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Book:
Katz, L.A. and Bhattacharya, D. (Editors). 2006. Genome Evolution in Eukaryotic Microbes. Oxford University Press. Submitted Articles:
Peer Reviewed Articles:
2012
Katz, LA, LW Parfrey, J Grant, JG Burleigh. 2012. Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst Biol. DOI:10.1093/sysbio/sys026 (PDF)Katz, LA, J DeBerardinis, MS Hall, AM Kovner, M Dunthorn, SV Muse. 2012. Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata. J. Mol. Evol. 73:266-272. (PDF)
2011
Parfrey, LW, LDJ G., AH Knoll, LA Katz. 2011. Estimating the timing of early eukaryotic diversification with multigene molecular clocks Proc. Natl. Acad. Sci. U. S. A. 108:13624-13629. (PDF)Tamura M, Katz LA, McManus GB. 2011. Distribution and diversity of oligotrich and choreotrich ciliates across an environmental gradient in a large temperate estuary. Aquatic Microbial Ecology 64:51-67 (PDF)
Lahr DJG, *Nguyen TB, *Barbero E, Katz LA. 2011. Evolution of the actin gene family in testate lobose Amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions. Mol. Biol. Evol. 28:223-236 (PDF)
Lahr, D. J. G., Grant, J. R., Nguyen, T., Lin, J.H. and L. A. Katz. 2011. Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSUrDNA and Actin Gene. PLOS One. 6(7). (PDF)
Katz, L. A., Grant, J. R., Parfrey, L. W., Gant, A., O'Kelley, C. J., Anderson, O. R., Molestina, R. E. & Nerad, T. 2011. Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes. Protist. (PDF)
Hall, MS and LA Katz. 2011. On the nature of species: insights from Paramecium and other ciliates. Genetica.139(5):677-84. (PDF)
Lahr, D. J. G., Parfrey, L. W., Mitchell, E. A., Katz, L. A. and E. Lara. 2011. The chasitity of amoebae: re-evaluating evidence for sex in amoebaoid organisms. Proc Biol Sci. 278(1715):2081-90. (PDF)
Dunthorn, M.S., W. Foissner and L.A. Katz. 2011. Expanding Character Sampling for Ciliate
Phylogenetic Inference Using Mitochondrial SSU-rDNA as a Molecular Marker. Protist. 162:85–99. (PDF)
2010
Parfrey LW and Katz LA. 2010. Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera). Genome Biology and Evolution 2:678-685. (PDF)Dunthorn, M. S., and L. A. Katz. 2010. Secretive ciliates and putative asexuality in microbial eukaryotes. Trends Microbiol.. 18: 183-188. (PDF)
Parfrey, L. W., and L. A. Katz. 2010. Dynamic genomes of eukaryotes and the maintenance of genomic integrity. Microbe 5:156-164. (PDF)
McManus, G. B., D. P. Xu, B. A. Costas, and L. A. Katz. 2010. Genetic identities of cryptic species in the Strombidium stylifer/apolatum/oculatum cluster, including a description of Strombidium rassoulzadegani n. sp. J. Eukaryot. Microbiol. 57:369-378.
Katz, L.A. and A. M. Kovner. 2010. Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata. J. Exp. Zool. Part B. (Mol. Dev. Evol.). Pub. online 10.1002/jez.b.21354 (PDF)
Tekle, Y. I., J. R. Grant, A. M. Kovner, J. P. Townsend, and L. A. Katz. 2010. Identification of new molecular markers for assembling the eukaryotic tree of life. Mol. Phylogenet. Evol. 55:1177-1182. (PDF)
Doherty, M., M. Tamura, J.A.C. Vriezen, G.B. McManus and L.A. Katz. 2010. Diversity of Oligotrich and Choreotrich ciliates in coastal marine sediments: relationships with overlying plankton. Appl. Environ. Microbiol. 76:3924-3935. (PDF)
Parfrey, L. W., J. R. Grant, Y. I. Tekle, E. Lasek-Nesselquist, H. G. Morrison, M. L. Sogin, D. J. Patterson, and L. A. Katz. In Press. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst. Biol. (PDF)
Doherty, M., B.A. Costas, M. Tamura, M.E. Ritchie, G.B. McManus and L.A. Katz. 2010. Ciliate diversity across an environmental and depth gradient in Long Island Sound, USA. Environ. Microbiol. 12: 886-898 (PDF)
Cole J., Andersen O.R., Tekle Y. I., J. Grant, Katz L. A., and T. Nerad. 2010. A description of a new ‘Amoebozoa’ isolated from the American Lobster, Homarus americanus. J. Euk. Micro. 57: 40-47. (PDF)
2009
