Alejandro Centeno-Cuadros

The Senegalese sole (Solea senegalensis Kaup, 1858) is a highly valuable species in European aquaculture and capture fisheries. Efficient monitoring of its populations is essential for sustainable management, yet traditional survey methods are invasive and labor-intensive. Environmental DNA (eDNA) analysis offers a powerful non-invasive alternative by detecting DNA fragments shed by organisms into the environment. In this study, we developed a species-specific TaqMan quantitative PCR (qPCR) assay targeting the mitochondrial cytochrome c oxidase subunit I (COI) gene to detect S. senegalensis eDNA. We evaluated assay performance, eDNA release, and persistence under controlled aquarium conditions. The assay demonstrated robust analytical sensitivity and specificity and showed an efficiency of 77.4%, an R² of 0.986, and an analytical limit of detection at the 10⁻⁵ dilution. Density had a statistically significant effect on the values observed (one-way ANOVA: F_3,16 = 3.903, p = 0.0287). To ensure accuracy, context-dependent operational quantification cycle (Cq) thresholds were defined: a stringent cutoff (Cq < 30) prevents false positives in complex marine environments, while a permissive cutoff (Cq < 36) maximizes detection in controlled settings. Aquarium trials confirmed that eDNA concentration correlates directly with fish density and accumulation time. Following fish removal, rapid eDNA degradation was observed, falling below strict quantifiable limits within 72 h, although trace signals persisted at late amplification cycles. This optimized qPCR protocol provides a foundational molecular tool that, pending further in situ validation, could support non-invasive S. senegalensis monitoring in ecological assessments and aquaculture management.

Two sibling bare-backed bat species (Pteronotus fulvus and P. gymnonotus) have been traditionally differentiated by their size. However, intermediate specimens between the two species have been found in sympatric populations along southern Mexico and it has been suggested that they may be the outcome of a hybridization process between the two species. We used one mitochondrial (COI), three nuclear markers (PRKCL, STAT5A and RAG2) and 13 microsatellites to explore the evolutionary relationships between these two species and elucidate whether the intermediate morphotypes correspond to hybrid individuals. These markers have been analyzed in sympatric and allopatric populations of the two species plus the closely related species Pteronotus davyi. We confirmed the species-level differentiation of the three lineages (P. fulvus, P. davyi and P. gymnonotus), but the phylogenetic hypotheses suggested by the nuclear and mitochondrial markers were discordant. We confirm that the discordance between markers is due to genetic introgression through the mitochondrial capture of P. fulvus in P. gymnonotus populations. Such introgression was found in all P. gymnonotus specimens across its sympatric distribution range (Mexico to Costa Rica) and is related to expansion/retraction species distribution pulses associated with changes in forest distribution during the Quaternary climate cycles. Microsatellite analyses showed contemporary genetic contact between the two sympatric species and 3.0% of the samples studied were identified as hybrids. In conclusion, we found a historical and asymmetric genetic introgression (through mitochondrial capture) of P. fulvus into P. gymnonotus in Mexico and Central America and a limited contemporary gene exchange between the two species. However, no relationship was found between hybridization and the intermediate-sized specimens from southern Mexico, which might likely result from a clinal variation with latitude. These results confirm the need for caution when using forearm size to identify these species in the field and when differentiating them in the laboratory based on mitochondrial DNA alone.

PCR is a universal tool for the multiplication of specific DNA sequences. For example, PCR‐based sex determination is widely used, and a diversity of primer sets is available. However, this protocol requires thermal cycling and electrophoresis, so results are typically obtained in laboratories and several days after sampling. Loop‐mediated isothermal amplification (LAMP) is an alternative to PCR that can take molecular ecology outside the laboratory. Although its application has been successfully probed for sex determination in three species of a single avian Family (raptors, Accipitridae), its generality remains untested and suitable primers across taxa are lacking. We designed and tested the first LAMP‐based primer set for sex determination across the modern birds (NEO‐W) based on a fragment of the gene chromo‐helicase‐DNA‐binding protein located on the female‐specific W chromosome. As nucleotide identity is expected to increase among more related taxa, taxonomically targeted primers were also developed for the Order Falconiformes and Families Psittacidae, Ciconiidae, Estrildidae and Icteridae as examples. NEO‐W successfully determined sex in a subset of 21 species within 17 Families and 10 Orders and is therefore a candidate primer for all modern birds. Primer sets designed specifically for the selected taxa correctly assigned sex to the evaluated species. A short troubleshooting guide for new LAMP users is provided to identify false negatives and optimize LAMP reactions. This study represents the crucial next step towards the use of LAMP for molecular sex determination in birds and other applications in molecular ecology.

Understanding the ecological, behavioural and evolutionary response of organisms to changing environments is of primary importance in a human‐altered world. It is crucial to elucidate how human activities alter gene flow and what are the consequences for the genetic structure of a species. We studied two lineages of the Egyptian fruit bat (Rousettus aegyptiacus) throughout the contact zone between mesic and arid Ecozones in the Middle East to evaluate the species' response to the growing proportion of human‐altered habitats in the desert. We integrated population genetics, morphometrics and movement ecology to analyse population structure, morphological variation and habitat use fromGPS‐ or radio‐tagged individuals from both desert and Mediterranean areas. We classified the spatial distribution and environmental stratification by describing physical–geographical conditions and land cover. We analysed this information to estimate patch occupancy and used an isolation‐by‐resistance approach to model gene flow patterns. Our results suggest that lineages from desert and Mediterranean habitats, despite their admixture, are isolated by environment and by adaptation supporting their classification as ecotypes. We found a positive effect of human‐altered habitats on patch occupancy and habitat use of fruit bats by increasing the availability of roosting and foraging areas. While this commensalism promotes the distribution of fruit bats throughout the Middle East, gene flow between colonies has not been altered by human activities. This discrepancy between habitat use and gene flow patterns may, therefore, be explained by the breeding system of the species and modifications of natal dispersal patterns.