W. Kelley Thomas

Publications


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PUBLICATIONS (Full Manuscripts)

2011

Abebe E., Abebe-Akele F., Morrison J., Cooper V., and Thomas W.K. 2011. An insect pathogenic symbiosis between a Caenorhabditis and Serratia. Virulence 2:158-161.

Abebe E.., Mekete T. and Thomas W.K. 2011. A critique of current methods in nematode taxonomy. African Journal of Biotechnology 10:312-323.

2010

Sung W., Tucker A., Bergeron R.D., Lynch M., and Thomas W.K. 2010. Simple sequence repeat variation in the Daphnia pulex genome. BMC Genomics 11:691. [Epub ahead of print]

Abebe E., Jumba M., Bonner K., Gray V., Morris K., Thomas, W.K. 2010. An entomopathogenic Caenorhabditis briggsae. J. Exp. Biol. 213: 3223-3229.

Bik H.M., Thomas W.K., Lunt D.H., and Lambhead P.J. 2010. Low Endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC Evol. Biol. 10:389.

Bik H.M., Lambshead P.J., Thomas W.K., Lunt D.H. 2010. Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades. BMC Evol. Biol. 10:353.

Creer S., Fonseca V.G., Porazinska D.L., Giblin-Davis R.M., Sung W., Power D.M., Packer M., Carvalho G R., Blaxter M.L., Lambshead P.J.D., and Thomas W.K. 2010. Ultrasequencing of the meiofaunal biosphere: practice, promises and pitfalls. Mol. Ecol. 19 (Suppl. 1):4-20.

Davies K.A., Ye W., Giblin-Davis R.M., Taylor G.S., Scheffer S., Thomas W.K. 2010. The nematode genus Fergusobia (Nematoda: Neotylenchidae): molecular phylogeny, descriptions of clades and associated galls, host plants and Fergusonina fly larvae. Zootaxa 2633: 1-6.

Fonseca V.G., Carvalho G.R., Sung W., Johnson H.F., Power D.M., Neill S.P., Packer M., Blaxter M.L., Lambshead P.J., Thomas W.K., Creer S. 2010. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat. Comm. 1:98.

Porazinska D.L., Giblin-Davis R.G., Esquivel A., Powers T.O., Sung W., Thomas W.K. 2010. Ecometagenetics confirm high tropical rainforest nematode diversity. Mol. Ecol. 19: 5521-5530.

Porazinska D.L., Sung W., Giblin-Davis R.M., and Thomas, W.K. 2010. Reproducibility of Read Numbers in High-Throughput Sequencing Analysis of Nematode Community Composition and Structure. Mol. Ecol. Res. 10:666-676.

Colbourne J.K., Pfrender M.E., Gilbert D., Thomas W.K., Tucker A., Oakley T.H., Tokishita S., Aerts A., Arnold G.J., Basu M.K., Bauer D.J., Caceres C.E., Carmel L., Casola C., Choi J.H., Detter J., Dong Q., Dusheyko S., Eads B.D., Frohlich T., Geiler-Samerotte K.A., Gerlach D., Hatcher P., Jogdeo S., Krijgsveld J., Kriventseva E.V., Kultz D., Laforsch C., Lindquist E., Lopez J., Manak J.R., Muller J., Pangilinan J., Patwardhan R.P., Pitluck S., Pritham E.J., Rechtsteiner A., Rho M., Rogozin I.B., Sakarya O., Salamov A., Schaack S., Shapiro H., Shiga Y., Skalitzky C., Smith Z., Souvorov A., Sung W., Tang Z., Tsuchiya D., Tu H., Vos H., Wang M., Wolf Y., Yamagata H., Yamada T., Ye Y., Shaw J.R., Andrews J., Crease T.J., Tang H., Lucas S.M., Robertson H.M., Bork P., Koonin E.V., Zdobnov E.M., Grigoriev I.V., Lynch M., Boore J.L. 2011. The ecoresponsive genome of Daphnia pulex. Science, 331:555-561.

2009

Porazinska D.L., Giblin-Davis R.M., Faller L. , Farmerie W. , Kanzaki N., Morris K., Powers T.O., Tucker A.E., Sung W., and Thomas W.K. 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode discovery. Mol. Ecol. Res. Online DOI 10.1111/j.1755-0998.2009.02611.x

Kanzaki, N., Giblin-Davis R.M., Davies K., Ye W., Center B.J., and Thomas W.K. 2009. Teratodiplogaster fignewmani gen. nov. sp. nov. (Nematoda: Diplogasteridae) from the synconia of Ficus racemose in Australia. Zool. Sci. 26:569-578.

