Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

Epistasis and the Dynamics of Reversion in Molecular Evolution

(2016) D. M. McCandlish et al.   GENETICS

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

(2016) Tanja Stadler et al.   SYSTEMATIC BIOLOGY

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

Nonadaptive Amino Acid Convergence Rates Decrease over Time

(2015) Richard A. Goldstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

No Genome-Wide Protein Sequence Convergence for Echolocation

(2015) Z. Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

(2015) G. W. C. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

(2015) Zhengting Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Contingency and entrenchment in protein evolution under purifying selection

(2015) Premal Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

(2015) Nicola De Maio et al.   SYSTEMATIC BIOLOGY

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

The Molecular Basis of Phenotypic Convergence

(2014) Erica Bree Rosenblum et al.   Annual Review of Ecology Evolution and Systematics

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES

(2013) Jeffrey C. Oliver   EVOLUTION

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models

(2013) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds

(2013) J. Projecto-Garcia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fitness conferred by replaced amino acids declines with time

(2012) S. A. Naumenko et al.   Biology Letters

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

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

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes

(2012) C. R. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase

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

Parallel Molecular Evolution in an Herbivore Community

(2012) Y. Zhen et al.   SCIENCE

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

Convergence in pigmentation at multiple levels: mutations, genes and function

(2010) M. Manceau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evidence for an ancient adaptive episode of convergent molecular evolution

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

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

(2008) Igor B Rogozin et al.   Biology Direct

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evolutionary Switch and Genetic Convergence on rbcL following the Evolution of C4 Photosynthesis

(2008) Pascal-Antoine Christin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Frequent and Widespread Parallel Evolution of Protein Sequences

(2008) A. Rokas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hemiplasy: A New Term in the Lexicon of Phylogenetics

(2008) John C. Avise et al.   SYSTEMATIC BIOLOGY