Evolutionary Applications最新文献

In recent decades, Dothistroma needle blight (DNB), a pine tree disease caused by the fungal pathogen Dothistroma septosporum, has severely damaged lodgepole pine (Pinus contorta Dougl. ex. Loud.) in British Columbia, Canada, and raised health concerns for jack pine (Pinus banksiana Lamb.). The pathogen has already shown signs of host shift eastward to the hybrid populations between lodgepole pine and jack pine (Pinus contorta × P. banksiana), and possibly into pure jack pine. However, we have little knowledge about mechanisms of resistance to D. septosporum, especially the underlying genetic basis of variation in pines. In this study, we conducted controlled inoculations to induce infection by D. septosporum and performed a genome-wide case–control association study with pooled sequencing (pool-seq) data to dissect the genetic architecture underlying response in lodgepole pine, jack pine, and their hybrids. We identified candidate genes associated with D. septosporum response in lodgepole pine and in hybrid samples. We also assessed genetic structure in hybrid populations and inferred how introgression may affect the distribution of genetic variation involved in D. septosporum response in the studied samples. These results can be used to develop genomic tools to evaluate DNB risk, guide forest management strategies, and potentially select for resistant genotypes.

Genetic factors can have a major influence on both short- and long-term success of reintroductions. Genomic monitoring can give a range of insights into the early life of a reintroduced population and ultimately can help to avoid wasting limited conservation resources. In this study, we characterise the genetic diversity of a reintroduced Carterocephalus palaemon (Chequered Skipper butterfly) population in England with respect to the spatial genetic structure and diversity of the source populations in south Belgium. We aim to evaluate the success of the reintroduction, including the effectiveness of the donor sampling strategy, and assess genetic vulnerabilities that may affect the population's future. We also use an isolation-by-distance approach to make quantitative inferences about dispersal, and we explore covariance between host mitochondrial and Wolbachia genomes. We find that, four generations following the initial release, the reintroduced population, founded by 66 wild-caught adults, has an effective size of c. 33, yet has retained similar levels of genomic heterozygosity to those in the source subpopulations in Belgium and shows low levels of inbreeding. However, the restricted number of founders and variance in reproductive success among the surviving families have resulted in a higher level of kinship, likely to result in somewhat higher rates of inbreeding in the future. Furthermore, there is a distinct split between two source landscapes in Belgium, and all genomic evidence suggests that the reintroduced population is descended from only one of these landscapes (called Fagne). We discuss potential causes behind these results, including whether Wolbachia strains are causing genetic incompatibility between clades. We conclude that a conservative strategy for any further translocations would prefer Fagne sites as sources because of the strong evidence of their ability to survive. However, our results warrant further investigation into the reasons for the divergence found in Belgium.

Although many tree species frequently hybridize and backcross, management decisions in forestry and nature conservation are usually concentrated on pure species. Therefore, understanding which environmental factors drive the distribution and admixture of tree species on a local stand scale is of great interest to support decision-making in the establishment and management of resilient forests. Here, we extensively sampled a mixed stand of hybridizing white oaks (Quercus petraea and Q. pubescens) near Lake Neuchâtel (Switzerland), where limestone and glacier moraine geologies coexist in proximity, to test whether micro-environmental conditions can predict taxonomic distribution and genetic admixture. We collected DNA from bud tissue, individual soil samples, and extracted high-resolution topographic data for 385 oak trees. We used 50 species-discriminatory single nucleotide polymorphism (SNP) markers to determine the taxonomic composition and admixture levels of individual trees and tested their association with micro-environmental conditions. We show that the trees' taxonomic distribution can be explained mainly by geographic position, soil pH, and potential rooting depth, a proxy for soil water availability. We found that admixed individuals tend to grow in habitats that are characteristic of the more drought-tolerant species Q. pubescens rather than in intermediate habitats. Using in situ measurements, we are the first to show that fine-scale variation in soil properties related to pH and water availability potentially drives the distribution of hybridizing tree species in a mixed stand. Microenvironmental variation therefore promotes local taxonomic diversity, facilitates admixture and adaptive introgression, and contributes to the resilience of forests under environmental change. Consequently, species such as white oaks should be managed and protected as a species complex rather than as pure species.

