Biology subjects

Viruel, J.

Publications and source records attributed to Viruel, J..

5 recordsLinked to original sources

bioRxiv2026

Reticulate evolution and climate driven diversification shaped the origin and geographic structure of Linum bienne

[vrecto] Hybridization, incomplete lineage sorting and climatic oscillations can interact across evolutionary timescales, but their combined effects on plant diversification remain difficult to resolve. We investigated how these processes shaped the origin and geographic structure of Linum bienne, the putative progenitor of cultivated flax. [vrecto]We integrated genus-level Angiosperms353 phylogenomics across Linum with plastome analyses, low-depth nuclear resequencing, demographic inference and environmental niche modelling across the range of L. bienne. This framework allowed us to assess phylogenetic discordance, test for reticulation and reconstruct lineage history through time. [vrecto]Phylogenetic discordance was widespread across our genus-level sampling and largely consistent with incomplete lineage sorting. However, branch-length and maximum-likelihood network analyses detected additional signal of gene flow at the node including L. bienne, cultivated flax and the closest relatives. Within L. bienne, plastid and nuclear data recovered four geographically structured lineages across the species range, with cytonuclear discordance and demographic analyses supporting repeated secondary contact. [vrecto]Our results show that the evolutionary history of L. bienne reflects the interaction between deep reticulation, incomplete lineage sorting and Pleistocene range dynamics. This multiscale perspective highlights L. bienne as a genetically complex species and illustrates how reticulate evolution and climatic change can jointly shape plant diversification.

evolutionary biology↗

bioRxiv2025

Placing very long branch taxa in the plant tree of life: a case study with Dioscoreales mycoheterotrophs

PremiseThe inclusion of heterotrophic plants in broadly focused systematic studies is challenging, reflecting substantial morphological modification, gene loss, and accelerated nucleotide substitution following photosynthesis loss. In particular, inclusion of very long branch (VLB) taxa with highly elevated rates may lead to phylogenomic misinference. MethodsWe explore how rapidly evolving plastomes behave in model-based phylogenetic inferences of the yam order Dioscoreales, which experienced convergent photosynthesis losses. The taxon sampling includes all photosynthetic genera, and mycoheterotrophic lineages with a broad range of substitution rates. ResultsWhen only moderately rapidly evolving heterotrophs are included, relationships within Dioscoreales are congruent with recent mitochondrial analysis, and generally strongly supported. Photosynthetic Stenomeris (represented by only three genes) is moderately supported as sister to Dioscoreaceae. Notably, Burmanniaceae and Thismiaceae, two mycoheterotrophic families including highly reduced plastomes, are strongly supported as distantly related within Dioscoreales. Constrained analysis rejects combining Thismiaceae with Burmanniaceae, conflicting with current angiosperm classification. Including VLB mycoheterotrophs in phylogenetic inference can lead to localized to broad reduction in branch support--substantially so for Afrothismiaceae, a family placing in disparate locations in Dioscoreales (and beyond) in variant analyses, with no ability to differentiate among its alternative placements. ConclusionsInclusion of highly rate-elevated taxa in analyses of Dioscoreales phylogeny can depress branch support. Inferred relationships in the order are otherwise congruent with studies based on mitochondrial data; the family-level classification needs updating. The extraordinarily rapidly evolving family Afrothismiaceae places inconsistently in diverse plastid analyses, pointing to probable analytical limits for plastid-based phylogenomic analyses of VLB heterotrophs.

evolutionary biology↗

bioRxiv2024

Genic and phylogenomic discordances reveal conflicting hybridization episodes in temperate Loliinae grasses

