Although there is huge variation in how mortality changes with age across species, in humans, all-causes mortality increases at a relatively constant rate across populations and time. However, individuals die due to specific causes that include extrinsic and intrinsic sources. Here, we compared the rate at which mortality increases with age (i.e., the rate of aging) for the causes of death supposedly referring to extrinsic (infectious and parasitic diseases) and intrinsic sources (cardiovascular diseases and malignant neoplasm) in 12 human populations. Given that individuals are exposed to infectious agents across their entire lifespan, it is straightforward to expect a shallower rate of aging for infectious compared to cardiovascular diseases and malignant neoplasm. However, infectious and noninfectious diseases might target the same tissues/organs and tissue-specific repair mechanisms may strongly affect the disease severity. We, therefore, also compared the rate of aging for transmissible and nontransmissible diseases targeting the same tissues/organs. Contrary to the pattern observed when comparing infectious and noninfectious diseases overall, we found that diseases with shared target organs had similar rate of aging, whatever their etiology. We went a step further by assessing the changes in the distribution of cause-specific mortality across ages (i.e., lifespan equality), between 1955 and 2020, and by investigating whether they were accounted for by changes in early-life mortality, adult mortality or the rate of aging. This analysis showed that temporal changes in lifespan equality were essentially driven by changes in early-life mortality, with modest or almost no contribution from changes in adult mortality or the rate of aging. Overall, these results show that the rate at which mortality increases with age is relatively invariant for diseases targeting the same tissues/organs, suggesting that shared tolerance mechanisms, independently from the etiology of the disease, might be important drivers of age-dependent mortality schedules.
ABSTRACT Demographic, geographic, and environmental factors such as effective population size, isolation, and habitat availability interact to shape contemporary levels of population genomic diversity. Such factors must be carefully evaluated and contextualized at both the intraspecific and interspecific levels when assessing the conservation status of imperiled species. Here, we studied the population genomics of a perching songbird, the California towhee (Melozone crissalis), by generating a high‐quality annotated reference genome assembly (N50 = 22 Mb among 627 contigs, max contig size 89.1 Mb) and conducting whole‐genome resequencing on n = 81 individual birds sampled from multiple geographic sites across much of the species' range. California towhee sampled from Inyo County and from Southern Oregon, on the periphery of their geographic range, showed reduced heterozygosity and elevated inbreeding compared (a) to other sampled California towhee populations and (b) to related Threatened songbirds. Contemporary effective population sizes (Ne) were low for these two peripheral populations, and ancestry patterns of the federally protected Inyo population reveal the remarkably clear genomic signature of a documented, human‐induced demographic bottleneck. Elevated genomic differentiation (FST) in the Oregon and Inyo populations, ecological niche modeling, and spatial patterns of gene flow all provide strong support for genetic isolation, limited connectivity, and demographic independence. Both peripheral populations show evidence indicative of local adaptation, as gauged by landscape genetic approaches. Our data highlight the tension that exists between the idealistic goal of conserving all the diversity in a gene pool (e.g., isolated peripheral populations that may contain locally adapted variants) versus the less desirable but more practical goal of focusing expensive conservation efforts on the core gene pool.
ABSTRACT Neotropical seasonally dry biomes are amongst the world's most threatened ecosystems and are predicted to lose more biodiversity with climate change. The capacity of natural populations to respond to these changes depends on their genetic variation, but is poorly understood in most Neotropical seasonally dry forest species. Here, we used genome‐wide single nucleotide polymorphism (SNP) data for 109 individuals across 12 Colombian populations of Enterolobium cyclocarpum, a widespread deciduous legume tree found in seasonally dry tropical forests, human‐disturbed and open landscapes from Central and Northern South America, to (1) explore population structure across the landscape, (2) determine local adaptation to heat and drought stress, and (3) assess genomic offset and adaptive potential under future climate change. Our results suggest clear genomic differentiation among regions and populations, as well as an uneven spatial distribution of adaptive alleles associated with drought and heat stress, together suggesting different degrees of local adaptation to climate across the landscape. Furthermore, all regions investigated (i.e., Caribbean, inter‐Andean valleys, and Orinoquía) showed limited adaptive potential under future climate change scenarios. For some regions, gene flow may help buffer the effects of environmental change by bringing in adaptive alleles, however, this will likely be insufficient to counteract predicted mal‐adaptation in certain regions, such as in the Orinoquía. Our results suggest that both barriers to gene flow (e.g., orography) and varying heat and drought stress conditions have shaped the genomic composition and adaptive potential of the species. Enterolobium cyclocarpum populations have adapted locally to current climate, but this adaptation may not be sufficient to cope with future climate change, particularly where population connectivity is low. Our findings have relevance for the conservation of species in highly threatened Neotropical biomes, such as seasonally dry tropical forests, which are expected to experience rising temperatures and greater drought under future climate change.
