Molecular Ecology最新文献

The frequency of emerging disease is growing with ongoing human activity facilitating new host-pathogen interactions. Novel infection outcomes can also be shaped by the host microbiota. Caenorhabditis elegans nematodes experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, have been shown to suffer higher mortality than those infected by the pathogen alone. Understanding the host responses to such microbiota-pathogen ecological interactions is key to pinpointing the mechanism underlying severe infection outcomes. We conducted transcriptomic analyses of C. elegans colonised by its native microbiota, S. aureus and both in combination. Correlations between altered collagen gene expression and heightened mortality in co-colonised hosts suggest the microbiota modified host resistance to infection. Furthermore, microbiota colonised hosts showed increased expression of immunity genes and variable expression of stress response genes during infection. Changes in host immunity and stress response could encompass both causes and effects of severe infection outcomes. 'Re-wilding' this model nematode host with its native microbiota indicated that typically commensal microbes can mediate molecular changes in the host that are costly when challenged by a novel emerging pathogen.

Ostrea edulis, the European flat oyster, was once a widespread economically and ecologically important marine species, but has suffered dramatic declines over the past two centuries. Consequently, there has been a surge in European restoration efforts, many of which focus on restocking as a conservation measure. In this study, we used whole-genome sequencing (WGS) data to investigate the population structure, demographic history, and patterns of local adaptation of O. edulis across its natural distribution with increased sampling densities at Scandinavian localities. Results revealed seven distinct genetic clusters, including previously undescribed complex population structure in Norway, and evidence for introgression between genetic clusters in Scandinavia. We detected large structural variants (SVs) on three pseudo-chromosomes. These megabase long regions were characterised by strong linkage disequilibrium and clear geographical differentiation, suggestive of chromosomal inversions potentially associated with local adaptation. The results indicated that genomic traces of past translocations of non-native O. edulis were still present in some individuals, but overall, we found limited evidence of major impacts of translocations on the scale of contemporary population structure. Our findings highlight the importance of considering population structure and signatures of selection in the design of effective conservation strategies to preserve and restore wild native European flat oyster populations, and we provide direct knowledge safeguarding sustainable mitigation actions in this important species.

Invasive species with native ranges spanning strong environmental gradients are well suited for examining the roles of selection and population history in rapid adaptation to new habitats, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill (Urosalpinx cinerea) is a marine snail whose native range spans the strongest coastal latitudinal temperature gradient in the world, with invasive populations established on the US Pacific coast. Here, we leverage this system using genome-wide SNPs and environmental data to examine invasion history and identify genotype-environment associations indicative of local adaptation across the native range, and then assess evidence for allelic frequency shifts that would signal rapid adaptation within invasive populations. We demonstrate strong genetic structuring among native regions which aligns with life history expectations, identifying southern New England as the source of invasive populations. Then, we identify putatively thermally adaptive loci across the native range but find no evidence of allele frequency shifts in invasive populations that suggest rapid adaptation to new environments. Our results indicate that while these loci may underpin local thermal adaptation in their native range, selection is relaxed in invasive populations, perhaps due to complex polygenic architecture underlying thermal traits and/or standing capacity for phenotypic plasticity. Given the prolific invasion of Urosalpinx, our study suggests population success in new environments is influenced by factors other than selection on standing genetic variation that underlies local adaptation in the native range and highlights the importance of considering population history and environmental selection pressures when evaluating adaptive capacity.

Environmental temperature shapes the ontogeny of ectotherms by influencing rates of growth and development which can be key determinants of survival. Whereas the escalating impacts of water management on freshwater ecosystems is well documented, the effects of cold-water releases from dams-which can alter downstream temperatures-remains relatively underexplored but may present novel challenges to endemic ectotherms. Specifically, little is known about how thermal depressions reshape phenotypic and genetic patterns during larval metamorphosis for fishes that evolved in warmwater systems. We assessed the effects of thermal shifts on larval ontogeny of the endangered razorback sucker (Xyrauchen texanus), which evolved in the warm waters of the Colorado River Basin, USA. We hypothesised that development is more sensitive to cold-water influences than growth and that temperature would influence patterns in gene expression related to development. Our results supported these hypotheses and showed that both wild and laboratory-reared larvae in slightly cooler temperatures exhibited delayed development, but similar growth compared to larvae reared in warmer conditions. These findings suggest growth and development in early ectotherm life stages can be decoupled, which follows patterns more like the temperature-size rule than allometric scaling of development by size. We also observed transcriptional differences related to genes associated with stress responses and development in our laboratory-reared fish; here, gene expression of fish from the coldest conditions at the end of the experiment was more similar to fish reared in warmer temperatures at the midpoint. Our findings suggest that modest temperature reductions can delay ontogeny and alter the transcriptional landscape while not necessarily limiting growth. This finding highlights the need for conservation practitioners to consider cascading impacts that even small temperature reductions can cause in riverine ecosystems.

