Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

Powerful methods for detecting introgressed regions from population genomic data

(2016) Benjamin K. Rosenzweig et al.   MOLECULAR ECOLOGY

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes

(2016) Britta S. Meyer et al.   SYSTEMATIC BIOLOGY

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

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

Genome-wide tests for introgression between cactophilicDrosophilaimplicate a role of inversions during speciation

(2015) Konrad Lohse et al.   EVOLUTION

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

(2015) Jeffrey M. Good et al.   EVOLUTION

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

(2015) Christopher H. Martin et al.   EVOLUTION

Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod ( Gadus morhua L.)

(2015) Paul R. Berg et al.   Genome Biology and Evolution

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Biased introgression of mitochondrial and nuclear genes: a comparison of diploid and haplodiploid systems

(2015) Manus M. Patten et al.   MOLECULAR ECOLOGY

High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

(2015) Antonia G. P. Ford et al.   MOLECULAR ECOLOGY

A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach

(2015) Britta S. Meyer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

The effect of temperature on the male and female recombination landscape of barley

(2015) Dylan Phillips et al.   NEW PHYTOLOGIST

Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets

(2015) Laura C. Norris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

The genomics of organismal diversification illuminated by adaptive radiations

(2015) Daniel Berner et al.   TRENDS IN GENETICS

The genomics of ecological vicariance in threespine stickleback fish

(2015) Marius Roesti et al.   Nature Communications

Ecology and Evolution of the African Great Lakes and Their Faunas

(2014) Walter Salzburger et al.   Annual Review of Ecology Evolution and Systematics

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evolutionary history and population genetics of a cyprinid fish (Iberochondrostoma olisiponensis) endangered by introgression from a more abundant relative

(2014) Carla Sousa-Santos et al.   CONSERVATION GENETICS

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

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

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

(2014) José L. Campos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

(2014) Zachariah Gompert et al.   MOLECULAR ECOLOGY

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

Theoretical models of the influence of genomic architecture on the dynamics of speciation

(2014) Samuel M. Flaxman et al.   MOLECULAR ECOLOGY

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Hybrid speciation through sorting of parental incompatibilities in Italian sparrows

(2014) Jo S. Hermansen et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Radiating genomes

(2014) Chris D. Jiggins   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

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

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Genome Sequencing Highlights the Dynamic Early History of Dogs

(2014) Adam H. Freedman et al.   PLoS Genetics

Genetic Diversity in the Interference Selection Limit

(2014) Benjamin H. Good et al.   PLoS Genetics

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

(2014) Cassandra N. Trier et al.   PLoS Genetics

Unsupervised genome-wide recognition of local relationship patterns

(2013) Neda Zamani et al.   BMC GENOMICS

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

(2013) James B. Pease et al.   EVOLUTION

GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

(2013) Samuel M. Flaxman et al.   EVOLUTION

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Hybridization is important in evolution, but is speciation?

(2013) G.-P. Saetre   JOURNAL OF EVOLUTIONARY BIOLOGY

Hybridization and speciation

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

Recombination in the threespine stickleback genome-patterns and consequences

(2013) Marius Roesti et al.   MOLECULAR ECOLOGY

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)

(2013) Caleb D. McMahan et al.   PLoS One

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

(2013) M. Friedman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content

(2012) Flavie Tortereau et al.   BMC GENOMICS

Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish

(2012) Juliana Mazzuchelli et al.   BMC GENOMICS

Evolution: Cichlid Models on the Runaway to Speciation

(2012) Hugo F. Gante et al.   CURRENT BIOLOGY

Convergent Evolution within an Adaptive Radiation of Cichlid Fishes

(2012) Moritz Muschick et al.   CURRENT BIOLOGY

AN EVALUATION OF THE HYBRID SPECIATION HYPOTHESIS FORXIPHOPHORUS CLEMENCIAEBASED ON WHOLE GENOME SEQUENCES

(2012) Molly Schumer et al.   EVOLUTION

Fine-Scale Maps of Recombination Rates and Hotspots in the Mouse Genome

(2012) Hadassa Brunschwig et al.   GENETICS

Spatially explicit models of divergence and genome hitchhiking

(2012) S. M. Flaxman et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

(2012) I. Keller et al.   MOLECULAR ECOLOGY

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau et al.   MOLECULAR ECOLOGY

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution

(2012) J. Schwarzer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How Cichlids Diversify

(2012) M. E. Santos et al.   SCIENCE

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Recombination Modulates How Selection Affects Linked Sites in Drosophila

(2012) Suzanne E. McGaugh et al.   PLOS BIOLOGY

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

(2012) Carolina Pardo-Diaz et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Repeated colonization and hybridization in Lake Malawi cichlids

(2011) Domino A. Joyce et al.   CURRENT BIOLOGY

Ancient Hybridization and Phenotypic Novelty within Lake Malawi's Cichlid Fish Radiation

(2011) M. J. Genner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

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

A framework for comparing processes of speciation in the presence of gene flow

(2011) CAROLE M. SMADJA et al.   MOLECULAR ECOLOGY

Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination

(2011) A. GERALDES et al.   MOLECULAR ECOLOGY

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Direct and indirect consequences of meiotic recombination: implications for genome evolution

(2011) Matthew T. Webster et al.   TRENDS IN GENETICS

An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci

(2011) Kevin M. Bradley et al.   G3-Genes Genomes Genetics

The evolution of cooperative breeding in the African cichlid fish, Neolamprologus pulcher

(2010) Marian Wong et al.   BIOLOGICAL REVIEWS

SPECIATION IN THE EUROPEAN RABBIT (ORYCTOLAGUS CUNICULUS): ISLANDS OF DIFFERENTIATION ON THE X CHROMOSOME AND AUTOSOMES

(2010) Miguel Carneiro et al.   EVOLUTION

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

Evolutionary history of the Lake Tanganyika cichlid tribe Lamprologini (Teleostei: Perciformes) derived from mitochondrial and nuclear DNA data

(2010) Christian Sturmbauer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recombination and Its Impact on the Genome of the Haplodiploid Parasitoid Wasp Nasonia

(2010) Oliver Niehuis et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Understanding the onset of hybrid speciation

(2010) Arne W. Nolte et al.   TRENDS IN GENETICS

Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies

(2010) Camilo Salazar et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish

(2009) B. NEVADO et al.   MOLECULAR ECOLOGY

Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini

(2009) Stephan Koblmüller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Hybrid speciation in angiosperms: parental divergence drives ploidy

(2009) Ovidiu Paun et al.   NEW PHYTOLOGIST

Recombinational Landscape and Population Genomics of Caenorhabditis elegans

(2009) Matthew V. Rockman et al.   PLoS Genetics

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

Genetic Analysis of Variation in Human Meiotic Recombination

(2009) Reshmi Chowdhury et al.   PLoS Genetics

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

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

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

(2008) Yoichiro Azuma et al.   BMC EVOLUTIONARY BIOLOGY

Homoploid hybrid speciation in animals

(2008) JESÚS MAVÁREZ et al.   MOLECULAR ECOLOGY

The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes

(2008) WALTER SALZBURGER   MOLECULAR ECOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Hybrid trait speciation and Heliconius butterflies

(2008) C. D Jiggins et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence

(2008) R. J. Kulathinal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How many species of cichlid fishes are there in African lakes?

(2003) George F. Turner et al.   MOLECULAR ECOLOGY