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

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

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Speciation in Freshwater Fishes

(2014) Ole Seehausen 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

Cichlid species-area relationships are shaped by adaptive radiations that scale with area

(2014) Catherine E. Wagner et al.   ECOLOGY LETTERS

Air breathing in Magadi tilapiaAlcolapia grahami, under normoxic and hyperoxic conditions, and the association with sunlight and reactive oxygen species

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Genomic atolls of differentiation in coral reef fishes (Hypoplectrusspp.,Serranidae)

(2014) O. Puebla et al.   MOLECULAR ECOLOGY

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

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

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

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Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish

(2013) Alan G Hudson et al.   BMC EVOLUTIONARY BIOLOGY

Genetic and morphological analyses indicate high population mixing in the endangered cichlid Alcolapia flock of East Africa

(2013) Serena Zaccara et al.   CONSERVATION GENETICS

Adaptive Radiation: Convergence and Non-equilibrium

(2013) Rosemary G. Gillespie   CURRENT BIOLOGY

FUNCTIONAL AND POPULATION GENOMIC DIVERGENCE WITHIN AND BETWEEN TWO SPECIES OF KILLIFISH ADAPTED TO DIFFERENT OSMOTIC NICHES

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Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

Pronounced genetic differentiation of small, isolated and fragmented tilapia populations inhabiting the Magadi Soda Lake in Kenya

(2013) Geraldine D. Kavembe et al.   HYDROBIOLOGIA

Conditions when hybridization might predispose populations for adaptive radiation

(2013) O. Seehausen   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2013) Paolo Franchini et al.   MOLECULAR ECOLOGY

Speciation in fishes

(2013) Giacomo Bernardi   MOLECULAR ECOLOGY

Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”

(2013) Andreas R. Dunz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish

(2013) Paul C. Kirchberger et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

Ecological speciation in postglacial European whitefish: rapid adaptive radiations into the littoral, pelagic, and profundal lake habitats

(2013) Kim Praebel et al.   Ecology and Evolution

Remote sensing the hydrological variability of Tanzania's Lake Natron, a vital Lesser Flamingo breeding site under threat

(2013) E.J. Tebbs et al.   ECOHYDROLOGY & HYDROBIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

CRATER LAKE COLONIZATION BY NEOTROPICAL CICHLID FISHES

(2012) Kathryn R. Elmer et al.   EVOLUTION

Coexistence and origin of trophic ecotypes of pygmy whitefish,Prosopium coulterii, in a south-western Alaskan lake

(2012) C. P. Gowell et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

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

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey 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

Eutrophication causes speciation reversal in whitefish adaptive radiations

(2012) P. Vonlanthen et al.   NATURE

Reconstructing Native American population history

(2012) David Reich et al.   NATURE

Inferring Phylogenies from RAD Sequence Data

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PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

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A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

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Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

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(2010) R. R. Bouckaert   BIOINFORMATICS

Phenotypic variation and sexual dimorphism in anadromous threespine stickleback: implications for postglacial adaptive radiation

(2010) WINDSOR E. AGUIRRE et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2010) Kathryn R Elmer et al.   BMC BIOLOGY

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes

(2010) Marta Barluenga et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

The sensitivity of East African rift lakes to climate fluctuations

(2010) Lydia A. Olaka et al.   JOURNAL OF PALEOLIMNOLOGY

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

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

Niche Dimensions in Fishes: An Integrative View

(2010) H. O. Pörtner et al.   PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

(2010) A. G. Hudson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe 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

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The root of the East African cichlid radiations

(2009) Julia Schwarzer et al.   BMC EVOLUTIONARY BIOLOGY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Ecological explanations for (incomplete) speciation

(2009) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Geomorphological contributions to palaeolimnology on the African continent

(2008) Sallie L. Burrough et al.   GEOMORPHOLOGY

Gene flow at the margin of Lake Matano’s adaptive sailfin silverside radiation: Telmatherinidae of River Petea in Sulawesi

(2008) Julia Schwarzer et al.   HYDROBIOLOGIA

Divergence along a steep ecological gradient in lake whitefish (Coregonussp.)

(2008) P. VONLANTHEN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Speciation through sensory drive in cichlid fish

(2008) Ole Seehausen et al.   NATURE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One