Highland islands: assessing gene flow among populations of an aquatic highland endemic

Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes

(2022) Kyle R. Piller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rio de Janeiro and other palaeodrainages evidenced by the genetic structure of an Atlantic Forest catfish

(2021) Sergio M. Q. Lima et al.   JOURNAL OF BIOGEOGRAPHY

Comparative riverscape genomics of the rainbow darter ( Etheostoma caeruleum ) in glaciated and unglaciated environments

(2021) Jon M. Luiken et al.   Ecology and Evolution

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

(2020) Nathan K. Lujan et al.   MOLECULAR ECOLOGY

Recent and rapid anthropogenic habitat fragmentation increases extinction risk for freshwater biodiversity

(2020) Chris J. Brauer et al.   Evolutionary Applications

Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus ) into the New World

(2019) Jessica A. Oswald et al.   MOLECULAR ECOLOGY

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

(2019) Nathan V. Whelan et al.   MOLECULAR ECOLOGY

Evolving in the highlands: the case of the Neotropical Lerma live-bearing Poeciliopsis infans (Woolman, 1894) (Cyprinodontiformes: Poeciliidae) in Central Mexico

(2018) Rosa Gabriela Beltrán-López et al.   BMC EVOLUTIONARY BIOLOGY

Going with the Flow: Testing the Role of Habitat Isolation among Three Ecologically Divergent Darter Species

(2018) David T. Camak et al.   COPEIA

Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White-collared Seedeater complex (Thraupidae: Sporophila torqueola )

(2018) Nicholas A. Mason et al.   Ecology and Evolution

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

(2018) Kevin Winker et al.   PeerJ

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

The architecture of river networks can drive the evolutionary dynamics of aquatic populations

(2016) Andréa T. Thomaz et al.   EVOLUTION

Phylogenetic relationships and evolutionary history of the Mesoamerican endemic freshwater fish family Profundulidae (Cyprinodontiformes: Actinopterygii)

(2016) Felipe Morcillo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

(2016) Michael G. Harvey et al.   SYSTEMATIC BIOLOGY

Checklist of the continental fishes of the state of Chiapas, Mexico, and their distribution

(2016) Ernesto Velázquez-Velázquez et al.   ZooKeys

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: study of a Neotropical fish of the Brazilian coastal Atlantic Forest

(2015) Andréa T. Thomaz et al.   JOURNAL OF BIOGEOGRAPHY

Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

(2015) W. C. Funk et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A new species of killifish of the family Profundulidae from the highlands of the Mixteca region, Mexico

(2015) Claudia Patricia Ornelas-García et al.   Revista Mexicana de Biodiversidad

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cryptic diversity in a widespread live-bearing fish (Poeciliidae:Belonesox)

(2013) Elizabeth A. Marchio et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

How does ecological disturbance influence genetic diversity?

(2013) Sam C. Banks et al.   TRENDS IN ECOLOGY & EVOLUTION

A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes ( Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq)

(2013) Hans Recknagel et al.   G3-Genes Genomes Genetics

From the mountains to the sea: phylogeography and cryptic diversity within the mountain mullet,Agonostomus monticola(Teleostei: Mugilidae)

(2012) Caleb D. McMahan et al.   JOURNAL OF BIOGEOGRAPHY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Middle America, not Mesoamerica, is the Accurate Term for Biogeography

(2011) Kevin Winker   CONDOR

Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks

(2011) YOICHIRO KANNO et al.   MOLECULAR ECOLOGY

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

Genes in Streams: Using DNA to Understand the Movement of Freshwater Fauna and Their Riverine Habitat

(2009) Jane M. Hughes et al.   BIOSCIENCE

DOES FISH ECOLOGY PREDICT DISPERSAL ACROSS A RIVER DRAINAGE DIVIDE?

(2008) Christopher P. Burridge et al.   EVOLUTION

Global patterns of genetic variation in plant species along vertical and horizontal gradients on mountains

(2007) Takafumi Ohsawa et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY