Molecular Ecology最新文献

The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesised to indirectly select for increases in the genome-wide recombination rate. This hypothesis is potentially consistent with theory on the evolution of the recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilise population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domesticated goats compared to bezoars but more mixed results in chicken and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in genome-wide recombination with domestication.

Pollinators harbour diverse RNA viromes that play a vital role in their health. Yet, factors that shape viral communities are often unclear. The European honey bee (Apis mellifera) is experiencing a viral epidemic since the emergence of the parasitic mite Varroa destructor (varroa) introduced vector-borne transmission, which has also been linked to increased viral spillover into wild pollinator communities. Varroa-free island populations provide natural laboratories to study the effect of varroa, while also allowing us to ask how islands affect viral communities. Barriers that restrict the dispersal of wild pollinators and their pathogens to islands may be overcome by human-mediated transport in managed honey bees. Here we used islands with and without varroa and matched mainland populations of honey bees (A. mellifera) and bumble bees (Bombus terrestris) from 2015 and 2021 to explore how varroa presence and island location affect the virome of managed and wild bees. We find lower viral richness on islands in both species. Bumble bees harbour a distinct viral community that was not affected by varroa but geographically structured. In honey bees, however, varroa-present populations contained more viral reads driven by a high abundance of deformed wing virus (DWV). Within the 6 years between the sampling events, DWV underwent a shift from mostly DWV-B towards a mix of DWV-B and recombinant strains. Surprisingly, these shifts appeared independent of varroa. Viewing pollinator virome composition within an ecological framework provides valuable insights into the barriers to virus spread and could help to predict drivers of disease emergence.

Environmental adaptation and speciation are key processes shaping biodiversity, especially in extreme environments. This study investigates the Yarkand hare (Lepus yarkandensis), inhabiting the arid Tarim Basin, and the Desert hare (Lepus tibetanus), residing in the cold and hypoxic Pamir Plateau. These species, facing distinct environmental pressures, provide an ideal model for understanding how organisms adapt to extreme conditions. Using whole-genome resequencing, we identified genomic regions associated with environmental adaptation in both species, and employed selective sweep and functional enrichment analyses to pinpoint important candidate genes. Additionally, we examined morphological adaptations, measuring body size, nasal bone structure and tympanic bulla, to explore how these traits facilitate survival in their respective environments. The results reveal common adaptive strategies, such as selection for genes related to energy metabolism and immune function. However, due to their distinct environments, the species exhibit different evolutionary paths. The Yarkand hare has larger tympanic bullae but a smaller body size, aiding heat dissipation and predator avoidance. In contrast, the Desert hare has a larger body size and longer nasal bones, reducing heat loss and warming the cold air at high altitudes. These findings highlight the crucial role of divergent selection in shaping adaptive traits, contributing to ecological isolation and supporting speciation in response to environmental challenges. This research enhances our understanding of adaptive evolution and has implications for conservation strategies aimed at addressing climate change impacts.

Humans have relied on animal fur for centuries, yet fur farming only began recently during the mid-19th Century. Little is known about this incipient domestication or the genomic processes involved. Domestication may involve founder effects, population bottlenecks and low population size, which, when combined with intense artificial selection, lead to inbreeding, a limited gene pool and reduced fitness. The arctic fox (Vulpes lagopus) has been farmed intensively since the early 1900s and has been artificially selected for economic phenotypes. We investigated the origin of these lineages and the genomic consequences of intensive farming by comparing the genomes of farmed and wild arctic foxes from across their range. Our research indicates recent inbreeding through long Runs of Homozygosity and reduced genomic variation in farmed foxes relative to their respective wild populations. We identified a coastal ecotype origin for all Fennoscandian farmed arctic foxes, aligning them phylogenetically with the wild Icelandic population, a geographically isolated and phenotypically distinct coastal lineage. The depleted genome-wide heterozygosity and increased recent inbreeding in farmed fox lineages is consistent with a heavy consequence of domestication, shedding light on the demographic history and genomic consequences of human manipulation. We highlight the need for increased genomic investigations into fur farm populations to understand the incipient domestication process and uncover the cost of intense farming. The genomic consequences of domestication must be considered in the management of fur farms, with actionable steps needed to prevent descendants of escaped farmed foxes from polluting the gene pool in the wild through introgression.

The degree or extent of gene reuse during repeated adaptation offers key insights into the genomic constraints on evolution. Although many studies have identified signs of genomic repeatability, a thorough synthesis of methods for detecting gene reuse and estimating its extent is missing. In this review, we first propose a simple framework for studies aimed at identifying gene reuse during repeated adaptation using genomic data. Next, we examine existing approaches to (i) detect gene set overlap, perform significance testing, and perform multivariate dimensionality reduction, (ii) distinguish between gene and allele reuse while emphasising methods for detecting allele reuse, (iii) explore models to identify the mechanisms behind repeated adaptation, and (iv) address issues and potential solutions to differentiate true gene reuse from methodological artifacts. Our review highlights standardised methods developed using genomic data to identify gene reuse. We also note that, although few studies quantify allele reuse, conducting such analyses is essential because it adds a more detailed layer to predicting evolutionary paths. Finally, several strategies can be used to cross-validate signals of gene reuse. These should be applied to confirm true positives, as biological and methodological artifacts can bias predictions. By synthesizing current methods and outlining a robust analytical framework, we provide a roadmap for enhancing the accuracy and reliability of gene reuse detection in adaptive evolution.

Tropical Asia's complex, dynamic geological and climatic history, coupled with its diverse topography, provides a fascinating setting to study evolutionary processes driving high biodiversity. This phylogenomic research reconstructs the evolutionary history of the strictly arboreal and forest-dependent Oriental Giant Squirrels (Ratufa) to gain insights into the interplay between paleo-forest distribution and regional diversification. By analysing genomic data (complete mitochondrial genomes and approximately 4000 nuclear ultraconserved elements) from historic museum specimens and conducting divergence time estimation and niche modelling, we uncover how global paleoclimate cooling, the uplift of the Himalayas and Tibetan Plateau, and habitat fragmentation led to allopatric speciation in refugia during the mid-Miocene, Miocene-Pliocene boundary, and late Pliocene, in synchrony with other evergreen forest-dependent species. Our findings underscore the potential role of grassland expansion during climatic oscillations and the North Sunda and Mekong paleorivers in isolating populations and promoting vicariance and speciation in this region. This research suggests a species-level diversity underestimation within R. bicolor and R. affinis, supporting the recognition of R. gigantea as a distinct species, along with several candidate species that warrant integrative taxonomic revision. Additionally, this study highlights the rapid and independent evolution of dwarfism in three Ratufa lineages and discusses challenges in museum genomics. Ultimately, this study serves as a valuable reference on the historical biogeography of tropical Asia, providing important insights for the conservation of these threatened taxa and the evolutionary processes that generate and maintain biodiversity in this hyperdiverse region.

Sponge microbial communities play a crucial role in marine ecosystem functioning and serve as a rich source of bioactive compounds. While host identity is recognised as a major determinant of microbiome diversity, the underlying evolutionary mechanisms remain poorly understood. This study aimed to comprehensively assess phylosymbiosis patterns within the sponge family Petrosiidae. In total 21 sponge species, collected across a broad geographic scale, were examined to investigate how host phylogeny influences microbiome composition. Using 28S rRNA, 18S rRNA and COI gene barcoding to identify host sponges, combined with 16S rRNA gene amplicon sequencing to characterise prokaryotic communities, we provide evidence of phylosymbiosis through multiple analytical approaches, including distance-based metrics and topological congruence. Our results show that host phylogeny and identity play a significant role in structuring sponge microbiomes, even at finer taxonomic resolutions. However, we observed notable incongruencies, where closely related sponge species exhibit divergent microbial communities that appear to be associated with depth or geographical location. This study represents the first large-scale investigation of phylosymbiosis in sponges at the family level, providing valuable insights into the evolutionary and ecological drivers shaping sponge microbiomes, particularly in the sponge family Petrosiidae.

