Biology subjects

Rozas, J.

Publications and source records attributed to Rozas, J..

12 recordsLinked to original sources

bioRxiv2026

Genomic signatures of positive selection and relaxed selective constraints associated with convergent dietary specialisation

Island radiations provide ideal frameworks for studying the molecular basis of convergent evolution. The rapid diversification of Dysdera spiders in Canary Islands provides a striking example, with repeated dietary shifts towards specialisation on woodlice, accompanied by morphological, metabolic, and behavioural modifications that facilitate the exploitation of this heavy-metal-rich prey. Here, we investigate two independent events of dietary specialisation on different islands. By analysing six high-quality genome-assemblies, including three newly generated in this study, we investigate the genomic signals of positive selection and relaxed selection in protein-coding genes, upstream regulatory regions, and gene family turnover rates. We detected signatures of positive selection associated with the two specialists, accompanied by a twofold increase in gene loss rates relative to generalist ancestors. Notably, positive selection targeted a smaller, functionally coherent set of genes, potentially involved in detoxification likely through heavy metal excretion. In contrast, relaxation of selection affected a broader set of genes associated with functions that may have become dispensable under the new dietary regime. Furthermore, we found contractions in gene families associated with vesicular transport, potentially reflecting a reduced reliance on vesicle-mediated metal accumulation. Overall, our findings suggest that similar ecological pressures can drive parallel, yet non-identical, adaptive and non-adaptive responses, pointing to partially predictable evolutionary trajectories in an island radiation.

evolutionary biology↗

bioRxiv2026

Highly prevalent cargo genes of F plasmids harbored in pathogenic Escherichia coli

Analysis of prevalent orthogroups (OGs) in a collection of F plasmids from extraintestinal Escherichia coli ST131 isolates has led to the identification of two groups of previously uncharacterized cargo genes that may be widely distributed among F plasmids of pathogenic E. coli. Group 1 comprises four OGs whose encoded proteins are predicted to be involved in transport-related functions. The corresponding genes cluster with other genes associated with metabolism and are highly prevalent in extraintestinal ST131 isolates. Group 2 comprises several OGs whose encoded proteins currently have unknown functions. These OGs are present in a large proportion of F plasmids from both intestinal and extraintestinal E. coli isolates. The corresponding genes cluster within an F-plasmid region that also contains genes involved in DNA metabolism, suggesting that the proteins encoded by these newly identified OGs may likewise contribute to F-plasmid DNA biology. Characterizing the functions of these newly identified proteins may improve our understanding of the contribution of F plasmid to E. coli virulence and reveal novel targets for antimicrobial intervention, either by limiting F-plasmid dissemination among multidrug-resistant (MDR) E. coli strains or by directly targeting plasmid-carrying bacteria.

genomics↗

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

How did evolution halve genome size during an oceanic island colonization?

Red devil spiders of the genus Dysdera colonised the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are nearly half the size of their mainland counterparts ([~]1.7 vs. [~]3.3 Gb). This offers a unique model to solve long-standing debates regarding the roles of adaptive and non-adaptive forces on shaping genome size genome size evolution. To address these, we conducted comprehensive genomic analyses based on three high-quality chromosome-level assemblies, including two newly generated ones. We find that insular species experienced a reduction in genome size, affecting all genomic elements, including intronic and intergenic regions, with transposable element (TE) loss accounting for most of this contraction. Additionally, autosomes experienced a disproportionate reduction compared to the X chromosome. Paradoxically, island species exhibit higher levels of nucleotide diversity and recombination, lower TE activity in recent times, and evidence of intensified natural selection, collectively pointing to larger long-term effective population sizes in species from the Canary Islands. Overall, our findings align with the non-adaptive mutational hazard hypothesis, supporting purifying selection against slightly deleterious DNA and TE insertions as the primary mechanism driving genome size reduction.

genomics↗

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↗

bioRxiv2024

Population genomics of adaptive radiations: Exceptionally high levels of genetic diversity and recombination in an endemic spider from the Canary Islands

The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, [~]60 endemic species originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterized by phenotypic modifications encompassing morphological, metabolic and behavioral changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low-coverage based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterized genome-wide levels of nucleotide polymorphism, divergence, and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. Furthermore, we identified genomic regions potentially under positive selection, shedding light on relevant biological processes, such as vision and nitrogen extraction as possible targets of adaptation and eventually, as drivers of the species diversification. This pioneering study in spiders endemic of an oceanic archipelago lays the groundwork for broader population genomics investigations aimed at understanding the genetic mechanisms driven adaptive radiations in island ecosystems.