Revealing the spatial distribution of adaptive genetic variation is both a challenging and crucial task in evolutionary ecology, essential for understanding local adaptation within species, and in management, for predicting species responses to future climate change. This understanding is particularly important for long-lived tree species, which may not be able to migrate quickly enough to adapt to rapid climate changes and may need to rely on their standing genetic variation. In this study, we focused on Cryptomeria japonica, a major component of Japan's temperate forests and an important forestry species adapted to the humid environment of monsoon Asia. We extracted climate-associated genetic variation from the entire genome and evaluated its distribution and vulnerability under future climate scenarios using spatial modeling techniques. We analyzed 31,676 high-quality SNPs from 249 individuals across 22 natural populations of C. japonica, covering its entire distribution range. We identified 239 candidate climate-associated SNPs and found winter temperature, summer precipitation, and winter precipitation as the most significant factors explaining the genetic variation in these SNPs. The climate-associated genetic variation deviated from non-associated (neutral) genetic variation in the opposite (the Sea of Japan and Pacific Ocean) sides of Japanese archipelago, suggesting natural selection of different climate conditions in these regions. Difference in estimated allele frequency at the climate-associated loci (genetic offset) between the present and future (2090 in the SSP5-8.5 scenario) climate conditions was predicted to be larger in three areas (not only southwestern Japan but also coastal area on the Sea of Japan side and inland area on the Pacific Ocean side in northeastern Japan). This prediction implies the discrepancy between standing genetic variation at the present and that adaptive to the future climate in these areas, which underscores the necessity for proactive management to adjust the adaptive genetic variation.

Antimicrobial peptides (AMPs) are essential immune effectors of multicellular organisms. Bacteria can evolve resistance to AMPs. Surprisingly, when used to challenge the yellow mealworm beetle, Tenebrio molitor, Staphylococcus aureus resistant to an abundant AMP (tenecin 1) of the very same host species did not increase host mortality or bacterial load compared to infections with wild-type S. aureus. A possible explanation is that antimicrobial resistance is costly due to the collaterally increased sensitivity of AMP-resistant strains to other immune effectors. Here, we study the sensitivity of a group of AMP-resistant S. aureus strains (resistant to tenecin 1 or a combination of tenecin 1 + 2) to other immune effectors such as phenoloxidase and other AMPs in vivo. Using RNAi-based knockdown, we investigate S. aureus survival in insect hosts lacking selected immune effectors. We find that all except one AMP-resistant strain displayed collateral sensitivity toward phenoloxidase. Some AMP-resistant strains show sensitivity to components of the yellow mealworm beetle AMP defense cocktail. Our findings are consistent with the idea that resistance to AMPs does not translate into changes in virulence because it is balanced by the collaterally increased sensitivity to other host immune effectors. AMP resistance fails to provide a net survival advantage to S. aureus in a host environment that is dominated by AMPs.

Large-bodied pelagic sharks are key regulators of oceanic ecosystem stability, but highly impacted by severe overfishing. One such species, the shortfin mako shark (Isurus oxyrinchus), a globally widespread, highly migratory predator, has undergone dramatic population reductions and is now Endangered (IUCN Red List), with Atlantic Ocean mako sharks in particular assessed by fishery managers as overfished and in need of urgent, improved management attention. Genomic-scale population assessments for this apex predator species have not been previously available to inform management planning; thus, we investigated the population genetics of mako sharks across the Atlantic using a bi-organelle genomics approach. Complete mitochondrial genome (mitogenome) sequences and genome-wide SNPs from sharks distributed across the Atlantic revealed contrasting patterns of population structure across marker types. Consistent with this species' long-distance migratory capabilities, SNPs showed high connectivity and Atlantic panmixia overall. In contrast, there was matrilineal population genetic structure across Northern and Southern Hemispheres, suggesting at least large regional-scale female philopatry. Linkage disequilibrium network analysis indicated that makos possess a chromosomal inversion that occurs Atlantic wide, a genome feature that may be informative for evolutionary investigations concerning adaptations and the global history of this iconic species. Mitogenome diversity in Atlantic makos was high compared to other elasmobranchs assessed at the mitogenome level, and nuclear diversity was high compared to the two other, highly migratory pelagic shark species assessed with SNPs. These results support management efforts for shortfin makos on at least Northern versus Southern Hemisphere scales to preserve their matrilineal genetic distinctiveness. The overall comparative genetic diversity findings provide a baseline for future comparative assessments and monitoring of genetic diversity, as called for by the United Nations Convention on Biological Diversity, and cautious optimism regarding the health and recovery potential of Atlantic shortfin makos if further population declines can be halted.

