Publications

Diatom abundance in the polar oceans is predicted by genome size

Roberts WR, Siepielski AM, Alverson AJ.

Looking for the oldest diatoms

Bryłka K, Richoz, S, Alverson AJ, Conley DJ.

Gene duplication, shifting selection, and dosage balance of silicon transporter proteins in marine and freshwater diatoms

Bryłka K, Pinseel E, Roberts WR, Ruck EC, Conley DJ, Alverson AJ.

Cooperative motility, force generation and mechanosensing in a foraging non-photosynthetic diatom

Zheng P, Kumadaki K, Quek C, Lim ZH, Ashenafi Y, Yip ZT, Newby J, Alverson AJ, Jie Y, Jedd G.

Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance

Roberts WR, Ruck EC, Downey KM, Pinseel E, Alverson AJ.

The dynamic response to hypo-osmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom

Downey KM, Judy KJ, Pinseel E, Alverson AJ, Lewis JA.

Uncertainties surrounding the oldest fossil record of diatoms

Bryłka K, Alverson AJ, Pickering RA, Richoz S, Conley DJ.

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.

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.

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.

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.

Phylogenetic analysis places Spicaticribra within Cyclotella

Downey KM, Julius ML, Theriot EC, Alverson AJ.

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.

Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332

Gargas CB, Roberts WR, Alverson AJ.

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.

Fascinorbis gen. nov., a new genus of Stephanodiscaceae (Bacillariophyta) from a Late Miocene lacustrine diatomite

Stone JR, Edlund MB, Alverson AJ.

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.

Diatoms diversify and turn over faster in freshwater than marine environments

Nakov T, Beaulieu JM, Alverson AJ.

A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta)

Onyshchenko A, Ruck EC, Nakov T, Alverson AJ.

Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time.

Nakov T, Beaulieu JM, Alverson AJ.

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.

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta).

Parks MB, Nakov T, Ruck EC, Wickett NJ, Alverson AJ.

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).

Nakov T, Beaulieu JM, Alverson AJ.

Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).

Parks MB, Wickett NJ, Alverson AJ.

Models with unequal transition rates favor marine origins of Cyanobacteria and photosynthetic eukaryotes.

Nakov T, Boyko JD, Alverson AJ, Beaulieu JM.

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.

Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales.

Ruck EC, Nakov T, Alverson AJ, Theriot EC.

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.

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.

Transcriptomic insights into the life history of bolidophytes, the sister lineage to diatoms.

Kessenich CR, Ruck EC, Schurko AM, Wickett NJ, Alverson AJ.

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.

Timing marine–freshwater transitions in the diatom order Thalassiosirales.

Alverson AJ.

Using phylogeny to model cell size evolution in marine and freshwater diatoms.

Nakov T, Theriot EC, Alverson AJ.

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.

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.

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.

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,.

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.

A multi-locus chloroplast phylogeny of Cucurbita: Evolution of the domesticated and wild species.

Zheng, Y-H, Alverson AJ, Wang Q-F, Palmer JD.

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.

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.

Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber.

Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD.

The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella.

Alverson AJ, Beszteri B, Julius ML, Theriot EC.

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.

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.

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.

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.

Reply to Medlin and Kaczmarska (2008).

Alverson AJ, Jansen RK, Theriot EC.

The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.

Theriot EC, Cannone JJ, Gutell RR, Alverson AJ.

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.

Molecular systematics and the diatom species.

Alverson AJ.

Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms.

Alverson AJ, Jansen RK, Theriot EC.

Strong purifying selection in the silicon transporters of marine and freshwater diatoms.

Alverson AJ.

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.

The evolution of elongate cell shape in diatoms.

Alverson AJ, Cannone JJ, Gutell RR, Theriot EC.

Comparative sequence analysis of diatom silicon transporters: towards a mechanistic model of silicon transport.

Thamatrakoln K, Alverson AJ, Hildebrand M.

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,.

Comments on recent progress toward reconstructing the diatom phylogeny.

Alverson AJ, Theriot EC.

Laboratory sources of error for community attributes from counting algae.

Alverson AJ, Manoylov KM, Stevenson RJ.

Temporal patterns of diatom ingestion by larval net-winged midges (Diptera: Blephariceridae: Blepharicera).

Alverson AJ, Courtney GW.

Niche overlap of sympatric Blepharicera larvae (Diptera: Blephariceridae) from the southern Appalachian Mountains.

Alverson AJ, Courtney GW, Luttenton MR.