Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

Conundrum of jumbled mosquito genomes

(2015) A. G. Clark et al.   SCIENCE

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

(2014) Konrad Lohse et al.   GENETICS

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

Interspecific introgressive origin of genomic diversity in the house mouse

(2014) Kevin J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

(2013) Yun Yu et al.   BMC BIOINFORMATICS

Likelihood-based inference of population history from low-coveragede novogenome assemblies

(2013) Jack Hearn et al.   MOLECULAR ECOLOGY

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu et al.   SYSTEMATIC BIOLOGY

Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees

(2013) Michael DeGiorgio et al.   SYSTEMATIC BIOLOGY

Computational approaches to species phylogeny inference and gene tree reconciliation

(2013) Luay Nakhleh   TRENDS IN ECOLOGY & EVOLUTION

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

(2012) Michael L. Moody et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

(2012) A. Eriksson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Yun Yu et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

(2012) Fabian Staubach et al.   PLoS Genetics

COALESCENT-BASED SPECIES TREE INFERENCE FROM GENE TREE TOPOLOGIES UNDER INCOMPLETE LINEAGE SORTING BY MAXIMUM LIKELIHOOD

(2011) Yufeng Wu   EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

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

Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees

(2010) Yufeng Wu   BIOINFORMATICS

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters

(2010) Leo van Iersel et al.   BIOINFORMATICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS