个人简介

I am an evolutionary biologist interested in systematics and molecular evolution. I use molecular data such as DNA sequences and gene order, in combination with other organismal characteristics, to reconstruct the evolutionary history of lineages over time. In order to best use molecular data in phylogenetics, you need an understanding both of molecular evolutionary processes and methods of analysis. My work therefore centers on the study of molecular evolution and the methods of analysis of molecular data for phylogenetics. I am also very interested in the application of phylogenies to address a variety of biological questions.

研究领域

Molecular Systematics, Evolution, Biogeography, and Phylogeography: Rates, patterns, and mechanisms of molecular evolution , including nucleotide sequence evolution and mitochondrial gene order change, and consequences for phylogenetic reconstruction and reconstruction of ancestral states. Integration of molecular data with paleontological and morphological data. Using phylogenies to address biological questions.

My current research program is focused on two different levels: 1) gene order as a tool for higher-level systematics among the molluscs and related phyla, and 2) rates and patterns of sequence evolution in the mitochondrial genome, and their effect, at various taxonomic levels, on the utility of classes of molecular characters and phylogenetic methods. The conservation of gene content and rarity of gene order rearrangements within the animal mitochondrial genome suggests its utility in resolving questions of relationships among ancient lineages. These gene order characters are not subject to the shortcomings that have been attributed to morphological data (functional convergence) and molecular sequence data (unequal rate effects) that bear on the question of higher level among phyla, and underscore the utility of mitochondrial genome rearrangements as a powerful class of molecular phylogenetic tools to complement morphological and primary sequence comparisons. Another area of interest is rates and patterns of sequence evolution, and variation in rates within and among groups. My research involving sequence comparisons of species pairs isolated by the Pliocene emergence of the Isthmus of Panama, as well as species that participated in the Pliocene Trans-Arctic Interchange between the Northern Pacific and Northern Atlantic. I have also examined rates of molecular evolution from fossil occurrences. Finally, I have been investigating the significance of changing frequencies of the 4 bases A, G, C, and T in DNA sequences (base compositional effects) in phylogenetic studies. Results to date indicate that currently used methods of weighting, character-state reconstruction, rate determination, and significance testing (of phylogenetic hypotheses) are sensitive to the degree of base compositional bias, and that in the case of animal mitochondrial genomes, these patterns of base compositional bias are at least partially driven by the necessity for large portions of animal mitochondrial protein encoding genes to be hydrophobic. Research in the near future will focus on collecting molecular, morphological, and paleontological data to arrive at a robust phylogeny of the gastropods as a test case of methods of determining degrees of confidence, congruence, and resolving conflict in phylogenetic studies.