Specific interactions between bacteria and ectomycorrhizal fungi (EcMF) can benefit plant health, and saprotrophic soil fungi represent a potentially antagonistic guild to these mutualisms. Yet there is little field-derived experimental evidence showing how the relationship among these three organismal groups manifests across time. To bridge this knowledge gap, we experimentally reduced EcMF in forest soils and monitored both bacterial and fungal soil communities over the course of a year. Our analyses demonstrate that soil trenching shifts the community composition of fungal communities towards a greater abundance of taxa with saprotrophic traits, and this shift is linked to a decrease in both EcMF and a common ectomycorrhizal helper bacterial genus, Burkholderia, in a time-dependent manner. These results not only reveal the temporal nature of a widespread tripartite symbiosis between bacteria, EcMF and a shared host tree, but they also refine our understanding of the commonly referenced 'Gadgil effect' by illustrating the cascading effects of EcMF suppression and implicating soil saprotrophic fungi as potential antagonists on bacterial-EcMF interactions.

Population genomics has great potential to inform applied conservation management and associated policy. However, the bioinformatic analyses and interpretation of population genomic datasets can be daunting and difficult to convey to nonspecialists, including on-the-ground conservationists that work with many state, federal and international agencies. We think that individual population genomic metrics of interest can be interpolated and ultimately distilled into thematic GIS layers that represent spatiotemporal genomic potential (or conversely, susceptibility) in conservation monitoring. As examples relevant to ongoing conservation efforts, we use introgressive hybridisation and individual heterozygosity to illustrate a conceptual approach for mapping population genomic susceptibility. The general framework of thematic layers could be extended to integrate key genomic metrics (e.g., runs of homozygosity and genomic load) that are relevant to many conservation efforts.

The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.

Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable versus dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable versus dynamic habitat specialists.

Climate change and human influence are transforming mountain ecosystems, significantly impacting species distributions and biodiversity. Among these changes, the upward migration of lowland species into mountain regions stands out. This study examines the ecogeographical niche overlap and genetic diversity among three Leucanthemum species distributed along an altitudinal gradient in the Carpathian Mountains: the lowland L. ircutianum (4x), the montane L. rotundifolium (2x) and the alpine L. gaudinii (2x). By genotyping over 600 individuals using SNP analysis, followed by principal coordinate analysis (PCoA), Neighbour-Net Network and Structure clustering, we reveal not just distinct genetic groups but also hybridisation across all species, suggesting the potential for triple hybrids. Genetic admixture is further supported by environmental background and niche overlap analyses that reveal substantial overlap among species, particularly in line with their vertical distribution. Climate envelope plots indicate a likely reduction in available habitat for mountainous species due to climate change, leading to an increase in competition and an intensification of hybridisation. Anthropogenic influences are further intensifying these hybridisation trends. Among the studied species, L. gaudinii is most at risk of overwhelming hybridisation, whereas L. ircutianum may experience habitat expansion. By providing a comprehensive genetic and ecological overview, our research highlights the significance of hybridisation in biodiversity conservation and the challenges posed by environmental changes and anthropogenic activities in mountain environments. This study not only contributes to the understanding of genetic diversity in the Carpathians but also underscores the broader implications for molecular ecology and conservation strategies in mountain ecosystems.

In most fishes, the number of offspring increases with maternal body size. Although this size-fecundity relationship often varies among species as a result of the coevolution of life-history traits, the genetic basis of such size-fecundity relationships remains unclear. We explored the genetic basis underlying this size-fecundity relationship in two small medaka species, Oryzias latipes and O. sakaizumii. Our findings showed that O. sakaizumii has a higher fecundity than O. latipes, and quantitative trait locus analysis using interspecific F₂ hybrids showed that chromosome 23 is linked to the size-fecundity relationship. In particular, the genes igf1 and lep-b in this region are known to be associated with life-history traits, including somatic growth, gonad maturation, and progeny numbers in various taxa. Because O. sakaizumii is distributed at higher latitudes and has a shorter spawning season than O. latipes in the wild, we propose that the relatively high fecundity observed in O. sakaizumii is an adaptation to high latitudes. We also discuss the potential ecological ramifications associated with the evolution of increased fecundity in this species.