Molecular Ecology最新文献

Visual communication in fish is often shaped by their light environment, which influences both sensory (e.g., eye size, opsin gene expression) and signalling traits (e.g., body reflectance). This study explores the phenotypic variation in the visual communication traits of six species of centrarchids (Centrarchidae) inhabiting two contrasting light environments. We measured morphological, molecular and signalling traits to determine their variation across photic conditions. Our findings reveal significant interspecific variation in sensory traits but no consistent phenotypic variation between light environments. Centrarchids showed robust visual systems with green-sensitive rh2 and red-sensitive lws opsin genes representing the main chromatic channels, with their expression remaining largely unaffected between distinct light habitats. We also found significant molecular evolution in the visual opsin genes, although these changes were not associated with environmental conditions. However, body reflectance displayed species-specific responses to environmental conditions, suggesting that signalling traits may be more flexible than sensory traits. Overall, our results challenge the generality of the current paradigm in visual ecology, which portrays visual systems in fish as highly tunable owing to photic conditions. Our study highlights the potential evolutionary or developmental constraints on centrarchid visual systems and their implications for adaptability to various habitats and novel environmental threats.

The Iberian lynx was at the brink of extinction by the year 2000 but has since then, and thanks to intensive conservation measures, gone through a remarkable recovery, providing a much-welcomed and encouraging conservation success story. Genetic issues have probably contributed to the decline in the past, and the genetic management of inbreeding and genetic diversity is likely contributing to its recent recovery. The species was an early adopter of genetic and genomic approaches, and the combination of an extreme decline, an intensive monitoring and management programme and extensive genomic resources and data makes the Iberian lynx an excellent model for conservation genomics. Here, we review how genetic and genomic data have contributed to the knowledge of the species evolutionary and demographic history, the evaluation of the genetic status of the species through time, including historical and ancient data, and how this information has prompted and guided conservation actions. In the process, genomics provided valuable insights into the dynamics of functional variation in bottlenecked populations and the consequences of intraspecific and interspecific admixtures. In more applied terms, the species is subjected to an ambitious genetic monitoring and management programme, covering captive, remnant and reintroduced populations, which has succeeded in improving the genetic status of the species and thereby contributed to its recovery. Current genomic work aims at expanding these contributions with novel genomic resources and data while capitalising on extensive demographic and genealogical data provided by the ongoing non-invasive genetic monitoring programme.

Most terrestrial insects have a layer of cuticular hydrocarbons (CHCs) protecting them from desiccation and mediating chemical communication. The composition of these hydrocarbons is highly plastic and changes during their lifetime and with environmental conditions. How these changes in CHC composition are achieved is largely unknown. CHC profiles of Apis mellifera honey bees vary among castes, task groups and subspecies adapted to different climates. This makes A. mellifera an excellent model for studying the molecular mechanism underlying CHC biosynthesis. We correlated the expression of specific elongase- and desaturase-encoding genes with the CHC composition in bees performing different social tasks in two highly divergent A. mellifera subspecies. Elongases are enzymes that lengthen the hydrocarbon chain, while desaturases introduce double bonds in it. We evaluated the hypothesis that the expression of the genes encoding these enzymes determines CHC profiles of the worker bees. Our results revealed that the specificity of desaturases and elongases shapes the CHC profiles of worker bees performing different social tasks. Expression of the desaturase-encoding gene LOC100576797 and the elongase-encoding gene LOC550828 seemed to be strongly associated with the abundance of compounds that were characteristic of the CHC profile of nurse bees. In contrast, the compounds that characterised the CHC profiles of the forager bees seemed to be associated with the desaturase-encoding gene LOC551527 and the elongase-encoding gene LOC409638. Our data shed light on the genetic basis for task-specific CHC composition differences in social hymenopterans and paved the ground for unravelling the genetic underpinning of CHC biosynthesis.

Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, as the Arctic is undergoing rapid physical, ecological and socio-economic changes. The abundant and widely distributed polar cod (Boreogadus saida) is highly adapted to Arctic waters, and its larvae and juveniles live in close association with sea ice. Through a reduced-representation sequencing approach, this study explored the spatial genetic structure of polar cod at a circum-Arctic scale. Genomic variation was partitioned into neutral and adaptive components to respectively investigate genetic connectivity and local adaptation. Based on 922 high-quality single nucleotide polymorphism (SNP) markers genotyped in 611 polar cod, broad-scale differentiation was detected among three groups: (i) Beaufort –Chukchi seas, (ii) all regions connected by the Transpolar Drift, ranging from the Laptev Sea to Iceland, including the European Arctic and (iii) West Greenland. Patterns of neutral genetic structure suggested broadscale oceanographic and sea ice drift features (i.e., Beaufort Gyre and Transpolar Drift) as important drivers of connectivity. Genomic variation at 35 outlier loci indicated adaptive divergence of the West Greenland and the Beaufort–Chukchi Seas populations, possibly driven by environmental conditions. Sea ice decline and changing ocean currents can alter or disrupt connectivity between polar cod from the three genetic groups, potentially undermining their resilience to climate change, even in putative refugia, such as the Central Arctic Ocean and the Arctic Archipelago.

Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in the evolution of adaptations in those species. Inversions are thought to operate as supergenes by trapping adaptive alleles at multiple linked loci through the suppression of recombination. While there is now considerable support for the supergene mechanism of inversion evolution, the extent to which inversions trap pre-existing adaptive genetic variation versus accumulate new adaptive variants over time remains unclear. In this study, we report new insights into the evolution of a locally adaptive chromosomal inversion polymorphism (inv_chr8A), which contributes to the adaptive divergence between coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. This research was enabled by the sequencing, assembly and annotation of new annual and perennial genomes of M. guttatus using Oxford Nanopore long-read sequencing technology. In addition to the adaptive inv_chr8A inversion, we identified three other large inversion polymorphisms, including a previously unknown large inversion (inv_chr8B) nested within inv_chr8A. Through population genomic analyses, we determined that the nested inv_chr8B inversion is significantly older than the larger chromosomal inversion in which it resides. We also evaluated the potential role of key candidate genes underlying the phenotypic effects of inv_chr8A. These genes are involved in gibberellin biosynthesis and anthocyanin regulation. Although little evidence was found to suggest that inversion breakpoint mutations drive adaptive phenotypic effects, our findings do support the supergene mechanism of adaptation and suggest it may sometimes involve nested inversions that evolve at different times.

Freshwater ecosystems and their biota are under increasing pressure from anthropogenic stressors. In response to declining fish stocks, hatchery and stocking programmes are widely implemented as core components of restoration and management strategies, with positive outcomes for some wild populations. Despite this, stocking remains contentious due to potential genetic and ecological risks to wild populations. Monitoring and evaluation of stocking outcomes are critical to ensuring the long-term sustainability of wild populations, but identification of stocked individuals post-release remains a key challenge, particularly for mobile species. In this study, we combined otolith (natal origin and age) and genomic data to identify stocked individuals and evaluate the genetic implications of stocking for a culturally and socioeconomically important and mobile freshwater fish, golden perch Macquaria ambigua (family: Percichthyidae), across Australia's Murray–Darling Basin (MDB). We also generated a chromosome-level genome assembly. Many close kin were detected across the MDB, increasing in prevalence over recent decades and mostly of hatchery origin. Rivers with many close kin were associated with low effective population sizes (N_e < 100). Genetic signatures of stocking varied according to local context, being most pronounced in but not restricted to rivers considered functionally isolated for management purposes. Where fish are stocked into rivers that are part of the connected metapopulation, there is scope to modify current stocking practices to avoid over-representation of related stocked individuals. Increased focus on the genetic diversity of stocked fish is likely to promote the long-term persistence of golden perch in the wild.

A good understanding of biotic interactions is necessary to accurately predict the vulnerability of ecosystems to climate change. Recently, co-occurrence networks built from environmental DNA (eDNA) metabarcoding data have arisen as a tool to explore interspecific interactions in ecological communities exposed to different human and environmental pressures. Such networks can identify environmentally driven relationships in microbial and eukaryotic communities, but whether inferred co-occurrences robustly represent biotic interactions remains unclear. Here, we tackle this challenge and compare spatio-temporal variability in the structure and complexity of inferred co-occurrence networks and food webs, using 60 eDNA samples covering vertebrates and other eukaryotes in a North Sea coastal ecosystem. We compare topological characteristics and identify highly connected species across spatial and temporal subsets to evaluate variance in community composition and structure. We find consistent trends in topological characteristics across eDNA-derived co-occurrence networks and food webs that support some ability for the co-occurrence networks to detect real ecological processes, despite trophic interactions forming a minority of significant co-occurrences. The lack of significant trophic interactions detected in co-occurrence networks may result from ecological complexities, such as generalist predators having flexible interactions or behavioural partitioning, the inability to distinguish age class with eDNA or co-occurrences being driven by non-trophic or abiotic interactions. We find support for using eDNA-derived co-occurrence networks to infer ecological interactions, but further work is needed to assess their power to reliably detect and differentiate different interaction types and overcome methodological limitations, such as species detection uncertainties, which could influence inferred ecosystem complexity.