Evolutionary Applications最新文献

Genetic rescue, specifically translocation to facilitate gene flow among populations and reduce the effects of inbreeding, is an increasingly used approach in conservation. However, this approach comes with trade-offs, wherein gene flow may reduce fitness when populations have adaptive differentiation (i.e., outbreeding depression). A better understanding of the interaction between isolation, inbreeding, and adaptive divergence in key traits, such as life history traits, will help to inform genetic rescue efforts. Stream-dwelling salmonids, such as the westslope cutthroat trout (Oncorhynchus lewisi; WCT), are well-suited for examining these trade-offs because they are increasingly isolated by habitat degradation, exhibit substantial variation in life history traits among populations, and include many species of conservation concern. However, few genomic studies have examined the potential trade-offs in inbreeding versus outbreeding depression in salmonids. We used > 150,000 SNPs to examine genomic variation and inbreeding coefficients in 565 individuals across 25 WCT populations that differed in their isolation status and demographic histories. Analyses of runs of homozygosity revealed that several isolated WCT populations had "flatlined" having extremely low genetic variation and high inbreeding coefficients. Additionally, we conducted genome scans to identify potential outlier loci that could explain life history differences among 10 isolated populations. Genome scans identified one candidate genomic region that influenced maximum length and age-1 to age-2 growth. However, the limited number of candidate loci suggests that the life history traits examined may be driven by many genes of small effect or phenotypic plasticity. Although adaptive differentiation should be considered, the high inbreeding coefficients in several populations suggest that genetic rescue may benefit the most genetically depauperate WCT populations.

Inbreeding depression is a highly relevant universal phenomenon in population and conservation genetics since it leads to a decline in the fitness of individuals. This phenomenon is due to the homozygous expression of alleles whose effects are hidden in heterozygotes (inbreeding load). The rate of inbreeding depression for quantitative traits can be quantified if the coefficient of inbreeding (F) of individuals is known. This coefficient can be estimated from pedigrees or from the information of molecular markers, such as SNPs, using measures of homozygosity of individual markers or runs of homozygosity (ROH) across the genome. Several studies have investigated the accuracy of different F measures to estimate inbreeding depression, but always assuming that this is only due to recessive or partially recessive deleterious mutations. It is possible, though, that part of the inbreeding depression is due to variants with overdominant gene action (heterozygote advantage). In this study, we carried out computer simulations to assess the impact of overdominance on the estimation of inbreeding depression based on different measures of F. The results indicate that the estimators based on ROH provide the most robust estimates of inbreeding depression when this is due to overdominant loci. The estimators that use measures of homozygosity from individual markers may provide estimates with substantial biases, depending on whether or not low-frequency alleles are discarded in the analyses; but among these SNP-by-SNP measures, those based on the correlation between uniting gametes are generally the most reliable.

Elevated temperatures inhibit the germination of a concerning number of crop species. One strategy to mitigate the impact of warming temperatures is to identify and introgress adaptive genes into elite germplasm. Diversity must be sought in wild populations, coupled with an understanding of the complex pattern of adaptation across a broad range of landscapes. By investigating the landraces, wild, and feral populations of Algeria, Italy, France, Slovenia, Spain, and Tunisia, we assessed the response of germination to temperature increase in an unexplored diversity of 117 accessions of Brassica rapa and 66 of Brassica oleracea. Our results show that both species exhibit heat tolerance to the temperature range tested, especially B. rapa, with an increase in speed and uniformity of germination time, as well as an increase in germination rate as temperature increased. As for B. oleracea accessions, the ability to germinate under heat conditions depended on the geographical origin; in particular, southern populations showed a higher germination rate than northern populations, possibly in relation to their warmer climates of origin. These findings highlight the complex interplay between domestication, feralization, and current agronomic practices in shaping germination characteristics in Brassica species.

Climate change may hinder species' ability to evolutionarily adapt to environmental shifts. Assisted gene flow, introducing adaptive alleles into target populations, could be a viable solution for keystone species. Our study aimed to evaluate the benefits and limitations of assisted gene flow in enhancing the evolutionary potential of Lupinus angustifolius L. (Fabaceae), considering both phenotypic and genomic perspectives. We collected seeds from four populations in Spain at two latitudes (north and south), and grew them in a common garden. We used pollen from southern individuals to pollinate northern plants and create an F1 gene flow line that would advance its flowering onset. In the next season, we allowed F1 plants to self-pollinate creating an F2 self-pollination line. We also created a backcross line by pollinating control northern plants with pollen from F1 plants. We measured flowering onset, reproductive success, and other plant traits in all resulting lines. In parallel, we sequenced genes related to reproduction, growth, stress, nitrogen, and alkaloids. All gene flow-derived lines flowered significantly earlier than the control lines from the northern populations. F1 gene flow line plants produced heavier seeds and had a lower shoot growth than those from the northern control lines. Genomic analyses identified 36 outlier SNPs between the control and the F1 gene flow lines, associated with differences in flowering onset, seed weight, and shoot growth. These results underscore that assisted gene flow can enhance a population's evolutionary potential by altering specific traits. However, altering one trait may impact others in a way that depends on the intrinsic characteristics of each population.

Density dependence describes the regulation of population growth rate by population density. This process is widely observed in insect populations, including vectors such as mosquitoes and agricultural pests that are targets of genetic biocontrol using gene drive technologies. While there continues to be rapid advancement in gene drive molecular design, most studies prioritise gene drive efficacy over ecology, and the role of density-dependent feedback on gene drives remains neglected. Furthermore, the details of density dependence experienced in these potential species of interest are usually poorly understood, creating additional constraints and challenges in evaluating the efficacy and efficiency of gene drive systems, especially those that promise local confinement after release. Here, we formulate and analyse a simple, non-species-specific mathematical model which integrates population dynamics by density dependence together with population genetics of a high-threshold two-locus underdominance system. Different models of density dependence and strengths of within-species competition are investigated alongside other genetic and ecological parameters. Our results suggest that for an underdominance gene drive system, density dependence processes, by acting on births or deaths, influence the population dynamics by leading to significantly different population-level suppression in the presence of a fitness cost. However, density dependence does not directly affect the fitness cost threshold for drive establishment. Moreover, we find that the magnitude and range of key ecological parameters (birth and death rates) could result in different outcomes depending on the type of density dependence employed. Our work highlights the importance of considering the ecological contexts in the design, development and deployment of gene drive molecular strategies.

The Anthropocene is marked by increased population extirpations and redistributions driven primarily by human-induced climate change and habitat loss. Habitat loss affects populations by removing occupiable area, which reduces carrying capacity through a reduction in resources, and fragmenting the landscape, which can reduce gene flow with potential consequences for adaptation to changing environmental conditions. Real patterns of habitat loss are non-random, often clustered in space and within a subset of environmental conditions (e.g., primarily in the valleys of a mountain–valley region). Spatial clustering of habitat loss can alter population connectivity, and environmental clustering can shift the mean as well as decrease the variance in environmental conditions available to populations. We evaluate how spatial and environmental biases underlying habitat loss impact the survival of populations (as a proxy of evolutionary rescue) exposed to both habitat loss and environmental change. To do this, we simulated landscapes with a spatially autocorrelated temperature gradient to which individuals were locally adapted. These landscapes were then subjected to both nonrandom habitat loss (e.g., clustered based on the temperature) and increasing temperatures. We find that evolutionary rescue in response to increasing temperatures is hampered when habitat loss results in small patches, reduces the breadth of environmental conditions, and is concentrated on the cooler end of the temperature gradient. Our findings highlight the importance of maintaining a wide breadth of environmental conditions available to populations subjected to habitat loss, and the disproportionate role that colder sites play as a buffer to increasing temperatures, compared to warmer sites. Our findings also add a new dimension to the single large or several small (SLOSS) conservation discussion, stressing the importance of environmental diversity regardless of patch size.

Host–parasitoid interactions are tied in coevolutionary arms races where parasitoids continuously have to evolve increased virulence as hosts evolve increased resistance. Over time, geographic structure in virulence and resistance can arise because of spatial and temporal differences in parasitoid communities, in the strength of reciprocal selection pressures, in genetic variation in local populations, and as trade-offs are balanced between defense and fitness traits. It is crucial to understand the resistance structure of pest populations to successfully implement biological control programs against invasive insect hosts. We investigated spatial and temporal variations in the resistance of the invasive Drosophila suzukii in seven geographically distinct populations in Michigan and of one population from Oregon against a newly approved biocontrol agent, the larval parasitoid Ganaspis brasiliensis. We found regional and temporal variations in the resistance (encapsulation rates of parasitoid eggs) of D. suzukii populations that ranged from 11% to 48%. The northernmost, and thus the coldest site, had the highest rate of parasitism and the lowest encapsulation rate. Large regional differences in the resistance of D. suzukii populations can render the ensuing biocontrol program more variable and less predictable, and release strategies may need to be altered at sites where flies have high resistance.

As anthropogenic disturbances rapidly change natural environments, species must respond to new selective pressures shaping rates of reproduction, growth, and mortality. One example is intense fisheries harvest, which can drive the evolution of heavily fished populations toward maturation at smaller sizes and younger ages. Changes in maturation have often been measured using probabilistic maturation reaction norms (PMRNs), which were originally designed to control for phenotypic plasticity while allowing for the detection of the evolution of maturation. However, multiple studies have highlighted issues with PMRN estimation, particularly with respect to their accuracy when parameterized with sparse data or when applied to populations experiencing myriad environmental stressors. We used a three-decade time series of Laurentian Great Lakes yellow perch (Perca flavescens Mitchill) data to develop a novel, hierarchical Bayesian PMRN estimation method that can explicitly account for these conceptual issues. Our results indicate that commercial fishing was a primary driver of maturation change in this population, and that the relaxation of harvest pressure via the closure of the commercial fishery in the late 1990s resulted in adaptation toward older ages and larger sizes at maturation within 2–3 generations. Future pairing of hierarchical Bayesian PMRN methods with genome-wide data will help reveal the genetic underpinnings of maturation, and could lead to new avenues for integrating PMRNs into fisheries management and policy.

Translocations are carried out either unintentionally or intentionally for conservation or management reasons. In both cases, translocated populations may genetically impact natural populations via introgression. Understanding how genetic background may affect an establishment in a novel environment and the potential risks for native populations is important for biodiversity conservation. Here, using a panel of 96 SNPs, we monitor the establishment of two genetically and ecologically distinct brown trout populations released into a mountain lake system in central Sweden where trout did not occur prior to the release. The release was carried out in 1979, and we monitor the establishment over the first three decades (5–6 generations) in seven lakes downstream of the release site. We find that extensive hybridization has occurred, and genes from both populations exist in all lakes examined. Genes from the population that was nonmigratory in its native environment have remained to a higher degree in the area close to the release site, while genes from the population that was more migratory in its native habitat have spread further downstream. All established populations exhibit higher levels of genetic diversity than the released populations. Natural, stream-resident brown trout populations occur ~15 km downstream of the release site and below a waterfall that acts as an upstream migration barrier. Released fish have spread genes to these populations but with low introgression rates of 3%–8%. Recently adopted indicators for monitoring genetic diversity were partly able to detect this introgression, emphasizing the usefulness of genetic indicators in management. The SNP panel used in this study provides a similar picture as previously used allozymes, showing that older marker systems with fewer loci may still be useful for describing the population structure.

Understanding how warming surface waters impact the larval growth of highly prized marine fishes such as the European seabass, Dicentrarchus labrax, is important for sustainable fisheries and aquaculture. We studied the growth of larvae from three genetically differentiated seabass populations, Atlantic (AT), Western Mediterranean (WM), and Eastern Mediterranean (EM), reared in a common garden under three thermal regimes, representative of seasonal changes in a relatively cold Atlantic (rAT), intermediate Western Mediterranean (rWM), and warm Eastern Mediterranean (rEM). Survival was higher in warmer regimes until larvae reached a length of 23 mm, after which there was no major difference. Growth was monitored from 20 days posthatch to 1.5 g, with individuals sampled at regular intervals and their population of origin identified by parentage assignment using their genotypes for 96 SNPs. Significant length differences emerged among populations, the AT population being longer than WM and EM in all thermal regimes. In conclusion, the AT population had higher growth than the WM and EM populations in all thermal regimes, not just in its own, and the AT population can be considered the most robust to temperature variations at the larval stage. Further research is required to understand whether the high growth rate of the AT population reflects a process of local adaptation to a relatively cold thermal regime.