Publications
- Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance and hemiplasy
Roberts WR, Ruck EC, Downey KM, Alverson AJ
bioRxiv (2022) 10.1101/2022.08.12.503770 - The dynamic response to hypoosmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom
Downey KM, Judy KJ, Pinseel E, Alverson AJ, Lewis JA
Mol Ecol (2022) : in press 10.1111/mec.16703 - Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
Çiftçi O, Alverson AJ, van Bodegom P, Roberts WR, Mertens A, Van de Vijver B, Trobajo R, Mann DG, Pirovano W, van Eijk I, Gravendeel B
J Phycol (2022) 58(5) : 643-656 - Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
Pinseel E, Nakov T, Van den Berge K, Downey KM, Judy KJ, Kourtchenko O, Kremp A, Ruck EC, Sjöqvist C, Töpel M, Godhe A, Alverson AJ
ISME J (2022) 16 : 1776-1787 - The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics
Lambert BS, Groussman RD, Schatz MJ, Coesel SN, Durham BP, Alverson AJ, White AE, Armbrust EV
Proc Natl Acad Sci U S A (2022) 119(7) : e2100916119 - The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis
Onyshchenko A, Roberts WR, Ruck EC, Lewis JA, Alverson AJ
New Phytol (2021) - Phylogenetic analysis places Spicaticribra within Cyclotella
Downey KM, Julius ML, Theriot EC, Alverson AJ
Diatom Res (2021) 36(2) : 93-99 10.1080/0269249X.2021.1926332 - Microbial biogeography through the lens of exotic species: The recent introduction and spread of the freshwater diatom Discostella asterocostata in the United States
Alverson AJ, Chafin TK, Jones KA, Manoylov KM, Johnson H, Julius ML, Ruck EC, Theriot EC, Yeager KM, Stone JR
Biol Invasions (2021) 23 : 2191-2204 10.1007/s10530-021-02497-5 - Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332
Gargas CB, Roberts WR, Alverson AJ
Microbiol Resour Announc (2020) 9(46) : e01030-20 - Transcriptional response of osmolyte synthetic pathways and membrane transporters in a euryhaline diatom during long-term acclimation to a salinity gradient
Nakov T, Judy KJ, Downey KM, Ruck EC, Alverson AJ
J Phycol (2020) 56(6) : 1712-1728 32750159 10.1111/jpy.13061 - Fascinorbis gen. nov., a new genus of Stephanodiscaceae (Bacillariophyta) from a Late Miocene lacustrine diatomite
Stone JR, Edlund MB, Alverson AJ
Diatom Res (2020) 35(3) : 127-139 - Improved reference genome for Cyclotella cryptica CCMP332: A model for cell wall morphogenesis, salinity adaptation, and lipid production in diatoms (Bacillariophyta)
Roberts WR, Downey KM, Ruck EC, Traller JC, Alverson AJ
G3 (2020) 10(9) : 2965-2974 - Diatoms diversify and turn over faster in freshwater than marine environments
Nakov T, Beaulieu JM, Alverson AJ
Evolution (2019) 73(12) : 2497-2511 - A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta)
Onyshchenko A, Ruck EC, Nakov T, Alverson AJ
Am J Bot (2019) 106(4) : 560-572 - Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time.
Nakov T, Beaulieu JM, Alverson AJ
ISME J (2018) 12(11) : 2807-2810 PMC6194113 - Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta).
Guillory WX, Onyshchenko A, Ruck EC, Parks MB, Nakov T, Wickett NJ, Alverson AJ
Genome Biol Evol (2018) 10 : 1504–1515 - Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta).
Parks MB, Nakov T, Ruck EC, Wickett NJ, Alverson AJ
Am J Bot (2018) 105(3) : 330-347 - Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).
Nakov T, Beaulieu JM, Alverson AJ
New Phytol (2018) 219(1) : 462-473 - Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).
Parks MB, Wickett NJ, Alverson AJ
Mol Biol Evol (2018) 35(1) : 80-93 - Models with unequal transition rates favor marine origins of Cyanobacteria and photosynthetic eukaryotes.
Nakov T, Boyko JD, Alverson AJ, Beaulieu JM
Proc Natl Acad Sci USA (2017) pii : 1-2 - Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta).
Ruck EC, Linard SR, Nakov T, Theriot EC, Alverson AJ
Curr Genet (2017) 63(3) : 499-507 - Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales.
Ruck EC, Nakov T, Alverson AJ, Theriot EC
Mol Phylogenet Evol (2016) 103 : 155-171 - A phylogenetic re-definition of the diatom genus Bacterosira (Thalassiosirales, Bacillariophyta), with the transfer of Thalassiosira constricta based on morphological and molecular characters.
Park JS, Alverson AJ, Lee JH
Phytotaxa (2016) 245(1) : 1-16 - Towards a phylogenetic classification of species belonging to the diatom genus Cyclotella (Bacillariophyceae): Transfer of species formerly placed in Puncticulata, Handmannia, Pliocaenicus and Cyclotella to the genus Lindavia.
Nakov T, Guillory WX, Julius ML, Theriot EC, Alverson AJ
Phytotaxa (2015) 217(3) : 249-264 - Transcriptomic insights into the life history of bolidophytes, the sister lineage to diatoms.
Kessenich CR, Ruck EC, Schurko AM, Wickett NJ, Alverson AJ
J Phycol (2014) 50(6) : 977–983 10.1111/jpy.12222 - Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms.
Ruck EC, Nakov T, Jansen RK, Theriot EC, Alverson AJ
Genome Biol Evol (2014) 63(3) : 644-654 PMC3971590 - Timing marine–freshwater transitions in the diatom order Thalassiosirales.