ABSTRACT Landscape context can influence demographic rates and, consequently, the population genetic processes determining levels of genetic diversity. However, the role of landscape context is not always sufficiently considered in conservation management. For species with complex life cycles, such as amphibians, landscape context is particularly relevant because they rely on both aquatic and terrestrial habitats, the quality of which can vary across landscapes. Understanding how landscape context may influence these genetic processes is therefore important for effective management. We used population viability analysis (PVA) to simulate how landscape context may influence genetic and demographic outcomes for the great crested newt (Triturus cristatus) using two landscape‐specific models representing boreal forest and agricultural landscapes. We assessed the sensitivity of model outcomes to parameter perturbations and evaluated management scenarios and potential threats at the metapopulation level. A key result was that environmental stochasticity strongly influenced genetic dynamics in both landscapes. The low‐stochasticity forest model retained genetic diversity, responded strongly to management actions, and relied less on gene flow. In contrast, the high‐stochasticity agricultural model experienced stronger genetic drift, responded weakly to management actions, and relied more on continuous gene flow. Our findings suggest that enhancing gene flow alone may be insufficient for maintaining genetic diversity, and that improving resilience to environmental stochasticity should be considered an important part of genetic management.
ABSTRACT Soil microbial communities underpin key ecosystem processes, including plant health, nutrient cycling and primary productivity. In agricultural soils, beneficial soil bacteria are often exposed to multiple stressors simultaneously, including fungicides, antibiotics, and warming temperatures. Despite their ecological importance, little is known about how beneficial soil bacteria respond to such combined stressors over evolutionary timescales. Here, we investigated how the model plant growth promoting rhizobacterium (PGPR) Pseudomonas fluorescens evolves resistance to the fungicide formulation Fubol Gold (metalaxyl‐M + mancozeb), under ambient or warming soil conditions. Using a 16‐week evolution experiment in soil microcosms with a fully factorial design (fungicide ± warming), we assessed the evolution of fungicide resistance via phenotypic assays and whole‐genome sequencing. Fungicide exposure rapidly selected for increased fungicide resistance, detectable as early as week 4, and co‐selected for resistance to chloramphenicol, sulphatriad and nalidixic acid antibiotics, likely through mutations in a mexS ortholog that may be associated with efflux pump overexpression. Warming did not alter the evolution of fungicide resistance; however, populations subjected to both fungicide and warming stress went extinct more rapidly, so that population evolutionary rescue was less effective under dual stress. Our findings show that fungicide alone can drive multidrug resistance in beneficial soil bacteria, suggesting that non‐antibiotic drivers of resistance in the environment should be incorporated into One Health frameworks for tackling AMR.
ABSTRACT Global climate change disproportionately threatens island endemics because their restricted ranges and limited dispersal opportunities constrain their ability to shift their distributions. Therefore, when developing conservation strategies for species, it is crucial to incorporate population genomics data with ecological information to evaluate resilience and forecast vulnerability. However, genomic case studies that explicitly link these factors in island endemics remain scarce. Here, we examine population genetic differentiation of the Formosan Duke (Euthalia formosana), an endemic butterfly in Taiwan, to evaluate its potential vulnerabilities under future climate conditions. Our results reveal that the combined effects of topographic barriers, historical connectivity, and climatic heterogeneity can drive rapid diversification, even in species with strong flight ability. The Central Mountain Range has shaped pronounced genetic structure, separating eastern and western lineages, with diversification stronger in the western lineage. This within‐island diversification appears to be shaped by environmental gradients, enhancing persistence in local habitats while reducing a lineage's niche breadth and resulting in different lineage‐specific climate vulnerability. Thus, we suggest that genomic approaches should be included to assess environmental constraints and to guide conservation planning on the persistence of lowland endemics such as the Formosan Duke. This framework also integrates the concepts of habitat restoration with lineage‐specific connectivity to enhance the species' genetic resilience while preserving its capacity for local adaptation. Moreover, this study provides an evidence‐based framework for insular biodiversity conservation under accelerating climate change.
ABSTRACT Introduced species often undergo genetic drift and natural selection, which can reduce genetic diversity and drive differentiation among populations. Intraspecific hybridization, outcrossing among individuals from genetically distinct groups, may counteract these effects by increasing heterozygosity, potentially improving performance. However, in classical biological control agents, genetic diversity is typically low due to small founding sizes, long‐term quarantine rearing, and single‐source collections from the native range. As a result, opportunities for beneficial hybridization may be limited. We evaluated whether intraspecific hybridization could enhance genetic diversity and performance of Hypena opulenta (Lepidoptera: Erebidae), a biological control agent of invasive swallow‐wort vines (Vincetoxicum spp.) in North America. We used two populations: one reared under laboratory conditions for 28 generations, and another established in the field in Canada, separated from the lab population for 14 generations. We created a third population by crossing individuals from the two source populations. We conducted Whole Genome Sequencing (WGS) on 15–20 individuals per population to assess genetic divergence and heterozygosity and compared performance of the three populations under both laboratory and field conditions. Despite relatively recent separation, clear genetic structure had developed between the lab and field populations. Both exhibited low genome‐wide heterozygosity, while the outbred population showed significantly higher heterozygosity. Hybridization also led to improved performance: outbred females produced more pupae in the laboratory, caused greater defoliation of host plants, and yielded the most second‐generation adults in the field. These results demonstrate that even short‐term isolation can lead to meaningful divergence and that intentional intraspecific hybridization can boost both genetic diversity and performance. Our findings suggest that outcrossing among recently separated populations could be a practical approach to improve performance of biological control agents prior to field release, with broader implications for managing genetic diversity in applied ecology and conservation contexts.
ABSTRACT Laboratory and field populations of insects can experience a decline in fitness and loss of genetic diversity due to inbreeding depression and genetic drift, respectively. Matings among related individuals and small population size may also influence insect host microbiomes with consequences for fitness. In the dengue vector mosquito, Aedes aegypti, the bacterial microbiome is largely environmentally determined, but recent studies have also revealed host genetic components. We generated a panel of 55 inbred lines from either of two founding outbred populations of Ae. aegypti to test for associations between life history traits, inbreeding, allelic diversity, and microbiome composition using ddRADseq and bacterial 16S rRNA gene sequencing on pools of mosquitoes. Effects of inbreeding were diverse, with severe composite fitness costs in many lines but minimal costs in others despite similar low levels of genetic diversity. We found no strong relationship between major life history traits across inbred lines, suggesting that any costs due to inbreeding were trait specific. Bacterial microbiome analysis of pooled samples from a subset of lines revealed common microbes across lines, with Elizabethkingia, Aeromonas, and Ralstonia being the most abundant. Despite bacterial composition varying widely, there was no clear relationship between microbiome composition and fitness or population origin. However, there were several significant positive correlations between the relative abundance of different microbial taxa across lines. Our results demonstrate diverse impacts of inbreeding on the fitness of mosquito populations but with limited impacts on the microbiome.
ABSTRACT Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne at the subpopulation, genetic unit, and metapopulation levels, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne < 50, and 28 subpopulations had Ne < 500, and three of six metapopulations fell below the Ne < 500 threshold once population structure was accounted for, suggesting compromised short‐term viability and long‐term adaptive potential in the most affected units. Nc significantly predicted inbreeding (R2 = 0.16), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north‐to‐south gradient in bottleneck timing: northern populations declined in ~1700–1780, central populations in ~1780–1860, and southern populations in ~1860–1940, broadly coinciding with the documented timing of climate shifts and anthropogenic disturbances in the region. Our findings identify at‐risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.
