Genome‐wide analysis resolves the radiation of New Zealand's freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

(2021) Bruno F Melo et al.   SYSTEMATIC BIOLOGY

Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences

(2020) J.M. Waters et al.   TRENDS IN ECOLOGY & EVOLUTION

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness

(2020) Alex Bush et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes

(2020) Christopher P. Burridge et al.   EVOLUTION

On the causes of geographically heterogeneous parallel evolution in sticklebacks

(2020) Bohao Fang et al.   Nature Ecology & Evolution

River Capture and Freshwater Biological Evolution: A Review of Galaxiid Fish Vicariance

(2020) Jonathan M. Waters et al.   Diversity-Basel

Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species

(2020) Tabitha Blackwell et al.   MOLECULAR ECOLOGY

Genomic basis of the loss of diadromy in Galaxias maculatus : insights from reciprocal transplant experiments

(2020) M. Lisette Delgado et al.   MOLECULAR ECOLOGY

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

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Drivers and dynamics of a massive adaptive radiation in cichlid fishes

(2020) Fabrizia Ronco et al.   NATURE

Politics and pride: Maintaining genetic novelty may be detrimental for the conservation of Formosa landlocked salmon Oncorhynchus formosanus

(2019) Christopher Paul Burridge   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments

(2019) Antonia G.P. Ford et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The effects of diadromy and its loss on genomic divergence: The case of amphidromous Galaxias maculatus populations

(2019) M. Lisette Delgado et al.   MOLECULAR ECOLOGY

Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia

(2018) James J. Shelley et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Breaking Barriers: Causes, Consequences, and Experimental Utility of Human-Mediated Hybridization

(2018) Kathryn C. Grabenstein et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation

(2018) Sean J. Buckley et al.   Royal Society Open Science

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

(2018) Iker Irisarri et al.   Nature Communications

Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy

(2018) Roberta Bisconti et al.   Scientific Reports

Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

(2018) Daniel J MacGuigan et al.   SYSTEMATIC BIOLOGY

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka)

(2017) Andrew J. Veale et al.   Genome Biology and Evolution

Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes

(2017) Graham P. Wallis et al.   MOLECULAR ECOLOGY

Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis )

(2017) Peter J. Unmack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation

(2017) Paul Sunnucks et al.   Frontiers in Genetics

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Evolution of the Taieri River catchment, East Otago, New Zealand

(2016) D Craw et al.   NEW ZEALAND JOURNAL OF GEOLOGY AND GEOPHYSICS

Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece

(2016) Silvia Perea et al.   PLoS One

Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms

(2015) Nicolas Dussex et al.   EVOLUTION

Fine-scale habitat preferences influence within-river population connectivity: a case-study using two sympatric New ZealandGalaxiasfish species

(2015) Jonathan M. Waters et al.   FRESHWATER BIOLOGY

Within-river genetic connectivity patterns reflect contrasting geomorphology

(2015) Jonathan M. Waters et al.   JOURNAL OF BIOGEOGRAPHY

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

(2015) Carly F. Graham et al.   Molecular Ecology Resources

Rapid biological speciation driven by tectonic evolution in New Zealand

(2015) Dave Craw et al.   Nature Geoscience

Geology shapes biogeography: Quaternary river-capture explains New Zealand's biologically ‘composite’ Taieri River

(2015) Jonathan M. Waters et al.   QUATERNARY SCIENCE REVIEWS

Genetic rescue to the rescue

(2015) Andrew R. Whiteley et al.   TRENDS IN ECOLOGY & EVOLUTION

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Life-history variation in a species complex of nonmigratory galaxiids

(2014) Peter E. Jones et al.   ECOLOGY OF FRESHWATER FISH

Interspecific differences in early life-history traits in a species complex of stream-resident galaxiids

(2014) Peter E. Jones et al.   ECOLOGY OF FRESHWATER FISH

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room?

(2014) Mark Adams et al.   SYSTEMATIC BIOLOGY

Fifteen from one: a revision of the Galaxias olidus Günther, 1866 complex (Teleostei, Galaxiidae) in south-eastern Australia recognises three previously described taxa and describes 12 new species

(2014) TARMO A. RAADIK   ZOOTAXA

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

TESTING MITOCHONDRIAL CAPTURE AND DEEP COALESCENCE IN AMAZONIAN CICHLID FISHES (CICHLIDAE:CICHLA)

(2013) Stuart C. Willis et al.   EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Evolutionary Drivers of Diversification and Distribution of a Southern Temperate Stream Fish Assemblage: Testing the Role of Historical Isolation and Spatial Range Expansion

(2013) Albert Chakona et al.   PLoS One

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

Tectonic controls on the evolution of the Clutha River catchment, New Zealand

(2012) Dave Craw et al.   NEW ZEALAND JOURNAL OF GEOLOGY AND GEOPHYSICS

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

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Marine dispersal as a pre-requisite for Gondwanan vicariance among elements of the galaxiid fish fauna

(2011) Christopher P. Burridge et al.   JOURNAL OF BIOGEOGRAPHY

Testing for Ancient Admixture between Closely Related Populations

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

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Cryptic Diversity of African Tigerfish (Genus Hydrocynus) Reveals Palaeogeographic Signatures of Linked Neogene Geotectonic Events

(2011) Sarah A. M. Goodier et al.   PLoS One

A Phylogenetic Analysis of Pygmy Perches (Teleostei: Percichthyidae) with an Assessment of the Major Historical Influences on Aquatic Biogeography in Southern Australia

(2011) Peter J. Unmack et al.   SYSTEMATIC BIOLOGY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Conservation biogeography of freshwater fishes: recent progress and future challenges

(2010) Julian D. Olden et al.   DIVERSITY AND DISTRIBUTIONS

Morphological and genetic analysis ofGalaxias‘southern’ andG. gollumoides:interspecific differentiation and intraspecific structuring

(2010) S. K. Crow et al.   JOURNAL OF THE ROYAL SOCIETY OF NEW ZEALAND

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Gene Trees versus Species Trees: Reassessing Life-History Evolution in a Freshwater Fish Radiation

(2010) Jonathan M. Waters et al.   SYSTEMATIC BIOLOGY

ASYMMETRIC VIABILITY OF RECIPROCAL-CROSS HYBRIDS BETWEEN CRESTED AND MARBLED NEWTS (TRITURUS CRISTATUSANDT. MARMORATUS)

(2009) Jan W. Arntzen et al.   EVOLUTION

Niche partitioning and the effect of interspecific competition on microhabitat use by two sympatric galaxiid stream fishes

(2009) S. K. CROW et al.   FRESHWATER BIOLOGY

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

DOES FISH ECOLOGY PREDICT DISPERSAL ACROSS A RIVER DRAINAGE DIVIDE?

(2008) Christopher P. Burridge et al.   EVOLUTION

Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency

(2008) C. P. Burridge et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying Canadian Freshwater Fishes through DNA Barcodes

(2008) Nicolas Hubert et al.   PLoS One

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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