Molecular Ecology最新文献

Adjusting reproduction timing to environmental cues is essential for lifetime fitness. In many insects, reproductive diapause shows clinal variation along environmental gradients such as photoperiod and temperature. How such continuous trait variation may be encoded at the molecular level and maintained in the presence of gene flow remains largely elusive. The fruit fly Drosophila triauraria is distributed across a wide latitudinal range of the Japanese archipelago. Northern strains exhibit a strong photoperiodic reproductive diapause in females, whereas southern strains fail to arrest ovarian development even under short-day conditions at low temperatures. These distinct phenotypes and the presumable clinal variation in between provide an ideal opportunity to examine the molecular basis of latitudinal divergence. We first investigated diapause induction in both females and males from previously reported and newly tested strains collected from the regions spanning ~26° N-43° N along the Japanese archipelago. The assessment revealed continuous geographic variation in sensitivity to photoperiod and temperature. We then analysed the whole-genome sequences of 21 strains, including 14 newly sequenced, to identify genomic regions underlying this divergence. In addition to the conventional F_ST analysis, we applied a "monophyletic window" approach suitable for limited sample sizes. The analysis identified a candidate region containing putative E-box and TER-box sequence motifs of the timeless (tim) gene, which has been previously implicated in diapause regulation in multiple insect species. The quantitative PCR analysis further supported a partial association between the tim expression and the incidence of female diapause. These findings reinforce the growing evidence for a role of circadian clock genes in the adaptive regulation of reproductive diapause and demonstrate the utility of tree-based approaches for detecting genomic regions of geographic divergence.

Urbanisation has led to increasing homogenization of plant communities across cities. However, it is unclear whether these patterns extend to cosmopolitan plant species at the genetic level. We examined genome-wide genetic patterns in six widespread plant species (three Poaceae and three Asteraceae) across five cities in the USA (Boston, Baltimore, Minneapolis-St. Paul, Phoenix, and Los Angeles) using reduced-representation sequencing. We assessed genetic structure, differentiation, and patterns of isolation by distance (IBD) and environment (IBE) to determine if species were genetically homogeneous or differentiated by city, percentage of impervious surface, or both. Most species exhibited limited population structure overall, with Poa annua (annual bluegrass), Taraxacum officinale (dandelion), and Cynodon dactylon (Bermuda grass) showing no significant genetic differentiation among cities, a pattern consistent with high gene flow mediated by human activity. Notable exceptions included city-level differences in Erigeron canadensis (horseweed) and Lactuca serriola (prickly lettuce), especially in Phoenix. We also observed low genetic diversity in Digitaria sanguinalis (crabgrass) from Phoenix, suggesting recent founder effects or selection via environmental filtering. Erigeron canadensis, the only native species studied, displayed stronger differentiation by city, along with significant isolation by temperature and distance. Among all species, we found no evidence for population structure by impervious surface. Our findings indicate that widespread population genetic structure patterns of cosmopolitan plants are likely to depend more on species attributes (e.g., self-compatibility) and human-mediated dispersal than on urbanisation per se.

Organisms living in arid environments are predicted to be at increased risk of extinction under climatic and anthropogenic change. Response to past climate change can provide some insights into these risks; however, our understanding of the diversification and evolutionary history of many arid-adapted species is still limited, particularly in Australia. Here, we evaluate the demographic and evolutionary history of a widespread Australian marsupial, the black-footed rock-wallaby (Petrogale lateralis), with a highly fragmented contemporary distribution across Australia's arid biome and offshore islands. Combining genomic data from historical and modern samples, we evaluate the divergence history of the five P. lateralis subspecies. Our results show that the species has experienced a Pleistocene-age demographic expansion across the Australian arid biome, with subsequent geographic fragmentation of populations and subspecies. We find negligible gene flow between most extant populations/subspecies, yet low divergence between populations of P. l. lateralis and currently recognised subspecies. Individuals on islands have extremely low genetic diversity and high inbreeding coefficients, in contrast to naturally fragmented mainland populations, suggesting a stronger bottleneck experienced on islands. Our results indicate connectivity of populations within the past ~160-640 kya despite their current disjunct distributions, providing important context for conservation management and potential genetic rescue. However, given the large ecological gradient and chromosomal variation within this species, assessment of ecological differences and risks of outbreeding depression will be important before decisions to mix across geographically distant populations and/or subspecies. This study demonstrates how museum genomics improves our ability to resolve complex evolutionary histories and guide conservation.

Mountain ranges like the European Alps harbour large endemic biodiversity shaped by Pleistocene climatic oscillations. The flightless bush-cricket Anonconotus italoaustriacus, endemic to the Southern Limestone Alps (SLA) and the eastern Central Alps (CA), provides an ideal model to study the evolutionary and refugial dynamics of endemic alpine arthropods. Using genomic SNP data, we employed phylogenetic analyses, Bayesian clustering, and demographic modelling to investigate the species' evolutionary history and its refugial dynamics. Our results support a scenario of survival in multiple peripheral refugia during the Last Glacial Period (LGP; 115-11.7 ka), with populations in the southern SLA and eastern CA exhibiting the highest private allelic richness. Postglacial recolonization of interior alpine regions occurred exclusively from refugia on the southeastern margin of the SLA, most likely facilitated by open habitat corridors along transversal valleys. In contrast, populations in the southern SLA exhibited long-term isolation and distributional stasis, emphasising the importance of small, stable refugia in preserving genetic diversity. These findings highlight the importance of integrating evolutionary history into conservation strategies, particularly for alpine endemics with fragmented distributions. Protecting both long-term stable refugia and dynamic evolutionary hotspots is critical for the conservation of A. italoaustriacus and other high-altitude arthropods in the face of ongoing environmental change.

