Molecular Ecology最新文献

Biogeographic barriers are typically considered prominent geographic features that block or severely restrict dispersal and gene flow. However, mating barriers can also emerge within continuous suitable habitats, driven by ecological or behavioural constraints. Migratory insects show an extraordinary capacity to traverse vast geographic ranges, as well as notable landscape features like mountains, deserts and oceans. Yet, their movements are not unrestricted: they are shaped by seasonal dynamics that dictate the feasibility of migration across these landscapes. Hemisphericity, the existence of inverted seasonal regimes and orientation cues in the two latitudinal hemispheres, has been proposed as a potential abiotic barrier involved in the diversification of migratory insects. Here, we use population genomic data to investigate patterns of diversification in migratory caper butterflies (Belenois spp.) across Africa. We identify a striking phylogeographic break around the equator in Belenois aurota, and emerging population structure between northern and southern African populations in Belenois creona, consistent with migratory divides aligned with hemispheric barriers. These divergences largely predate the Last Glacial Maximum, when major environmental changes such as contractions-expansions of equatorial rainforests and savannahs occurred. This reinforces the hypothesis that long-term abiotic factors, such as hemisphericity, had a role in limiting north-south dispersal. Given the absence of detectable gene flow detected even in sympatric populations of B. aurota in their contact zone in Kenya, Uganda, and Tanzania, we argue that populations from the Northern and Southern Hemispheres represent different species, and reinstate the taxon Belenois syrinx (Wallengren 1860) reinst. stat. for the Southern African lineage. Our findings provide genomic evidence of migratory divides in insects, which surprisingly emerge in the absence of physical barriers in the landscape, highlighting a role of hemisphere-specific adaptations in driving reproductive isolation and diversification in migratory insects.

Quaternary climate change has accelerated species evolution. Periodic climate oscillations have driven the migration of different species between boreal and temperate areas, which has facilitated hybridisation between different taxa. Drastic climate fluctuations have isolated populations, which has imposed new selection pressures and potentially led to speciation. In this study, we integrated SNP and mtDNA data to investigate the complex reticular evolution history of four hare species, Lepus yarkandensis, L. tibetanus, L. tolai and L. timidus in northwest China, a biodiversity hotspot with diverse environments. Analysis of population structure and mito-nuclear discordance revealed extensive hybridisation among the four hare species. Phylogenetic analysis, population structure analysis, and F3 statistics revealed several genomic islands of differentiation between two genetically similar species, L. tolai and L. timidus, which may affect mate preferences. F3 statistics detected the gene flow between L. tibetanus and other hare species. Then the introgression regions were found by fd analysis, which may have influenced the adaptive evolution of L. tibetanus. Population history further indicated that the four hare species have experienced two severe bottleneck events. The first event was triggered by the Mid-Brunhes Event (MBE), which drove the migration of hares to limited refuges and possibly facilitated the emergence of L. tibetanus. The second event was likely caused by human activities, possibly due to the hunting of hares by early humans. Our findings provide new insights into the evolutionary history and speciation of Lepus in northwest China.

The spread of staple crops to diverse environments over time and their current genetic structure may reflect historical dispersal by humans, sustained human preference for particular traits and adaptation to local environments. Sorghum is a drought-tolerant crop native to Africa cultivated by hundreds of millions of smallholders globally. Here we examined the ecological context of population-genomic structure of 1806 sorghum landraces across Africa and Eurasia to infer the relative contribution of environmental and cultural factors to sorghum genetic diversity across different relative time periods. Sorghum landraces were spatially and linguistically structured at a large scale and within subregions, following a pattern of isolation by distance. Within regions, much of the genomic structure was best explained by a mechanistic model of human travel time. In our assessment of hierarchical linguistic structure, we found that language families explain 4% of genomic variation while individual languages explain 13% of genomic variation, suggesting the importance of human culture and relationships in gene flow and selection. Variance partitioning showed that travel time, language and climate explain up to 27% of genomic variation among landraces. We also observed regional differences in the degree of genetic relatedness across space and time in our assessment of shared ancestry. East Africa showed particularly strong geographic turnover in genomic composition and haplotype sharing, while West Africa showed substantial haplotype sharing even over large distances, signifying some rapidly spreading lineages. Thus, space, travel time and culture likely capture important forces controlling sorghum genomic variation, but these factors operate heterogeneously over space.