Li W., Tucker A.E., Sung W., Thomas W.K., and Lynch M. 2009. Extensive, recent intron gains in Daphnia populations. Science. 326:1260-1262.

Denver D.R., Dolan P.C., Wilhelm L.J., Lucas-Lledó W.I., Howe D.K., Lewis S.C., Okamoto K., Thomas W.K., Lynch M., Baer C.F. 2009. A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. PNAS 106:16310-16314.

2008

Bobilya D.J., Gauthier N.A., Karki S., Olley B.J., and Thomas W.K. 2008. Longitudinal changes in zinc transport kinetics, metallothionein and zinc transporter expression in a blood-brain barrier model in response to a moderately excessive zinc environment. J Nutr. Biochem. 19:129-137.

Seyfert A.L., Cristescu M.E.A., Frisse L., Schaak S., Thomas W.K., and Lynch M.2008. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178:2113-2121.

Lynch M., Sung W., Morris K., Coffey N., Landry C.R., Dopman E.B., Dickinson W.J., Okamoto K., Kulkarni S., Hartl D.L. and Thomas W.K. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. PNAS 105:9272-9288.

Brites D., McTaggart S., Morris K., Anderson J., Thomas K., Colson I., Fabbro T., Little T.J., Ebert D., Du Pasquier L. 2008 The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. Mol Biol Evol. 25:1429-39. Epub.

Zhao Z., Ye W., Giblin-Davis R.M., Li D., Thomas W.K., Davies K.A., and Riley I.T. 2008. Morphological and molecular analysis of six aphelenchoids from Australian conifers and their relationship to Bursaphelenchus (Fuchs, 1937). Nematology 10:663-678.

Gulcu B., Hazir S., Giblin-Davis R.M., Ye W., Kanzaki N., Mergen H., Keskin N., and Thomas, W.K. 2008. Molecular variability of Schistonchus caprifici (Nematoda: Aphelenchoididae) from Ficus carica in Turkey. Nematology 10:639-649.

2007

Ye, W., Giblin-Davis R.M., Braasch, H., Morris, K., and Thomas, W.K., “Phylogenetic Relationships Among Bursaphelenchus species (Nematoda: Parastiaphelenchidae) Inferred from Nuclear Ribosomal and Mitochondrial DNA Sequence Data.J. Mol. Evol. 43:1185-1197, 2007.

Ye W., Giblin-Davis R.M., Davies K.A., Purcell M.F., Scheffer S.J., Taylor G.S., Center T.D., Morris, K. and Thomas W.K. 2007. Molecular phylogenetics and the evolution of host plant associations in the nematode genus Fergusobia (Tylenchida: Fergusobiinae)???Mol. Phylogenet. Evol. 45:123-141.

Ye W., Giblin-Davis R.M., Braasch, H., Morris K. and Thomas W.K. 2007. Phylogenetic relationships among Bursaphelenchus species (Nematoda: Parasitaphlenchidae) inferred from nuclear ribosomal and mitochondrial DNA sequence data. Mol. Phylogenet. Evol. 43:1185-1187.

Faller, Lina (Mentors: R.D. Bergeron and W.K. Thomas) 2007. Bioinformatics: merging computer science and genetics. Inquiry Journal (published by UNH) Spring 2007.

Porazinska D.L., Giblin-Davis R.M., Powers T.O.; Kanzaki N., Ye W., Morris K., et al. 2007. 454 pyrosequencing for metagenomic analysis of nematode diversity. J. Nematology 39: 90.

Zeng Y., Giblin-Davis R.M., Ye W., Bélair G., Boivin G., and Thomas W.K. 2007. Bradynema listronoti n. sp. (Nematoda: Allantonematidae), a parasite of the carrot weevil Listronotus oregonensis (Coleoptera: Curculionidae) in Quebec, Canada Nematology 9: 605-623.

2006

Giblin-Davis R.M., Ye W., Kanzaki N., Williams D., Morris K., and Thomas W.K. 2006. Stomatal ultrastructure, molecular phylogeny, and description of Parasitodiplogaster laevigata n. sp. (Nematoda: Diplogasteridae), a parasite of fig wasps. J. Nematology 38:137-149.

