Alverson:Publications

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==Angiosperm organelle genomes==
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# Sloan, D.B., <strong>A.J. Alverson</strong>, M. Wu, J.D. Palmer, and D.R. Taylor. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence within the angiosperm genus ''Silene''. Genome Biology and Evolution 4, 294-306. [http://dx.doi.org/10.1093/gbe/evs006 doi: 10.1093/gbe/evs006].
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# Sloan, D.B., <strong>A.J. Alverson</strong>, J.P. Chuckalovcak, M. Wu, D.E. McCauley, J.D. Palmer, and D.R. Taylor. Rapid evolution of enormous, multichromosomal genomes in flowering plants. PLoS Biology 10(1): e1001241 [http://dx.doi.org/10.1371/journal.pbio.1001241 doi: 10.1371/journal.pbio.1001241] [http://f1000.com/13755957 F1000]
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# <strong>Alverson, A. J.</strong>, Rice, D. W., Dickinson, S., Barry, K., and Palmer, J. D. 2011. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber (''Cucumis sativus''). The Plant Cell 23, 2499-2513. [http://dx.doi.org/10.1105/tpc.111.087189 doi: 10.1105/tpc.111.087189]  [http://dx.doi.org/10.1105/tpc.111.230711 Featured article]
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# <strong>Alverson, A. J.</strong>, Zhuo, S., Rice, D. W., Sloan, D. B., and Palmer, J. D. 2011. The mitochondrial genome of the legume ''Vigna radiata'' and the analysis of recombination across short mitochondrial repeats. PLoS ONE 6, e16404. [http://dx.doi.org/10.1371/journal.pone.0016404 doi: 10.1371/journal.pone.0016404]
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# <strong>Alverson, A. J.</strong>, Wei, X. X., Rice, D. W., Stern, D. B., Barry, K., and Palmer, J. D. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of ''Citrullus lanatus'' and ''Cucurbita pepo'' (Cucurbitaceae). Mol Biol Evol 27, 1436-1448. [http://dx.doi.org/10.1093/molbev/msq029 doi: 10.1093/molbev/msq029]
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# Sloan, D. B., MacQueen, A. H., <strong>Alverson, A. J.</strong>, Palmer, J. D., and Taylor, D. R. 2010. Extensive loss of RNA editing sites in rapidly evolving ''Silene'' mitochondrial genomes: selection vs. retroprocessing as the driving force. Genetics 185, 1369-1380. [http://dx.doi.org/10.1534/genetics.110.118000 doi: 10.1534/genetics.110.118000]
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# Sloan, D. B., <strong>Alverson, A. J.</strong>, Storchova, H., Palmer, J. D., and Taylor, D. R. 2010. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm ''Silene latifolia''. BMC Evol Biol 10, 274. [http://dx.doi.org/10.1186/1471-2148-10-274 doi: 10.1186/1471-2148-10-274]
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# Sanchez-Puerta, M. V., Cho, Y., Mower, J. P., <strong>Alverson, A. J.</strong>, and Palmer, J. D. 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Mol Biol Evol 25, 1762-1777. [http://dx.doi.org/10.1093/molbev/msn129 doi: 10.1093/molbev/msn129]
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# Jansen, R. K., Kaittanis, C., Saski, C., Lee, S. B., Tomkins, J., <strong>Alverson, A. J.</strong>, and Daniell, H. 2006. Phylogenetic analyses of ''Vitis'' (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6. [http://dx.doi.org/10.1186/1471-2148-6-32 doi: 10.1186/1471-2148-6-32]
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# Jansen, R. K., Raubeson, L. A., Boore, J. L., DePamphilis, C. W., Chumley, T. W., Haberle, R. C., Wyman, S. K., <strong>Alverson, A. J.</strong>, Peery, R., Herman, S. J., Fourcade, H. M., Kuehl, J. V., McNeal, J. R., Leebens-Mack, J., and Cui, L. 2005. Methods for obtaining and analyzing whole chloroplast genome sequences. In Molecular Evolution: Producing the Biochemical Data, Part B, pp. 348-384. [http://dx.doi.org/10.1016/S0076-6879(05)95020-9 doi: 10.1016/S0076-6879(05)95020-9]
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==Diatoms==
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# <strong>Alverson, A. J.</strong>, Beszteri, B., Julius, M. L., and Theriot, E. C. 2011. The model marine diatom ''Thalassiosira pseudonana'' likely descended from a freshwater ancestor in the genus ''Cyclotella''. BMC Evol Biol 11, 125. [http://dx.doi.org/10.1186/1471-2148-11-125 doi: 10.1186/1471-2148-11-125]
