Evolutionary Applications最新文献

This review seeks a deeper functional understanding of wild bee microbiomes by focusing on a tribe of bees where natural history and behavioral ecology are well known but investigations of microbiology are just beginning. Opportunities to improve our future knowledge of pathogens to insect pollinators are explored—which have broad ramifications for crop pollination services, considering the current overdependence on a few managed species that face a multitude of health threats. The bee tribe Allodapini (Apidae: Xylocopinae) has the potential to offer comparative insights on the evolution of bee microbiomes, owing to a unique combination of life history traits relevant to pollination service delivery across sub-Saharan Africa, Southern Asia, and Australia. Allodapines exhibit facultatively social colony organization that offer evolutionary perspectives on the formation of group living not afforded by obligately eusocial insects, which have already transgressed the solitary-social threshold. Progressive provisioning of brood (in the absence of brood cells) facilitates a network exchange of nutrients (via trophallaxis) that we speculate may culminate in an intra-colony “network microbiome”. A literature review of pathogenic (bacterial, fungal, viral, and protozoan) associates of allodapine bees reveals considerably less research than for carpenter (Ceratina, Xylocopa), bumble (Bombus), and honey (Apis) bees. Interrogation of published genomes (Exoneura, Exoneurella) discovered novel microsporidian and protozoan parasites and relatives of known bee bacteria (Commensalibacter, Sodalis). Some Xylocopa exhibit microbial profiles typical of corbiculate bee core gut microbiomes, but no comparative evidence among allodapines was found. Allodapines visit flowers of 13 horticultural crops (fruits, vegetables, oilseeds, tree-nuts) and 50 native genera (predominantly Myrtaceae, Proteacae, Myoporaceae, Goodeniaceae). The ability to parse intrinsic and extrinsic factors influencing microbiome patterns within and between species means that allodapine bees provide the opportunity for an integrated approach to bee socio-eco-evo-immunology.

Maternally transmitted symbionts such as Wolbachia spread within host populations by mediating reproductive phenotypes. Cytoplasmic incompatibility (CI) is a reproductive phenotype that interferes with embryonal development when infected males fertilize uninfected females. Wolbachia-based pest control relies on strong CI to suppress or replace pest populations. Host genetic background determines CI strength, and host suppressors that cause weak CI threaten the efficacy of Wolbachia-based pest control programs. In haplodiploids, CI embryos either die (Female Mortality, FM-CI) or develop into uninfected males (Male Development, MD-CI). The reciprocal spread of host suppressors and infection, as well as the interaction with the two CI outcomes in haplodiploids, remains poorly understood. The contribution of sex allocation distortion (Sd), an independent Wolbachia-mediated reproductive phenotype that causes a female-biased sex ratio, to infection persistence in haplodiploids is also poorly understood, especially with imperfect maternal transmission. To address these issues, we developed individual-based simulations and validated this computational tool by tracking Wolbachia spread in experimental Tetranychus urticae populations and by contrasting infection dynamics with deterministic mathematical models. Within ⁓14 host generations, we found that deterministic models inflate infection frequencies relative to simulations by ⁓8.1% and overestimate the driving potential of CI, particularly under low initial infection frequencies. Compared to MD-CI, we show that FM-CI strongly extends infection persistence when nuclear suppressors are segregating in the population. We also quantify how maternal transmission modulates the reciprocal spread of suppressors and infection. Upon loss of CI, we show that hypomorphic expression of Sd (~5%) is sufficient for a stable persistence of infection. We derive a mathematical expression that approximates the stable polymorphic infection frequencies that can be maintained by Sd. Collectively, our results advance our understanding of how symbiosis with CI-inducing Wolbachia and haplodiploid hosts might evolve and inform CI-based pest control programs of potential future risks.