Alverson AJ
Paleobiology (2014) 40(1) : 91-101 - Using phylogeny to model cell size evolution in marine and freshwater diatoms.
Nakov T, Theriot EC, Alverson AJ
Limnol Oceanogr (2014) 59(1) : 79-86 10.4319/lo.2014.59.1.0079 - Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.
Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD
Science (2013) 342(6165) : 1468-73 10.1126/science.1246275 - Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes.
Tuteja R, Saxena RK, Davila J, Shah T, Chen W, Xiao YL, Fan G, Saxena KB, Alverson AJ, Spillane C, Town C, Varshney RK
DNA Res (2013) 20(5) : 485-95 PMC3789559 - Unique role for translation initiation factor 3 in the light color regulation of photosynthetic gene expression.
Gutu A, Nesbit AD, Alverson AJ, Palmer JD, Kehoe DM
Proc Natl Acad Sci USA (2013) 110(40) : 16253-8 PMC3791720 [Available on 04/01/14] - Next-generation phenomics for the Tree of Life.
Burleigh JG, Alphonse K, Alverson AJ, Bik HM, Blank C, Cirranello AL, Cui H, Daly M, Dietterich TG, Gasparich G, Irvine J, Julius M, Kaufman S, Law E,
PLoS Curr. (2013) 5 PMC3697239 - The "fossilized" mitochondrial genome of Liriodendron tulipifera: Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate.
Richardson AO, Rice DW, Young GJ, Alverson AJ, Palmer JD
BMC Biol (2013) : 29 PMC3646698 - A multi-locus chloroplast phylogeny of Cucurbita: Evolution of the domesticated and wild species.
Zheng, Y-H, Alverson AJ, Wang Q-F, Palmer JD
J Syst Evol (2013) 51 : 326–34 10.1111/jse.12006 - Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene.
Sloan DB, Alverson AJ, Wu M, Palmer JD, Taylor DR
Genome Biol Evol (2012) 4(3) : 294-306 PMC3318436 - Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.
Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR
PLoS Biol (2012) 10(1) : e1001241 PMC3260318 - Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber.
Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD
Plant Cell (2011) 23(7) : 2499-513 PMC3226218 - The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella.
Alverson AJ, Beszteri B, Julius ML, Theriot EC
BMC Evol Biol (2011) 11 : 125 PMC3121624 - The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.
Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD
PLoS ONE (2011) 6(1) : e16404 PMC3024419 - Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia.
Sloan DB, Alverson AJ, Storchová H, Palmer JD, Taylor DR
BMC Evol Biol (2010) 10 : 274 PMC2942850 - Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: Selection vs. retroprocessing as the driving force.
Sloan DB, MacQueen AH, Alverson AJ, Palmer JD, Taylor DR
Genetics (2010) 185(4) : 1369-80 PMC2927763 - Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).
Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD
Mol Biol Evol (2010) 27(6) : 1436-48 PMC2877997 - Reply to Medlin and Kaczmarska (2008).
Alverson AJ, Jansen RK, Theriot EC
Mol Phylogenet Evol (2009) 50 : 409–410 - The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.
Theriot EC, Cannone JJ, Gutell RR, Alverson AJ
Eur J Phycol (2009) 44(3) : 277–290 PMC2835975 - Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria.
Sanchez-Puerta MV, Cho Y, Mower JP, Alverson AJ, Palmer JD
Mol Biol Evol (2008) 25(8) : 1762-77 PMC2727383 - Molecular systematics and the diatom species.
Alverson AJ
Protist (2008) 159(3) : 339-53 PMC2538954 - Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms.
Alverson AJ, Jansen RK, Theriot EC
Mol Phylogenet Evol (2007) 45(1) : 193-210 - Strong purifying selection in the silicon transporters of marine and freshwater diatoms.
Alverson AJ
Limnol Oceanogr (2007) 52(4) : 1420–1429 10.4319/lo.2007.52.4.1420 - Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: Effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.
Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H
BMC Evol Biol (2006) 6 : 32 PMC1479384 - The evolution of elongate cell shape in diatoms.
Alverson AJ, Cannone JJ, Gutell RR, Theriot EC
J Phycol (2006) 42 : 655–668 10.1111/j.1529-8817.2006.00228.x - Comparative sequence analysis of diatom silicon transporters: towards a mechanistic model of silicon transport.
Thamatrakoln K, Alverson AJ, Hildebrand M
J Phycol (2006) 42(4) : 822–834 10.1111/j.1529-8817.2006.00233.x - Methods for obtaining and analyzing whole chloroplast genome sequences.
Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR,
Meth Enzymol (2005) 395 : 348-84 - Comments on recent progress toward reconstructing the diatom phylogeny.
Alverson AJ, Theriot EC
J Nanosci Nanotechnol (2005) 5(1) : 57-62 - Laboratory sources of error for community attributes from counting algae.
Alverson AJ, Manoylov KM, Stevenson RJ
J Appl Phycol (2003) 15(5) : 357–369 - Temporal patterns of diatom ingestion by larval net-winged midges (Diptera: Blephariceridae: Blepharicera).
Alverson AJ, Courtney GW
Freshwater Biol (2002) 47(11) : 2087–2097 10.1046/j.1365-2427.2002.00951.x - Niche overlap of sympatric Blepharicera larvae (Diptera: Blephariceridae) from the southern Appalachian Mountains.
Alverson AJ, Courtney GW, Luttenton MR
J N Am Benthol Soc (2001) 20(4) : 564–581 10.2307/1468088