evolutionary biology↗

bioRxiv2024

GALEON: A Comprehensive Bioinformatic Tool to Analyse and Visualise Gene Clusters in Complete Genomes

MotivationGene clusters, defined as a set of genes encoding functionally-related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges. ResultsTo facilitate the identification, analysis, and visualisation of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families, and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families. Availability and ImplementationGALEON is freely available from http://www.ub.edu/softevol/galeon, and from https://github.com/molevol-ub/galeon

genomics↗

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↗

bioRxiv2020

Chromosome-level genome assembly of the common chaffinch (Aves: Fringilla coelebs): a valuable resource for evolutionary biology

The common chaffinch, Fringilla coelebs, is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87 Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian dataset. Around 7.8 % of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian and vertebrate evolution.

evolutionary biology↗

bioRxiv2020

Smelling in the dark: phylogenomic insights on the chemosensory system of a subterranean beetle

The chemosensory system has experienced relevant changes in subterranean animals, facilitating the orientation into darkness via the perception of specific chemical signals critical to survive in this particular environment. However, the genomic basis of chemoreception in cave-dwelling fauna is largely unexplored. We generated de novo transcriptomes for antennae and body samples of the troglobitic beetle Speonomus longicornis (whose characters suggest an extreme adaptation to the deep subterranean) in order to interrogate the evolutionary origin and diversification of the chemosensory gene repertoire across coleopterans through a phylogenomic approach. Our results suggested a diminished diversity of odorant and gustatory gene repertoires compared to polyphagous epigean beetles. Moreover, S. longicornis showed a large diversity of odorant-binding proteins, suggesting an important role of these proteins in capturing airborne chemical cues. We identified a gene duplication in the ionotropic co-receptor I R25a, a highly conserved single-copy gene in protostomes involved in thermal and humidity sensing. In addition, no homologous genes to sugar receptors or the ionotropic receptor IR41a were detected. Our findings suggest that the chemosensory gene repertoire of this cave beetle may have been reshaped by the low complexity of chemical signals of this particular environment, and that gene duplication and loss may have played an important role in the evolution of genes involved in chemoreception. Altogether, our results shed light on the genomic basis of chemoreception in a cave-dwelling invertebrate and pave the road towards understanding the genomic underpinnings of adaptation to the subterranean lifestyle at a deeper level.

evolutionary biology↗

bioRxiv2019

Genomic adaptations to aquatic and aerial life in mayflies and the origin of wings in insects

The first winged insects underwent profound morphological and functional transformations leading to the most successful animal radiations in the history of earth. Despite this, we still have a very incomplete picture of the changes in their genomes that underlay this radiation. Mayflies (Ephemeroptera) are one of the extant sister groups of all other winged insects and therefore are at a key phylogenetic position to understand this radiation. Here, we describe the genome of the cosmopolitan mayfly Cloeon dipterum and study its expression along development and in specific organs. We discover an expansion of odorant-binding proteins, some expressed specifically in the breathing gills of aquatic nymphs, suggesting a novel sensory role for gills. In contrast, as flying adults, mayflies make use of an enlarged set of opsins and utilise these visual genes in a sexually dimorphic manner, with some opsins expressed only in males. Finally, to illuminate the origin of wings, we identify a core set of deeply conserved wing-specific genes at the root of the pterygote insects. Globally, this is the first comprehensive study of the structure and expression of the genome of a paleopteran insect and shows how its genome has kept a record of its functional adaptations.

evolutionary biology↗

bioRxiv2019

BITACORA: A comprehensive tool for the identification and annotation of gene families in genome assemblies

Gene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families in the genomes of non-model organisms. Despite the recent progress in automatic methods, the tools developed for this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent gene models for many family copies, which require considerable extra efforts to be amended. Here we present BITACORA, a bioinformatics solution that integrates sequence similarity search tools and Perl scripts to facilitate both the curation of these inaccurate annotations and the identification of previously undetected gene family copies directly from DNA sequences. We tested the performance of the BITACORA pipeline in annotating the members of two chemosensory gene families of different sizes in seven available chelicerate genome drafts. Despite the relatively high fragmentation of some of these drafts, BITACORA was able to improve the annotation of many members of these families and detected thousands of new chemoreceptors encoded in genome sequences. The program generates an output file in the general feature format (GFF) files, with both curated and novel gene models, and a FASTA file with the predicted proteins. These outputs can be easily integrated in genomic annotation editors, greatly facilitating subsequent manual annotation and downstream evolutionary analyses.

bioinformatics↗