Biology subjects

Marcussen, T.

Publications and source records attributed to Marcussen, T..

10 recordsLinked to original sources

bioRxiv2026

No evidence that polyploids arise during periods of environmental upheaval. A reply to Chen et al. (2026)

Ancient whole-genome duplications (WGDs) are thought to have played a major role in plant evolution, but robust inference of the patterns and drivers of polyploid establishment through deep time remains challenging. We re-evaluate the recent large-scale study by Chen et al. (2026), which linked polyploid establishment throughout angiosperm evolution to periods of climatic instability and low species richness. We identify five conceptual and methodological issues that substantially affect these conclusions and collectively undermine the proposed temporal and ecological associations. We hope that clarifying these issues will support future efforts to understand the evolutionary role of polyploidy in plant evolution.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe

The reference genome of Androsace saussurei (Ericales: Primulaceae: Primuloideae) provides a valuable resource for understanding the mechanisms of plant adaptations to the most extreme environments 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.

genomics↗

bioRxiv2025

ERGA-BGE Reference Genome of Phyllidia flava (Nudibranchia: Phyllidiidae), a Relict Species Endemic to the Mediterranean Sea

Phyllidia flava, the only Mediterranean representative of the otherwise Indo-Pacific family Phyllididae, is a radula-less dorid nudibranch that feeds exclusively on toxic sponges, from which it derives defensive and camouflage compounds. Although not currently listed as endangered, this relict species remains vulnerable due to its restricted distribution and the rising temperatures of the Mediterranean Sea. A total of 13 contiguous chromosomal pseudomolecules were assembled, resulting in a chromosome-level genome spanning 1.9 Gb. This assembly comprises 2,032 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.4 Mb and 169.7 Mb, respectively. This reference genome will serve as a valuable resource for conservation efforts, provide a robust calibration point for studying nudibranch phylogenetics based on the Tethys Ocean closure, and lay the groundwork for research into toxic prey diet specialisation.

genomics↗

bioRxiv2025

Phylogenetic biome niche conservatism underlies the evolution of forest paleoendemic legume trees in tropical Africa

Niche conservatism is prevalent during the evolution of plant lineages. However, inferring biome niche lability and its impact on tropical tree species diversification is currently limited. To better understand biome niche lability and its effect on diversification rates, we analyzed an endemic lineage of African tropical trees, testing whether biome niche type (forest vs savanna) and biome lability are non-randomly distributed. We reconstructed a time-calibrated phylogeny of the Berlinia clade (16 genera, ca 201 species) using 140 nuclear genes, 75% of its extant species, and eight fossil calibrations. We also analyzed the phylogenetic signal of biome shifts across the group and its effect on diversification and extinction rates. We found the forest biome as the ancestral condition and a directional shift from forest to savanna (no reversals). The forest biome type is conserved in the Berlinia clade, but the lability to shift biomes is randomly distributed in the group. We did not find evidence that biome shift was associated with higher diversification or lower extinction rates. Our analyses identified five paleoendemic genera that have persisted solely in the forest biome since the Eocene. These paleoendemic and forest-restricted lineages are potentially more susceptible to habitat alterations of human related activities and future climate change, due to perhaps an innate limitation to adapt to new habitat types.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Erebia palarica Chapman, 1905: a montane butterfly endemic to North-West Iberia

The reference genome of Erebia palarica will provide valuable insights into evolutionary and conservation genomics. On one hand, the reference genome paves the way to unravel the speciation process, reproductive barriers, and putative hybridisation of E. palarica with its closely related sister species: Erebica meolans. On the other hand, the reference genome will play an important role in the genetic monitoring of this endemic species, facilitating the use of genomics to estimate population genomics parameters. The genome was assembled into 14 contiguous chromosomal pseudomolecules (Z chromosome included). This chromosome-level assembly encompasses 0.49 Gb, composed of 38 contigs and 17 scaffolds, with contig and scaffold N50 values of 34.2 Mb and 38.4 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of the Spanish Moon Moth Graellsia isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive

The reference genome of the Spanish Moon Moth, Graellsia isabellae, will be of great importance for evolutionary and conservation genomics. Firstly, this reference genome, alongside phylogenomic analyses, may finally resolve the longstanding debate regarding the scientific name of this iconic species--whether it should be Graellsia isabellae (Graells, 1849) or Actias isabellae (Graells, 1849). Secondly, the reference genome will be instrumental in the genetic monitoring of this protected species, enabling advanced methods to calculate contemporary population genomics estimates. The genome was assembled into 31 contiguous chromosomal pseudomolecules (Z chromosome included). The mitochondrial genome has also been assembled and is 15,247 bp in length. This chromosome-level assembly encompasses 0.56 Gb, composed of 38 contigs and 32 scaffolds, with contig and scaffold N50 values of 18.9 Mb and 20.4 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions

The reference genome of Gluvia dorsalis is the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.

genomics↗

bioRxiv2022

A revised phylogenetic classification for Viola (Violaceae)

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 Beckers 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 subdivide the 658 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, 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. Study on seed anatomy and morphology is required to understand the fossil record of the genus.

plant biology↗

bioRxiv2019

Hybridization preceded radiation in diploid wheats

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 (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). Scenarios of reticulation have been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.5 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~4.1 Ma ago, and did not indicate additional hybridization events. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into almost all diploid as well as allopolyploid wild wheats.

evolutionary biology↗

bioRxiv2018

The grass subfamily Pooideae: late Cretaceous origin and climate-driven Cenozoic diversification

* AimFrost 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 worlds seed plant families have temperate representatives. Here, we study the transition from tropical to temperate climates in the grass subfamily Pooideae, which dominates the northern temperate grass floras. Specifically, we investigate the role of climate cooling in diversification.\n\n* LocationGlobal, temperate regions\n\n* Time periodLate Cretaceous-Cenozoic\n\n* Major taxaThe grass subfamily Pooideae\n\n* MethodsWe date a comprehensive Pooideae phylogeny and test for the impact of paleoclimates on diversification rates. Using ancestral state reconstruction, we investigate if Pooideae ancestors experienced frost and winter. To locate the area of origin of Pooideae we perform biogeographical analyses.\n\n* ResultsWe estimated a late Cretaceous origin of the Pooideae (66 million years ago (Mya)), and all major clades had already diversified at the Eocene-Oligocene transition climate cooling (34 Mya). Climate cooling was a probable driving force of Pooideae diversification. Pooideae likely evolved in mountainous regions of southwestern Eurasia in a temperate niche experiencing frost, but not long winters.\n\n* Main conclusionPooideae originated in a temperate niche and experienced cold temperatures and frost long before the expansion of temperate biomes after the Eocene-Oligocene transition. This suggests that the Pooideae ancestor had adaptations to temperate climate and that extant Pooideae grasses share responses to low temperature stress in Pooideae. Throughout the Cenozoic falling temperatures triggered diversification. However, complex mechanisms for enduring strongly seasonal climate with long, cold winters most likely evolved independently in lower taxonomic lineages. Our findings provide insight into how adaptations to historic changes in chill and frost exposure influence distribution of plant diversity today.

evolutionary biology↗