Molecular Ecology最新文献

Photopigments, formed by an opsin protein bound to a light-sensitive chromophore, underlie vertebrate vision. Long-wavelength–sensitive (LWS) opsins mediate red-light detection, and most teleosts retain a single functional LWS1. A shorter-shifted green-sensitive paralog (LWS2) is found only in a few lineages. By mining teleost genomes and sequencing retinal transcriptomes, we identify elopomorphs as an additional lineage retaining LWS2 (alongside characins and osteoglossomorphs). Surprisingly, we reveal a previously overlooked, shorter-shifted paralog, LWS3, restricted to gobies (Percomorpha) and arising from an ancestral duplication either in the teleost or in the percomorph ancestor. Structural modelling of twelve LWS opsins reveals convergent evolution at four key amino acid sites (214, 259, 261, 269) in the retinal-binding pocket, indicating convergent substitutions in human MWS (an old-world primate-specific duplicate of the vertebrate LWS1), teleost LWS2, and goby LWS3 relative to red-sensitive counterparts, consistent with repeated spectral shifts towards greener wavelengths. In several lineages, including characins, mormyrids, gobies, and primates, these shorter-shifted LWS opsins have at least partially replaced the canonical green-sensitive RH2-based visual pigment. Retinal transcriptomes revealed variable lws3 expression across adult gobies, either complementing lws1 in most species, or dominating the visual opsin expression profile as in the sicydiines. In situ hybridisation in the whitebarred goby (Amblygobius phalaena; Valenciennes, 1837) showed that lws1 and lws3 are expressed in separate double-cone members, analogous to rh2 expression in other fish species. Together, these results show that repeated convergence towards shorter LWS sensitivity in vertebrate evolution involves coordinated changes at the molecular, regulatory, and functional levels, providing a striking example of multilevel sensory adaptation.

Environmental RNA (eRNA) has been increasingly used to move beyond ‘who is there’ toward ‘who is active’ and ‘what is happening’ in ecosystems. Yet, most workflows have been optimised for laboratory sequencing, and decision-grade field use has remained sporadic. In this article, field-ready eRNA panels are defined as curated sets of transcripts paired with process controls and a transparent scoring rule, and a build–test pathway is described from marker discovery to deployment. Candidate markers are prioritised with field constraints in mind (abundance, specificity, persistence, and confounding seasonality), and RNA class choice (mRNA, rRNA, small, and other non-coding RNAs) is treated as a design lever for robustness. Pre-analytics are discussed as panel engineering, with emphasis placed on capture, rapid stabilisation, and inhibitor management to preserve multi-marker relationships. Field readout options are then compared, including isothermal amplification, CRISPR-assisted detection, portable qPCR, and portable nanopore sequencing for on-site verification and panel refresh. Finally, minimum controls and staged validation levels are proposed to support defensible ecological claims. Deliberate attention is directed toward shared terminology and testable standards so that discussion within and between ecology, diagnostics, and conservation practice is stimulated and priorities for future investigations are sharpened.

The metallic colour variation of beetles is a spectacular feature that has inspired diverse human cultures. However, little is known about the genetic basis of this trait or its ecological importance. In this study, we characterize the geographical distribution, optical mechanism, genetic basis and ecological and evolutionary importance of metallic colour variation in the Nebria ingens complex, an alpine ground beetle in the Sierra Nevada, California. We find that elytral colour varies continuously across two allopatric species (from black N. ingens to green N. riversi), with hybrid populations showing intermediate coloration, and we demonstrate that the metallic colour is generated from multilayer reflectors in the epicuticle of the elytra. By applying association mapping in natural populations (wild-GWAS) using high-density genotype variants, we identify five promising candidate genes covarying with metallic variation, with known roles in cuticle formation and pigmentation pathways. This finding, together with a significant correlation between colour variation and water availability, suggests that metallic variation evolves as a local adaptation to environmental variation in the N. ingens complex.

Understanding how demography and natural selection interact during colonization of novel environments is a central question in evolutionary biology. The Baltic Sea region combines one of the world's strongest salinity gradients with a well-characterized postglacial history of less than ~12,000 years. The harbour porpoise (Phocoena phocoena) is distributed across this gradient as three populations—the North Sea, Belt Sea and Proper Baltic Sea populations. Using whole genome resequencing data from 59 individuals, we reconstructed the demographic history of Baltic colonization and identified genomic signatures of local adaptation. Demographic modelling supported a sequential colonization in which the Belt Sea population diverged first from an ancestral North Sea population, followed by an independent divergence of the Proper Baltic Sea population, with two equally supported timing hypotheses placing initial colonization either during the Yoldia Sea (~11,800 years ago) or the Baltic Sea period (~8000 years ago). The Proper Baltic Sea population showed drift-dominated divergence consistent with a founder effect, while two discrete genomic islands of differentiation with selective sweep signatures were identified between North and Belt Sea populations, pointing to recent positive selection. Both regions contain osmoregulatory candidate genes, most notably SCNN1D, encoding part of the epithelial Na⁺ channels, a key regulator of sodium homeostasis. A non-synonymous mutation in SCNN1D showed striking allele frequency divergence along the salinity gradient, confirmed across ~400 individuals. Together, these results reveal how genetic drift and divergent selection interact to drive rapid adaptation to a brackish environment, and identify SCNN1D as a compelling candidate for cetacean osmoregulatory adaptation.

As climate change drives rapid environmental shifts, crops face significant challenges due to their limited adaptive genetic diversity, threatening food security. Crop wild relatives and potentially feral populations can serve as valuable reservoirs of adaptive diversity for breeding. Exploring and conserving this diversity is therefore essential, as it may encompass a wide range of adaptations. In this study, we investigate the genetic basis of local climate adaptation and the risk of maladaptation under future conditions in spontaneous populations—naturally occurring in the wild—of Brassica rapa (field mustard). A total of 62 populations were sampled, revealing strong differentiation between feral (France, Slovenia) and wild (Algeria, Sicily) populations. A genome–environment association analysis identified genomic regions associated with climatic variables, with broader patterns suggesting a polygenic architecture. Feral populations broadened the climatic range explored, but their reduced genetic diversity limited our ability to capture the full spectrum of adaptive variation in wild populations, indicating that the genetic architecture of climate adaptation is only partly shared between the two groups. We also used genomic offset (GO) analyses to assess mismatches between current and predicted-optimal genetic composition under 2050 climate projections. A common garden experiment indicated that GO captures some component of fitness variation, with feral populations providing additional predictive information beyond the environmental space occupied by wild populations. These findings highlight the complex genetic architecture of climate adaptation in B. rapa, as well as the potential and limitations of genomic tools for guiding conservation and crop improvement under climate change.

The extraordinarily polymorphic Major Histocompatibility Complex (MHC) is an iconic genomic region that has been associated with, for example, disease susceptibility, mate choice, and fitness. Both the MHC class I and II gene families have expanded considerably in songbirds (Passeriformes) compared to other bird orders, but our understanding of the functional relevance of the large number of gene copies in songbirds is hampered by lack of data on gene expression. We therefore took advantage of longitudinal data from our wild long-term monitored population of great reed warblers Acrocephalus arundinaceus as well as a long-term experiment to study patterns of MHC class I (MHC-I) gene expression during individuals' lifetimes and across generations, and between tissues. As could be expected within a species, the expressed diversity increased linearly with genomic MHC-I diversity. However, most MHC-I alleles were expressed at low levels, with only a handful of alleles showing moderate to high expression in each individual. The MHC-I expression patterns in blood were highly consistent (i) over an individual's lifetime, (ii) between parents and offspring, and (iii) among siblings, and (iv) were strongly correlated with expression in other tissues. The moderately to highly expressed MHC-I genes likely play a key role in antigen presentation in adaptive immunity and thus comprise primary targets for studies of host-pathogen coevolution.

As human activity accelerates the spread of pathogens and other invasive species, reconstructing the cryptic early dynamics of undetected invasions has become a central challenge in disease ecology and invasion biology. Here, we leverage museum specimens to reconstruct the invasion of Batrachochytrium dendrobatidis (Bd), a fungal panzootic driving global amphibian biodiversity loss, across historically enigmatic declines in the Brazilian Atlantic Forest. Two hypotheses have been proposed to explain Bd's historical dynamics in this region: long-term enzootic persistence versus recent epizootic invasion coinciding with declines. Using molecular screening, histopathology, and genotyping of museum and modern specimens, we find no evidence of Bd infection prior to the decline, followed by widespread infection immediately thereafter. Only the global panzootic lineage (Bd-GPL) was detected during the first year of post-decline sampling, implicating its invasion in driving regional losses. Infection prevalence varied among species following the decline, likely reflecting species-specific interactions between baseline susceptibility and ecological exposure risk. Contemporary host populations exhibit more uniform prevalence regardless of decline history, consistent with the evolution of pathogen tolerance under enzootic conditions. Together, these results provide the first site-specific evidence linking Bd-GPL invasion to enigmatic amphibian declines in Brazil and demonstrate the power of museum collections for resolving detection lag dynamics in emerging infectious diseases.