thomarc

• Maurstad, Marius Filomeno; Kusy, Dominik; Undheim, Eivind Andreas Baste; Jakobsen, Kjetill Sigurd; Böhne, Astrid & Monteiro, Rita [Show all 20 contributors for this article] (2026). ERGA-BGE chromosome-level genome assembly of the giant stream lacewing  Osmylus fulvicephalus (Scopoli, 1763). Open Research Europe. 6. doi: 10.12688/openreseurope.23457.3. Full text in Research Archive Show summary

  The giant stream lacewing, Osmylus fulvicephalus (Scopoli, 1763), is a widespread European species belonging to the insect order Neuroptera. Its cryptic larvae are predators found at the banks of streams and smaller rivers where they use their piercing, lance-shaped stylets to inject venom into their arthropod prey. Here, we present the reference genome of the giant stream lacewing as a crucial resource for uncovering the genetic basis of venom evolution in Neuroptera. The chromosome-level genome encompasses 674.7 Mb and is composed of 60 contigs and 24 scaffolds where 99.2% of the assembly is distributed among the 6 contiguous chromosomal pseudomolecules and two sex chromosomes (X and Y). Contig and scaffold N50 have a value of 51.5 Mb and 116.2 Mb, respectively. This reference genome is the first genomic resource from the family of lance lacewings, providing valuable data for clarifying the phylogenetic placement of the family Osmylidae within Neuroptera.

• Taboada, Sergi; Gracia-Sancha, Carlota; Galià-Camps, Carles; Böhne, Astrid; Monteiro, Rita & Marcussen, Thomas [Show all 18 contributors for this article] (2026). ERGA-BGE reference genome of Xylophaga dorsalis - a common deep-sea wood-boring bivalve with Atlantic-Mediterranean distribution. Open Research Europe. 6. doi: 10.12688/openreseurope.22692.2. Full text in Research Archive Show summary

  Xylophaga dorsalis is a common Atlantic-Mediterranean mollusc that plays a crucial role in deep-sea habitats, where it digests wood that reaches the seabed through a unique symbiosis with specialised bacteria. The reference genome of X. dorsalis thus offers a crucial resource for uncovering the genetic basis of the species adaptability to wood bore in deep-water ecosystems. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules (superscaffolds) and 1 mitochondrial genome. This chromosome-level assembly encompasses 0.451 Gb, composed of 1,259 contigs and 320 scaffolds, with contig and scaffold N50 values of 1.30 Mb and 25.4 Mb, respectively. The genome assembly encodes 19,441 protein-coding genes (34,405 transcripts) and 6,716 non-coding genes.

• Manzano-Marín, Alejandro; Böhne, Astrid; Monteiro, Rita; Marcussen, Thomas; Struck, Torsten H. & Oomen, Rebekah Alice [Show all 15 contributors for this article] (2026). ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech. Open Research Europe. 5. doi: 10.12688/openreseurope.21672.2. Full text in Research Archive Show summary

  Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana . Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.

• Lavergne, Sébastien; Rosa, Zoé; Peng, Chuan; Monteiro, Rita; Böhne, Astrid & Marcussen, Thomas [Show all 20 contributors for this article] (2026). ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe. Open Research Europe. 5. doi: 10.12688/openreseurope.21922.1. Full text in Research Archive Show summary

  The reference genome of Androsace saussurei (Ericales: Primulaceae: Primuloideae) provides a valuable resource for understanding the mechanisms of plant adaptations to the highest altitudes where flowering plants can thrive and the speciation mechanisms of plants dwelling on high alpine sky islands. The entirety of the genome sequence was assembled into 20 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 413 Mb, composed of 253 contigs and 101 scaffolds, with contig and scaffold N50 values of 4.95 Mb and 21.2 Mb, respectively.

• Tomasello, Salvatore; Manzo, Eleonora; Monteiro, Rita; Böhne, Astrid; Marcussen, Thomas & Struck, Torsten H [Show all 19 contributors for this article] (2026). ERGA-BGE genome of Xanthium orientale subsp. italicum (Moretti) Greuter. A plant of American origin, now widespread and, in some cases, invasive in Europe. Open Research Europe. 5, p. 367–367. doi: 10.12688/openreseurope.21891.1. Full text in Research Archive Show summary

  The Xanthium orientale subsp. italicum (Asterales: Asteraceae: Asteroideae) reference genome offers a valuable resource for understanding the genetic basis of invasiveness and fitness differences among congeneric species. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.26 Gb, composed of 46 contigs and 32 scaffolds, with contig and scaffold N50 values of 98.8 Mb and 124 Mb, respectively.

• Aguado-Ramsay, Pablo; Lara, Francisco; Draper, Isabel; Conejero, Maria; Böhne, Astrid & Monteiro, Rita [Show all 18 contributors for this article] (2026). ERGA-BGE reference genome of Lewinskya acuminata, a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia. Open Research Europe. 5. doi: 10.12688/openreseurope.21670.1. Full text in Research Archive Show summary

  The reference genome of Lewinskya acuminata (H. Philib.) F. Lara, Garilleti & Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the Orthotrichaceae and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, 1 mitochondrial genome, and 2 plastid genomes. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.

• Faria, Rui; Vilela, Rocío Nieto; Lima, Fernando P; Monteiro, Rita; Böhne, Astrid & Marcussen, Thomas [Show all 18 contributors for this article] (2026). ERGA-BGE genome of Patella rustica Linnaeus, 1758: a resource to investigate responses to global warming in the intertidal. Open Research Europe. 5. doi: 10.12688/openreseurope.21608.2. Full text in Research Archive Show summary

  The reference genome of Patella rustica Linnaeus, 1758 will offer a unique opportunity to understand how intertidal organisms respond to the effects of global warming, contributing to improve our predictions about the impact of climate change on the maintenance and diversification of marine biodiversity. A total of 9 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 719 Mb, composed of 157 contigs and 24 scaffolds, with contig and scaffold N50 values of 8.52 Mb and 83.6 Mb, respectively.

• Hausdorf, Bernhard; Tapia, Elicio; Monteiro, Rita; Böhne, Astrid; Marcussen, Thomas & Struck, Torsten H [Show all 10 contributors for this article] (2026). ERGA-BGE genome of Anisus vorticulus (Troschel, 1834): the Lesser Ramshorn Snail, an endangered freshwater snail protected under the EU's Habitats and Species Directive. Open Research Europe. 5. doi: 10.12688/openreseurope.20499.1. Full text in Research Archive Show summary

  We have generated a high-quality reference genome for Anisus vorticulus to support monitoring of the genetic diversity of populations of this declining freshwater species. The chromosome-level genome assembly encompasses 1.04 Gb, composed of 835 contigs and 77 scaffolds, with contig and scaffold N50 values of 2.35 Mb and 59.2 Mb, respectively. The genome was assembled into 18 chromosomal pseudomolecules.

• Lopes, Ricardo Jorge; Böhne, Astrid; Marcussen, Thomas; Oomen, Rebekah Alice; Struck, Torsten H & Aguilera, Laura [Show all 12 contributors for this article] (2026). ERGA-BGE reference genome of the Azores Bullfinch - Pyrrhula murina Godman, 1866: an IUCN Vulnerable Species endemic to a single island in the Azores Archipelago (Portugal). Open Research Europe. 5, p. 1–16. doi: 10.12688/openreseurope.20666.3. Full text in Research Archive Show summary

  The reference genome of Pyrrhula murina’s reference genome will substantially enhance the current monitoring of genetic diversity and population viability and will allow us to understand the effective population size trends throughout time and recent bottlenecks and population expansions. A total of 42 contiguous chromosomal pseudomolecules were assembled from the genome sequence, using ONT, HI-C and Illumina data. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 65 Mb and 76 Mb, respectively.

• Aurelle, Didier; Guillemain, Dorian; Zuberer, Frédéric; Malengros, Denys; Böhne, Astrid & Monteiro, Rita [Show all 19 contributors for this article] (2025). ERGA-BGE reference genome of Eunicella cavolini, an IUCN Near Threatened Gorgonian of the Mediterranean Sea. Open Research Europe. 5. doi: 10.12688/openreseurope.21514.1. Full text in Research Archive Show summary

  The Eunicella cavolini reference genome provides an important resource to study the adaptation of this species to different environments and anthropic pressures. This species is impacted by human activities, including climate change, and this reference genome will be useful to study the genomic evolution of this species. The entirety of the genome sequence was assembled into 17 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.49 Gb, composed of 159 contigs and 46 scaffolds, with contig and scaffold N50 values of 7.7 Mb and 51.1 Mb, respectively.

• Vila, Marta; Marí-Mena, Neus; Vila, Roger; Riesgo, Ana; García-Souto, Daniel & Lopez-Vaamonde, Carlos [Show all 20 contributors for this article] (2025). ERGA-BGE genome of the Spanish moon moth Actias isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive. Open Research Europe. 5. doi: 10.12688/openreseurope.20658.2. Full text in Research Archive Show summary

  High-quality reference genomes are critical resources for understanding biodiversity and supporting conservation efforts. We present the chromosome-level assembly of the Spanish moon moth, Actias isabellae (Graells, 1849), a nocturnal lepidopteran protected under the EU Habitats Directive. The assembly spans 0.56 Gb across 31 pseudomolecules, including the Z chromosome, with a contig N50 of 18.9 Mb and a scaffold N50 of 20.4 Mb. The mitochondrial genome was also assembled into a 15,247 bp circular sequence. Annotation identified 11,805 protein-coding genes and 2,238 non-coding genes, with a BUSCO completeness of over 94%. Notably, no W chromosome was detected, suggesting a ZZ/Z0 sex determination system. This reference genome provides an essential foundation for studying sex chromosome evolution in Lepidoptera and enables advanced population genomics monitoring of this protected species. More broadly, it contributes to ongoing efforts within the European Reference Genome Atlas and the Earth BioGenome Project to harness genomics for biodiversity conservation.