Egg size and fecundity are both positively associated with maternal reproductive success, yet maternal resource limitations result in a trade-off between these two traits. Exploring this trade-off, the extent of genetic and environmental influences on egg size and fecundity and of correlations between these and other traits, and thus, the effects acting within vs. among generations is therefore a central goal in both evolutionary ecology and selective breeding. Using multi-generational captive Arctic charr (Salvelinus alpinus) records, we quantified genetic and environmental effects on and correlations between egg size and fecundity, body size (a proxy for growth) and condition prior to maturation, and body size at maturation. We estimated that genetic contributions to variation in egg size and fecundity are moderate to high. Egg size and fecundity do not significantly correlate at the genetic level but do correlate negatively at the environmental level. Growth prior to maturation and size at maturation are positively correlated with fecundity and egg size at the phenotypic level. Genetic correlations with growth are positive for both egg size and fecundity but weaker for egg size. Contrarily, the environmental correlations with growth are of the opposite sign, also weaker for egg size, and increasing growth leads to decreasing egg size but increasing fecundity. Consequently, reproductive success can be optimized across generations via independent selection responses of egg size or fecundity and by correlated selection responses with body size. Ultimately, the egg size-fecundity resource trade-off in Arctic charr is resolved via growth-controlled phenotypic plasticity acting within generations.

Historic and contemporary demography affect deleterious variation and inbreeding depression, meaning that measuring genetic diversity alone does not capture the nuances of genetic erosion. Contrasting genomic signatures generated by long-term evolutionary processes to those generated by contemporary changes may help differentiate between populations more or less likely to persist with low diversity or high genetic load. To better understand these interactions, we examined signatures of inbreeding and genetic load across three species of bears: American black (Ursus americanus), brown (U. arctos), and polar (U. maritimus). We sampled across each species' geographic range to represent intraspecific variation in demographic history and ecology. We found that ROH burden often varied more among populations within lineages of species than between species. Admixed populations generally had higher heterozygosity and lower ROH burden; this pattern reversed in small, isolated populations. Greater diversity, including harmful variation, was found in larger, admixed populations—especially those with higher historical effective population sizes (N_E). However, this did not necessarily correspond to more realized genetic load. While polar bears had low N_E and low realized load, brown and American black bears exhibited less realized load as N_E increased and greater realized load in populations with recent bottlenecks and/or indications of recent consanguineous matings. This vantage offers insight into genetic health and threats of genetic erosion within populations and species, which can meaningfully contribute to assessments of threat status. In American black bears, the composite of these metrics revealed a trend in the Louisiana population that may be diagnostic for management intervention based on contemporary demographic changes. In brown bears, the Apennine bear consistently fell outside of the range of values in other populations, reinforcing previous descriptions of isolation, inbreeding, and purging in this population. In polar bears, there were no regional trends that warranted concern with respect to genetic erosion.

Identifying suitable donor sites is an important component of successful restoration and reduces the likelihood that a restoration action will have negative impacts on surrounding populations. Whether the most suitable donor site has (1) fast-growing phenotypes, (2) high genetic diversity, or (3) harbors alleles that are beneficial for the current or future environment at the restoration site is an ongoing debate in restoration genomics. It is also debated whether one single donor site is the best choice, or if a mixed provenance strategy from sites with different characteristics is preferable. For eelgrass restoration, donor material is typically sourced within a few kilometers. It is therefore also this small spatial scale that needs to be considered when testing which local meadows harbor the most beneficial donor material for a given restoration site. We here assessed micro-habitat differences at 10 eelgrass meadows across 1.5–14 km and genotyped the 10 meadows at 1689 single nucleotide polymorphisms (SNPs). We observed substantial differences in temperature regimes, genetic differentiation, and genetic diversity. We found that even on this small scale, 10% of the overall genetic variation was explained by the local environment of the meadow as well as geographic distance and genetic differentiation. We also identified putative adaptive loci associated with environmental variables and detected differences in growth in common-garden mesocosm experiments simulating ambient summer conditions as well as a marine heatwave with concurrent freshening. We highlight that the variation in environment, genetic diversity, local adaptation, the potential for preadaptation for future conditions, and differences in individual growth can be strong in eelgrass meadows even on the small spatial scale. We suggest a donor registry to take into account these differences and narrow down the pool of potential donor meadows to source the most beneficial combination of donor material for any given restoration site.

