Publications

* equal contribution, § undergraduate coauthor
Brief summary for selected papers is in bold below the reference

Recent

2025

  • Alverson AJ, Roberts WR, Ruck EC, Nakov T, Ashworth MP, Bryłka K, Downey KM, Kociolek JP, Parks M, Pinseel E. Phylogenomics reveals the slow-burning fuse of diatom evolution. Proceedings of the National Academy of Sciences 122(22): e2500153122, 2025.

  • Pinseel E, Ruck EC, Nakov T, Jonsson PR, Kourtchenko O, Kremp A, Pinder MIM, Roberts WR, Sjöqvist C, Töpel M. Genome‐Wide Adaptation to a Complex Environmental Gradient in a Keystone Phytoplankton Species. Molecular Ecology, e17817, 2025.

2023

  • Pinseel E, Ruck EC, Nakov T, Jonsson PR, Kourtchenko O, Kremp A, et. al Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes. bioRxiv, 2023.09. 22.559080

2022

  • Pinseel E, Nakov T, Van den Berge K, Downey KM, Judy KJ, Kourtchenko O, Kremp A, Ruck EC, Sjöqvist C, Töpel M et al. Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. The ISME Journal 16: 1776-1787

2021

  • Alverson AJ, Chafin TK, Jones KA, Manoylov KM, Johnson H, Julius ML, Nakov T, Ruck EC, Therior EC, et al. Microbial biogeography through the lens of exotic species: the recent introduction and spread of the freshwater diatom Discostella asterocostata in the United States. Biological Invasions, 23: 2191-2204

  • Hamlin JAP, Nakov T, Williams-Newkirk A. tinselR–an R Shiny Application for Annotating Phylogenetic Trees. Microbiology Resource Announcements 10, e00227-21

2020

  • Nakov T, Judy KJ, Downey KM, Ruck EC and Alverson AJ. Transcriptional response of osmolyte synthetic pathways and membrane transporters in a euryhaline diatom during long-term acclimation to a salinity gradient. Journal of Phycology 56: 1712-1728

  • Ozersky T, Nakov T, Hampton S, Rodenhouse NL, Shchapov K, Woo KH, … and Timofeev MA. Hot and sick: Impacts of warming and oomycete parasite infection on endemic dominant zooplankter of Lake Baikal. Limnology and Oceanography 65: 2772-2786

2019

  • Nakov T, Beaulieu JM, and Alverson, AJ. Diatoms diversify and turn over faster in freshwater than marine environments. Evolution, 73: 2497-2511.

Many clades that span the marine-freshwater divide are disproportionately more diverse in the younger and short-lived freshwater environments than they are in the marine realm, which covers most of the biosphere. How these patterns have been shaped is an open question. Using a novel set of diversification models that control for the effects of interacting factors and unobserved variables, we show that freshwater diatoms both speciate and go extinct faster than marine clades. We also found that colonizations of alternate environments have had different probabilities across the tree leading to communities (e.g., marine vs. freshwater plankton) with vastly different phylogenetic and functional diversities.

  • Onyshchenko A, Ruck EC, Nakov T, and Alverson AJ. A single loss of photosynthesis in diatoms. American Journal of Botany, 106: 560– 572.

2018

  • Nakov T, Beaulieu JM and Alverson AJ. Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time. International Society of Microbial Ecology Journal (ISME-J), 2018 Jul 16:1

Metabarcoding offers unprecedented insights into microbial diversity, however, most analyses assume that taxonomic ranks are biologically meaningful and that identically ranked groups are comparable. In this study, using a Tara Oceans diatom metabarcode dataset, we illustrate the limits of this approach and the advantages of using a phylogenetic framework to make inferences about microbial ecology, diversity, and biogeography.

  • Guillori WX, Onyschenko A, Ruck EC, Parks M, Nakov T, Wickett N and Alverson AJ. Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta). Genome Biology and Evolution, 10: 1504–1515

  • Parks M, Nakov T, Ruck EC, Wickett NJ and Alverson AJ. Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). American Journal of Botany, 105: 330–347

The first phylogenomic study to assess polyploidy in diatoms. Our results, based on an array of methods for detecting whole genome duplications (WGD), suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that harbors substantial genomic diversity.

  • Nakov T, Beaulieu JM and Alverson AJ. Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta). New Phytologist, 219: 462–473

We constructed and time‐calibrated the largest-to-date diatom phylogeny and used it to estimate, for the first time, diversification rates across lineages and through time. We found that a clade with vegetative cells capable of active movement diversified much faster than other diatoms. We proposed that the evolution of motility facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence and accelerated diversification.

  • Mejdandžić M, Bosak S, Nakov T, Ruck EC, Orlić S, Gligora Udovič M, Peharec Štefanić P, Špoljarić I, Mršić G and Z Ljubešić. Phylogenetic and taxonomic diversity of the canal–raphe diatom genus Entomoneis (Bacillariophyta) in marine plankton: six new species from the Adriatic Sea. Journal of Phycology, 54: 275–298

Earlier

2017

  • Nakov T, Boyko JD, Alverson AJ and Beaulieu JM. Models with unequal transition rates favor marine origins for cyanobacteria and photosynthetic eukaryotes. Proceedings of the National Academy of Sciences USA, 114: 13055–13056.