• Żabicka, Justyna; Migdałek, Grzegorz; Marcussen, Thomas; Sliwińska, Elwira; Słomka, Aneta & Mackiewicz, Leszek [Show all 7 contributors for this article] (2025). Genetic diversity and phylogeography of the circumboreal peatland violets (Viola epipsila-V. palustris complex, Violaceae) as inferred from non-coding nuclear and chloroplast DNA regions. Taxon. ISSN 0040-0262. 74(2), p. 307–336. doi: 10.1002/tax.13299. Full text in Research Archive
• Scoppola, Anna; Cardoni, Simone; Marcussen, Thomas & Simeone, Marco Cosimo (2022). Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect. Bracteolatae (Viola Sect. Melanium, Violaceae) in Italy: Insights from 5S-IGS High-Throughput Sequencing and Plastid DNA Variation. Plants. 11(10). doi: 10.3390/plants11101294. Full text in Research Archive Show summary

  Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual pansies occur in Italy, four of which are morphologically very similar and belong to the informal ‘V. tricolor species complex’: V. arvensis (2n = 34), V. hymettia (2n = 16), V. kitaibeliana (2n = 16), and V. tricolor (2n = 26). Their field recognition is difficult and reflects a long-debated taxonomy often resulting in doubtful records in field inventories and across European herbaria. The current lack of comprehensive intra- and interspecific comparative studies and a relative scarcity of appropriate genetic markers coupled with unambiguous cytological descriptions are hindering clear taxa circumscription and phylogenetic inferences within this group. In this work, we tested DNA sequence variation of three highly variable plastid markers and High-Throughput Sequencing (HTS) of the nuclear ribosomal 5S-IGS region in an attempt to decipher species identity within the V. tricolor species complex and to obtain an insight on their genome organization and evolution. Our results document the close relationships within this species group, a reliable molecular resolution for V. tricolor, and the common ancestry of V. arvensis and the poorly differentiated V. kitaibeliana and V. hymettia. Evidence of an important inter-population geographical divergence was recorded in V. tricolor and V. arvensis, pointing at the existence of different eco-cytotypes within these entities. Overall diversity patterns and the occurrence of two to four differently diverging 5S-IGS lineages are discussed in the light of the acknowledged taxonomy and genomic evolutive trajectories of sect. Melanium.

• Marcussen, Thomas; Ballard, Harvey E.; Danihelka, Jiří; Flores, Ana R.; Nicola, Marcela V. & Watson, John M. (2022). A Revised Phylogenetic Classification for Viola (Violaceae). Plants. 11(17). doi: 10.3390/plants11172224. Full text in Research Archive Show summary

  The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

• Ammarellou, Ali; Żabicka, Justyna; Słomka, Aneta; Bohdanowicz, Jerzy; Marcussen, Thomas & Kuta, Elżbieta (2021). Seasonal and simultaneous cleistogamy in rostrate violets (Viola, subsect. rostratae, violaceae). Plants. 10(10), p. 1–13. doi: 10.3390/plants10102147. Full text in Research Archive Show summary

  The special mixed reproductive system, i.e., the ability of an individual plant to develop both open, chasmogamous (CH) flowers adapted to cross-pollination and closed, cleistogamous (CL) flowers with obligate self-pollinating, is a common phenomenon in Viola L. In most sections of Northern Hemisphere violets, cleistogamy is seasonal, and CH and CL flowers develop sequentially in the season. Non-seasonal cleistogamy (simultaneous) is a rare phenomenon in rostrate violets. In the current study, we focused on modification of the CH/CL mating system in V. caspia by environmental conditions, resulting in a gradual switch from temporal cleistogamy, occurring in nature, to simultaneous cleistogamy under greenhouse conditions. V. reichenbachiana with seasonal cleistogamy was the control for V. caspia with the labile seasonal/simultaneous cleistogamy system. In simultaneous cleistogamy, the CH and CL flowers, fruits and seeds developed on an individual plant at the same time on the same branch. The typical difference between CH and CL flowers’ pistils is a straight style ending with a head-like stigma in CH and a curved style in CL adapted to self-pollination. This trait persists in the fruit and seed stages, allowing for easy recognition of fruit of CL and CH flowers in simultaneous cleistogamy. Floral meristems of CH flowers of V. reichenbachiana developed on the rhizome at the end of the growing season under short-day conditions and remained dormant until the following season. The CL floral meristems formed under long-day conditions on elongating lateral branches in the upper leaf axils. The daily temperature influenced the variable CH/CL ratio of V. caspia in nature and greenhouse conditions. Regulation of the CL/CH flower ratio by modifying environmental factors is important for basic research on genetic/epigenetic regulation of cleistogamy and for practical use to produce genetically stable lines of economically important species via CL seeds.

• Lindberg, Camilla Lorange; Hanslin, Hans Martin; Schubert, Marian; Marcussen, Thomas; Trevaskis, Ben & Preston, Jill Christine [Show all 7 contributors for this article] (2020). Increased above-ground resource allocation is a likely precursor for independent evolutionary origins of annuality in the Pooideae grass subfamily. New Phytologist. ISSN 0028-646X. 228(1), p. 318–329. doi: 10.1111/nph.16666. Full text in Research Archive Show summary

  Semelparous annual plants flower a single time during their 1‐yr life cycle, investing much of their energy into rapid reproduction. By contrast, iteroparous perennial plants flower multiple times over several years, and partition their resources between reproduction and persistence. To which extent evolutionary transitions between life‐cycle strategies are internally constrained at the developmental, genetic and phylogenetic level is unknown. Here we study the evolution of life‐cycle strategies in the grass subfamily Pooideae and test if transitions between them are facilitated by evolutionary precursors. We integrate ecological, life‐cycle strategy and growth data in a phylogenetic framework. We investigate if growth traits are candidates for a precursor. Species in certain Pooideae clades are predisposed to evolve annuality from perenniality, potentially due to the shared inheritance of specific evolutionary precursors. Seasonal dry climates, which have been linked to annuality, were only able to select for transitions to annuality when the precursor was present. Allocation of more resources to above‐ground rather than below‐ground growth is a candidate for the precursor. Our findings support the hypothesis that only certain lineages can respond quickly to changing external conditions by switching their life‐cycle strategy, likely due to the presence of evolutionary precursors.

