Biology subjects

Sanchez-Gracia, A.

Publications and source records attributed to Sanchez-Gracia, A..

6 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↗

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

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009-2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species demographic history and identify novel signs of adaptation across spatial and temporal dimensions. We showed that patterns of secondary contact, originally characterized in North America, are replicated in South America and Australia. We also found that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatio-temporal patterns of genetic variation in this classic model system.

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↗

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↗