Arctic-alpine species are highly sensitive to long-term temperature changes and associated glacial cycles due to their occurrence in cold environments to which they are adapted and spatially restricted. Unravelling their evolutionary responses to past climatic fluctuations can provide new insights into their diversification. In this study, we investigated the evolutionary history of the Silene acaulis species complex and how it was shaped by past glacial cycles. We assembled the first high-quality reference genome for S. acaulis and analysed reduced representation sequencing data from 955 individuals spanning 132 populations across the Holarctic distribution range of these arctic-alpine cushion plants. We identified five evolutionary lineages and assessed their phylogeographical structure in relation to current subspecies classifications, refugia, and historic migration patterns. Phylogenetic dating revealed that lineage divergence largely coincided with repeated phases of glacial cooling over the last two million years and was driven by isolation in glacial refugia. Secondary contact in glacial refugia or during interglacial expansions promoted hybridization and further shaped the distribution of genetic diversity across the species complex. Adaptive divergence amongst sympatric genetic groups in the European Alps highlights the contribution of niche specialisation to intraspecific divergence, with evidence for ecotype differentiation in response to a combination of edaphic and climatic factors. The S. acaulis species complex has an intricate evolutionary history, shaped by glacial cycles in the Late Pleistocene that have driven lineage diversification, secondary contact and ecotype formation. Our study underscores the significance of glacial cycles in shaping genetic diversity in arctic-alpine plant species and improves our understanding of how arctic-alpine species have responded to past climate fluctuations.

Hybridization and introgression frequently occur even between distantly related species. A central question in speciation research is which genomic regions act as barriers to gene flow and how genome-wide differentiation persists despite hybridization between species. Ecological divergence is well known to promote genomic differentiation, especially during the early stages of speciation. However, the extent to which ecological divergence contributes to genomic divergence and the restriction of gene flow between more strongly isolated species, such as those exhibiting intrinsic hybrid incompatibilities, remains relatively unclear. One promising approach is to compare genomic differentiation and introgression patterns between sympatric sites of ecologically divergent distantly related species and those of ecologically similar species. Here, we identified a new sympatric site of threespine stickleback (Gasterosteus aculeatus) and Japan Sea stickleback (G. nipponicus) in the Okinebe River, Hokkaido, Japan. In this habitat, these two species differ in migratory life histories: G. nipponicus is anadromous (sea-run migratory), whereas G. aculeatus is resident. This contrasts with the other two previously studied sympatric sites, where both species are anadromous. We found that genomic differentiation in the Okinebe pair is maintained at high levels despite limited spatial isolation. Furthermore, the Okinebe pair had more genomic regions with high differentiation and fewer regions of introgression than the other sympatric pairs. These findings suggest that migratory differences may be able to contribute to the restriction of gene flow even between species with strong reproductive isolation. To better understand the role of ecological divergence in speciation, broader comparative studies across multiple sympatric species pairs with varying degrees of ecological differentiation and reproductive isolation are needed.

Conservation management of endangered species increasingly relies on genomic approaches to understand how long-term small population sizes affect the fitness of extant individuals. However, despite the growing investment in genomic resources by conservation programmes, the impact that sequencing methods have on the ability to detect inbreeding-related phenomena has been largely overlooked. Here, we compare the use of whole-genome and reduced-representation sequencing approaches in 148 individuals of the critically endangered parrot, the kākāpō (Strigops habroptilus), to assess inbreeding and its effects on female reproductive success. We explore how sequencing choice influences the identification of long stretches of homozygosity across the genome (runs of homozygosity, ROH), and compare the conservation implications of the results produced by each method. Both whole-genome and reduced-representation sequencing approaches provided comparable estimates of genome-wide inbreeding (F_ROH) and revealed consistent effects on egg hatching success, suggesting that reduced-representation sequencing is capable of detecting inbreeding depression in wild populations under certain conditions. Whole-genome sequencing enabled chromosome-level inbreeding analyses, which revealed no strong evidence of chromosome-specific effects beyond the genome-wide signal. These results suggest that inbreeding depression in kākāpō reflects small effects across many chromosomes rather than strong effects on only a few, and that the primary benefit of whole-genome sequencing lies in improving the precision of genome-wide inbreeding estimates rather than identifying chromosome-specific effects. Our findings highlight the distinct benefits of each sequencing approach in conservation, particularly within the context of resource limitations.

Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. This has paved the way to study the eco-evolutionary dynamics of SVs across the tree of life and within a population genomics framework. In this review, we provide the necessary fundamentals to help researchers generate and analyse population-level SV data. We discuss the unique properties of different SV groups and how these fundamental differences interact with important biological and evolutionary processes using both empirical results and theory. This includes discussion of unresolved issues around SVs, such as technical difficulties in identification, accounting for diversity and evaluating functional effects. We explicitly integrate into this discussion transposable elements, which are an important component of SVs often identified in population-level variant data. Finally, we focus on the practical side of SV analysis, offering a framework for SV identification and data analysis. In particular, we examine the heterogeneous nature of SV properties (type, length, sequence identity) that should be considered when studying them in ecology and evolution. This review aims to provide resources and guidelines to help researchers navigate the complexities of a relatively new field of eco-evolutionary genomics research.