Evolutionary Applications最新文献

Information on climate-associated phenotypic variation is essential for sourcing seed that matches restoration site conditions. Spatially explicit seed transfer models can effectively deliver this information. However, standard modeling approaches often do not provide flexibility for practical considerations and may not capture highly complex trait-climate associations. We characterized climate-associated variation in growth, reproduction, morphology, phenology, and survival across 98 source populations at 3 common gardens for the grass Elymus elymoides (bottlebrush squirreltail), an important restoration species in the Intermountain Region of the western USA. We developed fixed-boundary seed zones and focal-point seed transfer models using non-standard methods (regression trees and random forests). In general, source populations with larger plant sizes and later flowering originated from cooler and wetter or milder climates than those with smaller sizes and earlier flowering, though some associations were more complex. Populations from milder climates also had higher trait plasticity than populations from other climates, except for plasticity in seed maturation, which was highest in populations from warmer and drier climates. Seed zones identified through our approach consisted of three major zones with 2-7 subzones each (13 seed zones in total). Two subspecies groups had distinct trait-climate associations, and separate seed zone models were developed for each. Our modeling approach provides a hierarchical structure that partitions predictor variables based on their importance. This doubles as a prioritization framework that assists in navigating trade-offs between risk avoidance and practical constraints by explicitly defining how zones can be combined or subdivided in response to user needs. Our approach also captures trait-climate association nuances missed by standard approaches, increasing the precision of our focal-point seed transfer zones. Our findings emphasize the multifaceted nature of trait-climate associations and highlight the importance of seed transfer modeling to seed-sourcing decisions in a time of global change.

In the genomic era, phylogenomics is playing an increasingly important role in biological control research for prioritising species in host specificity testing, species delimitation, and elucidating the origins of introduced species. This paper outlines key concepts in phylogenomics relevant to biocontrol practitioners and provides practical guidance on the construction and interpretation of phylogenetic trees. We examine the patterns and distributions of degrees of separation and phylogenetic distance (also known as patristic distance) across different types of phylogenetic trees, including cladograms, phylograms, and chronograms, and offer recommendations for their application. Further, we consider the impact of topological uncertainty on these distance measures and the inferences they inform for decision-making in biological control. These concepts are illustrated through two case study datasets representing distinct evolutionary contexts. The first explores a recently published phylogeny of Asteraceae tribe Senecioneae derived from traditionally used nuclear and chloroplast Sanger molecular markers, using common groundsel (Senecio vulgaris) as the hypothetical target weed. The second case study dataset focuses on the biocontrol of stinking passionflower (Passiflora foetida) in Australia, presenting a novel target capture (Angiosperms353) phylogeny for this group. Equipping biocontrol practitioners with a deeper understanding of phylogenomics will facilitate more efficient and data-driven decision-making in biological control.

Subalpine larch (Larix lyallii Parl.) is a deciduous conifer that only grows at treeline in the Cascade Range and Rocky Mountains of western North America. This habitat is shrinking due to climate change but subalpine larch is unlikely to migrate or adapt in situ and is therefore at risk of maladaptation and eventual extirpation. Future conservation efforts should be informed by an understanding of local adaptation in key traits. In this study, cold tolerance was assessed for 18 populations of subalpine larch from the Canadian portion of the species range that are grafted ex situ at the Kalamalka Forestry Centre in Vernon, BC. Electrolyte leakage was measured after stem tissue was subjected to artificial freezing tests at a range of subzero temperatures (−10°C to −40°C) over 2 years and three seasons (winter, spring, and autumn). Adaptive clines in cold tolerance were observed, providing the first evidence of local adaptation in this species. Temperature-associated climate variables such as the length of the frost-free period (FFP), the Julian date for the end of the frost-free period, and mean coldest month temperature were significant predictors of cold injury at −40°C in all three seasons. Populations from colder sites with a shorter FFP were found to have significantly higher cold tolerance in all three seasons, with the biggest differences observed in spring and autumn. Future management strategies should prioritize the conservation of adaptive variation in cold tolerance.

