel Fitz-Gibbon et al.   GENOME

Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

(2017) Andrew L. Hipp et al.   NEW PHYTOLOGIST

A genetic legacy of introgression confounds phylogeny and biogeography in oaks

(2017) John D. McVay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary history and gene flow of an endemic island oak: Quercus pacifica

(2016) Janet Rizner Backs et al.   AMERICAN JOURNAL OF BOTANY

Endemism in native floras of California’s Channel Islands correlated with seasonal patterns of aeolian processes

(2016) Lynn Riley et al.   Botany

Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes , Dynastinae)

(2016) Jen-Pan Huang   MOLECULAR ECOLOGY

Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection

(2016) Jordan B. Bemmels et al.   MOLECULAR ECOLOGY

Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

(2016) Chris J. Brauer et al.   MOLECULAR ECOLOGY

Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant modelArabidopsis arenosa

(2016) Filip Kolář et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

Genomic and functional approaches reveal a case of adaptive introgression fromPopulus balsamifera(balsam poplar) inP. trichocarpa(black cottonwood)

(2016) Adriana Suarez-Gonzalez et al.   MOLECULAR ECOLOGY

Genomics of hybridization and its evolutionary consequences

(2016) Richard J. Abbott et al.   MOLECULAR ECOLOGY

Demographic history of speciation in aSenecioaltitudinal hybrid zone on Mt. Etna

(2016) Dmitry A. Filatov et al.   MOLECULAR ECOLOGY

Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus )

(2016) Laura Benestan et al.   MOLECULAR ECOLOGY

Impacts of human-induced environmental disturbances on hybridization between two ecologically differentiated Californian oak species

(2016) Joaquín Ortego et al.   NEW PHYTOLOGIST

Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

(2016) Maria Tereza C. Thomé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reticulation, divergence, and the phylogeography–phylogenetics continuum

(2016) Scott V. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

Landscape genetics and population structure in Valley Oak (Quercus lobata Née)

(2015) Mary V. Ashley et al.   AMERICAN JOURNAL OF BOTANY

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

(2015) Joaquín Ortego et al.   MOLECULAR ECOLOGY

Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape

(2015) Anthony J. Barley et al.   MOLECULAR ECOLOGY

Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

(2015) Hayley C. Lanier et al.   MOLECULAR ECOLOGY

Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island Complex

(2015) Anna Papadopoulou et al.   MOLECULAR ECOLOGY

The population demography ofBetula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing

(2015) Y. Tsuda et al.   MOLECULAR ECOLOGY

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Climatically stable landscapes predict patterns of genetic structure and admixture in the Californian canyon live oak

(2014) Joaquín Ortego et al.   JOURNAL OF BIOGEOGRAPHY

Influence of climatic niche suitability and geographical overlap on hybridization patterns among southern Californian oaks

(2014) Joaquín Ortego et al.   JOURNAL OF BIOGEOGRAPHY

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

(2014) Jeffrey W. Streicher et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)

(2014) Marcial Escudero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Interspecific introgressive origin of genomic diversity in the house mouse

(2014) Kevin J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen

(2013) A. Rieux et al.   ECOLOGY LETTERS

Higher Levels of Neanderthal Ancestry in East Asians than in Europeans

(2013) Jeffrey D. Wall et al.   GENETICS

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Hybridization and the origin of species

(2013) A. Hochkirch   JOURNAL OF EVOLUTIONARY BIOLOGY

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobataNée

(2013) Paul F. Gugger et al.   MOLECULAR ECOLOGY

Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion

(2013) Yongshuai Sun et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Efficient mitigation of founder effects during the establishment of a leading-edge oak population

(2013) A. Hampe et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs

(2013) Frank E. Rheindt et al.   SYSTEMATIC BIOLOGY

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

(2012) Toni I. Gossmann et al.   Genome Biology and Evolution

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Outlier loci highlight the direction of introgression in oaks

(2012) E. Guichoux et al.   MOLECULAR ECOLOGY

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

(2012) Kai N. Stölting et al.   MOLECULAR ECOLOGY

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

Efficient Long-Distance Gene Flow into an Isolated Relict Oak Stand

(2011) J. Buschbom et al.   JOURNAL OF HEREDITY

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

(2011) M. Currat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introgressive hybridization as a mechanism for species rescue

(2011) Marissa L. Baskett et al.   Theoretical Ecology

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Rapid spread of invasive genes into a threatened native species

(2010) Benjamin M. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

INCIPIENT SPECIATION DESPITE LITTLE ASSORTATIVE MATING: THE YELLOW-RUMPED WARBLER HYBRID ZONE

(2009) Alan Brelsford et al.   EVOLUTION

Short distance pollen movement in a wind-pollinated tree, Quercus lobata (Fagaceae)

(2009) Andrea R. Pluess et al.   FOREST ECOLOGY AND MANAGEMENT

The genomic legacy from the extinctLepus timidusto the three hare species of Iberia: contrast between mtDNA, sex chromosomes and autosomes

(2009) J. MELO-FERREIRA et al.   MOLECULAR ECOLOGY

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

Natural hybridisation between kermes (Quercus coccifera L.) and holm oaks (Q. ilex L.) revealed by microsatellite markers

(2009) Joaquín Ortego et al.   PLANT BIOLOGY

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Are hotspots of evolutionary potential adequately protected in southern California?

(2008) Amy G. Vandergast et al.   BIOLOGICAL CONSERVATION

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

(2008) ALEJANDRO NETTEL et al.   MOLECULAR ECOLOGY

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY