To aid in the empirical evaluation of species hypotheses / concepts we present a strategy that uses NGS whole nuclear genome assemblies to identify novel single-copy universal PCR targets whose sequences discriminate species-scale clades. Our approach begins by identifying UCEs within partial Illumina genome assemblies across a strategically-chosen taxa set and culminates with experimental validation of appropriate single-copy nuclear DNA regions for PCR/Sanger sequencing. The highly diverse ( 35 K species) group of eupulmonate gastropods was used as proof-of-concept. Among the 24 K ultraconserved elements identified across 14 de novo and publicly-available genome assemblies spanning eupulmonate phylogeny, 61 informative universal PCR targets were ultimately identified. These allow for targeted sequence recovery from loci known to contain useful phylogenetic signal and permit efficient scaling to larger sample sizes, something that is immensely important when working with issues as complex as evolution and biodiversity.
This study re-evaluates the Pleistocene history of the European hedgehog (Erinaceus europaeus) and the Northern white-breasted hedgehog (E. roumanicus), by integrating genetically verified occurrence records, complementary allopatric GBIF records and ecological niche modelling (ENM). We assessed differences in broad-scale environmental associations, identified climatic predictors associated with their distributions, and reconstructed potential past climatic suitability during the Last Glacial Maximum. Niche overlap, equivalency and similarity analyses were applied across allopatric regions and areas of sympatry. Human Footprint showed a strong signal in exploratory models for both species, with a stronger effect in the Northern white-breasted hedgehog. Climatic predictors differed between the species: predicted suitability for the Northern white-breasted hedgehog was more strongly associated with temperature-related variables, whereas the European hedgehog models were mainly influenced by annual temperature range and precipitation-related variables. Niche comparisons across the Central European (CE) and Russian–Baltic (RB) contact zones revealed contrasting patterns, with stronger realized climatic niche differentiation in the CE zone and apparently greater, but less clearly resolved, niche overlap in the RB zone. The location of the CE contact zone may partly coincide with the transition between oceanic and continental climates, consistent with the trapping hypothesis of hybrid zones. Palaeoclimatic projections indicated suitable areas beyond the classical Mediterranean peninsulas, supporting the possibility of northern or extra-Mediterranean refugial areas. Our results suggest that broad-scale environmental gradients may contribute to the spatial structuring of contact zones and may interact with species-boundary dynamics despite ongoing hybridization, while palaeoclimatic reconstructions support a more complex Pleistocene history than implied by the classical southern-refugia paradigm. These findings highlight the importance of considering both ecological and historical processes when interpreting the evolutionary history of European temperate taxa.
Mobile genetic elements drive horizontal gene transfer (HGT), which may have contributed to the functional diversity of termite gut microbiomes, although the environmental determinants of these processes remain poorly understood. Our proposed model integrates spatially resolved physicochemical gradients and mobile genetic element (MGE) dynamics to quantitatively predict HGT patterns in termite guts. The framework integrates high-resolution metabolomic and transcriptomic profiling data from gut compartments, sourced from published experimental studies, with a generalized additive model to forecast the rate of MGE transfer as a function of local environmental conditions, and goes beyond static cataloguing of HGT events. Moreover, metabolic network alignments have been used to predict MGE-host interactions based on functional complementarity, and a heterogeneous graph neural network is used to dynamically predict HGT hotspots using environmental, MGE, and microbial host data. Unlike traditional methods, our framework explicitly links microenvironmental variability with gene flow mediated by MGEs using taxonomic, metagenomic, and metabolic features. The framework incorporates state-of-the-art computational methods, such as nanoscale secondary ion mass spectrometry for spatial metabolite mapping and graph attention networks (GAT) for transfer-likelihood prediction. The study of physicochemical gradients in the context of MGE-host interactions offers a mechanistic framework for investigating HGT dynamics in complex microbial communities, with broader implications for understanding gene flow in other host-associated ecosystems.
Parental effects link parental phenotype and environmental variation to offspring performance and evolutionary trajectories. However, their role remains poorly resolved in species lacking post-oviposition care, where offspring development is shaped mainly by pre-hatching parental influences. We investigated how parental phenotype, reproductive investment, and parental relatedness were associated with offspring development in the Asiatic toad (Bufo gargarizans). Amplectant pairs were collected from the wild, and offspring were reared under standardized laboratory conditions from fertilization to metamorphosis. Parental relatedness was estimated using microsatellite markers to evaluate how parental genetic similarity was associated with offspring developmental and morphological traits. We detected positive assortative pairing by body mass in B. gargarizans and strong clutch effects across offspring developmental traits, indicating substantial among-family variation. After distinguishing among parental body size, body mass, and body condition, the most consistent associations involved paternal body condition, paternal investment, and parental relatedness. Paternal body condition was positively associated with offspring growth rate during the G25-G42 interval, suggesting faster mid-stage larval growth in offspring of males in better condition. Paternal reproductive investment was positively associated with post-metamorphic morphology, particularly tibiofibula length at G46. Parental relatedness was negatively associated with length-related morphology around metamorphosis, and this association varied among developmental stages. Maternal traits showed more limited and mainly stage-dependent associations with offspring traits. Our results show that offspring development in B. gargarizans is associated with parental phenotype, reproductive investment, and parental relatedness. Paternal body condition and paternal investment were associated with offspring growth and post-metamorphic morphology, whereas parental relatedness was negatively associated with length-related morphology around metamorphosis. These findings suggest that parental effects in this species are trait-specific and stage-dependent. They also highlight the importance of integrating paternal phenotype and parental relatedness into studies of amphibian reproductive ecology, especially in species without post-oviposition care.