Amidst global reef declines, large-scale coral aquaculture is being developed to support reef intervention. Genetic diversity underpins population resilience and therefore it is critical that aquaculture methods maintain diversity. However, it remains unclear how genetic diversity of coral progeny is shaped by (1) parental genetic composition, (2) winnowing during aquaculture grow-out, and (3) field deployment. We utilised single nucleotide polymorphisms to examine genetic diversity dynamics in two coral progeny cohorts produced from 5 and 14 parents, with standardised gamete input per parent. Cohorts were sampled over 1 month of aquarium rearing, and for the 14-parent cohort, again after 2 years of field deployment. Parentage analysis confirmed that all parents contributed genetic material to surviving offspring at each cohort's end-point. However, per-parent contributions differed significantly, indicating skewed reproductive success despite equal gamete inputs. Temporal and parent-pool differences in heterozygosity (H_o) were observed during larval stages. At 12 h post-fertilisation, H_o was highest in the 5-parent offspring cohort, and lowest in the 14-parent cohort, reflecting high and low parental genetic dispersion among parents, respectively. By 84 h post-fertilisation, H_o decreased in 5-parent and increased in 14-parent cohorts, suggesting early development purges genetic defects from outbreeding or inbreeding depression, respectively. Importantly, H_o was similar among cohorts and did not decline after 7 days in either cohort, nor after 2 years in the 14-parent cohort, suggesting no evidence of a genetic bottleneck after settlement competency. These findings highlight that parental genetic diversity, rather than the number of parents contributing per se, is crucial to maintain genetic diversity in coral aquaculture, with implications for restoration.

Natural populations are in constant need of balancing resource allocation to compensate for seasonal environmental variation. In many insects, a well-established trade-off between migration and reproduction exists. While this trade-off has been characterised phenotypically for decades, the underlying regulatory pathways are poorly understood. Here, we examined how resource-related environmental cues shape transcription across development in the long-distance migrant butterfly Vanessa cardui. In a multi-cue, developmental stage-specific design, adult females were exposed to host-plant presence or absence, while larvae experienced food limitation or crowding. Adult exposure to host plants was associated with differential expression in ecdysteroid and juvenile-hormone pathways, consistent with endocrine regulation of reproductive readiness and predictions of the oogenesis-flight syndrome. Larval resource limitation altered developmental and metabolic pathways, suggesting molecular predispositions and potential carry-over effects to adult traits. Across all contrasts, metabolism emerged as a shared axis linking responses across life stages. Together, our results show that resource-driven cues leave both stage-specific and general transcriptional signatures that connect environmental context with the molecular basis of migratory behaviour.

Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.

Fine-scale thermal heterogeneity within intertidal and subtidal microhabitats could drive divergence in organismal heat tolerance. Reef corals from the extreme intertidal may hold optimism for the future of coral reefs and give insights into the mechanisms by which coral may persist under future conditions. Here, we compared the thermal sensitivities of intertidal and subtidal Acropora digitifera and evaluated their bleaching phenotypes, transcriptomes, host genetic differentiation and bacterial communities. Results showed that only heat-exposed subtidal corals displayed significantly reduced photochemical efficiency, symbiont densities, pigment and host protein concentrations, suggesting bleaching and host starvation. Despite being genetically similar, heat-exposed subtidal corals mounted stronger immune activation and amino acid degradation but downregulated monocarboxylate transport and calcification compared to intertidal corals. In contrast to the prevalence of Cladocopium in subtidal corals, intertidal corals were dominated by Durusdinium, whose transcriptional signature was characterised by lineage-specific and constitutively high transcript abundance of orthologs involved in stress response, metabolism, photosynthesis, cell cycle and symbiotic interactions. Furthermore, 16S rRNA sequencing demonstrated an origin-dependent bacterial composition, with Endozoicomonas being more abundant and important in co-occurrence networks of intertidal corals. Our findings suggest that distinction in Symbiodiniaceae and bacterial communities and Symbiodiniaceae lineage-specific transcriptional footprint largely underpin the exceptional thermotolerance of intertidal Acropora. Although these corals provide promising avenues for restoration, such a mechanism may bring attention to the risk of using them in selective breeding, particularly given the horizontal transmission of algal symbionts in Acropora.

