Alverson:Publications

Angiosperm organelle genomes

1. Sloan, D.B., A.J. Alverson, 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. doi: 10.1093/gbe/evs006.
2. Sloan, D.B., A.J. Alverson, 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 doi: 10.1371/journal.pbio.1001241 F1000
3. Alverson, A. J., 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. doi: 10.1105/tpc.111.087189 Featured article
4. Alverson, A. J., 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. doi: 10.1371/journal.pone.0016404
5. Alverson, A. J., 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. doi: 10.1093/molbev/msq029
6. Sloan, D. B., MacQueen, A. H., Alverson, A. J., 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. doi: 10.1534/genetics.110.118000
7. Sloan, D. B., Alverson, A. J., 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. doi: 10.1186/1471-2148-10-274
8. Sanchez-Puerta, M. V., Cho, Y., Mower, J. P., Alverson, A. J., 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. doi: 10.1093/molbev/msn129
9. Jansen, R. K., Kaittanis, C., Saski, C., Lee, S. B., Tomkins, J., Alverson, A. J., 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. doi: 10.1186/1471-2148-6-32
10. Jansen, R. K., Raubeson, L. A., Boore, J. L., DePamphilis, C. W., Chumley, T. W., Haberle, R. C., Wyman, S. K., Alverson, A. J., 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. doi: 10.1016/S0076-6879(05)95020-9

Diatoms

1. Alverson, A. J., 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. doi: 10.1186/1471-2148-11-125
2. Theriot, E. C., Cannone, J. J., Gutell, R. R., and Alverson, A. J. 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. Eur J Phycol 44, 277-290. doi: 10.1080/09670260902749159
3. Alverson, A. J., Jansen, R. K., and Theriot, E. C. 2009. Response to Medlin and Kaczmarska (2008). Mol Phylogenet Evol 50, 409-410. doi: 10.1016/j.ympev.2008.11.006
4. Alverson, A. J. 2008. Molecular systematics and the diatom species. Protist 159, 339-353. doi: 10.1016/j.protis.2008.04.001
5. Alverson, A. J. 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnol Oceanogr 52, 1420-1429. doi: 10.4319/lo.2007.52.4.1420
6. Alverson, A. J., 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. doi: 10.1016/j.ympev.2007.03.024
7. Alverson, A. J., Cannone, J. J., Gutell, R. R., and Theriot, E. C. 2006. The evolution of elongate shape in diatoms. J Phycol 42, 655-668. doi: 10.1111/j.1529-8817.2006.00228.x
8. Alverson, A. J., 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. doi: 10.1080/0269249X.2006.9705667
9. Thamatrakoln, K., Alverson, A. J., and Hildebrand, M. 2006. Comparative sequence analysis of diatom silicon transporters: Toward a mechanistic model of silicon transport. J Phycol 42, 822-834. doi: 10.1111/j.1529-8817.2006.00233.x
10. Alverson, A. J., and Kolnick, L. 2005. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). J Phycol 41, 1248-1257. doi: 10.1111/j.1529-8817.2005.00136.x
11. Alverson, A. J., and Theriot, E. C. 2005. Comments on recent progress toward reconstructing the diatom phylogeny. J Nanosci Nanotechno 5, 57-62. doi: 10.1166/jnn.2005.007
12. Alverson, A. J., 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. doi: 10.1023/A:1026009724797
13. Alverson, A. J., and Courtney, G. W. 2002. Temporal patterns of diatom ingestion by larval net-winged midges (Diptera : Blephariceridae : Blepharicera). Freshw Biol 47, 2087-2097. doi: 10.1046/j.1365-2427.2002.00951.x
14. Alverson, A. J., 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.