Alverson:Publications

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==Angiosperm organelle genomes==
==Angiosperm organelle genomes==
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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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# 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 (in press) [http://dx.doi.org/10.1093/gbe/evs006 doi: 10.1093/gbe/evs006].
+
#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]
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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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# 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]
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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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# 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]
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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., <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., 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]
+
# 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]
-
# 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]
+
# 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.
-
# 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]
+
# <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]
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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]
+
# <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.
-
# 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]
+
# <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]
 +
 
==Diatoms==
==Diatoms==
-
# <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]
+
# <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., 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]
+
# 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>, 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]
+
# <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> 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> 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]
+
# <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>, 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]
+
# <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>, 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]
+
# <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>, 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]
+
# <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>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]
+
# 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]
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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]
+
# <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]
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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>, 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]
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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 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]
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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>, 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.
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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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# <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.

Revision as of 10:58, 24 July 2013

The Alverson Lab

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Angiosperm organelle genomes

  1. Tuteja, R., R.K. Saxena, J. Davila, T. Shah, W. Chen, Y.L. Xiao, G. Fan, K.B. Saxena, A.J. Alverson, 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. doi: 10.1093/dnares/dst025
  2. Richardson, A. O., D. W. Rice, G. J. Young, A. J. Alverson, 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. doi: 10.1186/1741-7007-11-29
  3. Zheng, Y-H., A. J. Alverson, 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. doi: 10.1111/jse.12006
  4. 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. 2012. Genome Biology and Evolution 4, 294-306. doi: 10.1093/gbe/evs006
  5. Sloan, D. B., A. J. Alverson, 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 doi: 10.1371/journal.pbio.1001241 F1000
  6. Mower, J. P., D. B. Sloan, and A. J. Alverson. 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.
  7. Alverson, A. J., 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. doi: 10.1105/tpc.111.087189 Featured article
  8. Alverson, A. J., 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.
  9. Alverson, A. J., 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. doi: 10.1093/molbev/msq029
  10. Sloan, D. B., A. H. MacQueen, A. J. Alverson, 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. doi: 10.1534/genetics.110.118000
  11. Sloan, D. B., A. J. Alverson, 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. doi: 10.1186/1471-2148-10-274
  12. Sanchez-Puerta, M. V., Y. Cho, J. P. Mower, A. J. Alverson, 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. doi: 10.1093/molbev/msn129
  13. Jansen, R. K., C. Kaittanis, C. Saski, S. B. Lee, J. Tomkins, A. J. Alverson, 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. doi: 10.1186/1471-2148-6-32
  14. Jansen, R. K., L. A. Raubeson, J. L. Boore, C. W. DePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman, A. J. Alverson, 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. doi: 10.1016/S0076-6879(05)95020-9


Diatoms

  1. Alverson, A. J., 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. doi: 10.1186/1471-2148-11-125
  2. Theriot, E. C., J. J. Cannone, R. R. Gutell, and A. J. Alverson 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. European Journal of Phycology 44, 277-290. doi: 10.1080/09670260902749159
  3. Alverson, A. J. 2008. Molecular systematics and the diatom species. Protist 159, 339-353. doi: 10.1016/j.protis.2008.04.001
  4. Alverson, A. J., R. K. Jansen, and E. C. Theriot. 2009. Reply to Medlin and Kaczmarska (2008). Molecular Phylogenetics and Evolution 50: 409–410.
  5. Alverson, A. J., 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. doi: 10.1016/j.ympev.2007.03.024
  6. Alverson, A. J. 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnology and Oceanography 52, 1420-1429. doi: 10.4319/lo.2007.52.4.1420
  7. Alverson, A. J., 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. doi: 10.1080/0269249X.2006.9705667
  8. Thamatrakoln, K., A. J. Alverson, and M. Hildebrand. 2006. Comparative sequence analysis of diatom silicon transporters: Toward a mechanistic model of silicon transport. Journal of Phycology 42, 822-834. doi: 10.1111/j.1529-8817.2006.00233.x
  9. Alverson, A. J., J. J. Cannone, R. R. Gutell, and E. C. Theriot. 2006. The evolution of elongate shape in diatoms. Journal of Phycology 42, 655-668. doi: 10.1111/j.1529-8817.2006.00228.x
  10. Alverson, A. J., 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. doi: 10.1111/j.1529-8817.2005.00136.x
  11. Alverson, A. J., and E. C. Theriot. 2005. Comments on recent progress toward reconstructing the diatom phylogeny. Journal of Nanoscience and Nanotechnology 5, 57-62. doi: 10.1166/jnn.2005.007
  12. Alverson, A. J., 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.
  13. Alverson, A. J. and G. W. Courtney. 2002. Temporal patterns of diatom ingestion by larval net-winged midges (Diptera: Blephariceridae: Blepharicera). Freshwater Biology 47: 2087–2097.
  14. Alverson, A. J., 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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