Evolutionary Applications最新文献

Pathological processes are often conceptualized as localized phenomena anchored in a primary tumor, a focal lesion, or a single organ. However, growing evidence indicates that many diseases persist and progress as complex distributed systems, maintained by interactions among multiple sites. Building on the emerging framework of selection for function, which can be applied to understand the evolutionary persistence of both replicating and non-replicating entities, we propose that metastases, amyloidoses, fibroses, autoimmune syndromes, granulomatous diseases, and multifocal reproductive disorders can all be understood as complex evolving pathological systems within individuals. In these contexts, local units such as metastatic nodules, amyloid plaques, or fibrotic foci act as semi-autonomous entities, yet achieve collective persistence through systemic flows, feedback loops, and network-level interactions, where local structuration gives rise to systemic effects. At certain points, lesions that produce mediators can trigger systemic alterations that, in turn, favor the emergence and persistence of additional lesions. This creates a vicious cycle in which local and systemic dynamics reinforce one another, helping these specific pathological networks to overcome host defense mechanisms and persist (i.e., be 'selected' via differential persistence). This perspective unifies seemingly disparate conditions under the principle of system persistence, reframing pathology as an emergent organizational property of a pathological system rather than as isolated local breakdowns of organismal components. It also carries important implications for evolutionary medicine, suggesting a taxonomy of diseases that distinguishes localized from distributed functional pathologies. Clinically, it underscores the need to go beyond focal interventions, advocating instead for therapies that disrupt pathological connectivity, destabilize network coherence, and monitor systemic biomarkers of disease persistence. Recognizing the role of selection for function in the emergence and persistence of complex pathological systems opens new avenues for both theoretical integration and therapeutic innovation in evolutionary medicine.

Direct-developing species lack the pelagic larval phase which facilitates connectivity in most marine species. Consequently, they tend to exhibit spatially restricted dispersal and increased population structure. When subject to harvesting, this biological constraint increases their vulnerability to localized depletion, as local aggregations may be unable to recover through dispersal from neighboring areas. In eastern Canada, the direct-developing whelk Buccinum undatum is targeted by commercial fisheries. Declining landings and catch per unit effort have raised concerns that the species' fully benthic life history renders it vulnerable to localized overexploitation. Here, we leverage a large genome-wide dataset to elucidate patterns of spatial genetic structure in B. undatum and gain insight into how seascape features influence genetic connectivity. We sampled hundreds of individuals throughout Canadian northwest Atlantic waters and genotyped them at 23,405 SNPs. We detected five major genetic clusters, and considerable genetic substructure within most of these groupings. In the St. Lawrence Estuary, where geographic sampling was most intensive, isolation by distance, driven by limited dispersal along continuous habitat, was observed. Deep water also serves as a major barrier to gene flow, leading to genetic divergence among populations separated by less than 50 km. Exploratory analyses also indicate the potential for isolation by environment across the seascape. Overall, our results confirm the limited vagility and gene flow of B. undatum, which leads to hierarchical genetic structure across the seascape. These findings highlight the importance of managing whelk populations at local scales to protect distinct conservation units and support sustainable harvesting.

Globally, corals face an increased frequency of mass mortality events (MMEs) as populations experience repeated marine heatwaves which disrupt their obligate algal symbiosis. Despite greater occurrences of MMEs, the relative roles of the environment, host, and symbiont genetic variation in survival, subsequent recovery, and carry-over effects to the next generation remain unresolved. High-resolution temporal and spatial whole genome sequencing of corals before, after, and several years following an MME reveal that host genetics have an impact on bleaching and mortality and that selected alleles important for adaptation persist through the next generation, demonstrating rapid evolution in this coral population. Bleaching resistance and survival following the bleaching event were highly polygenic, and allele frequency shifts show reef habitat specificity, emphasizing the spatial complexity of environmental selection and how it shapes population recovery following an MME. This study reveals how MMEs reshape the genomic landscape and the spatial and temporal distribution of genomic diversity within coral populations facing severe threats from global change.

