Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

From the mountains to the coast and back again: Ancient biogeography in a radiation of short-range endemic harvestmen from California

(2016) K.N. Emata et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

(2015) Anna Papadopoulou et al.   EVOLUTION

Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga,Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

(2015) Marshal Hedin et al.   MOLECULAR ECOLOGY

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

(2015) P. P. Sharma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

A Short Guide to the Climatic Variables of the Last Glacial Maximum for Biogeographers

(2015) Sara Varela et al.   PLoS One

Origins of Plant Diversity in the California Floristic Province

(2014) Bruce G. Baldwin   Annual Review of Ecology Evolution and Systematics

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America

(2014) Andrew D. Gottscho   BIOLOGICAL REVIEWS

Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact

(2014) Fiona C Gowen et al.   BMC EVOLUTIONARY BIOLOGY

Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

(2014) Sean B. Reilly 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

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Phylogeography of the Arizona hairy scorpion (Hadrurus arizonensis) supports a model of biotic assembly in the Mojave Desert and adds a new Pleistocene refugium

(2013) Matthew R. Graham et al.   JOURNAL OF BIOGEOGRAPHY

Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

(2013) Thomas J. Devitt et al.   MOLECULAR ECOLOGY

Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

(2013) E. A. Myers et al.   MOLECULAR ECOLOGY

Using genomic data to revisit an early example of reproductive character displacement in HaitianAnolislizards

(2013) Shea M. Lambert et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Bacterial endosymbiont infections in ‘living fossils’: a case study of North American vaejovid scorpions

(2013) Robert W. Bryson   Molecular Ecology Resources

Phylogeography of Beck’s Desert Scorpion, Paruroctonus becki, reveals Pliocene diversification in the Eastern California Shear Zone and postglacial expansion in the Great Basin Desert

(2013) Matthew R. Graham et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

As Old as the Hills: Montane Scorpions in Southwestern North America Reveal Ancient Associations between Biotic Diversification and Landscape History

(2013) Robert W. Bryson et al.   PLoS One

Species Delimitation and Morphological Divergence in the Scorpion Centruroides vittatus (Say, 1821): Insights from Phylogeography

(2013) Tsunemi Yamashita et al.   PLoS One

Multilocus Species Delimitation in a Complex of Morphologically Conserved Trapdoor Spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)

(2013) Jordan D. Satler 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

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

(2012) SEAN D. SCHOVILLE et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Early Cenozoic topography, morphology, and tectonics of the northern Sierra Nevada and western Basin and Range

(2012) Elizabeth J. Cassel et al.   Geosphere

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR 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

Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus) from California

(2012) Marshal Hedin et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

A simulation-based evaluation of methods for inferring linear barriers to gene flow

(2012) CHRISTOPHER BLAIR et al.   Molecular Ecology Resources

Climate Change Refugia for Biodiversity in the Klamath-Siskiyou Ecoregion

(2012) David Olson et al.   NATURAL AREAS JOURNAL

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

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

Phylogeography and Population Genetic Structure of the Ornate Dragon Lizard, Ctenophorus ornatus

(2012) Esther Levy et al.   PLoS One

Is Gene Flow Promoting the Reversal of Pleistocene Divergence in the Mountain Chickadee (Poecile gambeli)?

(2012) Joseph D. Manthey et al.   PLoS One

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics

(2011) Toni Safner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)

(2011) Jordan D. Satler et al.   PLoS One

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

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

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Elucidating the phylogeographic structure among a mosaic of unisexual and bisexual populations of the weevil Geodercodes latipennis (Coleoptera: Curculionidae) in the Transverse Ranges of southern California

(2010) MAXI POLIHRONAKIS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Multilocus phylogeography of the flightless darkling beetle Nyctoporis carinata (Coleoptera: Tenebrionidae) in the California Floristic Province: deciphering an evolutionary mosaic

(2010) MAXI POLIHRONAKIS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria

(2010) Dan L. Warren et al.   ECOLOGICAL APPLICATIONS

Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America

(2010) AARON B. A. SHAFER et al.   MOLECULAR ECOLOGY

Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance?

(2009) A. C. Frantz et al.   JOURNAL OF APPLIED ECOLOGY

Closing the ring: historical biogeography of the salamander ring speciesEnsatina eschscholtzii

(2009) Shawn R. Kuchta et al.   JOURNAL OF BIOGEOGRAPHY

Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008

(2009) SCOTT EDWARDS et al.   MOLECULAR ECOLOGY

Phylogeography’s past, present, and future: 10 years after Avise, 2000

(2009) M.J. Hickerson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California)

(2008) James F. Parham et al.   CONSERVATION GENETICS

Congruent population structure inferred from dispersal behaviour and intensive genetic surveys of the threatened Florida scrub-jay (Aphelocoma cœrulescens)

(2008) A. COULON et al.   MOLECULAR ECOLOGY

Pronounced phylogeographic structure on a small spatial scale: Geomorphological evolution and lineage history in the salamander ring species Ensatina eschscholtzii in central coastal California

(2008) Shawn R. Kuchta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION