HyDe: A Python Package for Genome-Scale Hybridization Detection

Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation

(2017) Michael L. Arnold et al.   TRENDS IN ECOLOGY & EVOLUTION

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

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

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu 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

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

(2011) David Gerard et al.   BMC EVOLUTIONARY BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Cython: The Best of Both Worlds

(2010) Stefan Behnel et al.   COMPUTING IN SCIENCE & ENGINEERING

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY