Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias

Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments

(2022) Andrew W Thompson et al.   G3-Genes Genomes Genetics

Filling the gaps: phylogeography of the self‐fertilizing Kryptolebias species (Cyprinodontiformes: Rivulidae) along South American mangroves

(2021) Mateus G. S. Lira et al.   JOURNAL OF FISH BIOLOGY

Fast two-stage phasing of large-scale sequence data

(2021) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Against the Odds: Hybrid Zones between Mangrove Killifish Species with Different Mating Systems

(2021) Waldir M. Berbel-Filho et al.   Genes

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

(2020) Melisa Olave et al.   SYSTEMATIC BIOLOGY

Extensive hybridization and past introgression between divergent lineages in a quasi‐clonal hermaphroditic fish: Ramifications for species concepts and taxonomy

(2020) Andrey Tatarenkov et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

(2019) Gustavo A. Bravo et al.   PeerJ

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

(2019) Scott A. Taylor et al.   Nature Ecology & Evolution

Local parasite pressures and host genotype modulate epigenetic diversity in a mixed‐mating fish

(2019) Waldir M. Berbel‐Filho et al.   Ecology and Evolution

Mating system variation in hybrid zones: facilitation, barriers and asymmetries to gene flow

(2019) Melinda Pickup et al.   NEW PHYTOLOGIST

Natural hybridization between divergent lineages in a selfing hermaphroditic fish

(2018) Andrey Tatarenkov et al.   Biology Letters

Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate

(2018) Luana S.F. Lins et al.   GENOME

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

(2017) Timothée Bonnet et al.   EVOLUTION

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

StructureSelector : A web-based software to select and visualize the optimal number of clusters using multiple methods

(2017) Yu-Long Li et al.   Molecular Ecology Resources

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Factors affecting egg production in the selfing mangrove rivulus ( Kryptolebias marmoratus )

(2017) Justin L. Lomax et al.   ZOOLOGY

The importance of autonomous selfing in preventing hybridization in three closely related plant species

(2016) Rein Brys et al.   JOURNAL OF ECOLOGY

First record of a male of Kryptolebias hermaphroditus Costa, 2011 (Cyprinodontiformes: Cynolebiidae)

(2016) Waldir M. Berbel-Filho et al.   Neotropical Ichthyology

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

Improving the estimation of genetic distances from Next-Generation Sequencing data

(2015) Filipe G. Vieira et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

(2015) Koen Herten et al.   BMC BIOINFORMATICS

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

Population genetics and evolution of the mangrove rivulusKryptolebias marmoratus, the world's only self-fertilizing hermaphroditic vertebrate

(2015) J. C. Avise et al.   JOURNAL OF FISH BIOLOGY

A Genetic Test for Whether Pairs of Hermaphrodites Can Cross-Fertilize in a Selfing Killifish

(2015) Andrew I. Furness et al.   JOURNAL OF HEREDITY

Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation

(2015) Shedrack R. Kitimu et al.   Frontiers in Plant Science

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Computational approaches to species phylogeny inference and gene tree reconciliation

(2013) Luay Nakhleh   TRENDS IN ECOLOGY & EVOLUTION

The biogeography of mitochondrial and nuclear discordance in animals

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Extreme homogeneity and low genetic diversity in Kryptolebias ocellatus from south-eastern Brazil suggest a recent foundation for this androdioecious fish population

(2011) A. Tatarenkov et al.   JOURNAL OF FISH BIOLOGY

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Androdioecy in Kryptolebias killifish and the evolution of self-fertilizing hermaphroditism

(2010) WILSON J. E. M. COSTA et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Long-term retention of self-fertilization in a fish clade

(2009) A. Tatarenkov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA