Thomas J Near

Summary

Affiliation: University of Tennessee
Country: USA

Publications

  1. ncbi request reprint Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA
    Thomas 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
  2. ncbi request reprint 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
  3. ncbi request reprint Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes
    Thomas J Near
    Center for Population Biology, One Shields Avenue, University of California, Davis, CA 95616, USA
    Mol Phylogenet Evol 32:344-57. 2004
  4. ncbi request reprint Dispersal, vicariance, and timing of diversification in Nothonotus darters
    Thomas 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
  5. pmc Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
    Thomas 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
  6. ncbi request reprint 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
  7. ncbi request reprint Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles
    Thomas J Near
    Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996 1610, USA
    Am Nat 165:137-46. 2005
  8. pmc Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting
    Matt Friedman
    Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK, Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA, Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA, Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Proc Biol Sci 280:20131733. 2013
  9. doi request reprint Piscivory limits diversification of feeding morphology in centrarchid fishes
    David C Collar
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Evolution 63:1557-73. 2009
  10. ncbi request reprint 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

Detail Information

Publications41

  1. ncbi request reprint Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA
    Thomas 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
    ....
  2. ncbi request reprint 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
    ....
  3. ncbi request reprint Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes
    Thomas 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...
  4. ncbi request reprint Dispersal, vicariance, and timing of diversification in Nothonotus darters
    Thomas 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...
  5. pmc Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
    Thomas 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...
  6. ncbi request reprint 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...
  7. ncbi request reprint Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles
    Thomas 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...
  8. pmc Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting
    Matt Friedman
    Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK, Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA, Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA, Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Proc Biol Sci 280:20131733. 2013
    ....
  9. doi request reprint Piscivory limits diversification of feeding morphology in centrarchid fishes
    David 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...
  10. ncbi request reprint 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...
  11. doi request reprint Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion
    Alex 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...
  12. doi request reprint Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia)
    Christen M Bossu
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
    Mol Ecol 22:5397-417. 2013
    ....
  13. doi request reprint Effects of climatic and geological processes during the pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (teleostei: amblyopsidae)
    Matthew L Niemiller
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Evolution 67:1011-25. 2013
    ..Finally, we conclude that climatic and geological processes have resulted in the formation of cryptic forms and advocate recognition of two distinct phylogenetic lineages currently recognized as A. spelaea...
  14. ncbi request reprint 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...
  15. doi request reprint Characterization of a contemporaneous hybrid zone between two darter species (Etheostoma bison and E. caeruleum) in the Buffalo River System
    Christen M Bossu
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Genetica 141:75-88. 2013
    ....
  16. doi request reprint Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes
    Samantha A Price
    Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA
    Evolution 67:417-28. 2013
    ..Whatever the cause, there is growing evidence that reef habitats stimulate morphological and functional diversification in teleost fishes...
  17. doi request reprint 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...
  18. ncbi request reprint 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...
  19. doi request reprint The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond
    Peter 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.]...
  20. doi request reprint Functional innovations and morphological diversification in parrotfish
    Samantha 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...
  21. ncbi request reprint 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...
  22. ncbi request reprint A genomic fossil reveals key steps in hemoglobin loss by the antarctic icefishes
    Thomas 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...
  23. doi request reprint Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)
    Matthew L Niemiller
    Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
    Evolution 67:732-48. 2013
    ..The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization...
  24. doi request reprint Phylogenetic inference of nuptial trait evolution in the context of asymmetrical introgression in North American darters (teleostei)
    Richard C Harrington
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Evolution 67:388-402. 2013
    ..Our results highlight the limited strategies available to account for introgressive hybridization in the inference of species relationships and the likely effects of this process on reconstructing trait evolution...
  25. doi request reprint Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes
    Jeremy J Wright
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Phylogenet Evol 63:848-56. 2012
    ....
  26. ncbi request reprint Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary
    C 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...
  27. ncbi request reprint 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...
  28. doi request reprint A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei: Percidae) endemic to the Cumberland River
    Benjamin 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...
  29. doi request reprint 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...
  30. doi request reprint 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...
  31. doi request reprint 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
    ....
  32. doi request reprint 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...
  33. ncbi request reprint 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...
  34. doi request reprint Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation
    Alex 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...
  35. doi request reprint 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...
  36. pmc An early fossil remora (Echeneoidea) reveals the evolutionary assembly of the adhesion disc
    Matt Friedman
    Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
    Proc Biol Sci 280:20131200. 2013
    ..This phylogenetic sequence of transformation finds some parallels in the order of ontogenetic changes to the disc documented for living remoras. ..
  37. ncbi request reprint Functional antifreeze glycoprotein genes in temperate-water New Zealand nototheniid fish infer an Antarctic evolutionary origin
    Chi Hing C Cheng
    Department of Animal Biology, University of Illinois, Urbana, USA
    Mol Biol Evol 20:1897-908. 2003
    ....
  38. doi request reprint Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences
    Thomas 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...
  39. ncbi request reprint 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...
  40. pmc Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes
    Daniel 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...
  41. ncbi request reprint Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography
    Gary 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...