ABSTRACT Understanding population structure and clarifying species boundaries are essential for the sustainable management of exploited marine species. Although genomic resources for shallow‐water taxa have expanded rapidly, open‐water species remain comparatively understudied. Here, we present a comprehensive genomic analysis of the white anglerfish ( Lophius piscatorius ), a commercially important species that occupies a wide depth range. We examined genetic structuring and verified species identity across its distribution range in the North Atlantic and Mediterranean. We combined whole‐genome sequencing of selected individuals with targeted SNP genotyping of 897 specimens from 35 locations. Our results support a panmictic or nearly panmictic population of white anglerfish throughout the Northeast Atlantic, consistent with earlier studies, here extended northward to about 68° N. We found no evidence of local adaptation or selection. Like earlier studies, we detected apparently misclassified specimens of the closely related black anglerfish ( L. budegassa ) and extensive hybridization with up to 20% hybrids in local samples from around the Celtic Sea and nearby waters. Most or all hybrids appear to be first generation (F1), with a few potential backcrossed individuals of less certain identification. Demographic analyses indicate a recent colonization of the North Atlantic, with black anglerfish diverging more recently and maintaining a smaller effective population size. These results underscore the value of integrating genomic tools into monitoring frameworks to improve species identification, delineate population units, and inform sustainable fisheries management.
ABSTRACT Saccharina latissima (sugar kelp) is a brown macroalga that forms kelp forests along North Atlantic coasts, playing a key role in coastal ecosystems. It is also of growing economic importance as the dominant species used in European kelp aquaculture. Both wild and cultivated kelps are increasingly threatened by marine heatwaves and elevated sea surface temperatures. Enhancing thermal tolerance could therefore benefit both conservation and production. Thermal priming, a method originating in agriculture where early life stages are exposed to moderate heat stress, can enhance resilience by inducing molecular stress memory. We applied a thermal priming treatment (20°C, 3 weeks) to S. latissima gametophytes before gametogenesis and sporophyte formation to test whether priming alters thermal responses in the derived sporophytes. Young sporophytes, produced by crossing primed or naïve (controls kept at 10°C) gametophytes, were reared at 10°C and then exposed to a heat stress (21.5°C for 48 h) before being allowed to recover at 10°C. Transcriptomic profiles and photophysiological characteristics were assessed before, during and after stress exposure to investigate priming‐induced changes in thermal stress resilience. Sporophytes derived from primed gametophytes showed stronger transcriptomic responses under heat stress; for example, upregulation of HSP90B was unique to primed samples. Naïve sporophytes exhibited a delayed response with extensive downregulation during recovery (2027 DEGs). Gene ontology enrichment analysis indicated higher expression of protein phosphorylation, chloroplast‐related functions, and post‐transcriptional regulation by ncRNA in primed sporophytes, suggesting a priming effect on their transcriptomic thermal response. Primed sporophytes exhibited a delayed reduction in photosynthetic performance compared with naïve throughout the heat stress. These findings suggest that thermal priming induces a transgenerational stress memory. Our results support the view that temperature priming alters the transcriptomic thermal response in kelp through regulatory changes in gene expression, in line with existing literature on priming.
ABSTRACT Insecticide resistance is a significant challenge for mosquito population control and disease prevention. This research investigated knockdown resistance ( kdr ) mutations V410L, V1016I, and F1534C in Aedes aegypti mosquitoes to address crucial gaps in understanding insecticide resistance evolution and management. Six common kdr genotypes were obtained through genetic crosses of three unique parental strains from the same location in Florida, USA. Through topical application of deltamethrin on both males and females, we quantified the resistance profiles of each genotype and sex. Triple homozygous mutants were over 52 times more resistant than the susceptible Rockefeller lab strain, with resistance ratios of the five other genotypes ranging from 8 to 19. We demonstrated that the resistant haplotypes I 1016 ‐ C 1534 (on V410L mutant background) and L 410 ‐ I 1016 (on F1534C mutant background) were incompletely recessive. Using these data in a simulation model, we show that the selective advantage is not constant but fluctuates within the window of selection. Selective advantage depended on the frequency of the resistance haplotype at the time of treatment, and both the level and dose of exposure. Finally, resistance profiles revealed that male mosquitoes had similar resistance profiles to females when sex and weight differences were accounted for, indicating that males could be used for resistance surveillance, which could enhance surveillance efforts. Overall, this study provides the first detailed quantification of dose–response curves and selection advantages for both sexes across multiple kdr genotypes. These results offer critical insights into the evolutionary dynamics of insecticide resistance and support the development of evidence‐based strategies for more sustainable mosquito control.
