Research Topics
Genomes and GenesSpecies | Thomas J NearSummaryAffiliation: University of Tennessee Country: USA Publications
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Publications
Rapid allopatric speciation in logperch darters (Percidae: Percina)Thomas J Near
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996 1610, USA
Evolution 58:2798-808. 2004..The empirical observation of high diversification rates in logperches demonstrates that allopatric speciation can occur rapidly...- Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae)Thomas J Near
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville 37996 1610, USA
Evolution 59:1768-82. 2005.... - Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genesThomas J Near
Center for Population Biology, One Shields Avenue, University of California, Davis, CA 95616, USA
Mol Phylogenet Evol 32:344-57. 2004..Slightly more than half of the 27 previously proposed hypotheses of centrarchid relationships were rejected based on the Shomodaira-Hasegawa test... - Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNAThomas J Near
Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN 37996 1610, USA
Mol Phylogenet Evol 32:881-91. 2004.... 
Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selectionThomas J Near
Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN 37669 1610, USA
Philos Trans R Soc Lond B Biol Sci 359:1477-83. 2004..In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model...- Dispersal, vicariance, and timing of diversification in Nothonotus dartersThomas J Near
Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, Tennessee, 37916 1610, USA
Mol Ecol 14:3485-96. 2005..Patterns of speciation in Nothonotus are similar to those discovered in recent efforts that have included speciation as a parameter into classic models of island biogeography... - Assessing concordance of fossil calibration points in molecular clock studies: an example using turtlesThomas J Near
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996 1610, USA
Am Nat 165:137-46. 2005..Many of the truly ancient lineages of turtles are currently represented by a few, often endangered species that deserve high priority as conservation targets... - Speciation in North American black basses, Micropterus (Actinopterygii: Centrarchidae)Thomas J Near
Center for Population Biology, University of California, One Shields Avenue, Davis, California 95616, USA
Evolution 57:1610-21. 2003..The application of the Gulf Coast allopatric speciation model to the remaining aquatic fauna of the Gulf of Mexico coast in North America will rely on robust phylogenetic hypotheses and accurate age estimations of speciation events... 
Piscivory limits diversification of feeding morphology in centrarchid fishesDavid C Collar
Section of Evolution and Ecology, University of California, Davis, California 95616, USA
Evolution 63:1557-73. 2009..These results suggest that piscivory limits feeding morphology diversification, but this effect is most severe in lineages that exhibit an extreme form of this diet...- Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusionAlex Dornburg
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Mol Phylogenet Evol 65:727-38. 2012..We propose a new classification for Holocentrinae, recognizing four lineages that are treated as genera: Sargocentron Fowler, 1904, Holocentrus Scopoli, 1777, Flameo Jordan and Evermann, 1898, and Neoniphon Castelnau, 1875... - Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae)Benjamin P Keck
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996 1610, USA
Mol Phylogenet Evol 46:708-20. 2008..Given the extensive lack of reciprocal monophyly of species observed in the S7 gene tree we predict that nuclear gene sequences may have limited utility in intraspecific phylogeographic studies of Nothonotus darters... - Phylogenetic and coalescent strategies of species delimitation in snubnose darters (Percidae: Etheostoma)Richard C Harrington
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Syst Biol 61:63-79. 2012..In addition, our analyses highlight the importance of phenotypic character information in providing an independent assessment of alternative species delimitation hypotheses in the E. simoterum species complex... - Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes?David C Collar
Section of Evolution and Ecology, University of California, Davis 95616, USA
Evolution 59:1783-94. 2005..4 and 7.7 times greater in Lepomis. Thus, time and phylogeny do not account for the differences in morphological disparity observed in Lepomis and Micropterus, and other diversity-promoting mechanisms should be investigated... - Functional innovations and morphological diversification in parrotfishSamantha A Price
Department of Evolution and Ecology, University of California, Davis, Davis, California 95616, USA
Evolution 64:3057-68. 2010..Interestingly, this morphological diversity may not have led to differential resource uses as available data suggest that members of this clade show remarkable homogeneity of diet... - Mitochondrial DNA, morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae)Thomas J Near
Center for Population Biology, One Shields Avenue, University of California, Davis, CA 95616, USA
Mol Phylogenet Evol 28:87-98. 2003..These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions... - A genomic fossil reveals key steps in hemoglobin loss by the antarctic icefishesThomas J Near
Department of Ecology and Evolutionary Biology, Yale University, USA
Mol Biol Evol 23:2008-16. 2006..ionah. We conclude that the globin pseudogene complex of N. ionah is a "genomic fossil" that reveals key intermediate steps on the pathway to loss of hemoglobin expression by all icefish species... - Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishesJeremy J Wright
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
Mol Phylogenet Evol 63:848-56. 2012.... - A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei: Percidae) endemic to the Cumberland RiverBenjamin P Keck
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Mol Ecol 19:5030-42. 2010..Our analyses reveal that geographic isolating mechanisms that result in similar phylogeographic patterns in the CRD are persistent through long expanses of evolutionary time... - Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundaryC Darrin Hulsey
Center for Population Biology, Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
Mol Phylogenet Evol 31:754-64. 2004..Our results indicate the 5-million-year-old extension of the Mexican Neovolcanic Plateau to the Gulf Coast of Mexico has strongly influenced the current transition between the vertebrate faunas of the Neotropics and Nearctic... - Geographic and temporal aspects of mitochondrial replacement in Nothonotus darters (Teleostei: Percidae: Etheostomatinae)Benjamin P Keck
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
Evolution 64:1410-28. 2010..Comparisons among darter subclades indicated that the mitochondrial lineage of the clade is most influential in determining if the lineage is a mitochondrial donor or recipient... - Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae)Matthew L Niemiller
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
Evolution 66:846-66. 2012..However, results depend on sampling of individuals and loci; this issue needs further study... - Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea)Alex Dornburg
Department of Ecology and Evolutionary Biology, Yale University, USA
Mol Biol Evol 29:721-36. 2012..We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages... - Relationship between species co-occurrence and rate of morphological change in Percina darters (Percidae: Etheostomatinae)Rose L Carlson
Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616, USA
Evolution 63:767-78. 2009..We find that morphology changes more quickly when co-occurrence is greater in Percina. Our results provide strong evidence that co-occurrence among close relatives is linked to the morphological diversification of this clade... - Temporal patterns of diversification and microendemism in Eastern Highland endemic barcheek darters (Percidae: Etheostomatinae)Phillip R Hollingsworth
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37916, USA
Evolution 63:228-43. 2009.... - Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (percidae: etheostoma)Christen M Bossu
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37917, USA
Syst Biol 58:114-29. 2009..spectabile species clade and may be relatively common among clades comprising the species-rich North American freshwater fauna... - Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimationAlex Dornburg
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Syst Biol 60:519-27. 2011..Additionally, this method is easily adapted to assess the consistency of potential calibrations to any one calibration in the candidate pool... - The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyondPeter C Wainwright
Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA
Syst Biol 61:1001-27. 2012..Acanthomorpha; Beloniformes; Centrogenyidae; key innovation; Labroidei; Ovalentaria; pharyngeal jaws; Perciformes.]... - The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae)Alex Dornburg
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
Evolution 65:1912-26. 2011..Together these findings suggest that the acquisition of a distinctive mode of locomotion drove an early radiation of shape and function in triggerfish, but not an early radiation of species... - Functional antifreeze glycoprotein genes in temperate-water New Zealand nototheniid fish infer an Antarctic evolutionary originChi Hing C Cheng
Department of Animal Biology, University of Illinois, Urbana, USA
Mol Biol Evol 20:1897-908. 2003.... - Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishesDaniel I Bolnick
Section of Integrative Biology, University of Texas, Austin, Texas 78712, USA
Genetics 178:1037-48. 2008..However, as with any comparative study, we cannot rule out the possibility that our results arise from a mutual correlation with a third variable such as body size... - Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae)Daniel I Bolnick
Section of Integrative Biology, University of Texas at Austin, Texas 78712 0253, USA
Evolution 59:1754-67. 2005..However, between-group comparisons require more careful molecular-clock calibration than has been the norm... - Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequencesThomas J Near
Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, 266 Whitney Ave, New Haven, CT 06520, USA
Mol Phylogenet Evol 47:832-40. 2008..However, we anticipate increased resolution of the notothenioid phylogeny from future analyses that sample DNA sequences from several nuclear genes... - Evolution and the latitudinal diversity gradient: speciation, extinction and biogeographyGary G Mittelbach
W K Kellogg Biological Station and Department of Zoology, Michigan State University, Hickory Corners, MI 49060, USA
Ecol Lett 10:315-31. 2007..Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research...