The grass subtribe Loliinae has great ecological and economic importance, as it includes community-dominant species of world mountain grasslands and the most extensively cultivated pasture, fodder and lawn grasses (fescues, ryegrasses). Resolving the phylogeny of recently evolved Loliinae lineages has proven challenging due to frequent introgressions and polyploidizations that occurred throughout their history. Evolutionary reconstruction based on genome-wide data sets is useful for large groups of species, enabling recovering phylogenetic trees, contrasting their topologies, unraveling the origins of the discordances, and testing hypotheses on their reticulate history. Here we present the first target-capture phylogeny of Loliinae using 234 single-copy nuclear coding loci for a large sample of 132 representative taxa, covering all its 29 evolutionary lineages. Additionally, we have completed organelle (plastome) sequences to elucidate the hybridogenic speciation history of the Loliinae from complementary genome sources. Concatenated maximum likelihood and multispecies coalescent trees of single-copy genes showed well-supported relationships for major lineages, which were generally consistent across analyses and genomes, and with previous taxonomic and phylogenetic findings. However, they also revealed high levels of both nuclear and cyto-nuclear discordances. The time-calibrated phylogeny of target-capture data supports an early Miocene origin for Loliinae and Mid-Late Miocene splits for its main broad-leaved and fine-leaved lineages, while current species-rich groups radiated in Plio-Pleistocene times. Hybridization and topological incongruence tests between the nuclear single-copy genes and plastome-based trees using multiple approaches and different sampling subsets confirmed the rampant introgression experienced by Loliinae at deep and shallow nodes. However, hybridization rates differed from lineage to lineage within the major clades and were not correlated with time or ploidy but rather depended on the "hybridogenous" nature of particular lineages. Our analyses detected high hybridization rates in four broad-leaved (Subulatae-Hawaiian, Tropical-South African, Mexico-Central-South American and Leucopoa p.p.) and five fine-leaved Loliinae lineages (American II, Aulaxyper, Afroalpine, American-Neozeylandic) containing rogue species that probably originated from trans-clade crosses and are more likely to hybridize greatly. In contrast, they recovered low hybridization rates in four broad-leaved (Schedonorus-Lolium, Subbulbosae, Drymanthele-Pseudoscariosae-Lojaconoa, Leucopoa pp) and six fine-leaved lineages (Festuca, Psilurus-Vulpia, American I, Exaratae-Loretia, American-Vulpia-Pampas, Eskia), with species derived from single ancestors that hybridize only with close congeners. The levels of intragenomic nuclear discordance could have been magnified by the prevalence of allopolyploids in the Loliinae and by methodological bias in the selection of orthologs; however, our nuclear and plastome trees have revealed key hybrid origins in these grasses. [allopolyploidization, lineage-specific hybridization rates, nuclear and cyto-nuclear discordances, Festuca and related genera, phylogenomics, nuclear single-copy genes, plastome].

evolutionary biology↗

bioRxiv2021

Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

Target capture has emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

evolutionary biology↗

bioRxiv2021

Molecular approaches reveal speciation between red and blue flowered plants in the Mediterranean Lysimachia arvensis and Lysimachia monelli (Primulaceae)

Flower colour constitutes a pivotal evolutionary force in speciation. The Mediterranean Lysimachia arvensis and L. monelli are morphologically variable species having both blue or red flowered plants. Previous studies suggested that L. arvensis plants differing in colour are diverging lineages, but this variation has not been considered in a phylogenetic context. We reconstruct the phylogenetic signal and the ancestral states of flower colour of Mediterranean Lysimachia species by using nuclear (ITS) and three plastid markers. Blue and red specimens are nested in two independent clades in the ITS tree, thus supporting that L. arvensis and L. monelli are polyphyletic, whereas low phylogenetic resolution was found in plastid markers. Blue-flowered L. arvensis is reconstructed sister to L. talaverae in a monophyletic clade sister to the remaining Lysimachia. Red-flowered L. arvensis is reconstructed sister to red-flowered L. monelli in a monophyletic clade sister to blue-flowered L. monelli and L. foemina. Our results suggest that colour lineages in L. arvensis and L. monelli constitute different species, but flower colour did not promote the separation of these lineages. We propose a new name for blue-flowered L. arvensis (L. loeflingii) and a new combination for red-flowered L. monelli (L. collina).

molecular biology↗