• Schubert, Marian; Marcussen, Thomas; Meseguer, Andrea S. & Fjellheim, Siri (2019). The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification. Global Ecology and Biogeography. ISSN 1466-822X. 28(8), p. 1168–1182. doi: 10.1111/geb.12923. Full text in Research Archive
• Kwiatkowska, Monika; Bohdanowicz, Jerzy; Cubala, Marlena; Slomka, Aneta; Zabicka, Justyna & Zabicki, Piotr [Show all 10 contributors for this article] (2019). A new pollination system in non-cleistogamous species of Viola results from nyctinastic (night-closing) petal movements – A mixed outcrossing-selfing strategy. Flora: Morphologie, Geobotanik, Oekophysiologie. ISSN 0367-2530. 253, p. 1–9. doi: 10.1016/j.flora.2019.01.007. Full text in Research Archive
• Bravo, Gustavo A.; Antonelli, Alexandre; Bacon, Christine D.; Bartoszek, Krzysztof; Blom, Mozes P.K. & Huynh, Stella [Show all 20 contributors for this article] (2019). Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics. PeerJ. 2019(2), p. 1–60. doi: 10.7717/peerj.6399. Full text in Research Archive Show summary

  Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

• Kwiatkowska, Monika; Żabicka, Justyna; Migdałek, Grzegorz; Żabicki, Piotr; Cubala, Marlena & Bohdanowicz, Jerzy [Show all 13 contributors for this article] (2019). Comprehensive characteristics and genetic diversity of the endemic Australian Viola banksii (section Erpetion, Violaceae). Australian Journal of Botany. ISSN 0067-1924. 67(2), p. 81–98. doi: 10.1071/BT18233. Full text in Research Archive
• Huynh, Stella; Marcussen, Thomas; Felber, Francois & Parisod, Christian (2019). Hybridization preceded radiation in diploid wheats. Molecular Phylogenetics and Evolution. ISSN 1055-7903. 139, p. 1–10. doi: 10.1016/j.ympev.2019.106554. Full text in Research Archive
• Blaxland, Kim; Ballard, Harvey E. & Marcussen, Thomas (2018). Viola pluviae sp. nov. (Violaceae), a member of subsect. Stolonosae in the Pacific Northwest region of North America. Nordic Journal of Botany (NJB). ISSN 0107-055X. 36(9), p. 1–9. doi: 10.1111/njb.01931. Full text in Research Archive
• Migdalek, Grzegorz; Nowak, J; Saluga, M; Cieslak, E; Szczepaniak, M & Ronikier, M [Show all 9 contributors for this article] (2017). No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae). Plant Biology. ISSN 1435-8603. 19(4), p. 542–551. doi: 10.1111/plb.12571. Full text in Research Archive
• Oxelman, Bengt; Brysting, Anne Krag; Jones, Graham R; Marcussen, Thomas; Oberprieler, Christoph & Pfeil, Bernard E. (2017). Phylogenetics of Allopolyploids. Annual Review of Ecology, Evolution and Systematics. ISSN 1543-592X. 48, p. 543–557. doi: 10.1146/annurev-ecolsys-110316-022729. Full text in Research Archive Show summary

  We give an overview of recently developed methods to reconstruct phylogenies of taxa that includes allopolyploids which have originated in relatively recent times, i.e., such that at least some of the parental lineages of lower ploidy levels are not extinct, and that there is clear ploidy information shown by variation in chromosome counts. We review how these methods have been applied to empirical data. The challenges are discussed and prospects for the future are outlined. The review includes a description of a new version of the AlloppNET method, which now can handle any number of species at the diploid and tetraploid level, and any num,ber of hybridisations. AlloppNET is an extension of the *BEAST model which can handle allotetraploids.

