Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae)

Leapfrogging the Mexican highlands: influence of biogeographical and ecological factors on the diversification of highland species

(2018) Itzue W Caviedes-Solis et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenomic insights into the diversification of salamanders in the Isthmura bellii group across the Mexican highlands

(2018) Robert W. Bryson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A multilocus phylogeny of the genus Sarcohyla (Anura: Hylidae), and an investigation of species boundaries using statistical species delimitation

(2018) Itzue W. Caviedes-Solis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Systematics of the frogs allocated to Sarcohyla bistincta sensu lato (Cope, 1877), with description of a new species from Western Mexico

(2018) JONATHAN A. CAMPBELL et al.   ZOOTAXA

A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

(2017) Robert W. Bryson et al.   JOURNAL OF BIOGEOGRAPHY

The K = 2 conundrum

(2017) Jasmine K. Janes et al.   MOLECULAR ECOLOGY

Willet be one species or two? A genomic view of the evolutionary history ofTringa semipalmata

(2016) Jessica A. Oswald et al.   AUK

Hidden histories of gene flow in highland birds revealed with genomic markers

(2016) Eugenia Zarza et al.   MOLECULAR ECOLOGY

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

(2016) James Starrett et al.   Molecular Ecology Resources

Exon capture optimization in amphibians with large genomes

(2016) Evan McCartney-Melstad et al.   Molecular Ecology Resources

Phylogenetics, classification, and biogeography of the treefrogs (Amphibia: Anura: Arboranae)

(2016) WILLIAM E. DUELLMAN et al.   ZOOTAXA

How Many Kinds of Birds Are There and Why Does It Matter?

(2016) George F. Barrowclough et al.   PLoS One

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans-Mexican Volcanic Belt

(2015) Alicia Mastretta-Yanes et al.   JOURNAL OF BIOGEOGRAPHY

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

Diversification and biogeographical history of Neotropical plethodontid salamanders

(2015) Sean M. Rovito et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

(2015) Fábio Raposo do Amaral et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

(2014) Jeffrey M. DaCosta et al.   PLoS One

The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

(2014) Robert W. Bryson et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Rediscovery of ‘lost’ treefrogs from the Oaxacan highlands of Mexico

(2013) Jesse R. J. Delia et al.   BIODIVERSITY AND CONSERVATION

Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south-eastern Mexico

(2013) Adam D. Leaché et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae:Thorius)

(2013) Sean M. Rovito et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Influence of the geological history of the Trans-Mexican Volcanic Belt on the diversification ofNolina parviflora(Asparagaceae: Nolinoideae)

(2013) Eduardo Ruiz-Sanchez et al.   JOURNAL OF BIOGEOGRAPHY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

The mitonuclear compatibility hypothesis of sexual selection

(2013) G. E. Hill et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Biodiversidad de anfibios en México

(2013) Gabriela Parra-Olea et al.   Revista Mexicana de Biodiversidad

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

A new species of Brush-Finch (Arremon; Emberizidae) from western Mexico

(2013) Adolfo G. Navarro-Sigüenza et al.   Wilson Journal of Ornithology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Species formation and geographical range evolution in a genus of Central American cloud forest salamanders (Dendrotriton)

(2012) Sean M. Rovito et al.   JOURNAL OF BIOGEOGRAPHY

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

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

Vulnerability of cloud forest reserves in Mexico to climate change

(2012) Rocío Ponce-Reyes et al.   Nature Climate Change

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

(2011) Robert W. Bryson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico

(2011) Robert W. Bryson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

ELUCIDATION OF CRYPTIC DIVERSITY IN A WIDESPREAD NEARCTIC TREEFROG REVEALS EPISODES OF MITOCHONDRIAL GENE CAPTURE AS FROGS DIVERSIFIED ACROSS A DYNAMIC LANDSCAPE

(2010) Robert W. Bryson Jr. et al.   EVOLUTION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes

(2010) Robert W. Bryson et al.   JOURNAL OF BIOGEOGRAPHY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A New Species of Stream-breeding Treefrog of the Genus Charadrahyla (Hylidae) from the Sierra Madre del Sur of Guerrero, Mexico

(2009) Jonathan A. Campbell et al.   COPEIA

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

(2009) SCOTT EDWARDS et al.   MOLECULAR ECOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina)

(2008) J. E. McCORMACK et al.   MOLECULAR ECOLOGY

Mitochondrial DNA under siege in avian phylogeography

(2008) ROBERT M. ZINK et al.   MOLECULAR ECOLOGY