
Thomas MarcussenUniversity of Oslo · Centre for Ecological and Evolutionary Synthesis
Thomas Marcussen
Dr.
About
85
Publications
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Introduction
Interests:
Inference of species phylogenies, especially homoploid and polyploid phylogenetic networks, from gene phylogenies under the multispecies coalescent (MSC), ancestral state reconstruction, phylogenetic dating techniques.
Research:
Taxonomy, evolution of Viola (Violaceae), Geranium (Geraniaceae) and grasses (Poaceae).
Additional affiliations
April 2015 - March 2017
Publications
Publications (85)
The allohexaploid bread wheat genome consists of three closely related subgenomes
(A, B, and D), but a clear understanding of their phylogenetic history has been lacking.
We used genome assemblies of bread wheat and five diploid relatives to analyze
genome-wide samples of gene trees, as well as to estimate evolutionary relatedness
and divergence ti...
Allopolyploidisation acounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for eva...
Aim
Frost is among the most dramatic stresses a plant can experience, and complex physiological adaptations are needed to endure long periods of sub‐zero temperatures. Owing to the need to evolve these complex adaptations, transitioning from tropical to temperate climates is regarded as difficult. Here, we study the transition from tropical to temp...
Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve
owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat
d-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome
lineage (progeni...
The genus Viola (Violaceae) is among the 40-50 largest genera among angiosperms, yet its 16 taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker 17 in 1925, the then known 400 species were distributed among 14 sections and numerous unranked 18 groups. Here we provide an updated, comprehensive classifica...
Current status of the genus Viola (Violaceae) in South America.
(Link to the Seminar replicated at Instituto de Botánica Darwinion in October 2023: https://www.youtube.com/watch?v=ON5gst06EII)
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...
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 s...
Taxonomic revision of Viola subg. Andinium. Originally described as section Andinium W.Becker, we combine this lineage to subgenus and classify its species in 11 sections: Confertae, Ericoidium, Grandiflos, Inconspicuiflos, Relictium, Rhizomandinium, Rosulatae, Sempervivum, Subandinium, Triflabellium, Xylobasis. We currently recognise c.140 describ...
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...
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 strat...
Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progeni...
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 s...
Viola banksii of the eastern Australian and Tasmanian sect. Erpetion produces exclusively chasmogamous flowers, unlike most other temperate taxa of Viola which additionally produce obligatory self-pollinated cleistogamous flowers. This study explored flower structure and nyctinastic flower movements (temporal flower closure), the correlation of the...
Viola banksii, the type species of section Erpetion, is endemic in eastern mainland Australia. In this paper we characterise morphological and anatomical features and assess genome size and genetic diversity in combination with the breeding system. V. banksii develops exclusively chasmogamous flowers. Ovules are anatropous, crassinucellate and bite...
Aim: Frost is among the most dramatic stresses a plant can experience and complex physiological adaptations are needed to endure long periods of sub-zero temperatures. Due to the need for evolving these complex adaptations, transitioning from tropical to temperate climates is regarded difficult and only half of the world's seed plant families have...
As hirtherto circumscribed, the allo‐octoploid Viola palustris L. exists in three distinct races in North America. The race occurring in the Pacific Northwest of North America has previously been shown to have originated by polyploidy from a different set of ancestral tetraploids than the nominal, Amphi‐Atlantic race. These two races differ also in...
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major 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-throug...
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major 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-throug...
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major 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-throug...
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major 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 next-genera...
Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, a...
We give an overview of recently developed methods to reconstruct phylog-enies of taxa that include allopolyploids that have originated in relatively recent times-in other words, taxa for which at least some of the parental lineages of lower ploidy levels are not extinct and for which ploidy information is clearly shown by variation in chromosome co...
Viola reichenbachiana (2 n = 4 x = 20) and V . riviniana (2 n = 8 x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by...
A new species, Viola barhalensis Knoche & Marcussen, from northeastern Turkey, is described and illustrated for the first time. It is found at elevations of 1050-1800 m, growing in shady crevices of igneous cliffs within the valley of the Barhal (or Altıparmak) river. It belongs to Viola subsection Viola, and is similar to Viola sandrasea and some...
