Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inconsistency of Species Tree Methods under Gene Flow

(2016) Claudia Solís-Lemus et al.   SYSTEMATIC BIOLOGY

Phylogenomics for Systematic Biology

(2016) David Posada   SYSTEMATIC BIOLOGY

Anthropogenic Impacts Facilitate Native Fish Hybridization in the Bonneville Basin of Western North America

(2016) Max R. Bangs et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

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

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

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Causes, consequences and solutions of phylogenetic incongruence

(2014) A. Som   BRIEFINGS IN BIOINFORMATICS

Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genusAnas)

(2014) Jeffrey L. Peters et al.   MOLECULAR ECOLOGY

Influence of Introgression and Geological Processes on Phylogenetic Relationships of Western North American Mountain Suckers (Pantosteus, Catostomidae)

(2014) Peter J. Unmack et al.   PLoS One

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

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

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

TESTING MITOCHONDRIAL CAPTURE AND DEEP COALESCENCE IN AMAZONIAN CICHLID FISHES (CICHLIDAE:CICHLA)

(2013) Stuart C. Willis et al.   EVOLUTION

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

Comparative Species Divergence across Eight Triplets of Spiny Lizards (Sceloporus) Using Genomic Sequence Data

(2013) Adam D. Leaché et al.   Genome Biology and Evolution

How to fail at species delimitation

(2013) Bryan C. Carstens et al.   MOLECULAR ECOLOGY

Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes

(2013) Matthew J. Phillips et al.   PLoS One

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

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

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Conservation Genomics of Threatened Animal Species

(2013) Cynthia C. Steiner et al.   Annual Review of Animal Biosciences

THE LANGUAGE OF SPECIATION

(2012) Richard G. Harrison   EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stream hierarchy defines riverscape genetics of a North American desert fish

(2012) Matthew W. Hopken et al.   MOLECULAR ECOLOGY

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

(2012) Ronald S. Burton et al.   MOLECULAR ECOLOGY

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

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

The Promises and Pitfalls of Next-Generation Sequencing Data in Phylogeography

(2012) Bryan Carstens et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Challenges and opportunities of genetic approaches to biological conservation

(2010) Richard Frankham   BIOLOGICAL CONSERVATION

CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

(2010) John E. McCormack et al.   EVOLUTION

Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds

(2010) ELIZABETH M. HUMPHRIES et al.   MOLECULAR ECOLOGY

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Widespread genomic divergence during sympatric speciation

(2010) A. P. Michel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENTHELIANTHUSSPECIES

(2009) Nolan C. Kane et al.   EVOLUTION

Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps)

(2009) Kurt E. Galbreath et al.   JOURNAL OF BIOGEOGRAPHY

Morphology and nuclear markers reveal extensive mitochondrial introgressions in the Iberian Wall Lizard species complex

(2009) JULIEN P. RENOULT et al.   MOLECULAR ECOLOGY

Frequent mitochondrial gene introgression among high elevation Tibetan megophryid frogs revealed by conflicting gene genealogies

(2009) WEI CHEN et al.   MOLECULAR ECOLOGY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences

(2009) Michael H. Doosey et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene Trees Reveal Repeated Instances of Mitochondrial DNA Introgression in Orangethroat Darters (Percidae: Etheostoma)

(2009) Christen M. Bossu et al.   SYSTEMATIC BIOLOGY

Factors affecting the concordance between orthologous gene trees and species tree in bacteria

(2008) Santiago Castillo-Ramírez et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeography: retrospect and prospect

(2008) John C. Avise   JOURNAL OF BIOGEOGRAPHY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One