Difference between revisions of "Alverson:Publications"

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==Angiosperm organelle genomes==
#Tuteja, R., R.K. Saxena, J. Davila, T. Shah, W. Chen, Y.L. Xiao, G. Fan, K.B. Saxena, <strong>A.J. Alverson</strong>, C. Spillane, C. Town, S. Mackenzie, and R. Kumar. 2013. Cytoplasmic male sterility associated chimeric ORFs identified by mitochondrial genome sequencing of four ''Cajanus'' genotypes. DNA Research ''in press''. [http://dx.doi.org/10.1093/dnares/dst025 doi: 10.1093/dnares/dst025]
# Richardson, A. O., D. W. Rice, G. J. Young, <strong>A. J. Alverson</strong>, and J. D. Palmer. 2013. The "fossilized" mitochondrial genome of ''Liriodendron tulipifera'': Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biology. 11:29. [http://dx.doi.org/10.1186/1741-7007-11-29 doi: 10.1186/1741-7007-11-29]
# Zheng, Y-H., <strong>A. J. Alverson</strong>, Q-F. Wang, and J. D. Palmer. 2013. A multi-locus chloroplast phylogeny of ''Cucurbita'': Evolution of domesticated and wild species. Journal of Systematics and Evolution 51(3), 326-334. [http://dx.doi.org/10.1111/jse.12006 doi: 10.1111/jse.12006]
# 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''. 2012. Genome Biology and Evolution 4, 294-306. [http://dx.doi.org/10.1093/gbe/evs006 doi: 10.1093/gbe/evs006]
# Sloan, D. B., <strong>A. J. Alverson</strong>, J. P. Chuckalovcak, M. Wu, D. E. McCauley, J. D. Palmer, and D. R. Taylor. 2012. 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]
# Mower, J. P., D. B. Sloan, and <strong>A. J. Alverson</strong>. 2012. Plant mitochondrial genome diversity: The genomics revolution. pp. 123–144 in Wendel, J. F., J. Greilhuber, J. Dolezel, and I. J. Leitch (eds). Plant Genomes, their Residents, and their Evolutionary Dynamics. Springer Verlag.
# <strong>Alverson, A. J.</strong>, D. W. Rice, S. Dickinson, Barry, K., and J. D. Palmer. 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]
# <strong>Alverson, A. J.</strong>, S. Zhuo, D. W. Rice, D. B. Sloan, and J. D. Palmer. 2011. The mitochondrial genome of the legume ''Vigna radiata'' and the analysis of recombination across short mitochondrial repeats. PLoS ONE 6(1): e16404.
# <strong>Alverson, A. J.</strong>, X. X. Wei, D. W. Rice, D. B. Stern, K. Barry, and J. D. Palmer. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of ''Citrullus lanatus'' and ''Cucurbita pepo'' (Cucurbitaceae). Molecular Biology and Evolution 27, 1436-1448. [http://dx.doi.org/10.1093/molbev/msq029 doi: 10.1093/molbev/msq029]
# Sloan, D. B., A. H. MacQueen, <strong>A. J. Alverson</strong>, J. D. Palmer, and D. R. Taylor. 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]
# Sloan, D. B., <strong>A. J. Alverson</strong>, H. Storchova, J. D. Palmer, and D. R. Taylor. 2010. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm ''Silene latifolia''. BMC Evolutionary Biology 10, 274. [http://dx.doi.org/10.1186/1471-2148-10-274 doi: 10.1186/1471-2148-10-274]
# Sanchez-Puerta, M. V., Y. Cho, J. P. Mower, <strong>A. J. Alverson</strong>, and J. D. Palmer. 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Molecular Biology and Evolution 25, 1762-1777. [http://dx.doi.org/10.1093/molbev/msn129 doi: 10.1093/molbev/msn129]
# Jansen, R. K., C. Kaittanis, C. Saski, S. B. Lee, J. Tomkins, <strong>A. J. Alverson</strong>, and H. Daniell. 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 Evolutionary Biology 6. [http://dx.doi.org/10.1186/1471-2148-6-32 doi: 10.1186/1471-2148-6-32]
# Jansen, R. K., L. A. Raubeson, J. L. Boore, C. W. DePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman, <strong>A. J. Alverson</strong>, R. Peery, S. J. Herman, H. M. Fourcade, J. V. Kuehl, J. R. McNeal, J. Leebens-Mack, and L. Cui. 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]
# <strong>Alverson, A. J.</strong>, B. Beszteri, M. L. Julius, and E. C. Theriot. 2011. The model marine diatom ''Thalassiosira pseudonana'' likely descended from a freshwater ancestor in the genus ''Cyclotella''. BMC Evolutionary Biology 11, 125. [http://dx.doi.org/10.1186/1471-2148-11-125 doi: 10.1186/1471-2148-11-125]
# Theriot, E. C., J. J. Cannone, R. R. Gutell, and <strong>A. J. Alverson</strong> 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. European Journal of Phycology 44, 277-290. [http://dx.doi.org/10.1080/09670260902749159 doi: 10.1080/09670260902749159]
# <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]
# <strong>Alverson, A. J.</strong>, R. K. Jansen, and E. C. Theriot. 2009. Reply to Medlin and Kaczmarska (2008). Molecular Phylogenetics and Evolution 50: 409–410.