Crassulacean acid metabolism (CAM) is a water-efficient photosynthetic strategy involving a coordinated suite of complex traits including metabolic, anatomical and regulatory aspects that shift across the diel cycle. While CAM has evolved repeatedly in land plants, the evolutionary routes enabling this convergence remain elusive. Whereas the same core CAM (de)carboxylation genes are consistently involved, a key question is whether distinct CAM phenotypes also depend on a shared set of auxiliary genes, reflecting a quantitative continuum of expression, or whether they can instead emerge through divergent or redundant peripheral solutions. The bromeliad subgenus Tillandsia, with diverse photosynthetic strategies, offers an ideal system to explore this question. Using physiological and transcriptomic analyses of well-watered and water-limited accessions of two closely related species, we characterised facultative and constitutive CAM. By comparing orthologous gene expression and orthogroup recruitment, we found that while both species performed CAM upon water-withholding, transcriptional shifts in pathways related to stomatal movement, sugar/malate transport, aquaporins and starch metabolism showed minimal overlap. Core enzymes involved in the CAM (de)carboxylation cycle exhibited broadly shared expression patterns, yet the facultative CAM species uniquely upregulated PPC2 at night instead of the canonical CAM-related PEPC ortholog PPC1. Our study reveals that, while the expression of certain core CAM enzymes is conserved, the surrounding transcriptional architecture can differ substantially even between closely related species. This supports a model in which CAM evolves through a mosaic recruitment of functionally equivalent, yet nonorthologous genes-underscoring its flexible and modular genetic architecture. These insights advance our understanding of the mechanisms enabling the repeated evolution of CAM and its capacity to facilitate adaptive diversification.

The Eastern Gulf Coastal Plain (EGCP) is a small region within the North American Coastal Plain (NACP), a recognised biodiversity hotspot. The EGCP has been described as 'one of the most important hotspots of speciation and endemism' in the United States, yet remains an anomaly relative to other regions with high biodiversity and endemism. In contrast to most biodiversity hotspots, the EGCP is homogeneous in elevation, coastal and geologically young. We here provide a novel synthesis of the origins and diversification of the EGCP biota. We review published phylogenies of range-restricted endemic vascular plant species in the EGCP to catalogue the geographic locations of their closest relatives. We find the EGCP to represent a crossroads where lineages from diverse locations have converged and, in some cases, diversified. To better understand mechanisms leading to species diversity, we review fine-scale phylogeographic and population genetic analyses across crown eukaryotes in the EGCP and create ecological niche models of overlapping sister species. We find that geographic barriers to dispersal (often rivers) have likely led to high species diversity in this region due to repeated bisection of the EGCP in times of cyclical inundation (e.g., following glaciation). This work has implications for understanding the formation of biodiversity hotspots at fine scales more generally and acts as a regional test case of an anomalous hotspot in a coastal lowland, showing that such areas can be as crucial for diversification and species richness as mountains or islands.

Intraspecific genetic diversity (ISD) underpins key eco-evolutionary processes, yet its spatial distribution across species' ranges remains poorly understood at broad scales. Combining mitochondrial sequence alignments, species distribution models and comparative analyses, we tested whether populations closer to current niche optima exhibit higher ISD-a prediction derived from the central-marginal paradigm. With this aim, we investigated how ISD varies in relation to both climatic and geographic centroids using data from 436 herptile species (248 reptiles and 188 amphibians) from six regions across the world. We adopted a meta-analysis approach based on publicly available data. For species presenting at least five georeferenced DNA sequences from unique locations (~2.5-km resolution) within their buffered geographic range, we generated spatially explicit ISD surfaces by interpolating gene-specific data. We then quantified the relationship between ISD and the distance to both climatic and geographic centroids using species-specific Spearman's ρ coefficients. To further explore the drivers of these patterns, we applied a Random Forest framework to predict Spearman's ρ as a function of climate, ecology, geography, morphology and demography. Contrary to prevailing assumptions, the strength and direction of ISD-centroid correlations proved highly variable and species-specific, and the models consistently showed poor predictive performance. These results suggest that no uniform macroecological or evolutionary processes govern ISD patterns across taxa, but rather that ISD reflects lineage-specific histories, ecological contexts and demographic contingencies. Our findings underscore the challenges of predicting genetic diversity patterns and highlight the relevance of species-tailored approaches in conservation planning.