The ability of plants to match their reproductive output with favorable environmental conditions has major consequences both for lifetime fitness and geographic patterns of diversity. In temperate ecosystems, some plant species have evolved the ability to use winter non-freezing cold (vernalization) as a cue to ready them for spring flowering. Howe...
Viola uliginosa is an endangered species throughout its range in Central Europe. Based on an unusual combination of morphological characters, including a reported lack of cleistogamous (CL) flowers, it was previously placed in the monotypic subsection Repentes, section Viola. Available individual phylogenetic analyses identify V. uliginosa as a lin...
Mayrose et al. (2011) and Arrigo and Barker (2012) concluded that neopolyploid lineages diversify more slowly than the diploid lineages from which they arise. We expressed concerns about this statement in Soltis et al. (2014a) to which Mayrose et al. (2014) responded. This article continues the discussion. We demonstrate a statistical problem with...
There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of the data) and coalescent stochasticity (presence of incomplete lineage sorting). Although most studies have b...
Dataset for:
Marcussen T., Heier L., Brysting A.K., Oxelman B., Jakobsen K.S. 2015. From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae). Systematic Biology 64:84–101.
Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be...
The comparative anatomy of three morphologically close taxa of Viola sect. Sclerosium W. Becker distributed in southern Iran is presented in this study: Viola behboudiana, Viola cinerea and Viola stocksii. Cross-sections of roots, stems, peduncles, petioles, leaves and the surface sections of leaves showed that the following properties were taxonom...
Pollen morphology of 17 species of Viola representing five sections, Melanium, Plagiostigma, 'Spathulidium' ined., Sclerosium, and Viola, was studied using light and scanning electron microscope. Pollen grains were usually symmetrical, tetrazonocolporate to pentazonocolporate in section Melanium and trizonocolporate to tetrazonocolporate in the oth...
The Violaceae consist of 1,000–1,100 species of herbs, shrubs, lianas, and trees that are placed in 22 recognized genera. In this study we tested the monophyly of genera with a particular focus on the morphologically heterogeneous Rinorea and Hybanthus, the second and third most species-rich genera in the family, respectively. We also investigated...
Primers and sequence variation for two low-copy nuclear genes (LCG) not previously used for phylogenetic inference in the genus Hypericum, PHYC and EMB2765, are presented here in comparison with the fast-evolving nuclear intergenic spacer ITS. Substitution rates in the LCG markers were two times lower than those reported in ITS for Hypericum, which...
The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence ti...
In this study, we provide additional evidence for the taxonomic delimitation of Viola stagnina based on a scanning electronic microscope study, a common garden experiment, a crossing experiment and chromosome counts. Plant height, leaf color, stipule size and shape, and differences in stigma shape all display large phenotypic plasticity among var....
Comparative anatomy of 7 taxa of Viola sect. Viola distributed in the north of Iran was studied. The investigated species are V. alba, V. odorata, V. sintenisii (subsect. Viola), V. caspia, V. reichenbachiana and V. rupestris (subsect. Rostratae). The following characters were determined to be taxonomically informative: presence or absence of phloe...
Op basis van al eerder gevonden genetische en morfologische verschillen en de uitkomsten van de hier gepresenteerde gegevens wordt voorgesteld dat de endemische vorm van V. stagnina als aparte variëteit lacteoides erkend moet blijven. Voor de taxonomische status van aparte (onder)soort verschillen de twee vormen nog te weinig en overlappen ze geogr...
Cross-sections of roots, stems, petioles and peduncles were investigated in 12 species of Viola distributed mainly in northern Iran: V . kitaibeliana , V. arvensis , V. occulta , V. tricolor (sect. Melanium ), V. somchetica (sect. Plagiostigma ), V. spathulata (sect. Spathulidium ined.), V . alba , V. odorata , V . sintenisii (sect. Viola subsect....
Viola sect. Melanium Ging. is represented in Iran with 5 species:
V. modesta, V. occulta, V. kitaibeliana, V. tricolor and V. arvensis.
During field research in Iran, approximately 250 specimens were
collected, studied, and compared to the material from the K, B and
RBGE herbaria. Viola kitaibeliana is introduced as rare species in flora
of Iran. V...
Premise of the study:
Climate change and shifts in land use are two major threats to biodiversity and are likely to disproportionately impact narrow endemics. Understanding their origins and the extent of their genetic diversity will enable land managers to better conserve these unique, highly localized gene pools. Viola guadalupensis is a narrow...
