List of works - Thomas J. Near

A New Species and a Molecular Phylogenetic Analysis of the Antarctic Fish Genus Pogonophryne (Notothenioidei: Artedidraconidae)

article

A genomic fossil reveals key steps in hemoglobin loss by the antarctic icefishes

scientific article

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

scientific article published on 11 September 2019

A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei: Percidae) endemic to the Cumberland River

scientific article published on 15 October 2010

AFLPs do not support deep phylogenetic relationships among darters (Teleostei: Percidae: Etheostomatinae).

scientific article published on 11 January 2012

Acanthocephalan phylogeny and the evolution of parasitism ⬇️

scientific article published on July 1, 2002

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

scientific article published on 01 December 2021

Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes

scientific article

An early fossil remora (Echeneoidea) reveals the evolutionary assembly of the adhesion disc

scientific article (publication date: 7 September 2013)

An inverse latitudinal gradient in speciation rate for marine fishes

scientific article published in Nature

Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes

scientific article

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

scientific article

Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles.

scientific article

Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae).

scientific article

Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes

scientific article published on 02 January 2014

Characterization of a contemporaneous hybrid zone between two darter species (Etheostoma bison and E. caeruleum) in the Buffalo River System ⬇️

scientific article published on February 27, 2013

Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes?

scientific article published on 01 August 2005

Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes

scientific article

Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes ⬇️

scientific article published on March 9, 2011

Cradles and museums of Antarctic teleost biodiversity

scientific article published on 24 July 2017

Cryptic species diversity in sub-Antarctic islands: A case study of Lepidonotothen

scientific article

Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae).

scientific article

Dispersal, vicariance, and timing of diversification in Nothonotus darters.

scientific article

Diversification of egg-deposition behaviours and the evolution of male parental care in darters (Teleostei: Percidae: Etheostomatinae).

scientific article

Diversity, relative abundance, new locality records and population structure of Antarctic demersal fishes from the northern Scotia Arc islands and Bouvetøya

Early bursts of body size and shape evolution are rare in comparative data

scientific article (publication date: August 2010)

Early members of 'living fossil' lineage imply later origin of modern ray-finned fishes.

scientific article

Ecological constraint and the evolution of sexual dichromatism in darters

scientific article

Effects of climatic and geological processes during the pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (teleostei: amblyopsidae).

scientific article published on 20 December 2012

Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes ⬇️

scientific article published on September 4, 2012

Erosion of heterogeneous rock drives diversification of Appalachian fishes

scientific article published on 25 May 2023

Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae).

scientific article published on 6 November 2012

Evolution and function of the globin intergenic regulatory regions of the antarctic dragonfishes (Notothenioidei: Bathydraconidae).

scientific article

Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography

scientific article (publication date: April 2007)

Evolution of the branchiostegal membrane and restricted gill openings in Actinopterygian fishes.

scientific article published on 11 February 2015

Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia).

scientific article published on 7 October 2013

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

scientific article published on 12 March 2018

Free from mitochondrial DNA: Nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae).

scientific article

Functional antifreeze glycoprotein genes in temperate-water New Zealand nototheniid fish infer an Antarctic evolutionary origin

scientific article published on 28 July 2003

Functional innovations and morphological diversification in parrotfish.

scientific article published on 19 August 2010

Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (percidae: etheostoma).

scientific article

Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes.

scientific article published on 14 March 2012

Genetic structure of midwestern Ascaris suum populations: a comparison of isoenzyme and RAPD markers

scientific article published on 01 June 1995

Geographic and temporal aspects of mitochondrial replacement in Nothonotus darters (Teleostei: Percidae: Etheostomatinae).

scientific article published on 6 November 2009

Hidden species diversity in an iconic living fossil vertebrate

scientific article published in November 2022

Historical contingency shapes adaptive radiation in Antarctic fishes

scientific article published on 10 June 2019

Historical contingency shapes adaptive radiation in Antarctic fishes:

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

scientific article

Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae)

scientific article (publication date: 7 October 2009)

Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation

scientific article published on 23 March 2011

Intraspecific phylogeography of Percina evides (Percidae: Etheostomatinae): an additional test of the Central Highlands pre-Pleistocene vicariance hypothesis.

scientific article

Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes

scientific article published in July 2004

Mitochondrial DNA, morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae).

scientific article published in July 2003

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

scientific article (publication date: 7 November 2013)

Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion

scientific article published on 3 August 2012

Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei

scientific article published on 8 August 2015

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

scientific article

On fossils, phylogenies and sequences of evolutionary change

scientific article (publication date: 7 June 2014)

Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)

Revised classification of of ray-finned (Actinopterygii) fishes using large molecular datasets (published in 2024)

Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations

scientific article published on 06 September 2018

Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei).

scientific article

Phylogenetic inference of nuptial trait evolution in the context of asymmetrical introgression in North American darters (teleostei).

scientific article published on 11 October 2012

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

scientific article

Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA.