Giblin-Davis R.M., Kanzaki N., Ye W., Mundo-Ocampo M., Baldwin J.G. and Thomas W.K. 2006. Morphology and description of Bursaphelenchus platzeri n. sp. (Nematoda: Parastiaphelenchidae), an associate of nitidulid beetles. J. Nematol. 38:150-157.

Kulkarni S., Bergeron R.D., and Thomas W.K. 2006. Multiple assembly viewer with enhanced navigation (MAVEN): interactive display of multiple genome assemblies. Eurographics/IEEE-VGTC Symposium on Visualization. Technical Report.

2005

De Ley, P., De Ley, I.T., Morris, K., Abebe, E., Mundo-Ocampo, M., Yoder, M., Heras, J., Waumann, D., Rocha-Olivares, A., Burr, J.A.H., Baldwin, J.G. and Thomas, W.K. An Integrated Approach to Fast and Informative Morphological Vouchering of Nematodes for Applications in Molecular Barcoding Philos. Trans. R. Soc. Lond. B. Biol. Sci. B 360:1945-1958, 2005.

Denver, D.R., Feinberg, S., Estes, S., Thomas, W.K. and Lynch, M. Mutations rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegansGenetics 170:107-113, 2005.

Denver, D.R., Morris, K., Streelman, J.T., Kim, S.K., Lynch, M. and Thomas, W.K. The Transcriptional Consequences of Mutation and Natural Selection in Caenorhabditis elegans.Nature Genetics 37:544-548, 2005. (PDF)

2004

Denver, D.R., Morris, K., Lynch, M., and Thomas, W.K. High Mutation Rate and Predominance of Insertions in the Caenorhabditis elegans nuclear genome.Nature 430:679-682, 2004. (PDF)

Denver, D.R., Morris, K., Kewalramani, A., Harris, K.E., Chow, A., Estes, S., Lynch, M., and Thomas, W.K. Abundance, Distribution, and Mutation Rates of HomopolymericNucleotide Runs in the Genome of Caenorhabditis elegans. J. Mol. Evol. 58:584-595, 2004. (PDF)

Estes, S., Phillips, P.C., Denver, D.R., Thomas, W.K., and Lynch, M. Mutation Accumulation in Populations of Varying Size: the Distribution of MutationalEffects for Fitness Correlates in Caenorhabditis elegans J. Mol. Evol. 166: 1269-1279, 2004.

Abebe, E., Grizzle, R.E., Hope, D., and Thomas, W.K. Nematode Biodiversity in the Gulf of Maine, USA, and a Web-Accessible, Relational Database.J. Mar. Biol. Ass. U.K. 84:1159-1167, 2004.

Giblin-Davis, R.M., Scheffer, S.J., Davies, K.A., Taylor, G.S., Curole, J., Center, T.D., Goolsby, J., and Thomas, W.K.,Coevolution Between Fergusobia and Fergusobiba Mutualists. Nematology Monographs & Perspectives 2:407-417., 2004.

2003

Denver, D.R., Morris, K., and Thomas, W.K. Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Mol. Biol. Evol. 20:393-400, 2003.

Giblin-Davis, R.M., Davies, K.A., Morris, K. and Thomas, W.K., Evolution of Parasitism in Insect-transmitted Plant Nematodes. J. Nematology 35:133-141, 2003.

prior to 2003

Denver, D.R., Morris, K., Lynch, M., Vassilieva, L.L. and Thomas, W.K. High Direct Estimate of the Mutation Rate in the Mitochondrial Genome of Caenorhabditis elegans. Science 289:2342-2344, 2000. (PDF)

Félix, M.-A., De Ley, P., Sommer, R.J., Frisse, L., Nadler, S., Thomas, K., Vanfleteren, J., and Sternberg, P.W.Evolution of Vulva Development in the Cephalobina (Nematoda). Dev. Biol. 221:68-6, 2000.

Kaplan, D.T., Thomas, W.K., Frisse, L.M., Sarah, J.L., Stanton, J.M., Speijer, P.R., Marin, D.H., and Opperman, C.H. Phylogenetic Analysis of Geographically Diverse Radopholus similus via rDNA Sequence Reveals a Monomorphic Motif. J. Nematol. 32:134-142, 2000.

Duncan, L.W., Inserra, R.N., Thomas, W.K., Dunn, D., Mustika, I., Frisse, L.M., Mendes, M.L., Morris, K., and Kaplan, D.T. Molecular and Morphological Analysis of Isolates of Pratylenchus coffeae and Closely Related Species. Nematropica 29:61-80, 1999.