• Park, Sungkyu; Yoo, Ki-Oug; Marcussen, Thomas; Backlund, Anders; Jacobsson, Erik & Rosengren, K Johan [Show all 8 contributors for this article] (2017). Cyclotide evolution: Insights from the analyses of their precursor sequences, structures and distribution in violets (Viola). Frontiers in Plant Science. 8. doi: 10.3389/fpls.2017.02058. Full text in Research Archive
• Malobecki, Andrzej; Marcussen, Thomas; Bohdanowicz, Jerzy; Migdalek, Grzegorz; Slomka, Aneta & Kuta, Elzbieta (2016). Cleistogamy and phylogenetic position of Viola uliginosa (Violaceae) re-examined. Botanical journal of the Linnean Society. ISSN 0024-4074. 182(1), p. 180–194. doi: 10.1111/boj.12460. Full text in Research Archive
• Toprak, Zeynep; Pfeil, Bernard E; Jones, Graham; Marcussen, Thomas; Ertekin, Alaattin Selcuk & Oxelman, Bengt (2016). Species delimitation without prior knowledge: DISSECT reveals extensive cryptic speciation in the Silene aegyptiaca complex (Caryophyllaceae). Molecular Phylogenetics and Evolution. ISSN 1055-7903. 102, p. 1–8. doi: 10.1016/j.ympev.2016.05.024. Full text in Research Archive
• Knoche, Gerd & Marcussen, Thomas (2016). Viola barhalensis (Violaceae), a new species from northeastern Turkey. Phytotaxa. ISSN 1179-3155. 275(1), p. 14–22. doi: 10.11646/phytotaxa.275.1.2. Full text in Research Archive
• McKeown, Meghan; Schubert, Marian; Marcussen, Thomas; Fjellheim, Siri & Preston, Jill C (2016). Evidence for an early origin of vernalization responsiveness in temperate pooideae grasses. Plant Physiology. ISSN 0032-0889. 172(1), p. 416–426. doi: 10.1104/pp.16.01023. Full text in Research Archive
• Bertrand, Yann J.K.; Scheen, Anne-Cathrine; Marcussen, Thomas; Pfeil, Bernard E.; Sousa, Filipe de & Oxelman, Bengt (2015). Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from fumaria (papaveraceae). Systematic Biology. ISSN 1063-5157. 64(3), p. 448–471. doi: 10.1093/sysbio/syv004. Full text in Research Archive
• Marcussen, Thomas; Heier, Lise; Brysting, Anne Krag; Oxelman, Bengt & Jakobsen, Kjetill Sigurd (2015). From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae). Systematic Biology. ISSN 1063-5157. 64(1), p. 84–101. doi: 10.1093/sysbio/syu071. Full text in Research Archive
• Sandve, Simen Rød; Marcussen, Thomas; Mayer, Klaus F X; Jakobsen, Kjetill Sigurd; Heier, Lise & Steuernagel, Burkhard [Show all 8 contributors for this article] (2015). Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D-genome. New Phytologist. ISSN 0028-646X. 208(1), p. 9–10. doi: 10.1111/nph.13487. Full text in Research Archive
• Shahrestani, Maryam Mohammadi; Marcussen, Thomas; Mehrvarz, Shahryar Saeidi & Yousefi, Narjes (2015). Morphological and phylogenetic relationships within Viola sect. Sclerosium (Violaceae) in Iran. Flora: Morphologie, Geobotanik, Oekophysiologie. ISSN 0367-2530. 215, p. 67–74. doi: 10.1016/j.flora.2015.07.008. Full text in Research Archive
• Marcussen, Thomas; Sandve, Simen Rød; Heier, Lise; Spannagl, Manuel; Pfeifer, Matthias & Genom, IWGSC The International Wheat [Show all 11 contributors for this article] (2014). Ancient hybridizations among the ancestral genomes of bread wheat. Science. ISSN 0036-8075. 345(6194). doi: 10.1126/science.1250092. Full text in Research Archive
• Elven, Reidar; Fremstad, Eli & Marcussen, Thomas (2013). Viola epipsila Ledeb. In Elven, Reidar; Fremstad, Eli & Pedersen, Oddvar (Ed.), Distribution maps of Norwegian vascular plants. IV The eastern and northeastern elements. Akademika forlag. ISSN 9788232102464. p. 447–450. Full text in Research Archive
• Nordal, Inger; Marcussen, Thomas & Elven, Reidar (2013). Viola rupestris F.W.Schmidt. In Elven, Reidar; Fremstad, Eli & Pedersen, Oddvar (Ed.), Distribution maps of Norwegian vascular plants. IV The eastern and northeastern elements. Akademika forlag. ISSN 9788232102464. p. 453–455. doi: 10.1111/j.1365-2699.2005.01257.x. Full text in Research Archive
• Marcussen, Thomas; Jakobsen, Kjetill Sigurd; Danihelka, Jiří; Ballard, Harvey E.; Blaxland, Kim & Brysting, Anne Krag [Show all 7 contributors for this article] (2012). Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae). Systematic Biology. ISSN 1063-5157. 61(1), p. 107–126. doi: 10.1093/sysbio/syr096. Full text in Research Archive
• Marcussen, Thomas & Borgen, Liv (2011). Species delimitation in the Ponto-Caucasian Viola sieheana complex, based on evidence from allozymes, morphology, ploidy levels, and crossing experiments. Plant Systematics and Evolution. ISSN 0378-2697. 291(3-4), p. 183–196. doi: 10.1007/s00606-010-0377-z. Full text in Research Archive
• Brysting, Anne Krag; Mathiesen, Cecilie & Marcussen, Thomas (2011). Challenges in polyploid phylogenetic reconstruction: A case story from the arctic-alpine Cerastium alpinum complex. Taxon. ISSN 0040-0262. 60(2), p. 333–347. doi: 10.1002/tax.602004. Full text in Research Archive
• Marcussen, Thomas; Oxelman, Bengt; Skog, Anna & Jakobsen, Kjetill Sigurd (2010). Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae). BMC Evolutionary Biology. 10(45). doi: 10.1186/1471-2148-10-45. Full text in Research Archive Show summary