Domestication involves huge phenotypic shifts via strong directional selection. The resulting changes, often termed the Domestication Syndrome, typically encompass numerous traits; however, the most universal of these are changes in reduced fear of humans (tameness) and brain composition. To assess how early domestication selection may have focused on tameness and its interaction with brain composition, a Red Junglefowl (Gallus gallus) population (the wild progenitor of the domestic chicken) was used to create two lines bidirectionally selected for fear of humans over eight generations of selection. These selection lines were then used to make an intercross population. Using a combination of genome-wide mapping in the intercross and between-line analysis of the selection lines, we show that the genetic loci for tameness co-localise with genetic loci for brain composition and anxiety behaviour. Furthermore, the detected loci for brain composition also co-localise with brain composition loci identified in a separate wild × domestic intercross. These results indicate that tameness and brain composition are either pleiotropic or genetically linked, and that tameness selection appears to recapitulate the same loci that have been selected by domestication itself. Therefore, selection for increased tameness could be the initial selection pressure driving the core of the domestication syndrome.

Environmental stressors and sex-specific life-history strategies synergistically shape senescence patterns in ectotherms, yet their interactive effects on telomere dynamics remain poorly understood. This study investigates how altitude-related environmental factors and sexual dimorphism drive telomere length variation in the montane salamander Pachytriton cheni across an elevational gradient (850-1350 m) in Qingliangfeng Nature Reserve, China. Using qPCR, skeletochronology and physiological assays, we analysed telomere length, age, oxidative damage markers and environmental parameters in 100 individuals. Results revealed a significant positive correlation between altitude and relative telomere length (RTL), with males exhibiting stronger elevational dependence than females. Multivariate models identified divergent environmental effects: higher flow velocity promoted telomere maintenance, whereas elevated water temperature, dissolved oxygen and dietary diversity accelerated attrition. Despite lower mobility, females maintained longer telomeres than males, suggesting sex-specific trade-offs favouring somatic maintenance over reproductive investment. Oxidative damage markers (malondialdehyde and protein carbonyls) were elevated at lower altitudes, aligning with free radical theory predictions. These findings highlight the interplay of environmental stressors (e.g., thermal and oxidative pressures) and sex-driven energy allocation in shaping telomere dynamics. Our work underscores the importance of integrating climate resilience into conservation strategies for high-altitude amphibians, particularly as habitat degradation and climate change threaten montane ecosystems. Our findings on the genotype-environment-sex interactions in P. cheni provide a conceptual framework for predicting how ectotherms may senesce in rapidly changing environments.

Moulting is fundamental to decapod growth and development, yet its molecular regulatory mechanisms and relationship with environmental adaptive evolution remain incompletely elucidated. Through comparative genomic and transcriptomic analyses, we identified six cuticle-associated gene families (CP8, CP AMP1A, pro-resilin, CP AM1199, CP575, and CP1246) that underwent significant expansion in decapods, displaying species-specific distribution patterns. Notably, the CP1246 family, specifically expanded in crabs and enriched with calcification-related cuticle domains, likely represents a key evolutionary innovation enabling adaptation to the physical impacts and predation pressures of intertidal environments. Transcriptomic analysis revealed that these expanded gene families exhibit highly specific spatiotemporal expression patterns during the moulting cycle: CP8, pro-resilin, and CP AMP1A show elevated expression during intermolt (InM3), contributing to endocuticle formation, while CP1246, CP575, and CP AM1199 maintain higher expression during other periods, potentially associated with the construction of different exoskeletal regions. Additionally, we identified the ecdysis triggering hormone (ETH) and its receptor (ETHR), confirming their gradually increasing expression pattern during moulting, and through co-expression network analysis, demonstrated that ETH likely coordinates the regulation of genes related to muscle development, immune response, and energy metabolism, collectively supporting the orderly progression of the moulting process. These findings establish an integrated model of decapod moulting regulation, elucidating how cuticle-associated gene family expansion and stage-specific expression promote adaptation to complex ecological environments in decapods, particularly crabs, providing new insights into the molecular foundations of adaptive evolution in crustaceans.