ABSTRACT As drought impacts on forests intensify, evaluating the potential for adaptation is critical for predicting forest responses and the impacts of management strategies. We assessed phenotypic and genomic variation in western larch (Larix occidentalis Nutt.) populations to evaluate the potential for drought adaptation across its range. First, we established a seedling common garden experiment outside the natural range with 52 populations subjected to two drought treatments. Second, we analyzed pooled targeted exome‐sequence capture data from 44 populations of an adult provenance trial to evaluate the relative ability of climate, geography, and neutral genetic structure to predict landscape genomic variation. We found that population differentiation for drought resistance was low. Drought reduced population differentiation for growth and bud set, and weakened clinal associations for growth. We found no antagonistic correlations between drought resistance and growth or phenology, indicating that trade‐offs are unlikely to constrain adaptation. Further, landscape genomic variation was primarily explained by neutral genetic structure, with little additional variation explained by climate or geography. Together, these findings demonstrate weak local adaptation to drought and reduced genetic variation in traits under drought indicate that natural populations of western larch may have limited potential to adapt to future drought conditions.
ABSTRACT Conservation translocations are widely used to increase population size and redundancy, yet their genetic consequences are often uncertain, particularly for clonal species with unknown rates of sexual reproduction. Propagation through asexual reproduction is frequently employed in these systems, but its effectiveness for preserving genomic diversity remains poorly evaluated. We used genome‐wide single nucleotide polymorphism (SNP) data to assess the genetic outcomes of translocation efforts in Pleuropogon oregonus , a critically endangered grass endemic to eastern Oregon, USA. We quantified genetic diversity, relatedness, and population structure across natural and introduced sites and used coalescent simulations to infer the divergence history between disjunct populations. Genetic analyses identified two divergent lineages corresponding to northern and southern regions, with divergence predating the last glacial period and limited subsequent gene flow. Within regions, natural populations exhibited high clonality but retained genetically distinct individuals. Introductions that used vegetative propagules from the northern region maintained heterozygosity and allelic diversity comparable to sources and captured multiple distinct genotypes, including alleles likely originating from an unsampled source, thereby increasing population redundancy. In contrast, the introduction derived from a low‐diversity, southern region source reflected similarly limited clonal diversity. Our results demonstrate that vegetative propagation can effectively preserve genomic diversity in clonal species when propagules are sampled representatively, but that evolutionary history may inform sourcing and mixing decisions. More broadly, this study provides an empirical framework for integrating genomic data into conservation translocations, highlighting conditions under which vegetative propagation maintains evolutionary potential and when it may pose risks to long‐term persistence.
ABSTRACT Life history diversity in salmonids contributes to population resilience, yet the mechanisms driving contemporary life history change remain difficult to disentangle from demographic and environmental processes. We evaluated long‐term changes in neutral genetic variation, adaptive haplotypes near the six6 gene, and life history traits in the Dworshak National Fish Hatchery steelhead ( Oncorhynchus mykiss ) broodstock by comparing archived scale samples from the founding broodstock and subsequent returns (1969–1976) with contemporary samples (2014–2016; 2019–2022). Neutral genetic diversity and population structure remained stable through time, consistent with prior evidence that observed life history shifts were not associated with erosion of neutral genetic diversity. In contrast, we detected pronounced temporal shifts in adaptive variation near the six6 gene on chromosome 25, including a decline in the long haplotype historically associated with extended years in the ocean and larger body size. Ocean age composition also shifted over time, with an increased proportion of 2‐ocean fish and altered age distributions within six6 genotype classes. Although six6 remained significantly associated with length‐at‐age, the magnitude of phenotypic differences among genotypes was substantially reduced in contemporary samples, indicating a weakening of the genotype–phenotype relationship. These results suggest that environmental conditions increasingly constrain, or otherwise alter, the expression of genetically based life history variation. Our findings demonstrate that life history change can occur without loss of neutral genetic diversity and highlight the importance of integrating genetic and demographic data to understand eco‐evolutionary responses of salmonids under changing ocean conditions.
