Molecular Ecology最新文献

Coral species abundance and biodiversity estimates are typically based on colony macromorphology. However, such measurements often underestimate the true diversity within coral communities because morphology does not necessarily reflect behavioral or genetic divergence. We previously reported on the unusual spawning behavior of the brain coral Diploria labyrinthiformis (Linnaeus, 1758) in Curaçao, Southern Caribbean, where this species spawns in both spring and autumn. Here, using data collected from 2013 to 2021, we show that in Curaçao, D. labyrinthiformis comprises two behaviorally and genetically distinct lineages, with 93% of colonies spawning exclusively in one season or the other. The two lineages could not be distinguished based on obvious macromorphological differences or depth but represented clearly distinct genetic clusters (F_ST = 0.098) based on genome-wide sequencing. We tested for prezygotic and postzygotic gametic barriers between them by fertilising eggs released in spring 2019 with sperm collected and cryopreserved in autumn 2018. Fertilisation in this unidirectional cross was successful and the resulting larvae developed normally, thus eliminating complete gametic incompatibility or early life postzygotic barriers as explanations for their divergence. Using observations from 19 other localities across the Wider Caribbean Region, we confirmed the co-occurrence of discrete spring- and autumn-spawning populations across a range of latitudes. Thus, we show that seasonal, temporal reproductive isolation (allochrony), but not gametic reproductive isolation, is a strong barrier to gene flow in sympatric lineages of this critically endangered reef-building coral. More broadly, our findings underscore the role of allochrony in the creation and maintenance of cryptic coral lineages and the urgency of identifying, quantifying, and conserving this diversity before it is lost.

Within the same species of eusocial insects, individuals of different castes typically display widely different life-history traits: sterile workers live for a few months, while queens can live for decades. Ageing theories emphasise the importance of metabolism and oxidative stress in explaining longevity, with mitochondrial bioenergetics standing at the crossroads of energy and reactive oxygen species production. The study of mitochondrial functioning is therefore of great relevance in determining the nature of the mechanisms that explain the contrasting longevities between insect social castes. We addressed this question in the eusocial black garden ant Lasius niger. Our findings reveal that caste differences in mitochondrial bioenergetics and the oxidative balance only partially align with oxidative stress theory predictions. Long-lived queens display lower metabolic rates and mitochondrial density, yet maintain higher cellular energy availability, as reflected by a high adenylate energy charge (AEC). This may result from enhanced mitochondrial maintenance processes and potentially a specific recourse to the purine salvage pathway, promoting ATP availability while limiting oxidative cost. Our study highlights so far unrevealed bioenergetic adaptations that might contribute to the queens' remarkable lifespan.

Anthropogenic land-use and climate change pose novel selection pressures on bees, yet their evolutionary responses in terms of morphological or physiological adaptations remain unclear. While adaptive responses are expected, these may be constrained by gene flow when changes in selection pressures are spatially heterogeneous. The buff-tailed bumblebee (Bombus terrestris) is a widespread species that copes well with anthropogenic land-use and climate change, suggesting high adaptive capacity or phenotypic plasticity. Here, we genotyped populations of native B. terrestris in south and central Sweden using RADseq to investigate genetic structure and local adaptation across a paired design of agricultural landscapes with high and low land-use complexity along a geographic climate gradient. We expected to find genetic structure reflective of regional barriers to gene flow, and molecular evidence for local adaptation to differing landscape and climate conditions. We found genetic structure separating southern Sweden from more northern regions, with a negative Tajima's D indicating a potential population expansion, likely northwards and inland into forested areas, consistent with observational data indicating a range shift. We found weak but significant evidence for local adaptation to climate and land use, specifically to agricultural land cover, including genes under putative selection linked to insecticide resistance. Signatures of selection were also identified in relation to latitude, temperature, and urban land cover, with other candidate SNPs associated with olfaction and immune response. Our results suggest that B. terrestris successfully responded to anthropogenic land-use and climate changes, likely due to its generalist traits, enabling phenotypic adaptation to changing environments.

Mitonuclear discordance—evolutionary discrepancies between mitochondrial and nuclear DNA phylogenies—can arise from various factors, including introgression, incomplete lineage sorting, recent or ancient demographic fluctuations, sex-biased dispersal asymmetries, among others. Understanding this phenomenon is crucial for accurately reconstructing evolutionary histories, as failing to account for discordance can lead to misinterpretations of species boundaries, phylogenetic relationships, and historical biogeographic patterns. We investigate the evolutionary drivers of mitonuclear discordance in the Tropidurus spinulosus species group, which contains nine species of lizards inhabiting open tropical and subtropical environments in South America. Using a combination of population genetic and phylogenomic approaches applied to mitochondrial and nuclear data, we identified different instances of gene flow that occurred in ancestral lineages of extant species. Our results point to a complex evolutionary history marked by prolonged isolation between species, demographic fluctuations, and potential episodes of secondary contact with genetic admixture. These conditions likely facilitated mitochondrial genome capture while diluting signals of nuclear introgression. Furthermore, we found no strong evidence supporting incomplete lineage sorting or natural selection as primary drivers of the observed mitonuclear discordance. Therefore, the unveiled patterns are most consistent with neutral demographic processes, coupled with ancient mitochondrial introgression, as the main factors underlying the mismatch between nuclear and mitochondrial phylogenies in this system. Future research could further explore the role of other demographic processes, such as asymmetric sex-biased dispersal, in shaping these complex evolutionary patterns.

Wolbachia is the most frequent bacterial endosymbiont of arthropods and nematodes. Although it is mostly vertically transmitted, from parent to offspring through the egg cytoplasm, horizontal transfer of Wolbachia is thought to be common over evolutionary timescales. However, the relative frequency of each transmission mechanism has not been studied systematically in closely related species. Additionally, while Wolbachia is generally regarded as a reproductive manipulator, it is unclear how frequently the symbiont induces such effects. In this study, we investigated the presence, phenotypes and phylogenetic relationships among Wolbachia strains in whole genome sequence data for 18 European butterfly sister-species pairs. We find that sister-species share Wolbachia strains more often than random species pairs and that the probability of strain sharing is higher for younger pairs of host species, especially those with greater range overlap. We also find that split times between Wolbachia strains that infect the same sister-species pair generally pre-date host divergence, ruling out co-divergence in favour of horizontal transfer. However, some strains are younger than the mitochondrial split times of their hosts, so introgressive transfer cannot be ruled out in some cases. In addition, all newly assembled Wolbachia genomes contained putative homologues of genes associated with cytoplasmic incompatibility and male killing. This supports the potential for reproductive manipulation in Wolbachia strains infecting European butterflies, which until now was only inferred from mitochondrial diversity patterns. Our results show that horizontal and introgressive transfer of Wolbachia are frequent even between recently speciated host taxa, suggesting the symbiont's turnover rate is higher than had been inferred previously from surveys of distantly related hosts.

Alpine plants restricted to rocky habitats exhibit intraspecific diversification due to range fragmentation during Holocene warming, complicating predictions of their climate vulnerability. A lack of understanding of eco-evolutionary mechanisms driving their response to climate change results in ineffective conservation efforts. To uncover the genomic basis of their diversification and explain spatial patterns of their vulnerability, we combine landscape genomics and species distribution modelling. Our model, the Campanula lehmanniana complex, occurs in three distinct central Asian mountain ranges, considered both a biodiversity hotspot and a vascular plant diversity darkspot. Genome–environment association confirmed the adaptive basis of intraspecific diversification, driven by numerous loci of small effect. Genomic and ecological data indicate mountain range–specific climate sensitivity driven by altitude, temperature and precipitation. The cold-dry adapted group from Zeravshan-Hissar Mts will face niche decline but show a higher degree of preadaptation to future climate, while the temperate-humid group from Tian Shan shows an opposite response, with a higher risk of maladaptation despite predicted niche expansion. Maladapted populations at northern margins may require an influx of adaptive variation to cope with predicted changes. However, limited landscape connectivity between island-like habitats, combined with long migration distances required to minimise genotype–environment disruption, highlights the role of human-assisted migration in enabling evolutionary rescue. These results underscore the need to facilitate gene flow from pre- to maladapted populations and the importance of population-specific approaches to inform effective conservation strategies in heterogeneous mountain ecosystems. The results may be relevant to numerous Central Asian mountain species that show similar phylogeographic patterns.

Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype-environment associations (GEA), are often used to detect potential loci causing local adaptation but are rarely followed by experimental validation. Here, we tested loci identified in three moisture-related GEA studies on Arabidopsis. We studied 42 GEA-identified genes using t-DNA knockout lines under drought and tested effects on flowering time, an adaptive trait, and genotype-by-environment (GxE) interactions for performance and fitness. In total, 16/42 genes had significant effects on traits involved in local adaptation or performance responses to the environment. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, and 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow-up experiments, wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA-identified genes were validated for GxE interactions for fitness, we likely overlooked some genes because experiments might not well represent natural environments and t-DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow-up experiments are straightforward to implement in model systems and demonstrate prospects for GEA discovery of new local adaptations.

Soil bacteria play a crucial role in soil processes, such as carbon sequestration and nutrient cycling. While soil bacterial communities and their interactions with pedo-climatic factors have been well documented, most studies typically focus on broad taxonomic levels, leaving distribution and responses at the genus level unexplored. This study optimized machine learning models to predict the distribution of dominant bacterial genera across Australia on a comprehensive dataset of 1971 topsoil samples. Our high-resolution digital maps (~1 km resolution) reveal four distinct distribution patterns for the dominant bacterial genera: coastal or inland enriched patterns and latitude-related patterns. Each genus exhibited unique responses to critical factors, including temperature, precipitation, soil organic carbon (SOC), and pH. Notably, our findings highlight the importance of genus-level analysis, as bacterial genera within the same phylum can respond markedly differently to pedo-climatic conditions. Intensive land use significantly homogenized bacteria composition and increased the relative abundance of Rubrobacter, RB41, Microvirga, and Sphingomonas. Overall, this study enhances our understanding of bacterial macroecological trends and offers insights for more precise interventions to improve soil health and resilience against environmental changes.