Courtright, E.M., Wall Freckman, D., Virginia, R.A., Frisse, L.M., Vida, J.T., and Thomas, W.K., Nuclear and Mitochondrial DNA Sequence Diversity in the Antarctic Nematode Scottnema lindsayae. J. Nematol. 32:143-153, 2000.

Luong, L.T., Platzer, E.G., De Ley, P, Thomas, W.K., Morphological, Molecular, and Biological Characterization of Mehdinema alii (Nematoda: Diplogasterida) from the Decorated Cricket (Gryllodes sigillatus), J. Parasit. 85:1053-1064, 1999.

De Ley, P., Félix, M.-A., Frisse, L.M., Nadler, S.A., Sternberg, P.W., and Thomas, W.K., Molecular and Morphological Characterisation of Two Reproductively Isolated Species with Mirror-image Anatomy (Nematoda: Cephalobidae). Nematology 1:591-612, 1999.

Goldstein, B., Frisse, L.M., and Thomas, W.K., Embryonic Axis Specification in Nematodes: Evolution of the First Step in Development. Curr. Biol. 8:157-160, 1998.

Blaxter, M.L., De Ley, P., Garey, J., Liu, L.X., Scheldemen, P., Vanfleteren, J., Mackey, L.Y., Dorris, M., Frisse, L.M., Vida, J.T., and Thomas, W.K., A Molecular Evolutionary Framework for the Phylum Nematoda. Nature 392:71-75, 1998.

Thomas, W. K., Vida, J.T., Frisse, L.M., Mundo, M., and Baldwin, J.G., DNA Sequences From Formalin-Fixed Nematodes: Integrated Molecular and Morphological Approaches to Taxonomy. J. Nematology 29:250-254, 1997.

Baldwin, J.G., Frisse, L.M., Vida, J.T., Eddleman, C.D., and Thomas, W.K., An Evolutionary Framework for the Study of Developmental Evolution in a Set of Nematodes Related to Caenorhabditis elegans (Nemata: Rhabditina). Mol. Phylogenet. Evol. 8:249-259, 1997.

Baldwin, J.G., Giblin-Davis, R.M., Eddleman, C.D., Williams, D.S., Vida, J.T., Thomas, W.K., Buccal Capsule of Aduncospiculum halicti (Nemata: Diplogasterina): An Ultrastructural and Molecular Phylogenetic Study. Can. J. Zool., 75:407-423, 1997.

Nielsen, J., Tupper, D., and Thomas, W., Mitochondrial DNA Polymorphism in Unique Runs of Chinook Salmon (Oncoryhynchus tshawutscha) From the Sacramento-San Joaquin River Basin. Cons. Biol. 8:882-884, 1994.

Nielsen, J.L., Gan, C. Wright J.M., Morris, D.B. and Thomas, W.K., Biogeographic Distributions of Mitochondrial and Nuclear Markers for Southern Steelhead. Mol. Mar. Biol. Biotech., 3:281-293, 1994.

Nielsen, J.L., Gan, C. and Thomas, W.K., Differences in Genetic Diversity for mtDNA between Hatchery and Wild Populations of Oncorhynchus. Can. J. Fish Aquat. Sci., 51:Suppl. 1, 1994.

Sidow, A. and Thomas, W.K., A Molecular Evolutionary Framework for Eukaryotic Model Organisms. Curr. Biol. 4:596-603, 1994.

Litvaitis, M., Nunn, G., Thomas, W., and Kocher, T. A Molecular Approach for the Identification of Meiofaunal Tubellarians (Platyhelminthes, Turbellaria). Mar. Biol. 120:437-442, 1994.

Janke, A., Feldmaier-Fuchs, G., Thomas, W.K., Von Haeseler, A. and Pääbo, S., The Marsupial Mitochondrial Genome and the Evolution of Placental Mammals. Genetics 137:243-256, 1994.

Zimmer, R., Erdtmann, B., Thomas, W.K. and Quinn, T.W., Phylogenetic Analysis of the Coscoroba coscoroba Using Mitochondrial srRNA Gene Sequences. Mol. Phylogenet. Evol. 3:85-91, 1994.

Thomas, W.K. and Martin, S.L., A Recent Origin of Marmots. Mol. Phylogenet. Evol. 2:330-336, 1993.

Kocher, T.D. and Thomas, W.K., PCR Mediated DNA Sequencing. Meth. Enzym. 224:391-399, 1993.

