Evolutionary Applications最新文献

The elongate ilisha (Ilisha elongata) is an important commercial species found along the Northwestern Pacific Coast. A sharp decline in the annual catch of I. elongata over recent decades implies a concerning situation regarding its fishery stocks. Nonetheless, inadequate knowledge of the genetic diversity, population structure, and historical demography of this species has hindered the establishment of sustainable fishery policies and appropriate conservation measures. In this study, the genetic structure and population demography of I. elongata stocks along the Northwestern Pacific Coast were examined using target-gene enrichment data from 144 I. elongata individuals collected from 18 locations. The analysis revealed an average heterozygosity value of 0.2321 across variable sites in all I. elongata populations. Furthermore, inter-population differentiation is relatively low, with most geographical populations displaying minimal genetic distinctions or none from one another. Population clustering analysis identified four lineages of I. elongata stocks. Through historical demography simulations, it was proposed that the Yalu River Estuary population diverged initially around 32,802 generations before present, while the remaining lineage split into two about 9120 generations ago. One lineage represents the southern population, while the other further separated into the northern population and the Japanese population approximately 4200 generations ago. Furthermore, secondary contact between the southern and northern population was evidenced by either population clustering or demography simulation results. These results underscore that the current phylogeographic patterns of I. elongata may result from directional selection due to low temperature and geographic barriers during and post glacial periods.

The fall armyworm (FAW), scientifically known as Spodoptera frugiperda, is an agricultural pest native to the American continents. Its larvae display voracious feeding behavior with a host range of over 350 plant species. The pest was first detected outside the Americas in 2016, subsequently spreading across Africa, Asia, and Oceania. As a country with substantial agricultural imports and exposure to regional migration routes, Malaysia presents a valuable case study for investigating the establishment and adaptation of invasive FAW populations. Forty-two novel Malaysian FAW genomes were sequenced on the DNBSEQ-G400 platform via DNBSeq. A subset of high-quality genome-wide single nucleotide polymorphisms was used to compare the evolution of both native and invasive FAW populations, with publicly available samples from another 18 countries from across the world. Our analyses revealed clear genetic differentiation between native and invasive FAW populations. We found little evidence to support West African populations as the founding source for Asian or East African invasions. Instead, Malaysian FAW clustered closely with populations from India, China, and East African countries, suggesting multiple, independent introductions into the region. Genomic outliers related to sensory perception, insecticide resistance, and heat tolerance were detected, likely contributing to the recent global success of FAW invasions. This study provides new genomic insights into the invasion history and adaptive strategies of FAW in Malaysia, contributing to a clearer picture of FAW movement across Asia and Africa. The results provide critical information for future pest management and policy-making to mitigate the spread of this invasive pest.

Musk deer (Moschus), the sole genus in the family Moschidae, are critically endangered and face an uncertain future due to the limited understanding of their taxonomy, evolutionary history, genetic load, and adaptive evolution. These knowledge gaps hinder conservation efforts at crucial stages. Here, we conducted a comprehensive conservation genomic analysis by sequencing eight M. anhuiensis genomes and integrating public data from 15 M. berezovskii individuals. Phylogenomic and population genomic analyses confirmed that M. anhuiensis is a distinct phylogenetic species that diverged approximately 260 thousand years ago (kya). Both species experienced severe population bottlenecks, subsequently exhibiting marked genetic divergence. Over the past 200 kya, M. berezovskii has undergone multiple admixture events and bottlenecks, whereas M. anhuiensis has steadily declined and maintained a small, stable population. Anthropogenic activities have intensified these pressures, leading to sharp declines in both species. Notably, M. anhuiensis has accumulated homozygous deleterious mutations, thereby heightening its extinction risk. Moreover, selective sweep analysis revealed 32 positively selected genes, including olfactory receptor genes (OLF3 and OR6B1), which are essential for foraging, reproduction, and social interactions; the proliferation-related gene (PDGFRA), which responds to environmental changes and injury; and the thermoregulation gene (CDH13), which helps maintain body temperature stability in extreme conditions. These findings shed light on the speciation and evolutionary history of musk deer, offering crucial insights into their local adaptations and vulnerabilities. This work provides a foundation for targeted conservation efforts to avert extinction and safeguard biodiversity.

Next-generation-sequencing has broadened perspectives regarding the estimation of the effective population size (Ne) by providing high-density genomic information. These technologies have expanded data collection and analytical tools in population genetics, increasing understanding of populations with high abundance, such as marine species with high commercial or conservation priority. Several common methods for estimating Ne are based on allele frequency spectra or linkage disequilibrium between loci. However, their specific constraints make it difficult to apply them to large populations, especially with confounding factors such as migration rates, complex sampling schemes or non-independence between loci. Computer simulations have long represented invaluable tools to explore the influence of biological or logistical factors on Ne estimation and to assess the robustness of dedicated methods. Here, we outline several Ne estimation methods and their foundational principles, requirements and likely caveats regarding application to populations of high abundance. Thereafter, we present a simulation framework built upon recent computational genomic tools that combine the possibility to generate biologically realistic data sets with realistic patterns of long-term neutral genetic diversity. This framework aims at reproducing and tracking the main critical features of data derived from a large natural population when running a simulation-based population genetics study, for example, evaluating the strengths and limitations of various Ne estimation methods. We illustrate this framework by generating genotype data sets with varying sample sizes and locus numbers and analysing them with three software tools (NeEstimator2, GONE and GADMA). Detailed and annotated simulation scripts are provided to ensure reproducibility and to support future research on Ne estimation. These resources can support method comparisons and validations, particularly for non-specialists, such as conservation practitioners and students.

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.