Evolutionary Applications最新文献

For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species-level consideration if other recent species elevations are retained.

Colyer, B., Bak, M., Basanta, D., & Noble, R. (2024). A seven-step guide to spatial, agent-based modelling of tumour evolution. Evolutionary Applications, 17, e13687.

The Acknowledgements section omitted to acknowledge funding from the National Cancer Institute of the National Institutes of Health under Award Number U54CA217376.

We apologize for this error.

The number of multidrug-resistant strains of bacteria is increasing rapidly, while the number of new antibiotic discoveries has stagnated. This trend has caused a surge in interest in bacteriophages as anti-bacterial therapeutics, in part because there is near limitless diversity of phages to harness. While this diversity provides an opportunity, it also creates the dilemma of having to decide which criteria to use to select phages. Here we test whether a phage's ability to coevolve with its host (evolvability) should be considered and how this property compares to two previously proposed criteria: fast reproduction and thermostability. To do this, we compared the suppressiveness of three phages that vary by a single amino acid yet differ in these traits such that each strain maximized two of three characteristics. Our studies revealed that both evolvability and reproductive rate are independently important. The phage most able to suppress bacterial populations was the strain with high evolvability and reproductive rate, yet this phage was unstable. Phages varied due to differences in the types of resistance evolved against them and their ability to counteract resistance. When conditions were shifted to exaggerate the importance of thermostability, one of the stable phages was most suppressive in the short-term, but not over the long-term. Our results demonstrate the utility of biological therapeutics' capacities to evolve and adjust in action to resolve complications like resistance evolution. Furthermore, evolvability is a property that can be engineered into phage therapeutics to enhance their effectiveness.

The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×–58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.

Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity, underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life histories still exist, despite reductions in spawning habitat and hatchery practices that have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River. To understand this diversity, we collected migration timing data and GREB1L genotypes from hook-and-line, acoustic tagging, and carcass surveys of Chinook salmon in the Yuba River between 2009 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in California's Central Valley. We found that the date Chinook salmon crossed the lowest barrier to Yuba River spawning habitat (Daguerre Point Dam) was tightly correlated with their GREB1L genotype. Importantly, our study confirms that ESA-listed spring-run Chinook salmon are spawning in the Yuba River, promoting a portfolio of life history and genetic diversity, despite the highly compressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems, to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

DNA cytosine methylation is an important epigenetic mechanism in genomic DNA. In most land plants, it is absent in the chloroplast DNA. We detected methylation in the chloroplast DNA of the kelp Saccharina latissima, a non-model macroalgal species of high ecological and economic importance. Since the functional role of the chloroplast methylome is yet largely unknown, this fundamental research assessed the chloroplast DNA cytosine methylation in wild and laboratory raised kelp from different climatic origins (High-Arctic at 79° N, and temperate at 54° N), and in laboratory samples from these origins raised at different temperatures (5, 10 and 15°C). Results suggest genome-wide differences in methylated sites and methylation level between the origins, while rearing temperature had only weak effects on the chloroplast methylome. Our findings point at the importance of matching conditions to origin in restoration and cultivation processes to be valid even on plastid level.

Introgression of non-native conspecifics changes the genetic composition of wild populations, potentially leading to loss of local adaptations and fitness declines. However, long-term data from wild populations are still relatively few. Here, we studied the effects of introgression in a Danish brown trout (Salmo trutta, L.) population, subjected to intensive stocking with domesticated hatchery fish of non-native origin. We used wild-caught genetically wild and admixed trout as well as fish from the partly domesticated hatchery strain used for stocking the river up until ~15 years prior to this study, to produce 22 families varying in hatchery/wild admixture. Following a replicated common-garden experiment conducted in fish tanks from first feeding through 23 weeks at 7, 12, and 16°C, we observed a significant positive relationship between family admixture and fish size upon termination, an effect observed through all levels of admixture. Furthermore, the admixture effect was most distinct at the higher rearing temperatures. Although the hatchery strain used for stocking had been in culture for ~7 generations, it had not been deliberately selected for increased growth. These data thus demonstrate: (i) that growth had increased in the hatchery strain even in the absence of deliberate directional selection for this trait, (ii) that the increasing effect of admixture by temperature could represent inadvertent selection for performance in the hatchery strain at higher temperatures, and most significantly, (iii) that despite undergoing up to five generations of natural selection in the admixed wild population, the genetically increased growth potential was still detectable and thus persistent. Our findings suggest that altered growth patterns and potentially their cascading effects are of importance to the severity of hatchery/wild introgression, especially under changing-climate scenarios and are of general significance to conservation practitioners seeking to evaluate long-term effects of intra-specific hybridization including under recovery.

The deliberate release of captive-bred individuals, the accidental escape of domesticated strains, or the invasion of closely related conspecifics into wild populations can all lead to introgressive hybridization, which poses a challenge for conservation and wildlife management. Rates of introgression and the magnitude of associated demographic impacts vary widely across ecological contexts. However, the reasons for this variation remain poorly understood. One rarely considered phenomenon in this context is soft selection, wherein relative trait values determine success in intraspecific competition for a limiting resource. Here we develop an eco-genetic model explicitly focussed on understanding the influence of such competitive interactions on the eco-evolutionary dynamics of wild populations experiencing an influx of foreign/domesticated individuals. The model is applicable to any taxon that experiences natural or human-mediated inputs of locally maladapted genotypes (‘intrusion’), in addition to phenotype-dependent competition for a limiting resource (e.g. breeding sites, feeding territories). The effects of both acute and chronic intrusion depended strongly on the relative competitiveness of intruders versus locals. When intruders were competitively inferior, density-dependent regulation limited their reproductive success (ability to compete for limited spawning sites), which prevented strong introgression or population declines from occurring. In contrast, when intruders were competitively superior, this amplified introgression and led to increased maladaptation of the admixed population. This had negative consequences for population size and population viability. The results were sensitive to the intrusion level, the magnitude of reproductive excess, trait heritability and the extent to which intruders were maladapted relative to locals. Our findings draw attention to under-appreciated interactions between phenotype-dependent competitive interactions and maladaptive hybridization, which may be critical to determining the impact captive breeding programmes and domesticated escapees can have on otherwise self-sustaining wild populations.

Mashlawi, A. M., Alqahtani, H., Abuelmaali, S. A., Gloria-Soria, A., Saingamsook, J., Kaddumukasa, M., … Walton, C. (2024). Microsatellite-based analysis reveals Aedes aegypti populations in the Kingdom of Saudi Arabia result from colonization by both the ancestral African and the global domestic forms. Evolutionary Applications, 17(2), e13661.

The authors would like to amend the Acknowledgments section of the above article and consolidate some of the resources mentioned in it. The Acknowledgments should read as follows:

Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype–environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant Arabis alpina L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.