Biology subjects

Riutort, M.

Publications and source records attributed to Riutort, M..

6 recordsLinked to original sources

bioRxiv2025

The first chromosome-scale Dugesia genomes shed light on structural rearrangements and genome size evolution in flatworms

AbstractHigh-quality, chromosome-scale genomes are crucial for understanding biological processes, yet many metazoan lineages, including most Lophotrochozoa, remain underrepresented in genome databases. Among these, planarians (Platyhelminthes, Tricladida), particularly Dugesia, are a globally distributed and phenotypically diverse group that has become an important model in evolutionary biology, notably for investigating the genetic effects of agametic asexuality. However, the lack of chromosome-scale assemblies has limited progress. Here, we present the first chromosome-scale genomes of four Western Mediterranean Dugesia species, displaying the first intra- and intergeneric comparisons. Comparison with the regeneration model organism Schmidtea mediterranea, rejects a whole-genome duplication as the cause of differences in chromosomal number and genome size between genera. Instead, Dugesia shows extensive lineage-specific and differential expansions of DNA transposable elements, likely contributing to genome size variation during diversification. Despite differences in the dynamics of structural genome rearrangements observed between genera, both groups lack the conservation of ancestral metazoan linkage groups, supporting the idea that genome structural instability is a key feature of flatworm genome evolution. Our newly generated genomic resources and findings offer vital insights into the genetic basis of diversification and establish Dugesia as a valuable model for studying metazoan genome dynamics, including the evolution of alternative reproductive systems.

genomics↗

bioRxiv2025

An integrative taxonomic approach reveals unexplored diversity in Croatian planarians

BackgroundFreshwater ecosystems are among the most endangered habitats on Earth, with approximately one-fourth of aquatic species at risk of extinction. Effective conservation efforts require comprehensive monitoring and accurate species identification, including often overlooked groups. DNA barcoding promises rapid and accessible species identification but requires the availability of "universal" primer pairs and robust, taxonomically curated reference libraries. Planarian flatworms are one such group for which these resources are currently lacking, even though they are common constituents of freshwater ecosystems worldwide. As a result, the true extent of planarian diversity remains underappreciated in many areas. ResultsMotivated by the highly skewed representation of planarian diversity in current GenBank records of the barcoding gene mitochondrial cytochrome c oxidase subunit I (COI), we optimised existing barcoding primers and tested them on planarians collected in a species-rich but, so far, poorly surveyed region of Croatia. Using an integrative approach combining the new primers, traditional taxonomy and karyology, we generated new taxonomically curated COI barcode sequences for European dugesiids, dendrocoelids and planariids, which, in the case of the latter two groups, represent a substantial increase of the number of entries for those families. Our efforts resulted in several significant findings, including the description of a new pigmented Dendrocoelum species, Dendrocoelum pigmentatum sp. nov, the discovery of two highly differentiated haplotypic clades in Schmidtea lugubris, and the rediscovery of Polycladodes alba in Croatia after a century. ConclusionsOverall, our work extends the utility of DNA barcoding for species-level identification of planarians to previously inaccessible groups. Additionally, it integrates Croatia as an underexplored but species-rich region into the endeavour to systematically describe the planarian fauna of Europe. The expansion of a known number of Croatian planarian species from eight to sixteen and the discovery of a new, large planarian species in continental Europe, Dendrocoelum pigmentatum, demonstrate the effectiveness of our integrative approach. Overall, our work highlights the underappreciated diversity of planarians, even in continental Europe and supports practical conservation efforts to preserve aquatic biodiversity.

zoology↗

bioRxiv2024

Pervasive and recurrent hybridisation prevents inbreeding depression in Europe's most threatened seabird