Thomas, W.K. and Pääbo, S., Diachronic Studies of DNA in Museum Specimens. Meth. Enzym. 224:406-419, 1993.

Prager, E.M, Sage, R.D., Gyllensten, U., Thomas, W.K., Hubner, R., Jones, C.S., Noble, L., Searle, J.B. and Wilson, A.C. Mitochondrial DNA Sequence Diversity and the Colonization of Scandinavia by House Mice from East Holstein. Biol. J. Linn. Soc. 50:85-122, 1993.

Smith, M.F., Thomas, W.K. and Patton, J.L., Mitochondrial DNA-like Sequence in the Nuclear Genome of an Akodontine Rodent. Mol. Biol. Evol. 9:204-215, 1992.

Pääbo, S., Thomas, W.K., Whitfield, K.M., Kumazawa, Y. and Wilson, A.C. Rearrangements of Mitochondrial tRNA Genes in Marsupials. J. Mol. Evol. 33:426-430, 1991.

Thomas, W.K. and Wilson, A.C., Mode and Tempo of Molecular Evolution in the Nematode Caenorhabditis. Genetics 128:269-279, 1991.

Thomas, W.K., Pääbo, S., Villablanca, F.X. and Wilson, A.C. Spatial and Temporal Continuity of Kangaroo Rat Population Shown by Sequencing Mitochondrial DNA from Museum Specimens J. Mol. Evol. 31:101-112, 1990.

Buroker, N.E., Brown, J.R., Gilbert, T.A., O'Hara, P.J., Beckenbach, A.T., Thomas, W.K. and Smith, M.J., Length Heteroplasmy of Sturgeon Mitochondrial DNA: an Illegitimate Elongation Model. Genetics 124:157-163, 1990.

Beckenbach, A.T., Thomas, W.K. and Sohrabi, H., Intraspecific Sequence Variation in the Mitochondrial Genome of Rainbow Trout (Oncorhynchus mykiss). Genome 33:13-15, 1990.

Thomas, W.K., Maa, J. and Wilson, A.C. Shifting Constraints on tRNA Genes during Mitochondrial DNA Evolution in Animals. New Biol. 1:93-100, 1989.

Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Pääbo, S., Villablanca, F.X. and Wilson, A.C. Dynamics of Mitochondrial DNA Evolution in Animals: Amplification and Sequencing with Conserved Primers. Proc. Natl. Acad. Sci. USA 86:6196-6200, 1989.

Thomas, W.K. and Beckenbach, A.T., Variation in Salmonid Mitochondrial DNA: Evolutionary Constraints and Mechanisms of Substitution. J. Mol. Evol. 29:233-245, 1989.

Wilson, G.M., Thomas, W.K. and Beckenbach, A.T., Mitochondrial DNA Analysis of Pacific Northwest Populations of Onchorhynchus tshawytscha Can. J. Fish. Aquatic Sci. 44:1301-1305, 1987.

Thomas, W.K. and Beckenbach, A.T., Mitochondrial DNA Restriction Site Variation in the Townsend's Vole, Microtus townsendii Can. J. Zool. 64:2750-2756, 1986.

Thomas, W.K., Withler, R.E. and Beckenbach, A.T., Mitochondrial DNA Analysis of Pacific Salmonid Evolution Can. J. Zool. 64:1058-1064, 1986.

Wilson, G.M., Thomas, W.K. and Beckenbach, A.T., Intra- and Inter-Specific Mitochondrial DNA Sequence Divergence in Salmo: Rainbow, Steelhead and Cutthroat Trouts Can. J. Zool. 63:2088-2094, 1985.

Book Chapters

Giblin-Davis, R.M., Davies, K.A., Taylor, G.S., and Thomas, W.K. “Entomophilic Nematode Models for Studying Biodiversity and Cospeciation.”in Nematology, Advances and Perspectives, Z.X. Chen, S.Y. Chen and D.W. Dickson, eds., pp 492-538, 2003.

Thomas, W. K. and Glover, “Direct Sequencing by TEM of Z-Substituted DNA Molecules. In Next Generation Genome Sequencing, ed. Michael Janitz. Wiley-VCH Verlag GmbH & Co., KGaA, Weinheim, 2008.

Fitch, D.H.A. and Thomas,W.K. “Evolution” in C. elegans II, D. Riddle, T. Blumenthal, B. Meyer, and J. Priess, eds., pp 815-850, 1997.