Local adaptation is a fundamental process that allows populations to thrive in their native environment, often increasing genetic differentiation with neighboring stands. However, detecting the molecular basis and selective factors responsible for local adaptation remains a challenge, particularly in sessile, non-model species with long life cycles, such as forest trees. Local adaptation in trees is not only modeled by climatic factors, but also by soil variation. Such variation depends on dynamic geological and ecological processes that generate a highly heterogeneous selective mosaic that may differentially condition tree adaptation both at the range-wide and local scales. This could be particularly manifest in species inhabiting mountain ranges that were formed by diverse geological events, like sacred fir (Abies religiosa), a conifer endemic to the mountains of central Mexico. Here, we used landscape genomics approaches to investigate how chemical edaphic variation influences the genetic structure of this species at the range-wide and local scales. After controlling for neutral genetic structure, we performed genotype-environment associations and identified 49 and 23 candidate SNPs at the range-wide and local scales, respectively, with little overlap between scales. We then developed polygenic models with such candidates, which accounted for ~20% of the range-wide variation in soil Ca²⁺ concentration, electric conductivity (EC), and pH, and for the local variation in soil EC and organic carbon content (OC). Spatial Principal Component Analyses further highlighted the role of geography and population isolation in explaining this genetic-soil co-variation. Our findings reveal that local adaptation in trees is the result of an intricate interaction between soil chemical properties and the local population's genetic makeup, and that the selective factors driving such adaptation greatly vary and are not necessarily predictable across spatial scales. These results highlight the need to consider edaphic variation in forest genetic studies (including common garden experiments) and in conservation, management and assisted migration programs.

Quantitative resistances are essential tools for mitigating epidemics in managed plant ecosystems. However, their deployment can drive evolutionary changes in pathogen life-history traits, making predictions of epidemic development challenging. To investigate these effects, we developed a demo-genetic model that explicitly captures feedbacks between the pathogen's population demography and its genetic composition. The model also links within-host multiplication and between-host transmission, and is built on the assumption that the coexistence of susceptible and resistant hosts imposes divergent selection pressures on the pathogen population at the landscape scale. We simulated contrasting landscapes of perennial host plants with varying proportions of resistant plants and resistance efficiencies. Our simulations confirmed that deploying resistances with nearly complete efficiency (> 99.99%) effectively reduces the severity of epidemics caused by pathogen introduction and promotes the specialization of infectious genotypes to either susceptible or resistant hosts. Conversely, the use of partial resistances induces limited evolutionary changes, often resulting in pathogen maladaptation to both susceptible and resistant hosts. Notably, deploying resistances with strong (89%) or moderate (60%) efficiencies can, under certain conditions, lead to higher host mortality compared to entirely susceptible populations. This counterintuitive outcome arises from the maladaptation of infectious genotypes to their hosts, which prolongs the lifespan of infected hosts and can increase inoculum pressure. We further compared simulations of the full model with those of simplified versions in which (i) the contribution of infected plants to disease transmission did not depend on the pathogen load they carried, (ii) plant landscapes were not spatially explicit. These comparisons highlighted the essential role of these components in shaping model predictions. Finally, we discuss the conditions that may lead to detrimental outcomes of quantitative resistance deployments in managed perennial plants.