Lahr, D.J.G. and L.A. Katz. 2009. Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. Biotechniques. 47: 857-866. (PDF)McManus, G.B. and L.A. Katz. 2009. Molecular and morphological methods for identifying plankton: what makes a successful marriage? J. Plank. Research. 31: 1119-1129. (PDF)
Tekle, Y.I., Parfrey, L.W., and L.A. Katz. 2009. Molecular data are transforming hypotheses on the origin and diversification of eukaryotes. BioScience 59: 471–481. (PDF)
Grant J.R., Tekle, Y.I., O.R. Anderson, Patterson D.J., and L.A. Katz. 2009. Multigene evidence for the placement of a heterotrophic amoeboid lineage Leukarachnion sp. among photosynthetic stramenopiles. Protist. 160: 376—385. (PDF)
Dunthorn, M. M. Eppinger, M. V. J. Schwarz, M. Schweikert, J. Boenigk, W. Foissner, L. A. Katz, T. Stoeck. 2009. A redescription of Aristerostoma marinum Kahl, 1931 and the phylogenetic placement of the Cyrtolophosididae Stokes, 1888 (Ciliophora; Colpodea). International Journal of Systematic and Evolutionary Microbiology. 59: 167–180 (PDF)
2008
Foissner, W., A. Chao and Laura A. Katz. 2008. Diversity and geographic distribution of ciliates (Protista: Ciliophora). Biodiv. Conserv. 17: 345-363. (PDF)Parfrey, L.W., D. Lahr and L.A. Katz. 2008. The dynamic nature of eukaryotic genomes. Mol. Biol. Evol. (PDF)
Tekle, Y.I., J.R. Grant, L. O.R. Anderson, J.C. Cole, T. Nerad, and L.A. Katz . 2008. Multigene phylogenetic analyses of diverse amoebae and assessment of stability of clades within ‘Amoebozoa’ based on rate corrected SSU-rDNA analysis. Mol. Phylogenet. Evol. 47: 339–352 (PDF)
2007
Yoon, H-S, J.R. Grant, Y.I. Tekle, M. Wu, B.C. Chao, J.C. Cole, J.M. Logsdon, D.J. Patterson, D. Bhattacharya, and L.A. Katz. 2007. A broadly sampled multigene tree of eukaryotes. BMC Evol. Biol. (PDF)
Dunthorn, M.S., W. Foissner, L.A. Katz. 2007. Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using increased taxon sampling. Mol. Phylogenet. Evol.
46: 316–327(PDF)*Robinson, T. and L.A. Katz. 2007. Non-Mendelian inheritance of two cytoskeletal genes in the ciliate Chilodonella uncinata. Mol. Biol. Evol. 24(11):2495–2503. (PDF)
Tilley, S.G., R.L. *Eriksen and L.A. Katz. 2008qa. Systematics of dusky salamanders, Desmognathus (Caudata: Plethodontidae) in the mountain and Piedmont regions of Virginia and North Carolina, USA. Zool. J. Linnean Soc. 152: 115-130. (PDF)
Doherty, M., B. Costas, G. McManus, and L.A. Katz. 2007. Culture independent assessment of planktonic ciliate in coastal northwest Atlantic waters. Aquat. Microb. Ecol. 48: 141-154 (PDF)
Costas, B, G. McManus, M. Doherty and L.A. Katz. 2007. Use of species-specific primers and PCR to measure the distributions of planktonic ciliates in coastal waters. Limnol. Ocean: Methods. 5: 163-173 (PDF)
Tekle, Y.I., J.R. Grant, O.R. Anderson, J.C. Cole, T. Nerad, D.J. Patterson and L.A. Katz. 2007. A multigene analysis of Corallomyxa tenera sp. nov. suggests its membership in a clade that include Gromia, Haplosporidia and Foraminifera. Protist. (PDF)
*McGrath, C., R. A. Zufall and L.A. Katz. 2007. Variation in macronuclear genome content of three ciliates with extensive chromosomal fragmentation: a preliminary analysis. J. Eukaryot. Microbiol. 54(3): 242-246. (PDF)
Zufall, R.A. and L.A. Katz. 2007. Micronuclear and macronuclear forms of β-tubulin genes in the ciliate Chilodonella uncinata reveal insights into genome processing and protein evolution. J. Eukaryot. Microbiol. 54(3): 275-282. (PDF)
2006
Parfrey, L.W., E. *Barbero, E. *Lasser, M.S. Dunthorn, D. Bhattacharya, D.J. Patterson and L.A. Katz. 2006. Evaluating support for the current classification of eukaryotic diversity. PLOS Genetics 2: 2062-2073. (PDF)Katz, L.A. 2006. Epigenomics and the Future of Genome Science. Current Biology . 16: R996-R997 (PDF)
Zufall, R.A., *C. McGrath, S. Muse and L.A. Katz. 2006. Genome architecture drives protein evolution in ciliates. Mol. Biol. Evol.23: 1681-1687. (PDF)