The African catfish (Clarias gariepinus) is a commercially important species, for both fisheries and aquaculture, and is now the most commonly farmed fish in sub-Saharan Africa. However, knowledge about the genetic diversity and population structure of natural and farmed populations, which is crucial for effective conservation and sustainable aquaculture management, is scarce. Using mitochondrial DNA (mtDNA) cytochrome c oxidase 1 gene (COI) sequencing and genomic analysis using triple restriction site-associated DNA sequencing (3RAD), we investigated the genetic diversity and population structure of farmed and natural C. gariepinus populations from Nigeria including an albino form found in the natural environment. Eleven COI haplotypes were identified, of which seven were unique to natural samples. From the 3RAD results, natural sampling sites had a slightly broader range and higher maximum values for observed heterozygosity (H_o = 0.150–0.178), expected heterozygosity (H_e = 0.173–0.213) and nucleotide diversity (pi = 0.181–0.228) compared to the farmed populations (H_o = 0.133–0.161, H_e = 0.116–0.149, pi = 0.121–0.156). Conversely, genetic differentiation (F_st) was higher among farmed sampling sites compared to the natural ones and there was high genetic differentiation between the farmed and natural C. gariepinus sampling sites (F_st = 0.29–0.44). Admixture patterns suggested occasional mixing, possibly driven by hydrological connectivity and fish transport practices. Notably, five albino individuals sampled from the wild supported evidence of farm escapees. Outlier analyses and GO enrichment revealed loci potentially under selection related to lipid metabolism, immune signalling and apoptotic processes, indicating metabolic and immune-related adaptations to environmental stress. Our finding of potential farm escapees highlights the potential risks associated with increasing aquaculture activities and the need for greater regulation of fish farms, which could aid monitoring and reduce the risk of escapes.

Applying environmental DNA (eDNA) metabarcoding to samples from waterholes and their surroundings offers a promising approach for monitoring terrestrial vertebrates in semi-arid and arid ecosystems, such as the southern African savannas. However, minimal guidance exists on key sampling design parameters for terrestrial ecosystems, which can significantly influence species detection. This study investigated the effects of sampled substrate, sampling season, and metabarcoding primer pair on species richness and taxonomic group detection in terrestrial vertebrates, with a focus on mammals, using eDNA samples from waterholes in Botsalano Game Reserve, South Africa. A total of 725 eDNA samples were collected from 94 sampling events across wet and dry seasons, detecting 95 species (45 birds, 42 mammals, 4 amphibians, 3 reptiles, and 1 fish). Sediment samples provided more reliable detection of abundant taxa, whereas water samples had higher detection frequencies of rare taxa. A mixed sampling approach yielded the highest species richness. Sampling during the wet season yielded higher species richness overall, while more mammal species were detected from dry season sampling. Overlap in species detection between the two metabarcoding primers tested was low (47%). We formulate recommendations for future eDNA metabarcoding study designs in similar systems, including remote sampling logistics and discuss potential sources of false positives in eDNA metabarcoding, including (1) secondary eDNA input, (2) incomplete genetic reference databases, and (3) the low genetic resolution of metabarcoding markers.

Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.

Effective population size (N_e) is a key concept in biology and conservation. Stripped to its bare essentials, it reflects how much genetic drift a population experiences, expressed as a number of individuals of an ideal theoretical population. Superficially, N_e seems like a fairly simple concept, but the more layers of the onion you peel, the more you feel like crying. Really understanding N_e in all its facets is daunting, as there are various temporal, spatial, biological, and mathematical ways in which N_e can be defined and approached, many of which are erroneously interchanged and often not distinguished. If that is not enough, understanding the intricacies and the assumptions of the many ways in which N_e can be calculated is required to make sense of the concept. This is why a special issue on this topic, especially in relation to biodiversity monitoring, is timely. We assembled 19 original papers, perspectives, and reviews on effective population size estimation in relation to conservation to help practitioners in conservation research and practical management see the forest for the trees with regards to N_e.

Ultraconserved elements (UCEs) have emerged as a powerful tool for resolving deep evolutionary relationships due to their low DNA quality requirements and broad taxonomic applicability. While their utility for intraspecific and shallow-divergence studies is growing, only a few studies have explored their performance in marine taxa, some of them with metapopulations spanning thousands of kilometers. Here, we employed the UCE approach to investigate the population genomics of Gigantidas platifrons—a deep-sea mussel with a long larval dispersal period that exhibits a panmictic genetic structure across its extensive distribution range in the chemosynthetic ecosystems of the Western Pacific. With its published whole genome and prior restriction site-associated DNA sequencing using IIB restriction enzymes (2b-RAD seq) study, this species is an excellent candidate for evaluating the effectiveness of UCEs. We conducted UCE target capture sequencing on 123 individuals collected from two hydrocarbon seeps and four hydrothermal vents, yielding 1960 UCEs. To assess the impact of different reference choices, we identified 11,870 single-nucleotide polymorphisms (SNPs) by mapping against the published genome and 8936 SNPs by mapping to the representative 1960 UCEs. Both datasets were similar, with over 80% of the SNPs located in intronic and intergenic regions. Analyses based on both datasets consistently implied a clear genetic divergence between the South China Sea (SCS) and Okinawa Trough-Sagami Bay (OT-SB) populations, with predominant gene flow from OT to SB, consistent with previously published 2b-RAD seq findings. Additionally, UCE-based SNPs identified a dynamic decline in population size for individuals in the three regions and revealed selective adaptation signals to their environments. Overall, our study serves as a proof-of-concept demonstrating that UCEs provide a comparable resolution to RAD-Seq in detecting shallow-level genetic divergence and delineating conservation units in a high-dispersal marine species, even when lacking a sequenced genome.

Herbicides are a valuable tool in agricultural ecosystems to manage nuisance species. Due to the reliance on herbicides for weed control, herbicide resistance is a growing concern. Herbicides are also used extensively in aquatic and natural systems, but the genetics and evolutionary dynamics of resistance are not as frequently incorporated into management plans in these systems. In Eurasian watermilfoil, a widespread and heavily managed invasive aquatic weed in the United States, clonal lineages have been characterized as resistant to fluridone, a commonly used phytoene desaturase (PDS)-inhibitor herbicide. In order to locate genomic loci associated with herbicide resistance, we created an F2 mapping population segregating for fluridone resistance. Using this population, we examined the pds gene for amino acid alterations in resistant individuals and performed bulk segregant analysis between the highly resistant and susceptible F2 individuals. Additionally, we compared pds gene expression between resistant and susceptible strains in control and treated environments using RT-qPCR. We found no evidence of amino acid alterations to the pds gene in fluridone resistant individuals or increased pds expression in the resistant strain, either in the presence or absence of fluridone. Our QTL mapping identified a putative QTL on chromosome seven, while the gene encoding fluridone's target molecule, phytoene desaturase (PDS) is located on chromosomes 10–12. Our results indicate that fluridone resistance in the Eurasian watermilfoil strain isolated from Lake Lansing, MI, is due to at least one non-target site mechanism. Characterizing mechanisms of herbicide resistance within invasive plants enables effective and thoughtful herbicide usage, as well as the development of diagnostic biomarkers for resistance in unknown populations.

Movement patterns of marine fish are often difficult to accurately define given seasonal variation, ontogenetic shifts, and changing environmental conditions. However, outlining movement is crucial for understanding population dynamics, as well as for conservation and management efforts. Here, we evaluate seasonal adult movement and juvenile spatial distribution of Pacific cod (Gadus macrocephalus), a highly mobile and commercially important species, by developing and applying a genotyping-in-thousands by sequencing (GT-seq) panel. This panel identifies four genetically distinct stocks within Alaska waters with high confidence in assignment (97% average accuracy across stocks). The application of this panel to adult, summer-caught Pacific cod identified limited seasonal movement within and between populations, with the exception of those in the Northern Bering Sea (NBS). Two stocks occupied this region during the summer, non-spawning season, and mixed at variable proportions in a west-to-east gradient potentially tied to the directionality of sea-ice retreat in the NBS. Juvenile results indicated that although a predominant westward advection of larvae was prevalent in the Gulf of Alaska (GOA), two major deviations from this overall trend were apparent: (i) an eastward advection of a western GOA stock into the eastern GOA that varied interannually and (ii) a consistently high proportion of eastern GOA individuals in a western GOA narrow strait. These two deviating patterns suggest that mesoscale oceanographic processes play an important role in transport dynamics in the GOA that may be contrary to patterns expected based on the prevailing current. Taken together, our study provides novel insights into the movement dynamics of Pacific cod that can be leveraged by managers to help guide decision-making for the species. Additionally, this inexpensive genetic panel can continue to be applied to further explore important questions about the ecology of Pacific cod in Alaska waters.