Molecular Ecology最新文献

Through genomic phylogeography, previously unrecognised biodiversity can be revealed. The alpine newt serves as a case in point: this taxon carries highly distinct mtDNA clades and has a severely fragmented range. We obtain genome-wide data with target enrichment by sequence capture to delineate cryptic species and disentangle their phylogenetic relationships. Furthermore, we explore potential niche divergence and glaciation-driven distribution dynamics. On the basis of the uncovered genetic structure, we distinguish five main groups that we propose should be treated as distinct species. Limited interspecific genetic admixture often occurs away from current contact zones between these species, in line with a scenario of current range reduction, compared to the Last Glacial Maximum. A decline in suitable habitat also explains the fragmented nature of current species ranges. We uncover pronounced mito-nuclear discordance. We show that an ancient mtDNA lineage endemic to the Vlasina Plateau on the border between Serbia and Bulgaria, previously interpreted to be a 'ghost lineage', in fact represents a distinct species. However, it is nested considerably deeper inside the alpine newt species complex than mtDNA suggests. Our study illustrates how genomic phylogeography allows intricate evolutionary histories to be untangled.

Anthropogenic disturbances can disrupt ecosystems and alter species population dynamics. Interspecific hybridization is common between genetically related organisms, especially once reproductive barriers such as spatial isolation have been removed. We used genotyping-by-sequencing data to assess outcomes of hybridization between several Leuciscidae minnow species and to identify to what extent land use type and environmental variables influence the frequency of hybridization. We found that both two-species and multi-species hybridization was widespread; hybrids were sampled at all 25 sampling sites and made up almost 30% of all individuals sampled. While most species hybridised with at least one other sampled species, the amount of hybridization was variable. We used logistic regression to estimate the influence of anthropogenic disturbance on hybridization, and found weak relationships between hybridization and environmental factors. This research improves our understanding of hybridization dynamics in species-rich clades like the Leuciscidae with low reproductive isolation, and points to the need for additional work to better understand predictors of hybridization in multi-species hybrid zones.

Plankton play a key role in biogeochemical cycles in aquatic environments, and their abundance and composition vary spatially and seasonally. We characterised the seasonal dynamics and environmental preferences of freshwater bacteria and microeukaryotes from four pelagic sites in the oligotrophic Lake Baikal and examined the spatio-seasonal niche of closely related taxa. Based on spatio-seasonal patterns, the amplicon sequence variants (ASVs) of bacterial 16S rRNA gene, microeukaryote 18S rRNA gene, and zooplankton 18S rRNA gene were divided into ubiquitous, seasonal (spring or summer-autumn), and episodic groups. Co-occurrence networks for each of the dominant bacteria (Iluma, acI, Cyanobium, Flavobacterium, Verrucomicrobiae) or microeukaryotes (Chrysophyceae, Chlorophyta, Cryptophyceae, Dinophyceae, Ciliophora) contained ubiquitous, seasonally similar, or divergent closely related ASVs. In co-occurrence networks of bacterial or microeukaryotic ASVs, related taxa showed more positive correlations with each other, whereas distantly related or unrelated ASVs showed more negative correlations. This study revealed the coexistence of closely related taxa for some bacterial or microeukaryotic groups and spatio-seasonal differentiation for others in a temperate freshwater environment.

Malaria, a febrile disease caused by the Plasmodium parasites and transmitted by mosquitoes, is a leading cause of mortality in children under 5 in endemic countries. The widespread deployment of insecticide-treated bed nets (ITNs) has significantly reduced malaria transmission, but rising levels of insecticide resistance threaten to halt the progress. Monitoring insecticide resistance is vital for effective vector control, particularly when deploying new tools. Understanding mosquito population responses to these interventions is crucial for guiding control programmes in making informed decisions about the selection, timing and geographic deployment of tools. This genomic study investigates the demographic and evolutionary consequences on the malaria vector Anopheles gambiae of deploying standard ITNs (containing only pyrethroids) and pyrethroid-PBO nets (containing pyrethroids plus the synergist piperonyl butoxide) during a clinical trial in Uganda. Despite substantial reductions in indoor mosquito densities in the clinical trial, estimates of nucleotide diversity (π) and linkage disequilibrium revealed no significant decline in effective population size, reflecting continued large population size even after effective control. Marked allele frequency shifts at resistance-associated loci indicated strong selection pressures driven by the interventions, with distinct selective dynamics between the two net types, highlighting alternative pyrethroid detoxification pathways in the presence of PBO. A duplication in the Cyp9k1 gene significantly increased in frequency in populations exposed to pyrethroid-only nets but decreased in populations exposed to PBO-treated nets, suggesting that selection for over-expression of this gene is removed when this resistance mechanism is impacted by PBO. An alternative potential detoxification mechanism was selected within a region of the 2La chromosomal inversion on chromosome 2 L, which encompasses the UDP-glucose 6-dehydrogenase gene. This variant consistently increased in frequency when exposed to PBO-treated nets. Additionally, pyrethroid-only nets selected for a novel locus on the X chromosome containing the diacylglycerol kinase gene, which is potentially linked to behavioural adaptations through its role in neurotransmission modulation. Our findings underscore the importance of genomic surveillance in vector control, revealing distinct evolutionary dynamics of insecticide resistance mechanisms in the presence of PBO. While ITNs remain effective, the persistence and evolution of resistance-associated alleles highlight the need for adaptive and dynamic resistance management strategies. By integrating high-resolution genomic data with epidemiological and entomological monitoring, this study offers actionable insights to sustain malaria control efforts amid the ongoing challenge of insecticide resistance.

Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host-associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical (Abudefduf vaigiensis) and one subtropical (Microcanthus strigatus) reef fish species, across three temperate reefs representing natural analogues of climate change: a present-day baseline ('cool reef'), a chronically warmed reef ('warm reef') and a reef experiencing combined warming and extreme acidification ('extreme reef'). We also examined gut microbiome changes in A. vaigiensis before and during a severe marine heatwave. A. vaigiensis had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio. A. vaigiensis also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre-heatwave individuals. In contrast, M. strigatus showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in Abudefduf vaigiensis but distinct restructuring in Microcanthus strigatus. We conclude that climate-driven microbiome reshuffling may alter host-microbiome relationships and functions in fishes in a future ocean.

The woodwasp, Sirex noctilio, and its mutualistic fungal symbiont, Amylostereum areolatum, are native to Eurasia and northern Africa. Sirex noctilio was first reported outside its native range in New Zealand in 1900, Tasmania in 1952 and mainland Australia in 1961. In this study, we consider the invasion history of these organisms across Australasia through population genetic analysis using mitochondrial sequence data and microsatellite markers and compared them with a previously published dataset from global collections. The study included contemporary (n = 461) and historical (n = 41) samples of S. noctilio dating back to 1952 and fungal (n = 176) samples from across the range. No population structure was found in Australian and New Zealand populations of S. noctilio or the fungal symbiont A. areolatum, reflecting both the natural (within the countries) and human-assisted (between the countries) spread of these symbionts. The S. noctilio populations in these countries had lower genetic diversity than other populations sampled globally. Amylostereum areolatum populations from Australia and New Zealand clustered separately from all other countries and were highly clonal. While the results suggested multiple early introductions in these two countries, it also reflected an efficient recent quarantine system that isolated these populations and reduced their complexity compared to other parts of the world. The findings also have relevance to the application of biological control for the pest complex.

Teleost fish exhibit a striking divergence from mammals in how they regulate their epigenome. Unlike mammals, they do not undergo the extensive DNA methylation erasure and resetting events that occur during early embryogenesis, germline specification, and spermatogenesis. Consequently, DNA methylation patterns in teleosts might persist across generations, making these species potentially valuable models for studying intergenerational and transgenerational epigenetic inheritance. Recent findings suggest that environmental perturbations can induce heritable epigenetic changes in teleosts, raising the possibility that, in the absence of global epigenetic reprogramming, such changes could have long-lasting consequences. This review summarises current knowledge on DNA methylation stability and inheritance in teleosts, with a particular focus on the two teleost models, zebrafish and medaka. Moreover, the review discusses the ecological and evolutionary implications of epigenetic inheritance and highlights emerging experimental approaches for rigorously assessing transgenerational epigenetic effects in fish.

Invasive species that undergo a founder event may experience a decline in genetic diversity yet still establish successful populations. A possible example is a population of the common wall lizard (Podarcis muralis) in Cincinnati, Ohio, USA, which was founded following an introduction in the 1950s of a small number of individuals from Europe. We used whole genome sequences of individuals from source and introduced populations to assess the origin, demographic history, population structure, and possible signatures of adaptation in this successful lizard introduction. We first confirmed that the introduced lizards in Ohio are Podarcis muralis using phylogenetic analysis. Patterns of genetic diversity indicate introduced lizards in Cincinnati went through a short-term bottleneck with increased inbreeding but then rapidly increased in population size, thus minimising losses in genetic diversity. Comparisons of genomic variation between source and introduced populations demonstrate that populations in Cincinnati represent a subset of source genetic variation and show minimal losses of overall genetic diversity. Comparisons of mutation load between source and introduced populations reveal only small increases in load in introduced populations. Finally, tests for selection on the basis of outlier analyses detect targets for potential positive selection in multiple regions of the genome of introduced individuals, suggesting possible adaptation to a novel environment. Overall, we suggest that rapid population growth and possible adaptation have allowed the founding population of introduced lizards to evade the potential negative genetic impacts of small population size and successfully colonise a novel environment.

Understanding factors influencing the dynamics and distribution of parasites is essential to decipher the mechanism behind their spread and the identification of populations with elevated risks of infection. Bats-together with the diverse parasites they host and the influence of their social behaviour on parasitism-offer a suitable system. We investigated the extent to which differences in life history traits between parasite species found on the same host influence their dispersal dynamics across bat metapopulations. To do so, we compared the population genetic structure of two obligate ectoparasites of the same bat, the Daubenton's bat (Myotis daubentonii): the specialist wing mite Spinturnix andegavinus and the more generalist bat fly Nycteribia kolenatii, and we expected the bat fly to exhibit a higher connectivity than the wing mites. Using double-digest restriction site-associated DNA sequencing (ddRADseq), we genotyped 426 bat flies and 171 wing mites across 13 maternity colonies and foraging sites and 1 putative swarming site in Switzerland. We found high genetic homogeneity across the metapopulations for both species, highlighting the dispersal capacity of N. kolenatii and S. andegavinus, probably driven by the high mobility of their bat hosts. The positive population-specific F_IS and the excess of low-frequency alleles in both species suggest within-site expansion and provide insights into the life cycle of these ectoparasites. Altogether, these findings enhance our understanding of the interplay between nycteribiid flies and spinturnicid mites and their host movement in shaping population structure in Europe, offering broader insights into their potential role in pathogen transmission across bat populations.