Katz, L.A., O.L.O. Snoeyenbos-West and F. P. Doerder. 2006. Unusual patterns of molecular evolution at the SerH surface antigen locus in Tetrahymena thermophila: implication for estimates of effective population. Mol. Biol. Evol. 23: 608-614.(PDF)
2005
Katz, L.A., G. B. McManus, O.L.O. Snoeyenbos-West, *K. Pirog, *A. Griffin, and W. Foissner. 2005. Reframing the Microbial 'Everything is Everywhere' Debate: evidence for high gene flow and diversity in ciliate morphospecies. Aquat. Microb. Ecol. 41: 55-65. (PDF)Zufall, R.A., *T. Robinson and L.A. Katz. 2005. Evolution of developmentally regulated genome rearrangements in eukaryotes. J. Exp. Zool. Part B. (Mol. Dev. Evol.) 304B: 448-455. (PDF)
2004
Snoeyenbos-West, O.L.O., *A. Campbell, J. Cole, D.W. Coats and L.A. Katz. 2004. Molecular phylogeny of phyllopharyngean ciliates and their group I introns. J. Eukaryot. Microbiol. 51: 441-450. (PDF)Katz, L.A., *E. Lasek-Nesselquist, J. Bornstein and S.V. Muse. 2004. Dramatic diversity of histone H4 sequences in ciliates. Mol. Biol. Evol.21: 555-562. (PDF)
*McGrath, C. and L.A. Katz. 2004. Genome diversity in microbial eukaryotes. Trends Ecol. Evol. 19: 32-38. (PDF)
2003
Katz, L.A., *E. Lasek-Nesselquist and O.L.O. Snoeyenbos-West. 2003. Structure of the micronuclear a-tubulin gene in the phyllopharyngean ciliate Chilodonella uncinata: implications for the evolution of chromosomal processing. Gene 315: 15-19. (PDF)Jacobs, M.E., A. Sanchez-Blanco, L.A. Katz, and L.A. Klobutcher. 2003. Tec3: A New Developmentally Eliminated DNA Element in Euplotes crassus. Eukaryot. Cell. 2: 103-114
2002
Snoeyenbos-West, O.L.O., *Salcedo, T., G.B. McManus and L.A. Katz. 2002. Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci. Int. J. Syst. Evol. Micro. 52: 1901-1913. (PDF)Katz, L.A. 2002. Lateral gene transfers and the evolution of eukaryotes: theories and data. Int. J. Syst. Evol. Micro. 52: 1893-1900. (PDF)
* Israel, R.I., S. L. Kosakovsky Pond, S. Muse and L.A. Katz. 2002. Evolution of duplicated alpha-tubulin genes in ciliates. Evolution. 56: 1110-1122.
2001
Mead, L.S., S.G. Tilley and L.A. Katz. 2001. Genetic structure of the Blue Ridge dusky salamander (Desmognathus orestes): inferences from allozymes, mitochondrial DNA and behavior. Evolution. 55: 2287-2302.* Lasek-Nesselquist, E. and L.A. Katz. 2001. Phylogenetic position of Sorogena stoianovitchae and relationships within the Class Colpodea (Ciliophora) based on ssu rDNA sequences. J. Euk. Micro. 48: 604-607. (PDF)
* Riley, J.L. and L.A. Katz. 2001. Widespread distribution of extensive chromosomal fragmentation in ciliates. Mol. Biol. Evol. 18: 1372-1377.
Katz, L.A. 2001. Evolution of nuclear dualism in ciliates: a reanalysis in light of recent molecular data. Int. J. Evol. Syst. Microbiol.51: 1587-1592. (PDF)
2000
Katz, L.A, *E.A. Curtis, M. Pfunder and L.F. Landweber. 2000. Characterization of novel sequences from distantly related taxa using walking PCR. Mol. Phylo. Evol. 14: 318-321.
1999
Katz, L.A. and J.D. Berger. 1999 Parade of the little millions. American Naturalist 154: S93-S95.Katz, L.A. 1999. The tangled web: gene genealogies and the origin of eukaryotes. American Naturalist 154: S137-S145.
1998
Katz, L.A. 1998. Changing perspectives on the origin of eukaryotes. Trends Ecol. Evol.13: 493-497.
1997
Katz, L.A. and R.G. Harrison. 1997. Balancing selection on electrophoretic variation of the phosphoglucose isomerase gene in two species of field crickets: Gryllus pennsylvanicus and G. veletis. Genetics. 147: 609-621.Katz, L.A. 1997. Characterization of the phosphoglucose isomerase gene from crickets: an analysis of phylogeny, amino acid conservation and nucleotide composition. Insect Mol. Biol.,6: 305-318.
1996
Katz, L.A. 1996. Transkingdom transfer of the phosphoglucose isomerase gene. J. Mol. Evol. 43: 453-459.
1991
Katz, A.M. and L.A. Katz. 1991. Molecular biology in cardiology: A paradigmatic shift J. Mol. Cell Cardiol. 23: 403-408.
