Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Species tree estimation using Neighbor Joining

(2017) Joseph Rusinko et al.   JOURNAL OF THEORETICAL BIOLOGY

Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation

(2017) Erin N. Peterson et al.   NATURWISSENSCHAFTEN

Ancient hybridization fuels rapid cichlid fish adaptive radiations

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

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

(2017) Chungang Feng et al.   eLife

Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation

(2017) Erin N. Peterson et al.   Science of Nature

Proximate and ultimate causes of variable visual sensitivities: Insights from cichlid fish radiations

(2016) Karen L. Carleton et al.   GENESIS

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Hugo F. Gante et al.   MOLECULAR ECOLOGY

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Environmental change explains cichlid adaptive radiation at Lake Malawi over the past 1.2 million years

(2016) Sarah J. Ivory et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

(2016) N. M. Reid et al.   SCIENCE

Geographical ancestry of Lake Malawi's cichlid fish diversity: Figure 1.

(2015) Martin J. Genner et al.   Biology Letters

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

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

(2015) Sangeet Lamichhaney et al.   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Lake Tanganyika—A 'Melting Pot' of Ancient and Young Cichlid Lineages (Teleostei: Cichlidae)?

(2015) Juliane D. Weiss et al.   PLoS One

Homeobox transcription factor Six7 governs expression of green opsin genes in zebrafish

(2015) Yohey Ogawa et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Ecology and Evolution of the African Great Lakes and Their Faunas

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

Determinants of Mutation Rate Variation in the Human Germline

(2014) Laure Ségurel et al.   Annual Review of Genomics and Human Genetics

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

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

Adaptive divergence between lake and stream populations of an East African cichlid fish

(2014) Anya Theis et al.   MOLECULAR ECOLOGY

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

(2014) Rezwana Reaz et al.   PLoS One

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Looking for trees in the forest: summary tree from posterior samples

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

(2012) Cameron J Weadick et al.   BMC EVOLUTIONARY BIOLOGY

Does the decline of gastropods in deep water herald ecosystem change in Lakes Malawi and Tanganyika?

(2012) BERT VAN BOCXLAER et al.   FRESHWATER BIOLOGY

Whole-Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins

(2012) Juan C. Opazo et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Molecular ecology and adaptation of visual photopigments in craniates

(2012) WAYNE I. L. DAVIES et al.   MOLECULAR ECOLOGY

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

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 genomics of speciation-with-gene-flow

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

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

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

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

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

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

(2011) H. Li   BIOINFORMATICS

Cone arrestin confers cone vision of high temporal resolution in zebrafish larvae

(2011) Sabine L. Renninger et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

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 linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

Adaptation and diversification on islands

(2009) Jonathan B. Losos et al.   NATURE

Rapidly evolving fish genomes and teleost diversity

(2008) Vydianathan Ravi et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY