Evolutionary Applications最新文献

Triploid oysters are commonly used as the basis for production in the aquaculture of eastern oysters along the USA East and Gulf of Mexico coasts. While they are valued for their rapid growth, incidents of triploid mortality during summer months have been well documented in eastern oysters, especially at low salinity sites. We compared global transcriptomic responses of diploid and triploid oysters bred from the same three maternal source populations at two different hatcheries and outplanted to a high (annual mean salinity = 19.4 ± 6.7) and low (annual mean salinity = 9.3 ± 5.0) salinity site. Oysters were sampled for gene expression at the onset of a mortality event in the summer of 2021 to identify triploid-specific gene expression patterns associated with low salinity sites, which ultimately experienced greater triploid mortality. We also examined chromosome-specific gene expression to test for instances of aneuploidy in experimental triploid oyster lines, another possible contributor to elevated mortality in triploids. We observed a strong effect of hatchery conditions (cohort) on triploid-specific mortality (field data) and a strong interactive effect of hatchery, ploidy, and outplant site on gene expression. At the low salinity site where triploid oysters experienced high mortality, we observed downregulation of transcripts related to calcium signaling, ciliary activity, and cell cycle checkpoints in triploids relative to diploids. These transcripts suggest dampening of the salinity stress response and problems during cell division as key cellular processes associated with elevated mortality risk in triploid oysters. No instances of aneuploidy were detected in our triploid oyster lines. Our results suggest that triploid oysters may be fundamentally less tolerant of rapid decreases in salinity, indicating that oyster farmers may need to limit the use of triploid oysters to sites with more stable salinity conditions.

Molecular methods are routinely used to estimate the effective size of populations (N_e). However, underlying model assumptions are frequently violated to an unknown extent. Although simulations can detect sources of bias and help to adjust sampling strategies and analyses methods, additional information from empirical data can also be used to calibrate methods and improve molecular N_e estimation methods. Here, we take advantage of long-term genetic and ecological monitoring data of the grey wolf (Canis lupus) in Germany, and detailed population genetic studies in Poland, Spain and Portugal to improve N_e estimation strategies in this species, and species with similar life history traits. We first calculated N_e from average lifetime reproductive success and detailed census data from the German population, which served as a baseline to compare to molecular estimates based on linkage disequilibrium and sibship frequency. This yielded a robust N_e/N_c estimation that we used to calibrate molecular estimates of German, Polish and Iberian wolf populations. The linkage disequilibrium method was strongly influenced by spatial genetic structure, much more than the sibship frequency method. When N_e was estimated in local neighbourhoods, both methods yielded comparable results. Estimates of the metapopulation effective size seemed to correspond generally well with the sum of the estimates of local neighbourhoods. Overall, we found that the number of packs is a good proxy of the effective population size. Using this as a rule of thumb, we evaluated for all European wolf populations the N_e 500 indicator and concluded that half of the European wolf populations do not yet fulfil this criterion.

While it is recognised that most, if not all, multicellular organisms harbour neoplastic processes within their bodies, the timing of when these undesirable cell proliferations are most likely to occur and progress throughout the organism's lifetime remains only partially documented. Due to the different mechanisms implicated in tumourigenesis, it is highly unlikely that this probability remains constant at all times and stages of life. In this article, we summarise what is known about this variation, considering the roles of age, season and circadian rhythm. While most studies requiring that level of detail be done on humans, we also review available evidence in other animal species. For each of these timescales, we identify mechanisms or biological functions shaping the variation. When possible, we show that evolutionary processes likely played a role, either directly to regulate the cancer risk or indirectly through trade-offs. We find that neoplastic risk varies with age in a more complex way than predicted by early epidemiological models: rather than resulting from mutations alone, tumour development is dictated by tissue- and age-specific processes. Similarly, the seasonal cycle can be associated with risk variation in some species with life-history events such as sexual competition or mating being timed according to the season. Lastly, we show that the circadian cycle influences tumourigenesis in physiological, pathological and therapeutic contexts. We also highlight two biological functions at the core of these variations across our three timescales: immunity and metabolism. Finally, we show that our understanding of the entanglement between tumourigenic processes and biological cycles is constrained by the limited number of species for which we have extensive data. Improving our knowledge of the periods of vulnerability to the onset and/or progression of (malignant) tumours is a key issue that deserves further investigation, as it is key to successful cancer prevention strategies.

In population genetics idealized Wright-Fisher (WF) populations are generally considered equivalent to real populations with regard to the major evolutionary processes that influence genotype and allele frequencies. As a result we often model the response of populations by focusing on the effective size N_e. The Diversity Partitioning Theorem (DPT) shows that you cannot model the behavior of a system solely on the basis of a diversity (accounting for unevenness among items) without taking richness into account. I show that the census population size (the number of adults, N_c) is equivalent to a richness, and that the effective size N_e is equivalent to a true diversity. It follows logically from the DPT that we require both N_e and N_c to understand how drift, selection, mutation, and gene flow interact to shape the course of evolution of populations. Here I review evidence that both N_c and N_e affect evolutionary trajectories of populations for neutral and adaptive processes. This also influences how we should consider evolutionary potential and genetic criteria for conservation of populations. The effective size of a population is of huge importance in evolutionary biology, but it should not be the sole focus when population size is concerned. Applied evolutionary studies need to integrate N_c in the equation more consistently when modeling the response to selection, mutation, migration, and drift.

In long-distance dispersal events, colonising species typically begin with a small number of founding individuals. A growing body of research suggests that establishment success of small founding populations can be determined by the context of the colonisation event and the new environment. Here, we illuminate the importance of these sources of context dependence. Using a spatially explicit, temporally dynamic, mechanistic, individual-based simulator of a model amphibian species, the cane toad (Rhinella marina), we simulated colonisation scenarios to investigate how (1) the number of founding individuals, (2) the number of dispersal events, (3) landscape's spatial composition and configuration of habitats (‘spatially heterogeneous landscapes’) and (4) the timing of arrival with regards to dynamic environmental conditions (‘dynamic environmental conditions’) influence the establishment success of small founding populations. We analysed the dynamic effects of these predictors on establishment success using running-window logistic regression models. We showed establishment success increases with the number of founding individuals, whereas the number of dispersal events had a weak effect. At ≥ 20 founding individuals, propagule size swamps the effects of other factors, to whereby establishment success is near-certain (≥ 90%). But below this level, confidence in establishment success dramatically decreases as number of founding individuals decreases. At low numbers of founding individuals, the prominent predictors are landscape spatial heterogeneity and dynamic environmental conditions. For instance, compared to the annual mean, founding populations with ≤ 5 individuals have up to 18% higher establishment success when they arrive in ‘packed’ landscapes with relatively limited and clustered essential habitats and right before the breeding season. Accounting for landscape spatial heterogeneity and dynamic environmental conditions is integral in understanding and predicting population establishment and species colonisation. This additional complexity is necessary for advancing biogeographical theory and its application, such as in guiding species reintroduction efforts and invasive alien species management.

Identification of the geographic origin of invasive species can be critical to effective management and amelioration of negative impacts in the introduced range. Liriomyza huidobrensis is a polyphagous leafmining fly that is a devastating pest of many vegetable and floriculture crops around the world. Considered native to South and possibly Central America, L. huidobrensis became invasive in the 1980s and has since spread to at least 30 countries on five continents. We used phylogeographic analysis of over 2 kb of mitochondrial cytochrome oxidase I and II sequence data from 403 field-collected specimens from both native and introduced populations to investigate the geographic origins of invasive L. huidobrensis worldwide. Within South America, there was substantial genetic variation, as well as the strong phylogeographic structure typical of a native range. In contrast, leafminers from the introduced range and Central America all contained little genetic variation and shared the same small set of haplotypes. These haplotypes trace to Peru as the ultimate geographic origin of invasive populations. Central America is rejected as part of the original geographic range of L. huidobrensis. Within Peru, the primary export region of Lima shared an extremely similar pattern of reduced haplotype variation to the invasive populations. An additional 18 specimens collected at US ports of entry did not share the same haplotype profile as contemporary invasive populations, raising perplexing questions on global pathways and establishment success in this species.

Fast-paced selective pressures imposed by climate change and anthropogenic activities call for adaptive evolutionary responses to emerge at ecological timescales. However, the evolution and heritability of genomic variation underlie mechanistic constraints, which dictate a slower pace of adaptation exclusively relying on standing genetic variation and novel mutations. Environmentally responsive epigenetic mechanisms can allow acclimatisation and adaptive phenotypes to arise faster than DNA sequence-based mechanisms alone. Nevertheless, the knowledge gap between identifying epigenetic marks and effectively deeming them functional is still wide in a natural context and often outside the scope of model organisms. With this Special Issue, we aimed to narrow this gap by presenting a compilation of original research articles, reviews and opinions on the topic of epigenetics in wild populations. We contextualised this collection within the overarching topic of conservation biology, as we firmly propose that epigenetic research can significantly enhance the effectiveness of conservation measures. Contributions highlighted the putative role of epigenetic variation in the acclimatisation and adaptive potential of species and populations directly and indirectly affected by climatic shifts and anthropogenic actions. They further exemplified how epigenetic variation can be used as biomarkers for monitoring variations in physiology, phenology and behaviour. Lastly, reviews and perspective articles illustrated the past and present of epigenetic research in wild populations while suggesting future research avenues.

Biological invasions have caused the loss of freshwater biodiversity worldwide. The interplay between adaptive responses and demographic characteristics of populations impacted by invasions is expected to be important for their resilience, but the interaction between these factors is poorly understood. The freshwater gastropod Amnicola limosus is native to the Upper St. Lawrence River and distributed along a water calcium concentration gradient within which high-calcium habitats are impacted by an invasive predator fish (Neogobius melanostomus, round goby), whereas low-calcium habitats provide refuges for the gastropods from the invasive predator. Our objectives were to (1) test for adaptation of A. limosus to the invasive predator and the low-calcium habitats, and (2) investigate if migrant gastropods could move from refuge populations to declining invaded populations (i.e., demographic rescue), which could also help maintain genetic diversity through gene flow (i.e., genetic rescue). We conducted a laboratory reciprocal transplant of wild F₀ A. limosus sourced from the two habitat types (high calcium/invaded and low calcium/refuge) to measure adult survival and fecundity in home and transplant treatments of water calcium concentration (low/high) and round goby cue (present/absent). We then applied pooled whole-genome sequencing of 12 gastropod populations from across the calcium/invasion gradient. We identified patterns of life-history traits and genetic differentiation across the habitats that are consistent with local adaptation to low-calcium concentrations in refuge populations and to round goby predation in invaded populations. We also detected restricted gene flow from the low-calcium refugia towards high-calcium invaded populations, implying that the potential for demographic and genetic rescue is limited by natural dispersal. Our study highlights the importance of considering the potentially conflicting effects of local adaptation and gene flow for the resilience of populations coping with invasive predators.

Many methods are now available to calculate N_e, but their performance varies depending on assumptions. Although simulated data are useful to discover certain types of bias, real empirical data supported by detailed known population histories allow us to discern how well methods perform with actual messy and complex data. Here, we focus on two genomic data sets of grey wolf populations for which population size changes of the past 40–120 years are well documented. We use this background to explore in what detail we can retrieve the known population history from these populations, in the light of pitfalls relating to population history, sampling design and the change in the spatial scale at which N_e is estimated as we go further back in time. The Scandinavian wolf population was founded in the early 1980s from a few individuals and has gradually expanded up to 510 wolves. Although the founder event of the Scandinavian population was detected by GONE, the founding effective population size was strongly overestimated when the most recent samples were used, but less so when older samples were considered. Nevertheless, the present-day N_e corresponds to theoretical expectations. The western Great Lakes wolf population of Minnesota is the only population in the contiguous United States that persisted throughout the 20th century, surviving intense persecution. We found a good concordance between the estimated N_e and trends in census size data, but the reconstruction of N_e clearly highlights the difficulty of interpreting results in spatially structured populations that underwent demographic fluctuations.

We are still largely reliant on pesticides for the suppression of arthropod pests which threaten human health and food production, but the recent rise of evolved resistance among important pest species has reduced pesticide efficacy. Despite this, our understanding of strategies that effectively limit the evolution of resistance remains weak. Male-killing sex ratio distorting microbes (SRDMs), such as Wolbachia and Spiroplasma, are common among arthropod species. Previous theoretical work has suggested that they could limit adaptive potential in two ways: first, because by distorting sex ratios they reduce the effective population size, and second, because infected females produce no male offspring which restricts gene flow. Here we present the results of a novel experiment in which we test the extent by which these two mechanisms limit the adaptive response of arthropods to pesticide. Using a fully factorial design, we manipulated the adult sex ratio of laboratory populations of Drosophila melanogaster, both in the presence and absence of SRDMs, and exposed these populations to six generations of pesticide poisoning. This design allows the effects of SRDMs on sex ratio and their effects on gene flow to be estimated separately. After six generations, individuals from populations with even sex ratios displayed a higher resistance to pesticide relative to individuals from female-biased populations. By contrast, we found no effect of the presence of SRDMs in host populations on pesticide resistance independent of sex ratio. In addition, males were more susceptible to pesticide than females—this was true of flies from both naïve and previously exposed populations. These findings provide the first empirical proof of concept that sex ratio distortion arising from SRDMs can limit adaptation to pesticides, but cast doubt on the theoretical effect of male-killers limiting adaptation by disrupting gene flow.