ABSTRACT Despite the important role that species concepts and taxonomy play in understanding the evolution of species, taxonomists have struggled to describe the relationship between many organisms. Here, using Cutthroat Trout as a case study, we illustrate how full mitochondrial genomes and broad taxonomic sampling can provide further insight on disputed taxonomic relationships, and aid in management and conservation decisions of different species. Inconsistencies in the taxonomy of Cutthroat Trout inspired a special workshop at the 2015 annual meeting of the American Fisheries Society that emphasized the need for revision. To further resolve the relationship between different Cutthroat Trout groups, we sequenced and assembled full mitochondrial genomes from 123 Cutthroat Trout from across their native range. We used maximum likelihood and Bayesian phylogenetic approaches to examine the evolutionary relationships between all named Cutthroat Trout subspecies. Through these analyses, we find eight lineages of Cutthroat Trout that diverged more than one million years ago, and at least 12 lineages that diverged more than 790 thousand years ago, highlighting that despite the ancient split with Rainbow Trout at around ten million years ago, the modern diversity seen within the Cutthroat Trout Species Complex is much more recent. We do not find that Coastal, Westslope, or Lahontan Cutthroat Trout are substantially more different than the lineages in the Yellowstone complex. As such, we continue to recognize a single Cutthroat Trout species (Oncorhynchus clarkii) comprised of eleven distinct subspecies level clades, maintaining consistency with ongoing conservation efforts, management plans and ESA‐related decisions, while also preserving stability associated with historical nomenclature. Overall, we highlight that using full mitochondrial genomes can increase phylogenetically informative information and that the consistent nature of mitochondrial genomes across the tree of life allows for a valuable and measurable comparison of different species concepts in closely related taxa.
ABSTRACT Little is known about local adaptation to temperature in bacterial pathogen populations in nature. For plant‐pathogenic bacteria, local thermal adaptation may influence the evolution of virulence, which has strong implications for disease management and mitigation. Xylella fastidiosa ( Xf ) is an insect‐transmitted bacterial pathogen that infects over 700 plant species globally and causes Pierce's disease of grapevines. Here, we compared in vitro growth and in planta virulence of multiple strains from two genetically distinct Xf populations from California regions having either a colder climate (Hopland) or warmer climate (Bakersfield). Xf strains from a warmer climate grew faster than cold‐climate strains under suboptimal (20°C) temperatures, suggesting a lower thermal optimum. In reciprocal field experiments, infections of plants by Xf strains from a colder climate were more likely to survive the winter. After a mild winter in Bakersfield (warmer climate), there were severe symptoms and some vine mortality the following growing season in vines infected with the non‐local, cold‐climate (Hopland) strains, pointing to a potential trade‐off between virulence and transmission due to vine mortality. Our data suggest that Xf populations in CA are locally adapted to temperature, with cold‐climate strains exhibiting hypervirulence when transplanted to warmer climates, whereas warm‐climate strains survive at lower rates when transplanted to colder climates. Thus, local thermal adaptation in bacterial pathogens may influence the optimum virulence phenotype across the landscape.
