Molecular Ecology最新文献

Advances in sequencing and chromosome-scale assembly have brought non-model animals into focus, deepening our understanding of genome and chromosome evolution. Here, we present the waterbuck (Kobus ellipsiprymnus) as an emerging model antelope for studying population dynamics and chromosome evolution. Waterbuck evolutionary history has been shaped by both climatic and geographic changes, as well as structural chromosome changes, principally Robertsonian (Rb) fusions. To provide new insights into waterbuck evolution, we generated a chromosome-level genome assembly for the species using PacBio HiFi and Hi-C sequencing. We further leveraged museum collections to perform whole genome sequencing (WGS) of 24 historical specimens. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date and reveals previously unrecognised population structure and gene flow between waterbuck populations, alongside several regions of high genomic differentiation between the two recognised subspecies. Notably, several differentiation hotspots occur near the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. These regions contain genes involved in development, fertility, and recombination. Our findings underscore the value of chromosome-level genome assemblies, the critical role of historical collections in capturing fine-scale population structure and gene flow in species with wide-ranging distributions, and the potential evolutionary impacts of Rb fusions on genomic differentiation and recombination landscapes.

The Lansing effect is a transgenerational age effect by which old parents tend to produce less viable descendants. Despite its importance for the evolution of lifespan and parental effects, the transgenerational nature of age effects and the underlying mechanisms are poorly understood. In an experiment using the three-spined stickleback, we test whether the age of mothers (generation P0) at reproduction affects parental traits of the F1 offspring, and whether they subsequently influence the early development and viability of the F2 descendants. Daughters (F1 females) of old (2-year-old) and young (1-year-old) mothers showed comparable body size, spawning rate, clutch size and egg telomere length (TL). However, sons (F1 males) of old mothers had a smaller adult body size and produced sperm with shorter TL than those of younger mothers. Structural equation model analysis revealed that P0 female age influenced embryo TL and hatching success of the F2 descendants through its effect on sperm TL of F1 males. There was also an interacting effect of P0 female age and telomerase reverse transcriptase gene (tert) mRNA level in eggs of the F1 females on the hatching success of the F2 descendants. Our results provide novel evidence that maternal age can have transmissive effects on successive generations through the gamete traits of their offspring, especially sperm TL and egg tert gene transcripts. We conclude that this transmissible age effect on grandoffspring TL and viability can shape the evolution of life histories because TL is related to health, ageing and lifespan.

Understanding how dispersal impacts the genetic makeup of populations is essential for predicting their responses to environmental change. Gene flow—via within-population dispersal and external immigration—shapes population health and evolutionary potential by boosting genetic diversity, but it can also counteract local adaptation. We investigate these processes in a population of great tits (Parus major) in Wytham Woods, United Kingdom. This system represents a large, continuous population of a vagile, widely distributed species. Using a comprehensive social pedigree alongside two genomic datasets, one with 949 individuals genotyped at 600,000 SNPs and another with 2644 individuals typed at 10,000 SNPs, we demonstrate spatial genetic structure largely driven by the spatial and temporal clustering of close kin. We quantify how temporally persistent this pattern is and find that relatedness declines with geographic distance in a consistent manner across years, without a consistent genetic basis, a pattern which is frequently renewed due to high population turnover. Immigrants make up a substantial portion of the breeding population, yet are often assumed to be genetically distinct, unrelated and outbred—assumptions that can bias population inferences. We show that immigrants are indeed outbred, as are local birds; have fewer close relatives within the population, and are less likely to be related to their neighbours than locally born birds. Despite low F_ST and no clear genome-wide population structure, immigrants and locals can be distinguished above chance using a Random Forest classifier trained on SNP data. Our study highlights the complex interplay between dispersal, population turnover and spatial population structure, and suggests that great tits in Wytham Woods experience substantial gene flow within the population and from immigrants, maintaining high genetic diversity and reducing the possibility of local adaptation at this spatial scale.