  Background DNA-dependent RNA polymerase IV and V (Pol IV and V) are multi-subunit enzymes occurring in plants. The origin of Pol V, specific to angiosperms, from Pol IV, which is present in all land plants, is linked to the duplication of the gene encoding the largest subunit and the subsequent subneofunctionalization of the two paralogs (NRPD1 and NRPE1). Additional duplication of the second-largest subunit, NRPD2/NRPE2, has happened independently in at least some eudicot lineages, but its paralogs are often subject to concerted evolution and gene death and little is known about their evolution nor their affinity with Pol IV and Pol V. Results We sequenced a ~1500 bp NRPD2/E2-like fragment from 18 Viola species, mostly paleopolyploids, and 6 non-Viola Violaceae species. Incongruence between the NRPD2/E2-like gene phylogeny and species phylogeny indicates a first duplication of NRPD2 relatively basally in Violaceae, with subsequent sorting of paralogs in the descendants, followed by a second duplication in the common ancestor of Viola and Allexis. In Viola, the mutation pattern suggested (sub-) neofunctionalization of the two NRPD2/E2-like paralogs, NRPD2/E2-a and NRPD2/E2-b. The d N/d Sratios indicated that a 54 bp region exerted strong positive selection for both paralogs immediately following duplication. This 54 bp region encodes a domain that is involved in the binding of the Nrpd2 subunit with other Pol IV/V subunits, and may be important for correct recognition of subunits specific to Pol IV and Pol V. Across all Viola taxa 73 NRPD2/E2-like sequences were obtained, of which 23 (32%) were putative pseudogenes - all occurring in polyploids. The NRPD2 duplication was conserved in all lineages except the diploid MELVIO clade, in which NRPD2/E2-b was lost, and its allopolyploid derivates from hybridization with the CHAM clade, section Viola and section Melanium, in which NRPD2/E2-a occurred in multiple copies while NRPD2/E2-b paralogs were either absent or pseudogenized. Conclusions Following the relatively recent split of Pol IV and Pol V, our data indicate that these two multi-subunit enzymes are still in the process of specialization and each acquiring fully subfunctionalized copies of their subunit genes. Even after specialization, the NRPD2/E2-like paralogs are prone to pseudogenization and gene conversion and NRPD2 and NRPE2 copy number is a highly dynamic process modulated by allopolyploidy and gene death.

• Malecot, V; Marcussen, Thomas; Munzinger, J; Yockteng, R & Henry, M (2007). On the origin of the sweet-smelling Parma violet cultivars (Violaceae): Wide intraspecific hybridization, sterility, and sexual reproduction. American Journal of Botany. ISSN 0002-9122. 94(1), p. 29–41. Full text in Research Archive
• Marcussen, Thomas (2007). Lifiol er død - leve engfiol! en kritisk morfologisk gjennomgang av komplekset i Norge. Blyttia : Norsk botanisk forenings tidsskrift. ISSN 0006-5269. 65(3), p. 195–207. Full text in Research Archive
• Marcussen, Thomas (2006). Allozymic variation in the widespread and cultivated Viola odorata (Violaceae) in western Eurasia. Botanical journal of the Linnean Society. ISSN 0024-4074. 151, p. 563–571. Full text in Research Archive
• Nordal, Inger; Jonsell, Bengt & Marcussen, Thomas (2005). Viola rupestris: molecular analyses to elucidate postglacial migration in Western Europe. Journal of Biogeography. ISSN 0305-0270. 32, p. 1453–1459. Full text in Research Archive
• Nordal, Inger & Marcussen, Thomas (2005). Kalkfiol Viola rupestris ssp. relicta er bisentrisk i Skandinavia - ny forekomst på Møre. Blyttia : Norsk botanisk forenings tidsskrift. ISSN 0006-5269. 63(2), p. 67–71. Full text in Research Archive
• Marcussen, Thomas; Borgen, Liv & Nordal, Inger (2005). New distributional and molecular information call into question the systematic position of the West Asian Viola sintenisii (Violaceae). Botanical journal of the Linnean Society. ISSN 0024-4074. 147, p. 91–98. Full text in Research Archive
• Marcussen, Thomas; Borgen, Liv & Nordal, Inger (2001). Viola hirta (Violaceae) and its relatives in Norway. Nordic Journal of Botany (NJB). ISSN 0107-055X. 21(1), p. 5–17. Full text in Research Archive Show summary

  Viola hirta is widespread in most of Europe but rare in Norway, occurring in four isolated enclaves around the Oslo Fjord. Allozymic and morphological patterns of variation were studied in 320 individuals of Viola hirta (2n = 20) and its relatives V. collina (2n = 20), V. odorata (2n = 20), and V. suavis (2n = 40) from 22 Norwegian populations. Ongoing introgression from both V. collina and V. odorata, as hypothesised by several authors, was not supported by our data. All hybrids proved to be primary ones and, apparently, introgression is rare. However, allozyme markers suggested that V. hirta may have been affected by ancient introgression from V. collina and possibly also from the East European V. ambigua (2n = 40) during its evolutionary history. Geographical differentiation, presumably relatively recent and post-glacial, was evident in V. hirta. Variation occurred also between and within V. odorata populations, most likely a consequence of independent introductions by man. No variation was observed in V. collina or in V. suavis. A key to the Norwegian species of subsection Viola and their primary hybrids based on morphological characters is provided in Flora Nordica note No. 26.

• Marcussen, Thomas & Borgen, Liv (2000). Allozymic variation and relationships within Viola subsection Viola (Violaceae). Plant Systematics and Evolution. ISSN 0378-2697. 223, p. 29–57. Full text in Research Archive Show summary

  Allozyme markers from ten European taxa of Viola subsection Viola suggests that this group is allotetraploid, based on x=5. All taxa had distinct multilocus phenotypes except V. alba sspp. alba and scotophylla, which were identical and different from ssp. dehnhardtii. Variation was consistently higher in Mediterranean populations than in North European ones. Hybridisation seems extensive but putative F1 hybrids were distinctly less fertile than the parental species. Nevertheless, increased fertility in later-generation hybrids and shared band patterns among taxa indicate an important role of hybridisation and introgression in past and present evolution within the subsection. The octoploid V. ambigua shows affinity to V. hirta (tetraploid). The octoploid V. suavis probably originated from V. pyrenaica and other unidentified tetraploids, and high variability suggests polytopy or even polyphyly. The stoloniferous condition (series Flagellatae) seems to be primitive in the subsection but the reduction of stolons (series Eflagellatae) may have originated multiple times.

