New prospects in the detection and comparative analysis of hybridization in the tree of life

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

(2017) Andrew A. Crowl et al.   EVOLUTION

Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America

(2017) John D. McVay et al.   GENOME

Is homoploid hybrid speciation that rare? An empiricist’s view

(2017) G Nieto Feliner et al.   HEREDITY

Genomic evidence of gene flow during reinforcement in Texas Phlox

(2017) Federico Roda et al.   MOLECULAR ECOLOGY

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

(2017) Nicolás García et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Expected pairwise congruence among gene trees under the coalescent model

(2017) Yuan Tian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas et al.   NEW PHYTOLOGIST

Ancient hybridization fuels rapid cichlid fish adaptive radiations

(2017) Joana I. Meier et al.   Nature Communications

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

Past, future, and present of state-dependent models of diversification

(2016) Brian C. O'Meara et al.   AMERICAN JOURNAL OF BOTANY

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction

(2016) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

Anderson's and Stebbins' Prophecy Comes True: Genetic Exchange in Fluctuating Environments

(2016) Michael L. Arnold   SYSTEMATIC BOTANY

Allopatric hybrids as evidence for past range dynamics in Sempervivum (Crassulaceae), a western Eurasian high mountain oreophyte

(2016) Johannes T. Klein et al.   Alpine Botany

Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

(2016) I. Marques et al.   Scientific Reports

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

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

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

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

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

(2015) D. Lopez-Alvarez et al.   AMERICAN JOURNAL OF BOTANY

Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species

(2015) Rajanikanth Govindarajulu et al.   AMERICAN JOURNAL OF BOTANY

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

(2015) Jeffrey M. Good et al.   EVOLUTION

Deep phylogenetic incongruence in the angiosperm clade Rosidae

(2015) Miao Sun et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

(2015) Jessica D. Stephens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

On the relative abundance of autopolyploids and allopolyploids

(2015) Michael S. Barker et al.   NEW PHYTOLOGIST

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

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

Cytonuclear Coordination Is Not Immediate upon Allopolyploid Formation in Tragopogon miscellus (Asteraceae) Allopolyploids

(2015) Tina Sehrish et al.   PLoS One

The polyploidy revolution then...and now: Stebbins revisited

(2014) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

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

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

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayroseet al. (2011)

(2014) Douglas E. Soltis et al.   NEW PHYTOLOGIST

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

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies

(2013) Katherine L Thompson et al.   BMC BIOINFORMATICS

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification

(2013) Matthew P Davis et al.   BMC EVOLUTIONARY BIOLOGY

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

(2013) Stuart C. Willis et al.   EVOLUTION

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data

(2013) Noah M. Reid 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

Predicting present and future intra-specific genetic structure through niche hindcasting across 24 millennia

(2012) Anahí Espíndola et al.   ECOLOGY LETTERS

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

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

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

JML: testing hybridization from species trees

(2011) SIMON JOLY   Molecular Ecology Resources

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

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

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus

(2010) Kenneth D. Whitney et al.   NEW PHYTOLOGIST

Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of ‘rear edge’ populations

(2010) Paul F. Gugger et al.   NEW PHYTOLOGIST

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Potential Role of Androgenesis in Cytoplasmic–Nuclear Phylogenetic Discordance

(2010) Shannon M. Hedtke et al.   SYSTEMATIC BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers

(2008) Julianno B. M. Sambatti et al.   ECOLOGY LETTERS

Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges

(2008) Eric Waltari et al.   JOURNAL OF BIOGEOGRAPHY

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

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY

Phylogeographic insights into cryptic glacial refugia

(2008) J PROVAN et al.   TRENDS IN ECOLOGY & EVOLUTION