Biology subjects

Rios, D.

Publications and source records attributed to Rios, D..

5 recordsLinked to original sources

bioRxiv2026

Population genomics of nicotinic acetylcholine receptors in Anopheles funestus reveals rapid evolution of the α9 and β2 subunits within a constrained gene family

The deployment of clothianidin-based insecticide formulations in malaria vector control has highlighted the capacity of Anopheles funestus to displace more susceptible mosquito species in treated areas and to rapidly evolve resistance under selection pressure. Metabolic detoxification, together with structural and genetic changes in nicotinic acetylcholine receptors (nAChRs), the primary molecular targets of neonicotinoids, can reduce insecticide efficacy. Here, we characterized amino acid substitutions across all 11 nAChR subunits in An. funestus to assess standing variation that may facilitate adaptive responses to chemical exposure. Using whole-genome sequencing data from 656 mosquitoes sampled in 13 African countries, we found marked contrasts in the distribution of nonsynonymous variants among nAChR subunits. Most subunits are strongly constrained and carry no missense variants, whereas two loci (3 and 7) display three geographically widespread amino acid substitutions across the continent. In contrast, 9 and {beta}2 accumulate dozens of nonsynonymous mutations occurring at intermediate to high frequencies, including within domains involved in orthosteric ligand binding and channel gating. Genetic differentiation at nAChR loci among populations from different countries is low to moderate, although several nonsynonymous mutations display high FST values consistent with geographic structuring. These results highlight relaxed constraint on two subunits that may provide opportunities for evolutionary diversification within a conserved family of multimeric receptor assemblies. Such diversification has not been observed in vector species displaced by An. funestus in indoor residual spraying areas, and the potential implications for reduced sensitivity to neonicotinoids are discussed.

evolutionary biology↗

bioRxiv2025

Behavioral divergence between a generalist and a specialist mosquito despite minimal differentiation across chemosensory receptor gene families

Oviposition site choice is a major determinant of habitat selection in insects, yet its behavioral and genetic bases remain poorly understood. Although model organisms such as Drosophila melanogaster provide well-established systems for studying oviposition, disentangling foraging from egg-laying decisions remains challenging because females use the same substrates for feeding and reproduction. Here, we identify a pair of sister mosquito species that exhibit contrasting oviposition strategies and provide a promising system for investigating how divergence in sensory information processing shapes behavioral shifts between generalist and specialist taxa. Using binary-choice assays, we tested oviposition preferences in 1,046 gravid females from both field and laboratory populations. Anopheles gambiae females were highly selective and deposited nearly all eggs in a single water source, consistent with specialist behavior. In contrast, females of its sibling species, An. coluzzii, adopted a generalist strategy marked by a more even distribution of eggs across available substrates. To identify chemosensory receptor genes that diverge between the cryptic species and may underlie these behavioral differences, we analyzed amino acid substitutions across odorant, ionotropic, and gustatory receptor families using whole-genome sequencing data. Although differentiation was limited at the gene-family level, several individual divergent loci associated with carboxylic acid, amine, and other volatile detection pathways emerged as candidate drivers of species-specific oviposition behavior. These findings suggest that shifts in sensory perception during egg laying may facilitate behavioral and ecological specialization, and that phenotypic divergence in environmental sensing can arise before substantial genome-wide differentiation.

evolutionary biology↗

bioRxiv2025

Standing genetic variation underlies divergence of nicotinic acetylcholine receptor subunits among cryptic species of the Anopheles gambiae complex