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# Theriot, E. C., Cannone, J. J., Gutell, R. R., and <strong>Alverson, A. J.</strong> 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. Eur J Phycol 44, 277-290. [http://dx.doi.org/10.1080/09670260902749159 doi: 10.1080/09670260902749159]
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# <strong>Alverson, A. J.</strong>, Jansen, R. K., and Theriot, E. C. 2009. Response to Medlin and Kaczmarska (2008). Mol Phylogenet Evol 50, 409-410. [http://dx.doi.org/10.1016/j.ympev.2008.11.006 doi: 10.1016/j.ympev.2008.11.006]
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# <strong>Alverson, A. J.</strong> 2008. Molecular systematics and the diatom species. Protist 159, 339-353. [http://dx.doi.org/10.1016/j.protis.2008.04.001 doi: 10.1016/j.protis.2008.04.001]
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# <strong>Alverson, A. J.</strong> 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnol Oceanogr 52, 1420-1429. [http://dx.doi.org/10.4319/lo.2007.52.4.1420 doi: 10.4319/lo.2007.52.4.1420]
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# <strong>Alverson, A. J.</strong>, Jansen, R. K., and Theriot, E. C. 2007. Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Mol Phylogenet Evol 45, 193-210. [http://dx.doi.org/10.1016/j.ympev.2007.03.024 doi: 10.1016/j.ympev.2007.03.024]
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# <strong>Alverson, A. J.</strong>, Cannone, J. J., Gutell, R. R., and Theriot, E. C. 2006. The evolution of elongate shape in diatoms. J Phycol 42, 655-668. [http://dx.doi.org/10.1111/j.1529-8817.2006.00228.x doi: 10.1111/j.1529-8817.2006.00228.x]
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# <strong>Alverson, A. J.</strong>, Kang, S.-H., and Theriot, E. C. 2006. Cell wall morphology and systematic importance of ''Thalassiosira ritscheri'' (Hustedt) Hasle, with a description of ''Shionodiscus'' gen. nov. Diatom Res 21, 251-262. [http://dx.doi.org/10.1080/0269249X.2006.9705667 doi: 10.1080/0269249X.2006.9705667]
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# Thamatrakoln, K., <strong>Alverson, A. J.</strong>, and Hildebrand, M. 2006. Comparative sequence analysis of diatom silicon transporters: Toward a mechanistic model of silicon transport. J Phycol 42, 822-834. [http://dx.doi.org/10.1111/j.1529-8817.2006.00233.x doi: 10.1111/j.1529-8817.2006.00233.x]
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# <strong>Alverson, A. J.</strong>, and Kolnick, L. 2005. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus ''Skeletonema'' (Bacillariophyta). J Phycol 41, 1248-1257. [http://dx.doi.org/10.1111/j.1529-8817.2005.00136.x doi: 10.1111/j.1529-8817.2005.00136.x]
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# <strong>Alverson, A. J.</strong>, and Theriot, E. C. 2005. Comments on recent progress toward reconstructing the diatom phylogeny. J Nanosci Nanotechno 5, 57-62. [http://dx.doi.org/10.1166/jnn.2005.007 doi: 10.1166/jnn.2005.007]
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# <strong>Alverson, A. J.</strong>, Manoylov, K. M., and Stevenson, R. J. 2003. Laboratory sources of error for algal community attributes during sample preparation and counting. J Appl Phycol 15. [http://dx.doi.org/10.1023/A:1026009724797 doi: 10.1023/A:1026009724797]
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# <strong>Alverson, A. J.</strong>, and Courtney, G. W. 2002. Temporal patterns of diatom ingestion by larval net-winged midges (Diptera : Blephariceridae : Blepharicera). Freshw Biol 47, 2087-2097. [http://dx.doi.org/10.1046/j.1365-2427.2002.00951.x doi: 10.1046/j.1365-2427.2002.00951.x]
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# <strong>Alverson, A. J.</strong>, and Courtney, G. W. 2001. Niche overlap of sympatric Blepharicera larvae (Diptera : Blephariceridae) from the southern Appalachian Mountains. J North Am Benthol Soc 20, 564-581.
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