The heavy reliance on pyrethroid-based interventions has largely driven insecticide resistance in malaria vectors, accelerating the spread of resistant strains, including resistant Anopheles funestus strains. The efficacy of insecticide-based interventions, especially insecticide-treated nets (ITNs), the cornerstone of malaria control and management, is threatened by the widespread occurrence of resistance, jeopardising malaria control efforts. Alpha-cypermethrin, a type II pyrethroid, is increasingly utilised in various ITN formulations, including those combined with piperonyl butoxide (PBO) and chlorfenapyr-based Interceptor G2 (IG2) nets, to enhance effectiveness against resistant mosquito populations. Therefore, understanding the molecular basis of resistance is essential to monitor and track resistance trends for an effective malaria control program. In this study, we identified a 1.4 Mb QTL on the telomeric end of the left arm of chromosome 2, conferring resistance to α-cypermethrin (rap1 QTL). Different crossing schemes and sequencing approaches were explored to determine the most effective strategy. Individual-based QTL mapping performed on segregating individuals from an isofemale family identified a QTL at the F₇ generation. Higher recombination density relative to the physical genome in the F₇ isofemale family, with a recombination every 240 kb, facilitated the detection of a QTL compared to the F₂ family (335 kb/cM). Additionally, we exploited bulk segregant analysis (BSA) between susceptible and resistant phenotypes from the F₇ isofemale family and an F₇ mixed cross-family to perform cost-effective and rapid QTL-mapping discovery. The strongest signal in both independent BSA analyses overlaps with the rap1 QTL, further supporting its role in α-cypermethrin resistance. The known resistant alleles of the cytochrome P450 CYP6P9a and 6.5-kb structural variant within the rap1 QTL strongly correlate with survival to α-cypermethrin. In this study, we validated that previously developed DNA-based assays, originally designed to monitor permethrin resistance, are effective for tracking resistance to α-cypermethrin as well. Additionally, we identified candidate variants that can serve as reliable markers for monitoring α-cypermethrin resistance.

Salinity—an essential factor shaping marine species distributions—is rapidly shifting due to global change, yet the mechanisms of salinity tolerance and adaptation remain poorly understood. We investigated local adaptation in the calanoid copepod Acartia tonsa, a broadly distributed marine species that thrives in the brackish Baltic Sea. Using a common-garden design, we compared physiological and transcriptomic responses to low salinity between populations from the North Sea (> 25 PSU) and the Baltic Sea (< 15 PSU). Baltic copepods exhibited significantly higher survival under low salinity, indicating local adaptation. While both populations shared a core osmoregulatory strategy involving active ion transport and regulation of amino acids, transcriptomic profiles revealed population-specific differences. Baltic individuals showed a reduced overall gene expression response, yet maintained higher relative expression of osmoregulatory genes—suggesting a more efficient and primed transcriptomic response. In contrast, North Sea copepods exhibited broader transcriptional shifts, including downregulation of metabolic and developmental pathways after prolonged stress exposure, possibly reflecting energy conservation mechanisms. These findings reveal that A. tonsa possesses both a plastic osmoregulatory strategy and population-level adaptation that enable survival in extreme salinity conditions. While both populations tolerate short-term exposure to low salinity, local adaptation has enhanced the Baltic population's resilience. This suggests that A. tonsa is broadly tolerant of moderate climate-driven salinity declines across most of its distribution. However, our data also indicate potential range contractions in the lowest salinity zones of the Baltic Sea, underscoring the importance of identifying physiological and genetic thresholds in climate resilience studies.

Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.

Submarine groundwater discharge (SGD) supplies large quantities of nutrients and other terrestrial elements to coastal ecosystems, impacting marine biota and ecosystem functioning. Despite the relevance of prokaryotes for marine biogeochemistry, little is known about their responses to groundwater inputs. Here we explored the impact of SGD on the spatiotemporal patterns of prokaryotic communities from the Mar Menor (Murcia, Spain), a highly anthropized hypersaline coastal lagoon that receives large amounts of nutrient-polluted SGD. Using 16S rRNA amplicon sequencing, activity assays, and flow cytometry, we investigated the dynamics of prokaryotic communities across the lagoon and its connected environments (freshwater streams, groundwater, soils, the sea) on two occasions. We found that the lagoon areas most influenced by SGD (i.e., sites closest to the shore) presented on average three-fold higher heterotrophic prokaryotic protein production than the inner lagoon samples, and 2.7-fold higher taxonomic richness. This spatial pattern was likely influenced by solutes supplied by SGD, as higher concentrations of dissolved nitrogen, silicate and SGD tracers (radium [Ra] isotopes) were found in nearshore waters. Increases in these elements also influenced the relative abundance of dominant bacterial groups (e.g., Flavobacteriales, Rhodobacterales). In autumn, increases in lagoon ²²⁴Ra were strongly linked to higher taxonomic richness in microbial assemblages and the influx of allochthonous taxa from the catchment, pointing to seasonally variable transport of coastal groundwater microorganisms via SGD. Our study highlights SGD as an overlooked driver of prokaryotic dynamics in coastal ecosystems, and suggests that changes in this process may significantly impact microbial community structure and functioning.