Evolutionary Applications最新文献

Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.

The adaptation of Anopheles malaria vectors to domestic settings is directly linked to their ability to feed on humans. The strength of this species–habitat association is unequal across the species within the genus, with the major vectors being particularly dependent on humans. However, our understanding of how blood-feeding behavior interacts with and adapts to environmental settings, including the presence of humans, remains limited. Using a field-based approach, we first investigated Anopheles community structure and feeding behavior patterns in domestic and sylvatic settings in La Lopé National Park in Gabon, Central Africa. We characterized the preference indices using a dual-host choice sampling approach across mosquito species, habitats, and seasons. We then quantified the plastic biting behavior of mosquito species in each habitat. We collected individuals from 16 Anopheles species that exhibited significant differences in species composition and abundance between sylvatic and domestic settings. The host-seeking behavior also varied among the seven most abundant species. The general attractiveness to each host, human or animal, remained relatively constant for each species, but with significant variations between habitats across species. These variations, to more generalist and to more anthropophilic behavior, were related to seasonal changes and distance from the village, respectively. Finally, we pointed out that the host choice of major malaria vectors changed in the absence of humans, revealing a plastic feeding behavior of these species. This study highlights the effect of humans on Anopheles distribution and feeding evolution. The characterization of feeding behavior in wild and domestic settings provides opportunities to better understand the interplay between genetic determinants of host preference and ecological factors. Our findings suggest that protected areas may offer alternative thriving conditions to major malaria vectors.

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1–17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild − wild] < [wild − cultured] < [cultured − cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.

Spreading of bacterial and fungal strains that are resistant to antimicrobials poses a serious threat to the well-being of humans, animals, and plants. Antimicrobial resistance has been mainly investigated in clinical settings. However, throughout their evolutionary history microorganisms in the wild have encountered antimicrobial substances, forcing them to evolve strategies to combat antimicrobial action. It is well known that many of these strategies are based on genetic mechanisms, but these do not fully explain important aspects of the antimicrobial response such as the rapid development of resistance, reversible phenotypes, and hetero-resistance. Consequently, attention has turned toward epigenetic pathways that may offer additional insights into antimicrobial mechanisms. The aim of this review is to explore the epigenetic mechanisms that confer antimicrobial resistance, focusing on those that might be relevant for resistance in the wild. First, we examine the presence of antimicrobials in natural settings. Then we describe the documented epigenetic mechanisms in bacteria and fungi associated with antimicrobial resistance and discuss innovative epigenetic editing techniques to establish causality in this context. Finally, we discuss the relevance of these epigenetic mechanisms on the evolutionary dynamics of antimicrobial resistance in the wild, emphasizing the critical role of priming in the adaptation process. We underscore the necessity of incorporating non-genetic mechanisms into our understanding of antimicrobial resistance evolution. These mechanisms offer invaluable insights into the dynamics of antimicrobial adaptation within natural ecosystems.

Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture–recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32–79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.

Knowledge of functional dispersal barriers in the marine environment can be used to inform a wide variety of management actions, such as marine spatial planning, restoration efforts, fisheries regulations, and invasive species management. Locations and causes of dispersal barriers can be studied through various methods, including movement tracking, biophysical modeling, demographic models, and genetics. Combining methods illustrating potential dispersal, such as biophysical modeling, with realized dispersal through, e.g., genetic connectivity estimates, provides particularly useful information for teasing apart potential causes of observed barriers. In this study, we focus on blue mussels (Mytilus edulis) in the Skagerrak—a marginal sea connected to the North Sea in Northern Europe—and combine biophysical models of larval dispersal with genomic data to infer locations and causes of dispersal barriers in the area. Results from both methods agree; patterns of ocean currents are a major structuring factor in the area. We find a complex pattern of source-sink dynamics with several dispersal barriers and show that some areas can be isolated despite an overall high dispersal capability. Finally, we translate our finding into management advice that can be used to sustainably manage this ecologically and economically important species in the future.