# <strong>Alverson, A. J.</strong>, R. K. Jansen, and E. C. Theriot. 2007. Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Molecular Phylogenetics and Evolution 45, 193-210. [http://dx.doi.org/10.1016/j.ympev.2007.03.024 doi: 10.1016/j.ympev.2007.03.024]
# <strong>Alverson, A. J.</strong> 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnology and Oceanography 52, 1420-1429. [http://dx.doi.org/10.4319/lo.2007.52.4.1420 doi: 10.4319/lo.2007.52.4.1420]
# <strong>Alverson, A. J.</strong>, S-H. Kang, and E. C. Theriot. 2006. Cell wall morphology and systematic importance of ''Thalassiosira ritscheri'' (Hustedt) Hasle, with a description of ''Shionodiscus'' gen. nov. Diatom Research 21, 251-262. [http://dx.doi.org/10.1080/0269249X.2006.9705667 doi: 10.1080/0269249X.2006.9705667]
# Thamatrakoln, K., <strong>A. J. Alverson</strong>, and M. Hildebrand. 2006. Comparative sequence analysis of diatom silicon transporters: Toward a mechanistic model of silicon transport. Journal of Phycology 42, 822-834. [http://dx.doi.org/10.1111/j.1529-8817.2006.00233.x doi: 10.1111/j.1529-8817.2006.00233.x]
# <strong>Alverson, A. J.</strong>, J. J. Cannone, R. R. Gutell, and E. C. Theriot. 2006. The evolution of elongate shape in diatoms. Journal of Phycology 42, 655-668. [http://dx.doi.org/10.1111/j.1529-8817.2006.00228.x doi: 10.1111/j.1529-8817.2006.00228.x]
# <strong>Alverson, A. J.</strong>, and L. Kolnick. 2005. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus ''Skeletonema'' (Bacillariophyta). Journal of Phycology 41, 1248-1257. [http://dx.doi.org/10.1111/j.1529-8817.2005.00136.x doi: 10.1111/j.1529-8817.2005.00136.x]
# <strong>Alverson, A. J.</strong>, and E. C. Theriot. 2005. Comments on recent progress toward reconstructing the diatom phylogeny. Journal of Nanoscience and Nanotechnology 5, 57-62. [http://dx.doi.org/10.1166/jnn.2005.007 doi: 10.1166/jnn.2005.007]
# <strong>Alverson, A. J.</strong>, K. M. Manoylov, and R. J. Stevenson. 2003. Laboratory sources of error for community attributes from counting algae. Journal of Applied Phycology 15: 357–369.
# <strong>Alverson, A. J.</strong> and G. W. Courtney. 2002. Temporal patterns of diatom ingestion by larval net-winged midges (Diptera: Blephariceridae: ''Blepharicera''). Freshwater Biology 47: 2087–2097.
# <strong>Alverson, A. J.</strong>, M. R. Luttenton, and G. W. Courtney. 2001. Niche overlap of sympatric ''Blepharicera'' larvae (Diptera: Blephariceridae) from the southern Appalachian Mountains.  Journal of the North American Benthological Society 20: 564–581.

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