• Marcussen, Thomas & Nordal, Inger (1998). Viola suavis, a new species in the Nordic flora, with analyses of the relation to other species in the subsection Viola (Violaceae). Nordic Journal of Botany (NJB). ISSN 0107-055X. 18(2), p. 221–237. Full text in Research Archive Show summary

  Evidence from cytology, enzyme markers and morphometry suggests that a species of Viola (Violaceae) collected in southeastern Norway should be referred to V. suavis, although differing in some phenotypic traits. Viola suavis is not previously known from the Nordic countries, but must now be regarded as an established member of the Norwegian flora. It was probably introduced more than a century ago, providing an interesting analogy to the situation of V. alba in Öland (Sweden). Thus, it seems like human activity has played a role for expanding the distribution areas of several of the species within Viola (V. alba, V. hirta, V. odorata and V. suavis). Electrophoretic evidence showed that the basal chromosome number of the subsection is x=5. Viola suavis is allo-octoploid, and closely related tetraploid taxa were easily reconised. However, it is difficult to trace its origin back to lower-ploid ancestors, and it seems likely that the complex may have contained extinct taxa with other allelic combinations that would better explain the origin of V. suavis.

• Marcussen, Thomas & Nordal, Inger (1998). Viola suavis - a new species in the Nordic flora - with comparisons with other species in the subsection Viola. Nordic Journal of Botany (NJB). ISSN 0107-055X. 18, p. 221–237. Full text in Research Archive

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• Marcussen, Thomas & Struck, Torsten H (2025). Door 5: Horsetail (Equisetum) species still hybridise, 100 million years after they diverged. doi: https:/blog.annelida.de/2025/12/05/door-5-horsetail-equisetum-species-still-hybridise-100-million-years-after-they-diverged/. Full text in Research Archive
• Marcussen, Thomas & Struck, Torsten H (2025). The marsh violets – a lineage where hybridisation creates, modifies and deletes diversity. doi: https:/blog.annelida.de/2025/06/01/the-marsh-violets-a-lineage-where-hybridisation-creates-modifies-and-deletes-diversity/. Full text in Research Archive
• Marcussen, Thomas & Jakobsen, Kjetill Sigurd (2023). En nasjonal dugnad for å kartlegge genomene til alle artene i Norge – EBP-Nor. Biolog. ISSN 0801-0722. 41(1), p. 6–12. Full text in Research Archive
• Schubert, Marian; Grønvold, Lars; Marcussen, Thomas; Meseguer, Andrea; Sandve, Simen Rød & Hvidsten, Torgeir Rhoden [Show all 7 contributors for this article] (2019). Evolution of tolerance to temperate climates in the grass subfamily Pooideae. Full text in Research Archive
• Fjellheim, Siri; Marcussen, Thomas; Schubert, Marian & Meseguer, Andrea (2018). Evolution of adaptations to temperate climate in the grass subfamily Pooideae. Full text in Research Archive
• Vivian-Smith, Adam; Sønstebø, Jørn Henrik; Marcussen, Thomas; Uleberg, Eivind; Graham, Julie & Sønsteby, Anita [Show all 7 contributors for this article] (2015). Genomic Survey Sequences and the Structure of the Rubus chamaemorus L. and Rubus arcticus L. Genomes As Determined By Double Digest Restriction Associated Digest-(ddRAD) Tags. Full text in Research Archive
• Marcussen, Thomas; Nordal, Inger & Jonsell, Bengt (2001). Phylogeography in the Viola rupestris and V. riviniana complexes ¿ a preliminary study. Full text in Research Archive Show summary

  As widely distributed, Viola rupestris has probably recolonised the deglaci-ated areas of Europe from numerous refugia. Viola riviniana, on the other hand, with its relatively restricted distribution and notable absence from the Caucasus, seems to have recolonised Europe from considerably fewer refugia. There is evidence that the alloploid Viola riviniana has been substantially affected by postglacial introgression from one of its parental species, V. reichenbachiana. More generally, introgression from parental taxa is an important, if not crucial, factor increasing the variability of (nascent) allo-ploids.

• Marcussen, Thomas (2000). Phylogeography in Viola elucidated by allozymes. Full text in Research Archive Show summary

  The three taxa Viola alba, V. odorata, and V. suavis are closely related. In spite of much similar present distributions (South Europe and West Asia), allozymic analyses have revealed their phylogeographical histories to be widely dissimilar. The Viola alba complex is usually divided in several more or less geographical races. The mostly white-flowered morphs from Central Europe (ssp. alba and ssp. scotophylla) and the purple-flowered Caucasian morph ("V. besseri") proved identical and must all be included in ssp. alba. The Mediterranean morph (ssp. dehnhardtii) is, however, distinct. Higher levels of variation in the Caucasus indicate recruitment of European ssp. alba from glacial refuges in this region. The Mediterranean ssp. dehnhardtii was also variable, suggesting a separate refuge for this taxon. The transition zone between the two subspecies across southern Europe may be considered a persistent hybrid zone. Viola odorata. Allozymes suggested that the European and Caucasian materials of this species were recruited from different refugia. The Macaronesian V. maderensis was not recognised, and any original geographical patterns within Europe may have been homogenised by extensive cultivation. Viola suavis is critical and has been divided into numerous morphs, which are not supported by allozymes nor by chromosome counts. However, the investigated materials from Europe and the Caucasus proved widely different, both in allozymic composition and in ploidal levels (2n=40 vs. 2n=20). Conclusively, these represent two quite distinct species: Either (i) the Caucasian materials belong to the true V. suavis (type from Kiew) and the European taxon must take the newer name V. sepincola, or (ii) they represent a new and yet undescribed species.