ABSTRACT Viral infections and the microsporidian Vairimorpha ceranae (‘vairimorpha’) have been involved in elevated honey bee ( Apis mellifera ) colony losses as a result of their individual or combined actions, with the ectoparasitic mite Varroa destructor (‘varroa’) often exacerbating these effects. This study investigates the relationship between vairimorpha and several common honey bee viruses within the unique ecological context of the remote mid‐Atlantic Azores archipelago, which comprises three main islands where varroa is present and six islands where varroa is still absent. We sampled 494 colonies across these islands and employed RT‐qPCR to detect and quantify vairimorpha and nine common honey bee viruses, of which seven were detected. The data were modelled using a Bayesian approach, which estimated the likelihood of an effect of the presence of vairimorpha on the loads of each of the viruses on varroa‐infested and varroa ‐ free islands. Both vairimorpha and the seven bee viruses were differentially distributed among the islands. An additive relationship was found between vairimorpha and both black queen cell virus (BQCV) and Lake Sinai virus (LSV), the latter driven almost exclusively by one strain (LSV‐2), and this relationship was stronger on the varroa‐infested islands (Pr = 96.2%) than on the varroa‐free islands (Pr = 69.1%). No association was found between vairimorpha and the two main strains of DWV (DWV‐A and DWV‐B) across all islands, although an antagonistic relationship may exist between vairimorpha and the rare DWV‐C strain, found only on varroa‐free islands. This study supports previous findings and shows the importance of possible additive relationships among co‐infecting honey bee pathogens and parasites.
Genetic assessments serve as powerful tools to evaluate the effects of anthropogenic habitat fragmentation on natural populations. In the Klamath River Basin, construction of four dams from 1912 to 1962 had a profound impact on the distribution of anadromous fishes, blocking access to over 751 river kilometers of critical habitat. To characterize the genetic diversity and connectivity among Oncorhynchus mykiss in the basin prior to the historic removal of the four dams in 2024, we genotyped 2466 samples at 193 presumably neutral and 105 putatively adaptive markers. Using complementary population genetic analyses, we found a clear division between coastal and inland O. mykiss lineages located primarily downstream and upstream of the outlet of Upper Klamath Lake, and little genetic structure associated with dams. Further, we detected distinct inland and coastal genetic lineages upstream of the lake outlet supporting the hypothesis that ancestral inland O. mykiss were secondarily invaded by a coastal lineage. We found that neutral genetic diversity was significantly greater in collections consisting primarily of anadromous O. mykiss compared to collections of adfluvial, fluvial, and resident fish while genetic diversity was significantly lower in adfluvial collections. Based on the chromosome Omy5 markers associated with anadromous/resident phenotypes, we found that anadromous and heterozygous genotypes were more prevalent downstream of the lake outlet while resident genotypes were prevalent upstream of the outlet. Based on the chromosome Omy28 markers associated with adult migration timing, we found that late-migration timing and heterozygous genotypes were numerous downstream of the lake outlet while early-migration timing genotypes were prevalent upstream of the outlet. The results of our population genetic analyses highlight the genetic diversity and structure of O. mykiss in the Klamath River Basin and will serve as a critical baseline for future assessments post dam removal.
Recent kelp forest declines and growth in the kelp aquaculture industry have fueled increasing interest in ecological and evolutionary research on kelp forests, including kelp population genomics. Although many kelp management activities have inherent genetic and evolutionary implications, kelp management in the Pacific Northwest (PNW) of North America has to date made only limited use of species-specific population genetic knowledge. We believe that kelp managers in the PNW are well positioned to begin routinely incorporating population genomic perspectives into their work. Here, we review the state of genetic knowledge in the canopy-forming kelps Nereocystis and Macrocystis from Washington to Alaska and highlight how this knowledge can support four key kelp management activities: restoration, aquaculture, wild harvest, and biobanking. We discuss several potential paradigms for geographic transfer of genetic material, consider the likely impacts of inbreeding and genetic drift in the management of small kelp populations, and suggest strategies for protecting the genetic integrity of populations during wild harvest. To inform optimal sourcing strategies for biobanking and outplanting, we also reanalyze genomic data to explore how the number of individuals sampled impacts retention of genetic diversity. In many cases, predictions derived from molecular data and models have accumulated faster than the research community's ability to validate them in the field. We propose that experimental tests be incorporated into ongoing kelp management operations as an immediate step in transitioning toward a management framework informed by population genomic data and perspectives. Adopting such a framework will improve the likelihood of attaining desirable outcomes in kelp conservation and aquaculture, including as kelp populations adapt to future challenges.
