Biology subjects

Guirao-Rico, S.

Publications and source records attributed to Guirao-Rico, S..

8 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

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

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

Transposable elements identify previously overlooked regions undergoing parallel evolution in response to diverse selective pressures

Evolve and Resequence (E&R) studies have contributed to closing the gap between adaptive phenotypic traits and their underlying genomic basis. Unlike other popular approaches, E&R studies provide a unique opportunity to understand the degree of repeatability and constraints of the evolutionary process. Still, one of the major challenges is to accurately identify the genetic variants targeted by selection. Traditionally, E&R studies have only explored part of the variation present in the genomes, SNPs, thus neglecting other sources of adaptive variation such as transposable elements (TEs). In this work, we analyzed the Pool-seq data of five published Drosophila melanogaster E&R studies in the context of TEs. We found some candidate TEs inserted in the same or nearby regions to significant SNPs/genes. As such, these TEs should be added to the set of possible targets of selection. However, we also found a subset of significant TEs that were not associated with previously identified significant SNPs/genes. Most of these TEs are inserted within or flanked by genes related to the trait of interest and thus they are the only potential targets of selection identified in these regions. Functional enrichment analysis of the genes located nearby all candidate adaptive TEs allowed to identify new relevant biological functions. Finally, the replicability of candidate TEs was similar or higher than that reported for SNPs. We argue that TE variants should also be considered as candidate targets of selection in E&R studies and we also provide guidelines to improve the detection of TEs as targets of selection.

evolutionary biology↗

bioRxiv2022

Basal and stress-induced expression changes consistent with water loss reduction explain desiccation tolerance of natural Drosophila melanogaster populations

BackgroundClimate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Integrating transcriptomics and physiology is key to advancing our knowledge on how species cope with desiccation stress, and these studies are still best accomplished in model organisms. ResultsHere, we characterized the natural variation of European D. melanogaster populations across climate zones and found that strains from arid regions were similar or more tolerant to desiccation compared with strains from temperate regions. Tolerant and sensitive strains differed not only in their transcriptomic response to stress but also in their basal expression levels. We further showed that gene expression changes in tolerant strains correlated with their physiological response to desiccation stress and with their cuticular hydrocarbon composition. Transposable elements, which are known to influence stress response across organisms, were not found to be enriched nearby differentially expressed genes. Finally, we identified several tRNA-derived small RNA fragments that differentially targeted genes in response to desiccation stress. ConclusionsOur results showed that by integrating transcriptomics with physiological trait analysis we can pinpoint the genetic basis of the differences in tolerance to desiccation stress found in natural D. melanogaster populations. Moreover, we showed that, beyond starvation and aging, tRNA-derived small RNA fragments (tRFs) appear to be relevant post-transcriptional gene regulators in response to desiccation stress.

evolutionary biology↗

bioRxiv2021

Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and associated with adaptive signatures in Drosophila melanogaster

High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generated 32 high-quality reference genomes for the well-known model species D. melanogaster and focused on the identification and analysis of transposable element variation as they are the most common type of structural variant. We showed that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identified hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

evolutionary biology↗

bioRxiv2020

Pervasive selection pressure in wild and domestic pigs

Animal domestication typically affected numerous polygenic quantitative traits, such as behaviour, development and reproduction. However, uncovering the genetic basis of quantitative trait variation is challenging, since it is probably caused by small allele-frequency changes. To date, only a few causative mutations related to domestication processes have been reported, strengthening the hypothesis that small effect variants have a prominent role. So far, the studies on domestication have been limited to the detection of the global effect of domestication on deleterious mutations and on strong beneficial variants, ignoring the importance of variants with small selective effects. In addition, very often, the study of the effects of selection are conducted on genome sequences that contain a non-negligible fraction of missing data, especially in non-model organisms. Hence, appropriate methods to account for these positions are needed. To overcome these difficulties, here we propose to estimate the proportion of beneficial variants using the asymptotic MacDonald-Kreitman (MK) method based on estimates of variability that summarizes the site frequency spectrum (SFS) while accounting for missing data and use them to perform an Approximate Bayesian Computation (ABC) analysis to infer the Distribution of Fitness Effects (DFE) of each population. We applied this approach to 46 genome sequences of pigs from three different populations, one wild and two domestics, with very different demographic histories and selective pressures. The obtained results showed that domestic and wild pig populations do not differ in nonsynonymous fixed mutations. Therefore, differences in estimation among breeds are determined by their polymorphisms. The comparison of for total and exclusive mutations suggests that the different domestic populations have suffered recent divergent changes in their functional versus neutral polymorphisms ratio, while the wild population is compatible with =0. Besides, the DFE inferred with ABC indicates that both wild and domestic pigs display a large number of deleterious mutations at low frequency and a high number of neutral and/or nearly-neutral mutations that may have a significant effect on the evolution of domestic and wild populations. In addition, models not considering beneficial mutations have higher posterior probabilities, suggesting that beneficial mutations are difficult to detect or are scarce. Indeed, for all three populations, the median proportion of the strong favourable mutations are very low ([≤] 0.1%) in those models that includes positive selection, with the average values of weak beneficial mutations around 0.6% for wild boar and 0.8-1.0% for the domestic pigs. Lastly, the analysis based on exclusive mutations showed that recent demographic changes may have severely affected the fitness of populations, especially that of the local Iberian breed.

evolutionary biology↗