scientific article

Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi).

scientific article

Phylogenetic relationships of Goneaperca and the evolution of parental care in darters (Teleostei: Percidae).

scientific article published on 20 January 2015

Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences

scientific article

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

scientific article published on 01 March 2019

Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes

scientific article

Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

scientific article

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

scientific article

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

scientific article (publication date: 30 July 2013)

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

scientific article

Piscivory limits diversification of feeding morphology in centrarchid fishes

scientific article published on 14 January 2009

Relationship between species co-occurrence and rate of morphological change in Percina darters (Percidae: Etheostomatinae).

scientific article

Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).

scientific article published on 15 September 2011

Resolution of ray-finned fish phylogeny and timing of diversification

scientific article (publication date: 21 August 2012)

Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes

scientific article published on 5 November 2008

Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary.

scientific article

Temporal patterns of diversification and microendemism in Eastern Highland endemic barcheek darters (Percidae: Etheostomatinae).

scientific article published on 29 September 2008

The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond

scientific article published on 27 June 2012

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

scientific article

The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae).

scientific article published on 25 March 2011

The reproductive behaviour of Pogonophryne scotti confirms widespread egg-guarding parental care among Antarctic notothenioids

scientific article published on 04 May 2012

Two waves of colonization straddling the K-Pg boundary formed the modern reef fish fauna

scientific article (publication date: 22 May 2014)

List of works by Thomas J. Near

A New Species and a Molecular Phylogenetic Analysis of the Antarctic Fish Genus Pogonophryne (Notothenioidei: Artedidraconidae)

A genomic fossil reveals key steps in hemoglobin loss by the antarctic icefishes

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei: Percidae) endemic to the Cumberland River

AFLPs do not support deep phylogenetic relationships among darters (Teleostei: Percidae: Etheostomatinae).

Acanthocephalan phylogeny and the evolution of parasitism ⬇️

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes

An early fossil remora (Echeneoidea) reveals the evolutionary assembly of the adhesion disc

An inverse latitudinal gradient in speciation rate for marine fishes

Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles.

Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae).

Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes

Characterization of a contemporaneous hybrid zone between two darter species (Etheostoma bison and E. caeruleum) in the Buffalo River System ⬇️

Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes?

Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes

Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes ⬇️

Cradles and museums of Antarctic teleost biodiversity

Cryptic species diversity in sub-Antarctic islands: A case study of Lepidonotothen

Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae).

Dispersal, vicariance, and timing of diversification in Nothonotus darters.

Diversification of egg-deposition behaviours and the evolution of male parental care in darters (Teleostei: Percidae: Etheostomatinae).

Diversity, relative abundance, new locality records and population structure of Antarctic demersal fishes from the northern Scotia Arc islands and Bouvetøya

Early bursts of body size and shape evolution are rare in comparative data

Early members of 'living fossil' lineage imply later origin of modern ray-finned fishes.

Ecological constraint and the evolution of sexual dichromatism in darters

Effects of climatic and geological processes during the pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (teleostei: amblyopsidae).

Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes ⬇️

Erosion of heterogeneous rock drives diversification of Appalachian fishes

Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae).

Evolution and function of the globin intergenic regulatory regions of the antarctic dragonfishes (Notothenioidei: Bathydraconidae).

Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography

Evolution of the branchiostegal membrane and restricted gill openings in Actinopterygian fishes.

Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia).

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

Free from mitochondrial DNA: Nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae).

Functional antifreeze glycoprotein genes in temperate-water New Zealand nototheniid fish infer an Antarctic evolutionary origin

Functional innovations and morphological diversification in parrotfish.

Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (percidae: etheostoma).

Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes.

Genetic structure of midwestern Ascaris suum populations: a comparison of isoenzyme and RAPD markers

Geographic and temporal aspects of mitochondrial replacement in Nothonotus darters (Teleostei: Percidae: Etheostomatinae).

Hidden species diversity in an iconic living fossil vertebrate

Historical contingency shapes adaptive radiation in Antarctic fishes

Historical contingency shapes adaptive radiation in Antarctic fishes:

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae)

Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation

Intraspecific phylogeography of Percina evides (Percidae: Etheostomatinae): an additional test of the Central Highlands pre-Pleistocene vicariance hypothesis.

Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes

Mitochondrial DNA, morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae).

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion

Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

On fossils, phylogenies and sequences of evolutionary change

Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)

Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations

Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei).

Phylogenetic inference of nuptial trait evolution in the context of asymmetrical introgression in North American darters (teleostei).

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA.

Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi).

Phylogenetic relationships of Goneaperca and the evolution of parental care in darters (Teleostei: Percidae).

Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences

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

Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes

Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

Piscivory limits diversification of feeding morphology in centrarchid fishes

Relationship between species co-occurrence and rate of morphological change in Percina darters (Percidae: Etheostomatinae).

Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).

Resolution of ray-finned fish phylogeny and timing of diversification

Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes

Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary.