Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids

What big lips are good for: on the adaptive function of repeatedly evolved hypertrophied lips of cichlid fishes

(2015) Lukas Baumgarten et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

(2015) Scott P. Egan et al.   ECOLOGY LETTERS

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

Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?

(2015) B. Eldon et al.   GENETICS

Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source

(2015) A Benazzo et al.   HEREDITY

Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus

(2015) Aaron B. A. Shafer et al.   MOLECULAR ECOLOGY

On the occurrence of false positives in tests of migration under an isolation-with-migration model

(2015) Jody Hey 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

Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum

(2015) Jonathan Terhorst 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 Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

The Evolutionary Genomics of Cichlid Fishes: Explosive Speciation and Adaptation in the Postgenomic Era

(2014) Frederico Henning et al.   Annual Review of Genomics and Human Genetics

SPECIES-SPECIFIC DIFFERENCES IN ADAPTIVE PHENOTYPIC PLASTICITY IN AN ECOLOGICALLY RELEVANT TROPHIC TRAIT: HYPERTROPHIC LIPS IN MIDAS CICHLID FISHES

(2014) Gonzalo Machado-Schiaffino et al.   EVOLUTION

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

(2014) Verena E. Kutschera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes

(2014) Christopher H. Martin et al.   MOLECULAR ECOLOGY

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

(2014) Aurélien Tellier 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

Genetics of ecological divergence during speciation

(2014) Matthew E. Arnegard et al.   NATURE

Genomic divergence in a ring species complex

(2014) Miguel Alcaide et al.   NATURE

Thinking too positive? Revisiting current methods of population genetic selection inference

(2014) Claudia Bank et al.   TRENDS IN GENETICS

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

(2014) Kathryn R. Elmer et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Geographic Mode of Speciation and Genomic Divergence

(2013) Jeffrey L. Feder et al.   Annual Review of Ecology Evolution and Systematics

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

(2013) Pierre-Alexandre Gagnaire et al.   EVOLUTION

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

(2013) Samuel M. Flaxman et al.   EVOLUTION

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

(2013) P.-R. Loh et al.   GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

(2013) Paolo Franchini et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Crater Lake Apoyo Revisited - Population Genetics of an Emerging Species Flock

(2013) Matthias F. Geiger et al.   PLoS One

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

(2013) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild

(2013) C. H. Martin et al.   SCIENCE

Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs

(2013) Frank E. Rheindt et al.   SYSTEMATIC BIOLOGY

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

CRATER LAKE COLONIZATION BY NEOTROPICAL CICHLID FISHES

(2012) Kathryn R. Elmer et al.   EVOLUTION

Sympatric Speciation in the Post “Modern Synthesis” Era of Evolutionary Biology

(2012) Christopher E. Bird et al.   Evolutionary Biology

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

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

Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

(2012) Tereza Manousaki et al.   MOLECULAR ECOLOGY

Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid fishes

(2012) Andreas F. Kautt et al.   MOLECULAR ECOLOGY

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage

(2012) F. Hailer et al.   SCIENCE

The genomics of speciation-with-gene-flow

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

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

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

Population divergence with or without admixture: selecting models using an ABC approach

(2011) V C Sousa et al.   HEREDITY

Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

(2011) JUNRUI LI et al.   MOLECULAR ECOLOGY

Speciation with gene flow on Lord Howe Island

(2011) Alexander S. T. Papadopulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations

(2011) J. Melo-Ferreira et al.   SYSTEMATIC BIOLOGY

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

(2010) Kathryn R Elmer et al.   BMC BIOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

MorphoJ: an integrated software package for geometric morphometrics

(2010) CHRISTIAN PETER KLINGENBERG   Molecular Ecology Resources

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Not a simple case – A first comprehensive phylogenetic hypothesis for the Midas cichlid complex in Nicaragua (Teleostei: Cichlidae: Amphilophus)

(2010) Matthias F. Geiger et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

(2010) K. R. Elmer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Description of two new species of the Midas cichlid complex (Teleostei: Cichlidae) from Lake Apoyo, Nicaragua

(2010) Matthias F. Geiger et al.   PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Pattern, process and geographic modes of speciation

(2009) B. M. FITZPATRICK et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Space, sympatry and speciation

(2009) J. MALLET et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish

(2009) B. NEVADO et al.   MOLECULAR ECOLOGY

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Natural selection in action during speciation

(2009) S. Via   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecologically dependent postmating isolation between sympatric host forms of Neochlamisus bebbianae leaf beetles

(2009) S. P. Egan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

What, if anything, is sympatric speciation?

(2008) B. M. FITZPATRICK et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Speciation with gene flow could be common

(2008) PATRIK NOSIL   MOLECULAR ECOLOGY