Understanding the evolutionary history of biological control agents in their native ranges is crucial for improving their selection, establishment, and performance across environmentally diverse regions. Phytophagous insects that specialize on aquatic plants offer particularly valuable models, as their evolutionary trajectories may be shaped by a combination of climatic variation, host plant availability, and the fragmented nature of aquatic habitats. Megamelus scutellaris is a monophagous planthopper native to South America that has been introduced into the United States and South Africa as part of biological control programs targeting the highly invasive aquatic plant, Pontederia crassipes. In this work, we combined nuclear SNP and mitochondrial sequence data to investigate the genetic structure, demographic history, and environmental drivers of population divergence in M. scutellaris across its native range in Argentina and Paraguay. We identified three main genetic lineages broadly associated with major river basins and ecoregions. Demographic modeling supported an early divergence, likely linked to Pleistocene climatic shifts and hydrological changes, followed by a more recent split dated to the early Holocene. Contemporary gene flow was asymmetric and varied in magnitude among lineages, reflecting differences in connectivity and environmental conditions. Lastly, landscape genomic analyzes revealed a strong association between genetic differentiation and climatic variation, supporting models of isolation by environment and resistance. These findings highlight the role of evolutionary and ecological processes in shaping the genetic landscape of M. scutellaris and provide key insights for selecting source populations better suited to different environments in introduced regions.

Global warming and rising sea temperatures are pushing many reef-building coral species towards extinction. As thermal tolerance in corals is partially heritable, identifying genes under thermal selection is critical for targeted biodiversity management. However, it remains unclear how large connectivity breaks (> 100 km of open sea) might affect the spread of adaptive alleles for different coral species in discontinuous reef networks such as the Western Indian Ocean (WIO). To address this, we applied a seascape genomics approach to model (i) population structure and (ii) thermal adaptive potentials for two keystone coral species, Acropora muricata and Pocillopora damicornis, across the WIO. Northern reefs in the Seychelles were largely genetically isolated from southern reefs in Rodrigues and Mauritius for both species, potentially driven by regional oceanographic barriers. Isolation-by-resistance calculated from ocean currents during reproductive months better explained regional genetic differences than isolation-by-distance alone. Spatial patterns of genetic variation were best captured by variables representing thermal stress, including sea surface temperature variability, accumulating heat stress, and fine-scale reef structure. Using these variables in genotype–environment association (GEA) analyses identified hundreds of loci under putative thermal selection, including several linked to genes involved in heat stress responses. We detected 12 molecular functions enriched in A. muricata and 20 enriched in P. damicornis, generally pertaining to cellular signalling, transport mechanisms, metabolism, and protein quality control, including six genes annotated as the heat-shock chaperone protein Sacsin for A. muricata. We produce species-specific maps estimating the putative thermally adaptive seascape across the WIO, which, when combined with population structure and previous ocean current models, indicate that the spread of heat adapted genotypes may be inhibited across the WIO. This research provides valuable insights into WIO coral population structure and thermal adaptive potentials to inform local and regional conservation management across the region.

Climate change is the greatest challenge to modern agriculture. It significantly impacts agricultural systems through an increased frequency and intensity of extreme environmental events. Maize, a vital crop for global food security, is particularly vulnerable to these changes, highlighting the urgent need to develop resilient varieties. This study aims to identify significant genes for adaptation to environmental conditions in 140 individuals derived from 28 Italian maize landraces using a landscape genomics approach to support the development of resilient maize genotypes. Landraces were genotyped using genotyping-by-sequencing, and the resulting genetic matrix was used to characterize the collection's diversity. Population genetic studies were conducted to investigate the genetic diversity and structure of the collection. Partial redundancy analysis (pRDA) was subsequently employed to analyze the relationship between climate variables and genetic variation of the materials. Among the 12 ancestral populations identified, both well-defined populations and highly admixed groups were observed. This degree of admixture was reflected in the clustering analysis and principal component analysis (PCA), although clear differentiation of individual populations was still apparent. pRDA revealed that 30% of the genetic variance in the collection was explained together by climate (45%), geography (11%), and genetic structure (31%). Three potential genomic signals of adaptation were identified in relation to the environmental variability across the sampling sites. The results highlight significant intra-landrace variability within the examined germplasm and reveal unique landraces tied to ancestral lineages. Notably, we identify distinct genetic markers strongly correlated with environmental factors. This discovery opens new avenues for potential genetic improvement in maize cultivation. Landraces preserve vital traits for the adaptation of maize to environmental stresses, thereby serving as key sources for breeding programs aimed at improving stress tolerance and yield stability under climate change.

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.