近期论文

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Pemberton, R.W., Collins, T.M., and Koptur, S. 2008. An asian orchid, Eulophia graminea (Orchidaceae: Cymbidieae), naturalizes in Florida. Lankesteriana 8:5-14. Buendia, P., Collins, T.M. & Narasimhan, G. 2008. The role of internal node sequences and the molecular clock in the analysis of serially-sampled data. International Journal of Bioinformatics Research and Applications 4:107-121. Almodovar, S., del Colon, M.C., Malodnado, I.M., Villafane, R., Abreu, S., Melendez, I., Dominguez, C., Cuevas, W., Collins, T.M. & Lorenzo, E. 2007. HIV-1 infection of monocytes is directly related to the success of HAART. Virology 369:35-46. Freeman, B., Nico, L.G., Osentoski, M., Jelks, H.L. & Collins, T.M. 2007. Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories. Zootaxa 1484:1-38. open access link Rawlings T.A., Hayes, K.A., Cowie, R.H. & Collins, T.M. 2007. The identity, distribution, and impacts of non-native apple snails in the continental United States. BMC Evolutionary Biology 7:97 (14 pages). open access link Buendia, P., Collins T. M. & Narasimhan, G. 2006. Reconstructing ancestor-descendant lineages from serially-sampled data: A comparison study. Lecture Notes in Computer Science 3992: 807-814. Collins, T.M., Fedrigo, O. and Naylor, G.J.P. 2005. Choosing the best genes for the job: The case for stationary genes in genome-scale phylogenetics. Systematic Biology 54: 493-500. Medina, M., T. M. Collins, and Walsh P.J. 2005. Phylogeny of Sea Hares in the Aplysia clade based on mitochondrial DNA Sequence Data. Bulletin of Marine Science 76: 691-698. Rawlings, T. A., Collins, T. M., and R. Bieler. 2003. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. PNAS 100:15700-15705. Collins T.M., Trexler J., Nico L., and T. A. Rawlings. 2002. Genetic diversity in a morphologically conservative invasive taxon: Multiple introductions of swamp eels to the southeastern United States. Conservation Biology 16: 1024-1035. Rawlings, T. A., Collins T. M., and R. Bieler 2001. A major mitochondrial gene rearrangement among closely related species. Molecular Biology and Evolution v. 18, n. 8 p. 1604-1609. Lee, D. W. and Collins, T. M. 2001. Phylogenetic and ontogenetic influences on the distribution of red pigments in leaves of tropical plants. International Journal of Plant Sciences 162:5:1141-1153. Medina, M., Collins, T.M., and P.J. Walsh. 2001. MtDNA Ribosomal Gene Phylogeny of Sea Hares in the Genus Aplysia (Gastropoda, Opisthobranchia, Anaspidea): Implications for Comparative Neurobiology. Systematic Biology 50: 676-688. Lorenzo, E., Collins T. M., Fisher, E., Herrera R. J., 2001 The Use of tat and env Sequences from Human Immunodeficiency Virus 1 in Phylogenetic Epidemiological Studies. Electrophoresis 22:3 438-444. Cunningham, C. W., and Collins, T. M. 1998. Beyond area relationships: Extinction and recolonization in molecular marine biogeography. p. 297-321 in Molecular Approaches to Ecology and Evolution Birkhauser, DeSalle R. and Schierwater, B. eds. Verlag, Basel, Switzerland. Collins, T. M., Frazer, K. S., Palmer, A. R. ,Vermeij, G. J. and W. M. Brown. 1996. Evolutionary history of Northern Hemisphere Nucella: Molecules, morphology, ecology, and fossils. Evolution v.50, n. 4, p. 2287-2304. Collins, L. S. and Collins, T. M. 1996 Evolution of Life. MacMillan Encyclopedia of Earth Sciences p. 552-555 Brawn, J. D., Collins, T. M., Medina, M. and E. Bermingham. 1996. Associations between physical isolation and geographic variation within three species of Neotropical birds. Molecular Ecology v.5, n. 1, p. 33-46. Collins, T. M. 1996. in Molecular comparisons of transisthmian species pairs: Rates and patterns of evolution. in: Environmental and Biological Change in Neogene and Quaternary Tropical America. Jackson, J .B. C., Coates, A. G., and A. Budd eds. Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L., and W. M. Brown. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature v. 376 163-165. Naylor, G. J. P., Collins, T. M., and W. M. Brown. 1995. Hydrophobicity and Phylogeny. Nature v.373, p. 565-566. Collins, T. M., Kraus, F., and G. Estabrook. 1994. Compositional effects and weighting of nucleotide sequences for phylogenetic analysis. Systematic Biology. v. 43, n. 3, p. 449-459. Cunningham, C. W., and Collins, T. M. 1994. Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates. p. 406-433. in: Molecular Ecology and Evolution: Approaches and applications. B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle eds. Birkhauser Verlag, Basel, Switzerland. Collins, T. M., Wimberger, P., and G. J. P. Naylor. 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology v. 43, n.4, p. 482-496. Vermeij, G. J. and Collins, T. M. 1988. Nerita fortidentata, a new gastropod from the Neogene of Panama, with comments on the fossil record of Nerita in Tropical America. Nautilus 102 (3) p.102-105.