Most malaria (Plasmodium spp.) parasite species undergo asexual replication synchronously within the red blood cells of their vertebrate host. Rhythmicity in this intraerythrocytic developmental cycle (IDC) enables parasites to maximise exploitation of the host and align transmission activities with the time of day that mosquito vectors blood feed. The IDC is also responsible for the major pathologies associated with malaria, and plasticity in the parasite's rhythm can confer tolerance to antimalarial drugs. Both the severity of infection (virulence) and synchrony of the IDC vary across species and between genotypes of Plasmodium; however, this variation is poorly understood. The theory predicts that virulence and IDC synchrony are negatively correlated, and we tested this hypothesis using two closely related genotypes of the rodent malaria model Plasmodium chabaudi that differ markedly in virulence. We also test the predictions that, in response to perturbations to the timing (phase) of the IDC schedule relative to the phase of host rhythms (misalignment), the virulent parasite genotype recovers the correct phase relationship faster, incurs less fitness losses and so hosts benefit less from misalignment when infected with a virulent genotype. Our predictions are partially supported by results suggesting that the virulent parasite genotype is less synchronous in some circumstances and recovers faster from misalignment. While hosts were less anaemic when infected by misaligned parasites, the extent of this benefit did not depend on parasite virulence. Overall, our results suggest that interventions to perturb the alignment between the IDC schedule, and host rhythms and increase synchrony between parasites within each IDC, could alleviate disease symptoms. However, virulent parasites, which are better at withstanding conventional antimalarial treatment, would also be intrinsically better able to tolerate such interventions.

Genetic assessment of species that have experienced dramatic population declines provides critical information that is instrumental for the design of conservation recovery programs. Here, we use different sources of molecular data (mtDNA and ddRAD-seq) to evaluate the genetic status of wild and captive populations of marbled teal (Marmaronetta angustirostris), a duck species classified as critically endangered in Spain and near threatened at a global scale. First, we determined the evolutionary and demographic trajectories of the wild population from Spain and the currently much larger population from Iraq, which is also the documented source of European zoo stocks. Second, we evaluated the suitability of the different captive populations for ongoing restocking programs in Spain and assessed their potential impact on the genetic composition of wild populations. Populations from Spain and Iraq were assigned to distinct genetic clusters, albeit with an overall low level of genetic differentiation, in line with their recent divergence (<8000 years ago) and lack of phylogeographic structure in the species. Demogenomic inferences revealed that the two populations have experienced parallel demographic trajectories, with a marked bottleneck during the last glacial period followed by a sudden demographic expansion and stability since the onset of the Holocene. The wild population from Spain presented high levels of inbreeding, but we found no evidence of recent genetic bottlenecks compatible with the human-driven decline of the species during the past century. The captive populations from the two Spanish centers involved in restocking programs showed genetic introgression from European zoos; however, we found limited evidence of introgression from the zoo genetic stock into the wild population from Spain, suggesting captive-bred birds have limited breeding success in the wild. Our study illustrates how ex situ conservation programs should consider the genetic distinctiveness of populations when establishing breeding stocks and highlights the importance of genetically assessing captive populations prior to reinforcement actions.

Conservation is prioritized based on accepted taxa. As a consequence, a conservation incentive exists to emphasize inter-population differences to define taxa, potentially leading to taxonomic inflation. But stressing the uniqueness of threatened populations has the side effect of hindering conservation actions that promote inter-population gene flow, such as genetic rescue. These actions may be of critical importance for severely inbred populations involved in extinction vortices, for which an inflated taxonomy can become a conservation trap. Here, we exemplify this scenario with the western capercaillie (Tetrao urogallus, Phasianidae) population in the Cantabrian Mountains, described and legally listed as a subspecies not supported by recent molecular data. The Cantabrian capercaillie population is Critically Endangered after a long-lasting decline and a recent demographic collapse. It shows clear signs of inbreeding depression, including striking clutch size decreases as well as reduced hatchability and chick survival. This critical situation could be alleviated through a genetic rescue, but this possibility is hindered by inertias rooted in the putative uniqueness of the Cantabrian capercaillie. It had been previously argued that poor taxonomy could hamper conservation, through the oblivion of populations deserving, but not having, a taxonomic status. We show that taxonomic inflation can also become an obstacle for effective conservation.