Molecular Ecology最新文献

Intraspecific competition due to for example, density, has substantial influence on fitness dynamics and life histories, but the underlying physiological mechanisms are often complex and the molecular basis unclear. Further, designing laboratory experiments to measure physiological responses that reflect natural conditions is challenging. Here, we reared Atlantic salmon juveniles in semi-wild conditions in two densities to investigate the molecular mechanism of density-related changes in the hypothalamus, a key brain region regulating stress and energy homeostasis. We measured density-dependent changes in the expression of 12 genes involved in appetite and stress regulation and 16 genes involved in post-transcriptional regulation of gene expression via m⁶A RNA methylation. We also quantified genotype-environment interactions between density and two major life-history loci, vgll3 and six6. We found significant density-related differences in the expression of genes coding for corticotropin-releasing factors, appetite stimulators and inhibitors and m⁶A RNA methylation actors. Moreover, a paralogue of an appetite inhibitor showed a density-dependent pattern that was the opposite of what was expected. Six6 locus was also associated with changes in the expression of epitranscriptomic markers, including two writers and one eraser. Our results highlight that individuals' response to density in natural conditions is shaped by a complex interplay between stress, appetite and epitranscriptomic pathways in the hypothalamus. In addition, the functional divergence of paralogs indicates a potential role of genome duplication shaping such a response. We emphasise the value of integrating different physiological responses at the molecular level to better understand ecological processes affected by environmental change.

Parthenogenesis, or all-female clonal reproduction, is rare among vertebrates. This is often attributed to the selective disadvantages of assumed reduction of genetic diversity in the absence of sex. However, parthenogenetic vertebrates have highly complex evolutionary histories, with most arising through hybridisation and many being polyploid. Here, we show that geographically widespread triploid parthenogenetic forms of the Australian gekkonid Heteronotia binoei are considerably diverse despite their clonal reproductive mode, with patterns of variation consistent with two previously identified reciprocal hybrid origins and numerous backcrossing events. We also confirm a two-fold increase in genome-wide heterozygosity among parthenogens (10.6%) compared with the sexual progenitors (4.63%). Our SNP-based diversity estimates exceed prior predictions for clonal H. binoei lineages based on karyotype and allozyme data. We also find evidence of repeated and geographically widespread backcrossing in both western and central Australia. This supports the long-standing hypothesis that parthenogens are able to partially recover parental niches by 'freezing' genotypic diversity present within the sexual forms. Understanding how asexual clones attain ecological success has implications for managing both invasive species, many of which are clonal, and threatened species, which often face similar challenges associated with reduced genetic diversity. Overall, our findings demonstrate that sex, historical or ongoing, is instrumental in the persistence of asexual lineages, contributing to a broader understanding of the evolutionary dynamics of parthenogenesis.

Anthropogenic salinisation of freshwater ecosystems represents a major threat to biodiversity. While the ecological consequences of freshwater salinisation have received extensive investigation, our knowledge of the evolutionary responses to projected salinisation is more limited. Phenotypic plasticity can be an important first step to facilitate population persistence in stressful environments. Here, we combined high-resolution environmental data with a laboratory-based experiment to investigate the time-course of gene expression plasticity in response to projected salinisation in two populations of the western mosquitofish (Gambusia affinis) with different histories of salt exposure. We found significant differences in transcriptional plasticity between populations as well as a general tendency for non-parallel expression change in salinity-responsive genes identified in both populations. Despite this pattern, we identified a core set of genes that showed parallel responses to salinity in both populations across all time points. However, these parallel responses in gene expression were putatively regulated by largely non-overlapping sets of microRNAs in each population. Finally, we found that genes expressed in parallel showed greater nucleotide diversity than genes with non-parallel responses, possibly providing standing genetic variation to facilitate population persistence under changing salinity conditions. Our results provide insights into the evolutionary consequences of freshwater salinisation and demonstrate the potential of freshwater fish to cope with projected salinisation.

Marine microbial communities are structured by a complex interplay of deterministic and stochastic processes, yet how these vary across latitudes remains poorly understood. Most long-term microbial observatories are restricted to temperate regions, limiting our ability to assess latitudinal contrasts in microbial dynamics. Here, we compare coastal microbial communities from two contrasting marine time-series stations using standardised molecular protocols: a new tropical site in the Equatorial Atlantic (EAMO, 6° S) and a well-studied temperate site in the Mediterranean Sea (BBMO, 41° N). Monthly 16S and 18S rRNA gene sequencing of two size-fractions (0.22-3 μm and > 3 μm) over 41 months (from April 2013 to August 2016) revealed marked differences in taxonomic composition, temporal variability and ecological assembly processes. Temperate communities exhibited strong seasonal turnover, higher beta-diversity and tighter coupling with environmental variables such as temperature and daylength. In contrast, tropical communities were compositionally more stable and more governed by biotic factors and stochastic processes such as historical contingency and ecological drift. These patterns were consistent across taxonomic domains and size-fractions, though selection was generally stronger in prokaryotes and the smallest size-fraction. Co-occurrence networks at the temperate site were more densely connected and environmentally responsive compared to tropical networks, where stochastic processes and putative biological interactions gain prominence. This study highlights the importance of integrating observatories from underrepresented latitudes into global microbial monitoring efforts, particularly as climate change alters the amplitude and frequency of environmental drivers across the ocean.