• Henriksen, Olaf; Corey, Linda A.; Pellock, John M.; Berg, Kåre; Solaas, Marit Hornberg & Refsland, Grethe B. [Show all 7 contributors for this article] (1999). The roleof genetics in epilepsy is demonstrated through studies of Norwegian and Virginian twins. Full text in Research Archive
• Marcussen, Thomas & Borgen, Liv (1999). Variation and relationships within Viola, subsect. Viola. Full text in Research Archive
• Nordal, Inger; Marcussen, Thomas & Berg, Tore (1999). Fagerfiol Viola suavis - ny, men likevel gammel i norsk flora! Blyttia : Norsk botanisk forenings tidsskrift. ISSN 0006-5269. 57(3), p. 109–116. Full text in Research Archive Show summary

  This paper is a popular presentation of data from Marcussen & Nordal (1998) and previously unpublished data on Viola suavis M. Bieb. from France. The identity of a Viola population from SE Norwat (Kragerø) is established by data from isoenzymes, morphometry and chromosome number, which points to V. suavis. The Norwegian name"fagerfiol" is proposed for V. suavis. The species, which was introduced to Norway more than 100 years ago, is fully naturalized. It grows in close proximity to V. hirta and V. odorata without any signs of hybridization, even though such hybrids are reproted from Central Europe.

• Lindberg, Camilla Lorange; Fjellheim, Siri; Marcussen, Thomas & Hanslin, Hans Martin (2016). Evolution of growth rates in Pooideae (Poaceae). Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  The temperate grasses in the subfamily Pooideae (Poaceae) has a limited distribution range The species are mainly distributed to the Northern Temperate regions and are known to be adapted to the strong seasonality this region possess. To be able to grow in such conditions, the plants have to edapt to the shift between the mild but short growing seasons and the harsh, long winters. In this study, I ask if the distribution of the subfamily is linked to the species growth rate traits. To be able to reproduce before winter returns in Northern temperate regions, it is an advantage to grow fast. The fundamental process of plant growth can be quantified using various growth rate traits, such as Relative Growth Rate (RGR), Standardised Growth Rate (SGR) and Allometric Slope. In order to analyse the evolutionary history of growth rates within Pooideae, a growth experiment were done. Here, traits related to growth were measured. Chloroplast sequences were retrieved from all the 64 populations of 55 species included in the experiment. The acquired datasets consisting of values of growth rate traits connected to chloroplast sequences were used in joint phylogenetic analyses with Ancestral State Reconstruction (ASR). Pooideae species in the Northern temperate lineages allocate more biomass to the shoots than to the roots. The results suggests that the most recent common ancestor (MRCA) of the monophyletic group core Pooideae made a switch in growth rate and Allometric Slope around 34 Ma, during a global cooling event.

• Marcussen, Thomas (1998). Viola L. subsection Viola: Variation, hybridization, and relationships among taxa. Biologisk institutt, UiO. Full text in Research Archive Show summary

  Morphological and allozyme (AAT, AMP, GPI, IDH, PGM, SKD) variation was investigated from a total of 64 European populations (547 individuals) of Viola alba Bess. (2n=20), V. ambigua Waldst. & Kit. (2n=40), V. collina (2n=20), V. hirta L. (2n=20), V. jaubertiana Marès & Vigin. (2n=20), V. odorata L. (2n=20), V. suavis M.Bieb. (2n=40), and several hybrid generations. Allozymes revealed that the 2n=20 taxa should be regarded as tetraploids, hence a new basic chromosome number (x=5) is revealed for Section Viola. Most taxa were enzymatically distinct and only little intraspeciefic variation was revealed. However, high amounts of morphological variation and regoional differentiation was found , especially in V. alba, V. hirta, and V. suavis. Multiple introductions of V. odorata into southern Norway is suggested. Considerable morphological and enzymatical overlap was found between V. alba ssp. alba and ssp. scotophylla, which seem to differ only in pigmentation. Ssp. dehnhardtii, on the other hand, was distinct. Viola jaubertiana seemed isolated from the other European species, at least morphologically, and also differed slightly from descriptions from the type locality. Hybrids were generally intermediate betwen the parental species, displaying low fertility and variable amounts of heterosis. Whereas stabilized individuals of V. alba x odorata and V. collina x hirta were found in the European material, hybrids of further generations could not be positively identified in the Norwegian populations. However, several F2 and F3 hybrid generations could be raised. Hybrids of further generations generally displayed reduced heterozygosity accompanied by increased fertility. Reticulation seemed to have played a certain role in the past evolution of subsection Viola. A large proportion of alleles were mosaically shared among taxa, indicating hybrid satbilization at the 2n=20 level. Viola ambigua and V. suavis were best interpreted as allo-octoploids having originated from tetraploid taxa. Their parentages were, however, difficult to trace, but V. ambigua seemed particularly closely related to V. hirta, and V. suavis to both V. odorata, V. collina, and somewhat to V. jaubertiana.

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