Arthropod species differ in insecticide susceptibility, yet how pre-existing polymorphism at target sites shapes variable responses within and among populations remains poorly understood. Recently diverged taxa provide ideal systems to test how target-site divergence modulates species sensitivity. Using whole-genome sequencing data from 573 mosquitoes representing six cryptic species of the Anopheles gambiae complex, we analyzed standing genetic variation across all 11 nicotinic acetylcholine receptor (nAChR) subunit genes to establish a baseline for natural diversity before the large-scale deployment of nAChR-targeting insecticides in Africa. We detected no previously reported resistance alleles from agricultural pests and found no evidence of selective sweeps or loss-of-function mutations across the nAChR gene family. Patterns of polymorphism were consistent with strong purifying selection. Most nonsynonymous variants were rare, predicted to be tolerated by SIFT (score [≥] 0.05), present almost exclusively in heterozygotes, and occurred outside ligand-binding and transmembrane domains. However, the 6 subunit exhibited relaxed constraint, with two high-frequency substitutions (I198M and D202E) that defined haplotypes segregating by species. The derived alleles represented ancient polymorphisms, showed evidence of introgression, and were fixed in populations with reduced larval susceptibility to spinosad. Our findings show that modest standing variation can shape divergence at insecticide target sites within a highly constrained gene family and underscore the need to monitor interspecific variation during the deployment of nAChR-targeting insecticides.

evolutionary biology↗

bioRxiv2024

Evolutionary genomics of two co-occurring congeneric fore reef coral species on Guam (Mariana Islands).

Population structure provides essential information for developing meaningful conservation plans. This is especially important in remote places, such as oceanic islands, where limited population sizes and genetic isolation can make populations more susceptible and self-dependent. In this study, we assess and compare the relatedness, population genetics and molecular ecology of two sympatric Acropora species, A. surculosa sensu Randall & Myers (1983) and A. cf. verweyi Veron & Wallace, 1984 around Guam, using genome-wide sequence data (ddRAD). We further contrast our findings with the results of a recent study on back reef A. cf. pulchra (Brook, 1891) to assess the impact of habitat, colony morphology and phylogenetic relatedness on these basic population genetic characteristics and generate testable hypotheses for future studies. Both target species were found to have small effective population sizes, low levels of genetic diversity, and minimal population structure around Guam. Nonetheless, A. cf. verweyi had significantly higher levels of genetic diversity, some population structure as well as more clones, close relatives and putative loci under selection. Comparisons with A. cf. pulchra indicate a potentially significant impact by habitat on population structure and genetic diversity while colony morphology seems to significantly impact clonality. This study revealed significant differences in the basic population genetic makeup of two sympatric Acropora species on Guam. Our results suggest that colony morphology and habitat/ecology may have a significant impact on the population genetic make-up in reef corals, which could offer valuable insights for future management decisions in the absence of genetic data.

evolutionary biology↗

bioRxiv2024

Population genomics for coral reef restoration - a case study of staghorn corals in Micronesia

Staghorn Acropora corals are ecological keystone species in shallow lagoons and back reef habitats throughout the tropics. Their widespread decline coupled with their amenability for asexual propagation propelled them to the forefront of global coral restoration efforts - albeit frequently without much scientific input. To guide these efforts and as a blueprint for similar projects, we conducted a comprehensive population genomic study of Acropora cf. pulchra, a major restoration target species in the Indo-Pacific. Our results revealed that A. cf. pulchra populations in the Mariana Islands are characterized by large clonal clusters and extremely low levels of genetic diversity. Differentiation among populations followed a significant isolation-by-distance pattern and delineated two distinct metapopulations on Guam. Our investigation identified critical population genetic parameters, necessitating targeted management strategies, and provides actionable guidelines for effective conservation efforts. For management and conservation, two populations emerged as pivotal connectivity hubs with elevated genetic diversity. For restoration, we show that A. cf. pulchra populations demonstrated a suitability for extensive asexual propagation and provide guidelines how to best apply that. To preserve and augment genetic diversity, strategies to mitigate inbreeding are crucial until sexual reproduction can be fully integrated into restoration protocols. Critical sites for restoration include local connectivity hubs, fringing lagoons that connect metapopulations, and back reefs around a particularly isolated population. These findings offer crucial insights into the genetic landscape of a keystone coral species and provide actionable recommendations for coral conservation and restoration. By advocating for the preservation of population connectivity and the promotion of genotypic, genetic, and symbiont diversity in coral restoration, our study serves as a blueprint for leveraging population genomic studies to enhance the efficacy and resilience of restoration projects on remote islands.

evolutionary biology↗