Short-term responses to temperature stress, such as heat waves and long-term acclimation to temperature changes, including seasonal shifts, are expected to be mediated by distinct molecular pathways. However, in ectotherms, such as reptiles, the effects of exposure duration on molecular responses to temperature change remain unclear. In this study, we investigated temperature-induced molecular changes across distinct timescales in a newly established reptilian model species, the Madagascar ground gecko (Paroedura picta). To determine temperature-responsive phenotypes and assess phenotypic plasticity under long-term temperature changes, we compared thermal traits in individuals acclimated to 25°C and 30°C for more than 30 days. We found significant differences in the critical thermal minimum and maximum as well as sprint speed between the two groups. We then employed RNA sequencing and the assay for transposase-accessible chromatin using sequencing to analyse gene expression, splicing and chromatin states across multiple temperature conditions and durations. Results revealed that abrupt temperature shifts activated known heat stress pathways, whereas prolonged temperature acclimation altered immune function. In the liver, the predicted occupancy of some transcription factors diverged between short- and long-term temperature stimuli. These findings indicate that transient temperature stress responses and long-term temperature acclimation in P. picta involve distinct molecular mechanisms.

Sympatric morphs provide valuable systems for studying incipient divergence despite incomplete reproductive isolation. In connected waterbodies with spatially heterogeneous habitats, one or more morphs may form metapopulation structures, generating eco-evolutionary dynamics unlike those in single lakes. We studied the phenotypic and genome-wide differentiation in Arctic charr (Salvelinus alpinus) in two Icelandic lakes: Thingvallavatn, known to harbour four distinct morphs, and a smaller downstream lake, Ulfljotsvatn. Our analyses confirm a single origin of charr polymorphism in this system, with all morphs present in both lakes. Relative morph abundances differ between the lakes: PL-charr dominate in Thingvallavatn, whereas LB-charr are most abundant in Ulfljotsvatn. Three morphs, large- (LB-), small (SB-) benthivorous and planktivorous (PL-) charr, are genetically distinct. The system likely forms a source-sink structure for both PL- and SB-charr, though migration rates from Thingvallavatn vary remarkably, resulting in distinct population dynamics. Conversely, LB-charr exhibit genetic differentiation between the lakes, suggesting the presence of a separate population in Ulfljotsvatn. While piscivorous (PI-) charr appear genetically similar to PL-charr, evidence suggests hybridisation between PI- and LB-charr in both lakes. Moreover, the higher hybridisation in the downstream lake likely contributes to the observed erosion of genetic separation between LB- and PL-charr in Ulfljotsvatn. These findings suggest that the complex interplay of habitat heterogeneity and morph-specific migrations shapes the coexistence and eco-evolutionary dynamics of sympatric charr morphs in the connected lakes. Our study highlights the importance of investigating early divergence in spatially complex systems to advance eco-evolutionary research.

Reef-building corals face continued declines due to climate change-amplified marine heatwaves. In addition to affecting coral heat tolerance, corals' algal endosymbionts (family Symbiodiniaceae) can reflect their prior heatwave exposure, although understanding is often limited to heatwave-induced shifts between symbiont genera. Here, we used ITS2 metabarcoding to characterise Symbiodiniaceae assemblages in 293 individuals of the common Indo-Pacific coral Acropora aff. digitifera in Palau (Western Pacific), between two outer-reef regions with contrasting heatwave histories. During the strongest recorded heatwaves, southwestern 'hotspot' reefs have typically accrued an additional 2°C-weeks of heat stress compared to thermal 'refugia' located 60 km north. In contrast to previous studies that observed declines in symbiont richness following heat stress, we found a greater diversity of symbiont taxa and low-abundance sequence variants in 'hotspot' corals, predominantly within the C40 lineage in genus Cladocopium. Combining these data with experimental heatwave performance from 168 of these corals revealed that approximately 10% of heat tolerance variability at hotspot reefs was associated with hosting different symbiont taxa. Compared to other hotspot corals, those hosting symbionts with the C15h sequence variant suffered bleaching mortality at 0.8°C-weeks lower heat stress. Despite higher variability in heat tolerance among corals from thermal refugia compared to hotspot reefs, we found no association between heat tolerance and the symbionts hosted by refugium corals. As the world's coral reefs are exposed to intensifying marine heatwaves under accelerating climate change, the low-abundance variants that characterise symbionts within genera or lineages may become increasingly important indicators of poor heatwave tolerance.