There is strong epidemiological evidence that development of various cancer types is linked to infection with flukes (Platyhelminthes: Trematoda) in Africa, Asia and the Middle East. The exact nature of the mechanism by which cancer is induced by these parasites is unknown. Here, we provide a new hypothesis suggesting that flukes are not the primary cause of cancer but act as vectors of cancer-inducing microbial pathogens. These pathogens adaptively induce tumours to attract and help flukes to feed on blood from the tumour. Pathogen take-up by fluke vectors also takes place in the tumour; therefore, tumour formation in this case is the result of a mutualistic and adaptive relationship between the microbe and the helminth parasite. The suggested mechanism for cancer induction provided here may help us gain deeper understanding about cancer in general and its relationship with microbes and parasites. By further elaborating the unique nexus between flukes, carcinogenic microbes and cancer, in the future it will also help us to broaden our oncological perspective to reduce human death and suffering from this serious disease group.

Translocating individuals from multiple source populations is one way to bolster genetic variation and avoid inbreeding in newly established populations. However, mixing isolated populations, especially from islands, can potentially lead to outbreeding depression and/or assortative mating, which may limit interbreeding between source populations. Here, we investigated genetic consequences of mixing individuals from two island populations of the dibbler (Parantechinus apicalis) in an island translocation. Despite a high level of genetic divergence between the source populations (F_ST ranges 0.33–0.64), and significant differences in body size, individuals with different ancestries were able to successfully interbreed in captivity and in the wild. However, the genetic contributions from each source population were unequal initially despite each of the source populations contributing an equal number of founders. Mating success of captive animals based on the pedigree suggests that this bias toward one source population was due to founder mortality and the mating success of younger and heavier animals. Nevertheless, genetic contributions in the translocated population became equal over time with no parental purebreds, suggesting an extreme excess of hybrids across multiple years. While genetic variation in the translocated population was comparable or higher than the source populations, the increase was short-lived. Genetic composition of captive animals may not reflect what happens in the wild. These changes post-translocation highlight the need for continued genetic monitoring.

Conservation efforts are leading to demographic growth and spatial expansion of some previously endangered species. However, past population bottlenecks or population size fluctuations can have lasting effects on effective population size (N_e), even when census size (N_c) appears large or recovered. The UK metapopulation of Eurasian otters (Lutra lutra) has a well-documented history of population recovery over recent decades, with indicators of presence (faeces and footprints) increasing in distribution and number over successive national surveys. To determine whether this increase in N_c is reflected in increased N_e, we analysed a large-scale microsatellite dataset (21 years: 1993–2014; 407 individuals) for signals of recent N_e change using BOTTLENECK and LDNe, and evaluated potential biases associated with unaccounted spatial genetic structuring and inclusion of admixed genotypes. We obtained clear bottleneck signals in East England, and signals of recent population expansion in Wales and South West England in some analyses, consistent with national otter surveys and recent findings from whole-genome sequencing. Analyses that did not account for spatial genetic structuring yielded strong spurious signals of United Kingdom-wide population expansion, and N_e estimates from these analyses were suppressed by a factor of 3–4. Inclusion of admixed individuals had weaker impacts on N_e estimates, with overlapping 95% confidence intervals from different analyses. Notably, total N_e summed across regions was small and well below the N_e = 500 size deemed necessary for long-term population viability (sum of river basin district groups: 170.6, 95% C.I.: 102.1–348.3). Conclusions drawn from UK otter surveys, which had suggested a robust population close to panmixia, are therefore not supported by our genetic evidence. Our study highlights the value of including genetic monitoring of endangered or recovering species in monitoring plans, while also providing methodologically important information about N_e estimation from real-world datasets.

Island ecosystems, particularly vulnerable to environmental challenges, host many endangered native species. Diadromous fish, in particular, are threatened throughout their marine and freshwater habitats. The conservation of these species requires an in-depth understanding of their genetic diversity and structure, to better understand their adaptive potential. We investigated fine-scale population diversity and structure in native brook charr (Salvelinus fontinalis) by genotyping 10 microsatellite loci in 244 individuals at three spatial scales in Saint-Pierre and Miquelon, France. We found limited genetic variability across the archipelago, with particularly low genetic diversity in one island, Langlade. A significant difference in allelic richness was also detected among the three islands, indicating a difference in genetic composition across the archipelago, probably induced by historical stocking actions on both Saint-Pierre and Miquelon. Finally, a strong genetic structure was detected across the archipelago among hydrosystems (overall F_ST = 0.19) and even within several of them. The presence of predominant interisland gene flow combined with complete genetic isolation from certain hydrosystems suggests that this contemporary genetic structure is the result of both natural demographic processes during the species postglacial colonization and recent restocking actions. The complex genetic structure of such isolated brook charr subpopulations highlights the importance of considering fine-scale genetic structure in conservation management.