Hybridisation is a double-edged sword: while it can erode distinct evolutionary lineages, it can also introduce genetic diversity and adaptive potential into dwindling populations. In the Critically Endangered Balearic shearwater (Puffinus mauretanicus), this dilemma is exacerbated by a limited understanding of the extent and consequences of hybridisation with the Yelkouan shearwater (P. yelkouan). This knowledge gap has limited the scope of science-based conservation strategies to avoid the Balearic shearwaters imminent extinction. Here, we investigate shearwater hybridisation dynamics and their effect on genome-wide diversity in the Balearic shearwater. Divergence dating, demographic modelling and admixture analyses suggest that these two poorly-differentiated shearwater lineages experienced recurrent episodes of divergence and widespread hybridisation during glacial cycles. Selection scans reveal a 500 kb region hosting an adaptive haplotype that potentially underpins interspecific differences in migratory behaviour, and which has been repeatedly introgressed between taxa. Moreover, we show that interspecific gene flow has prevented increases in homozygosity and genetic load, and through forward simulations we illustrate how it can enhance the Balearic shearwaters resilience to future population bottlenecks. Our findings illustrate how introgression can be crucial for maintaining genetic diversity in threatened taxa, and highlight the need for considering the protection of hybridisation in conservation plans.

evolutionary biology↗

bioRxiv2022

First molecular phylogeny of the freshwater planarian genus Girardia (Platyelminthes, Tricladida) unveils hidden taxonomic diversity and initiates resolution of its historical biogeography

The genus Girardia (Platyhelminthes: Tricladida) comprises several species of which some have spread from their original areas of distribution in the Americas to other parts of the globe. Due to great anatomical similarities between species, morphology-based phylogenetic analyses struggled to resolve the affinities between species and species-groups. This problem is exacerbated by the fact that populations of Girardia may show only asexual reproduction by fissiparity and, thus, do not exhibit a copulatory apparatus, which hampers taxonomic identification and extraction of phylogenetic characters. In the present work this problem has been resolved by constructing a molecular phylogeny of the genus. Although our samples do not include representatives of all known species, they cover a large part of the original distributional range of the genus Girardia. Our phylogenetic results suggest the presence of two main clades, which are genetically and karyologically highly differentiated. North and South American nominal G. tigrina actually constitute two sibling species that are not even closely related. The South American form is here described as a new species. The phylogenetic tree brings to light that Girardia arose on the South American portion of Gondwanaland, from which it, subsequently, dispersed to the Nearctic Region, probably more than once.

evolutionary biology↗

bioRxiv2021

The genome of the Balearic shearwater (Puffinus mauretanicus), a Critically Endangered seabird: a valuable resource for evolutionary and conservation genomics

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the population size. Currently, populations continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, and some studies predict their extinction by 2070. We present the first high-quality reference genome for the species which was obtained by a combination of short and long-read sequencing. Our hybrid assembly includes 4,169 scaffolds, with a scaffold N50 of 2.1 Mbp, a genome length of 1.2 Gbp, and BUSCO completeness of 96%, which is amongst the highest across sequenced avian species. This reference genome allowed us to study critical aspects relevant to the conservation status of the species, such as an evaluation of overall heterozygosity levels and the reconstruction of its historical demography. Our phylogenetic analysis using whole-genome information resolves current uncertainties in the order Procellariiformes systematics. Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision and the development of natriuresis. This reference genome will be the keystone for future developments of genetic tools in conservation efforts for this Critically Endangered species.

genomics↗

bioRxiv2021

Island-specific evolution of a sex-primed autosome in the planarian Schmidtea mediterranea

The sexual biotype of the planarian Schmidtea mediterranea is a hermaphrodite indigenous to Tunisia and several Mediterranean islands. Here, we isolated individual chromosomes and used sequencing, Hi-C and linkage mapping to assemble a chromosome-scale genome reference. The linkage map revealed an extremely low rate of recombination on chromosome 1. We confirmed suppression of recombination on chromosome 1 by quantifying recombination events in individual sperm and oocytes. We showed that the extensive heterozygous regions, previously designated as J and V haplotypes, comprise essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicated that this heterozygosity has evolved specifically in populations from Sardinia and Corsica. We found that chromosome 1 acquired many genes that determine the development of female and male reproductive systems, along with haplotype-specific expression of such sex specific genes. These molecular signatures and restricted recombination in a hermaphrodite led us to propose that chromosome 1 is a sex-primed autosome, providing direct molecular evidence for the traditional model of how sex chromosomes may have evolved from autosomes.

genetics↗