The agromyzid leafminer Liriomyza trifolii (Burgess) is an important polyphagous pest of vegetable crops and ornamental plants. It is native to the Americas but has spread throughout the world over the past 50 years. Previous molecular research has indicated that this species contains highly distinct mitochondrial lineages suggestive of cryptic species. To better interpret the mitochondrial divergence, we used anchored hybrid enrichment datasets in order to conduct genome-wide phylogenetic analyses. We found that individuals of L. trifolii from pepper and tomatillo populations form a monophyletic group (“PT group”) distinct from the remaining L. trifolii (“non-PT group”). These results corroborate previous mitochondrial and nuclear datasets and indicate an absence of gene flow between the PT and non-PT groups. This is consistent with previous work on reproductive isolation and oviposition preferences, and provides substantial evidence that the PT group represents a distinct and previously unrecognized species. The presence of two species within a nominally single pest species has important implications for management. Although there was only weak genetic differentiation between geographically disparate groups of non-PT L. trifolii, a monophyletic group of Chinese specimens was found in a coalescent-based analysis that is concordant with the history of invasions in Asia. Our study provides important new insight into geographic and host-associated structure in L. trifolii.

Dispersal impacts individual fitness and influences local dynamics, stability and adaptation in interconnected populations. Anadromous salmonid fishes are renowned for their precise homing and adaptations to local aquatic environments, while navigating between multiple connected habitats. However, recent studies have demonstrated considerable straying among systems, generating metapopulation dynamics among connected subpopulations or demes. Salmonids constitute valuable economic and ecological resources, yet many populations are declining due to multifaceted anthropogenic-induced disturbances. This context of reduced populations inhabiting altered environments may impact both population viability and dispersal. To explore if metapopulation processes are present among impacted neighbouring populations of anadromous brown trout (Salmo trutta), a 4-year study of individual (N = 84) dispersal behaviour (using biotelemetry) and genetic analysis was conducted in four populations, connected by an extensive (> 200 km), semi-enclosed fjord system, Sognefjorden, Norway. To estimate the demographic status of each study population, life-table matrices were built, from which a potential source–sink structure among demes could be identified. Sognefjorden brown trout formed a metapopulation consisting of multiple sink populations, primarily supplemented from a single source. Only one population exhibited intrinsic growth (i.e., λ > 1), with excess recruits in this population attributed to high survival within the fjord. Among potential spawners, dispersal movements were performed by 55% of the total population, with individual age and migration extent affecting the probability of this behaviour. Successful dispersal (straying) was performed by 25% of the total spawning population. The extensive hydroscape generated directional gene flow from the innermost to outermost populations, with the highest rates observed among neighbouring populations. Although most dispersal resulted in unsuccessful spawning events and/or was not intended for spawning (e.g., conducted for overwintering purposes), connectivity among population demes was significant. This connectivity likely enhances the overall resilience of the metapopulation to variation and shifts in contemporary conditions within the fjord.

Anthropogenic pollution can have detrimental effects on organismal physiology, behavior, and fitness, but the underlying genomic mechanisms mediating these effects are not well understood. Epigenetic regulation, such as DNA methylation, has been proposed as a potential mechanism mediating these effects, but currently, there are few studies in wild populations. Here, we examined the methylation patterns of liver tissues from black guillemot (Cepphus grylle) in regions of the Canadian Arctic with different histories of exposure to polycyclic aromatic compounds (PACs)—contaminants associated with hydrocarbons and petrochemicals. As compared to a reference site with minimal PAC exposure, the two sites with exposure to anthropogenic sources of PACs (shipping and spills) shared more differentially methylated regions (DMRs) than they did with the site experiencing chronic exposure to natural PACs (a hydrocarbon seep). Furthermore, we found that guillemots that have been exposed to anthropogenic PACs are characterized by having DMRs with significantly greater ratios of hypermethylated to hypomethylated DNA versus the population experiencing chronic exposure to natural PACs. However, birds from all three sites with elevated PAC exposure shared a core set of DMRs, implying that there are some consistent methylation responses to this family of compounds. Taken together, these results imply that the specific composition and exposure length of PACs can influence the direction of the epigenetic response. The identified DMRs serve as a genomic resource for further research investigating the functional role of DNA methylation in response to anthropogenic oil pollution.