  • Ruck EC, Linard SR, Nakov T, Theriot EC and Alverson AJ. Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom Toxarium undulatum (Bacillariophyta). Current Genetics 63: 499–507.

  • Chust G, Vogt M, Benedetti F, Nakov T, Villéger S, Aubert A, Vallina SM, Righetti D, Not F, Biard T, Bittner L, …, Ayata S-D. Mare incognitum: A glimpse into future plankton diversity and ecology research. Frontiers in Marine Science 4 (122).

2016

  • Ruck EC and Nakov T. Nomenclatural transfers associated with the phylogenetic reclassification of the Surirellales and Rhopalodiales. Notulae algarum 1–4.

  • Ruck EC, Nakov T, Alverson AJ and Theriot EC. Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhpalodiales. Molecular Phylogenetics and Evolution 103: 155–171.

2015

  • Nakov T, Guillory WX§, Julius ML, Theriot EC and Alverson AJ. Towards a phylogenetic classification of species belonging to the diatom genus Cyclotella (Bacillariophycae): Transfer of species formerly placed in Puncticulata, Handmannia, Pliocaenicus and Cyclotella to the genus Lindavia. Phytotaxa 217: 249–264.

  • Theriot EC, Ashworth MP, Nakov T, Ruck EC and Jansen RK. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution 89: 28–36.

2014

  • Nakov T, Ashworth MP and Theriot EC. Comparative analysis of the interaction between habitat and growth form in diatoms. International Society of Microbial Ecology Journal (ISME-J) 9: 246–255.

  • Nakov T, Ruck EC, Galachyants Y, Spaulding SA and Theriot EC. Molecular phylogeny of the Cymbellales (Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites. Phycologia 53: 359–373.

  • Ruck EC, Nakov T, Jansen RK, Theriot EC and Alverson AJ. Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms. Genome Biology and Evolution 6: 644–654.

  • Jovanovska E§, Buczkó K, Nakov T and Levkov Z. Diploneis transylvanica (Bacillariophyceae), a new diatom species from a Neogene fossil deposit in Romania. Nova Hedwigia 98: 3–4.

2013

  • Nakov T, Theriot EC and Alverson AJ. Using phylogeny to model the evolution of cell size in marine and freshwater diatoms. Limnology and Oceanography 59: 79–86.

Virtually any ecological and physiological feature of phytoplankton is related to cell size, so the evolution of cell size is central to phytoplankton biology. Here, for the first time, we investigated phytoplankton cell size evolution in a phylogenetic framework revealing an adaptive divergence between marine and freshwater lineages related to differences in nutrient regimes and sinking rates between habitats with different salinities.

  • Ashworth MP, Nakov T and Theriot EC. Revisiting Ross and Sims (1971): Towards a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae). Journal of Phycology 6: 1207–1222.

  • Jovanovska E§, Buczkó K, Ognjanova-Rumenova N, Nakov T and Levkov Z. Identity and typification of Diploneis ostracodarum, Diploneis budayana, and Diploneis praeclara (Bacillariophyta). Phytotaxa 137: 15–26.

  • Jovanovska E§, Nakov T and Levkov Z. Observations of the genus Diploneis (Ehrenberg) Cleve from Lake Ohrid, Macedonia. Diatom Research 28: 237–262.

2010

  • Theriot EC, Ashworth MP, Ruck EC, Nakov T and Jansen RK. A preliminary multigene phylogeny of the diatoms (Bacillariophyta): challenges for future research. Plant Ecology and Evolution 143: 278–296.

2009

  • Pavlov A§, Nakov T, Levkov Z, Furey P, Lowe R and Ector L. Luticola grupcei (Bacillariophyceae)–a new freshwater diatom from Mountain Baba (Macedonia) and Great Smoky Mountains National Park (USA): comparison with the type material of L. goeppertiana (Bleisch) D.G. Mann. Nova Hedwigia 89: 147–164.

2008

  • Levkov Z and Nakov T. Rhoicosphenia tenuis, a new diatom species from Lake Ohrid. Diatom Research 23: 377–388.

  • Levkov Z, Edlund MB and Nakov T. Identity and typification of Navicula hasta (Bacillariophyceae). Phycological Research 56: 46–57.

2007

  • Levkov Z, Blanco S, Krstic S, Nakov T and Ector L. Ecology of benthic diatoms from Lake Macro Prespa (Macedonia). Algological Studies 124: 71–83.

2006

  • Edlund MB, Brant LA, Levkov Z, and Nakov T. An emended description of Decussata (Patrick) Lange-Bertalot and Metzeltin that includes protoplast organization and detailed valve and cingulum ultrastructure. Diatom Research 21: 269–280.

2005

  • Levkov Z, Krstic S, Nakov T and Melovski L. Diatom assemblages on Shara and Nidze mountains, Macedonia. Nova Hedwigia 81: 501–538.