The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high polyploids (i.e., organisms with more than six sets of nuclear chromosomes), the signatures of gene homoeolog loss, deep coalescence, and polyploidy may become confounded, with the result that gene trees may be...
Information from allozymes, ploidy levels, morphology, cross-compatibility and biogeography suggests that the easternmost
occurrences of the Ponto-Caucasian Viola sieheana should be considered to belong to a separate species, V. caspia. Morphological characters delimitating V. sieheana and V. caspia are presented and discussed. The main distributio...
Here we illustrate and discuss the major challenges involved in reticulate phylogenetic reconstruction, with special reference to single- and low-copy nuclear data (the RNA polymerase genes) produced for the polyploid Cerastium alpinum group and close relatives. The dynamic nature of polyploid genomes paves the way for evolutionary novelty, and is...
The taxonomic and nomenclatural histories of Viola elatior Fr. (1828), V. pumila Chaix (1785) and V. stagnina Kit. ex Schult. (1814) in central and western Europe are discussed. The names V. stagnina and V. elatior are lectotypified with specimens corresponding to the current use of these names. The neglected lectotypification in 1988 of V. montana...
The taxonomic and nomenclatural histories of Viola elatior Fr. (1828), V. pumila Chaix (1785) and V. stagnina Kit. ex Schult. (1814) in central and western Europe are discussed. The names V. stagnina and V. elatior are lectotypified with specimens corresponding to the current use of these names. The neglected lectotypification in 1988 of V. montana...
A nomenclatural and taxonomic analysis has shown that Viola elatior Fr. (l.c.) is a legitimate name and its type specimen taxonomically corresponds to the Euro-Siberian species usually referred to by this name (Danihelka & al., l.c: 1869–1878 – this issue). However, there exist four earlier legitimate names, V. montana L. (Sp. Pl.: 935. 1753), V. p...
DnaSP Positive selection sliding window matrix. This file represents the alignment of 27 NRPD2/E2 exon sequences from Violaceae taxa used to examine dN/dS ratios with a sliding window approach using the DnaSP software.
PAML positive selection matrix. This file represents the 54 basepair alignment of NRPD2/E2 exon sequences for 44 Violaceae taxa.
Violaceae matrix. This file represents the NRPD2/E2 alignment from 8 Violaceae taxa aligned to exon sequences of a non-Violaceae outgroup.
Viola matrix. This file represents the alignment of NRPD2/E2 copies from 18 Viola taxa aligned to Allexis batangae as outgroup.
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). Ad...
[In Norwegian with English abstract]
[Norwegian title: Lifiol er død – leve engfiol! En kritisk morfologisk gjennomgang av komplekset i Norge]
A revision of all 1939 Norwegian specimens of Viola canina L. deposited in the Oslo herbarium (O) was performed. A subset of 162 specimens was analysed morphometrically for six characters considered diagnost...
Parma violets are reputed for their double, fragrant flowers and have been cultivated for centuries in Europe. However, due to a rather atypical morphology their taxonomic affinity has not been clarified. Authors have proposed an origin from three possible species, Viola alba, V. odorata, or V. suavis, or a hybrid origin. Using both ITS sequence va...
Viola odorata has been cultivated for cosmetics and medicine in Europe since antiquity. The spread by humans has expanded its distribution considerably beyond its original range in parts of the Mediterranean region, south-western Europe, and western Asia. One hundred and sixty-five plants of V. odorata from 52 collection sites from throughout most...
Aim Our aim was to elucidate the postglacial migration of Viola rupestris F.W. Schmidt, with its two subspecies, rupestris and relicta Jalas, in Europe, using molecular methods.
Location Norway, Sweden, Finland, England, the Netherlands, France and Switzerland.
Methods Isoenzymes were analysed from 49 populations of Viola rupestris s.lat. Based on...
Viola rupestris F.W.Schmidt ssp. relicta Jalas, formerly believed to be «northern unicentric» in Scandinavia, has been discovered in Fræna, Møre og Romsdal County. Comparative isoenzyme analyses were undertaken, and plants from this population show full agreement with N Scandinavian plants, and differ in three isoenzymes from the more southern ssp....