Evolutionary Applications最新文献

Cancer progression following treatment failure is an evolutionary process in which therapy acts as a selection pressure driving Darwinian selection on heritable variation to favor resistant clones. Heritable variation is a key determinant of how rapidly tumors can adapt to therapy. Heritable variation arises through various mechanisms such as genetic mutations, epigenetics, chromosomal rearrangements, and copy number variations, resulting in a lack of replicative fidelity. We consider evolvability as a property or trait of the cancer cells that influences the rate at which fitness-relevant heritable variation is generated. Using this as our definition, we present an evolutionary game-theoretic model to evaluate how evolvability shapes resistance dynamics under two treatment modalities: targeted therapy and chemotherapy. We first compare cancer populations with fixed evolvabilities: low or high. Targeted therapy imposes a steep selection gradient, enabling rapid resistance evolution, while chemotherapy imposes a flatter selection gradient but drives tumors toward more extreme resistance strategies. We show that targeted therapy works better in cancers with low evolvability, whereas chemotherapy better controls cancers with high evolvability. We then extend the model to incorporate “plastic evolvability,” in which cancer cells can adjust their evolvability in response to therapy-induced stress. In this case, cells fine-tune the trade-off between acquiring higher resistance and limiting the costs of resistance and evolvability. Plastic evolvability sustains a higher tumor burden than fixed-evolvability. To address the challenge of plastic evolvability, we develop and simulate an evolutionary double bind using sequential cycles of chemotherapy and targeted therapy. With an appropriate sequence and timing, the double bind can drive cancers with plastic evolvability to extinction. Our results highlight the importance of evolvability in shaping treatment response and underscore the need to incorporate evolutionary principles into therapy design.

Comb morphology is a salient chicken trait of biological and breeding interest. We analyzed whole-genome data from 228 birds representing 10 breeds, including Hetian (HTC) and Xiangdong (XDC)—the only two Chinese breeds with carnation combs—to investigate population structure, diversity, and genomic correlates of comb type. Population analyses revealed clear breed stratification, with clustering that partly tracked comb type; breeds subjected to strong artificial selection or bottlenecks showed reduced genetic diversity. The integrated fixation index (F_ST) and genome-wide association study (GWAS) approach highlighted multiple regions differentiating carnation- from non-carnation-comb birds, with the strongest, most consistent signal at HSF5. Additional associated loci included EDN3, ITGB8, PDE4B, SDK1, MC1R, CDKL5, NRXN1, and STAG3. Gene-set enrichment pointed to pathways involved in vascular development and embryogenesis, processes plausibly contributing to comb morphogenesis. Notably, while HTC and XDC maintained distinct global genomic backgrounds, they exhibited high similarity within the major candidate genes influencing the carnation comb phenotype, suggesting that independent breed differentiation occurred alongside a shared genetic basis for this trait. While causative variants were not established, these results nominate tractable candidates and pathways for functional validation and inform marker development for conservation and selection in indigenous breeds.

Reintroducing wildlife into anthropogenic landscapes is challenging, particularly for wide-ranging species. Extensive habitat fragmentation and limited carrying capacities pose genuine risks of population isolation and subsequent genetic erosion. A current example includes the fragmented populations of the Eurasian lynx (Lynx lynx carpathicus) in Central Europe, where isolated demes currently rely on ex situ sourced or wild-caught releases to buffer inbreeding accumulation over short timescales. Due to management trade-offs, however, such assisted migration can only function as a transitional remedy, whereas long-term stability hinges on inherent growth rates and vital genetic exchange in a metapopulation framework. We here use analytic modelling to examine potential scenarios and requirements for a vital metapopulation of the Eurasian lynx in Central Europe. To inform conservation management in the early stages of formation, we considered scenarios that describe the current and near-future status of the metapopulation, as well as anticipated—but not yet established—scenarios that would ensure long-term genetic stability. We find that current and near-future effective sizes and migration rates among demes are far from sufficient to reach long-term stability (Ne_meta > 500), even given hundreds of generations. Model-derived management targets suggest that robust configurations require significant increases in deme sizes (> 150%), diversity (Ne/Nc > 0.4), and average pairwise migration rates (> 10%), in order to advance towards stable metapopulation dynamics. This, however, entails potential distribution trade-offs from limited capacities in ex situ and/or wild population sourcing. Here, our model outcomes caution against diverting resources towards new introductions, and highlight the need for ongoing reinforcement of existing demes on the one hand, and the mitigation of dispersal barriers and threats on the other hand.

Genetic diversity is shaped by multiple factors, including life-history traits, contemporary range distributions, niche constraints, and historical demography. The interplay of these drivers remains largely unexplored, particularly at scales proven to be relevant to conservation management of tropical biodiversity hotspots. Here, we investigate the relative contribution of each of these factors in shaping the current patterns of genetic diversity of 13 plant species occurring in Carajás, Southeastern Amazon, Brazil. We further test whether species associated with iron-rich substrates in Carajás, known as cangas, share a common demographic history despite their differences in life-history traits, distributions, and niches. We found that inbreeding levels are likely determined by mating systems, while both observed and expected heterozygosity were negatively associated with niche marginality. Surprisingly, distribution range and niche breadth had no effects on genetic parameters, likely due to the absence of correlations with ecological specialization. Demographic reconstructions revealed a lack of synchronous population histories across co-distributed cangas plants, which likely reflects variation in the diversified life-history traits affecting the timing of their responses to past climatic changes. Our results offer valuable insights into future demographic trends of cangas-associated species, refining predictions on the fate of species in the face of anthropogenic pressures such as habitat loss and climate change. Our data further contribute to subsidizing analyses to determine priority areas and species for conservation.

Understanding how populations are structured and adapt to their local environment is critical for developing effective management strategies. We used the commercially and culturally valued marine teleost Chrysophrys auratus (the Australasian snapper) as an exemplar of a high-gene-flow species to study genetic structure, population connectivity, and local adaptation. We performed whole-genome sequencing of 382 individuals across 13 sample locations, covering the range of the species in New Zealand. We find that snapper consist of two genetic clusters with low levels of genetic differentiation (F_ST = 0.0031): a northeastern (NE) and a southwestern (SW) cluster, with genetic discontinuities around the Tauroa and Mahia Peninsulas. We further observe widespread admixture and dispersal events, which are indicative of ongoing gene flow, in particular around the areas of the genetic discontinuities near the Tauroa and Mahia Peninsulas. Selection scans identified 25 regions of interest (ROIs) throughout the genome. The haplotype-based statistic XP-nSL was used to identify which genetic cluster each ROI was most likely under selection, 12 and 13 ROIs for the NE and SW clusters, respectively. The identification of candidate genes with similar molecular functions provided tentative evidence of polygenic adaptation to local environments. Finally, we discuss how monitoring genetic variation contributes to fisheries management by maintaining genetic diversity and resilience in commercial fish. These insights into genetic structure, connectivity, genetic diversity, and local adaptation are critical for protecting species under increased pressure from anthropogenic threats like fishing and climate change, and are thus directly applicable to fisheries management.

In the Canadian Maritimes, the eastern oyster (Crassostrea virginica) industry has been shaped by population-scale events, including ~90% reductions of natural beds from Malpeque disease. For many years, Maritime oyster populations were considered genetically homogenous due to large-scale transplants to rehabilitate depleted beds; however, recent studies suggest that ancestral populations survived. We characterized genetic diversity and geographical genetic structure (using ddRAD-seq) of wild oysters from 24 locations (n = 1409) across New Brunswick (NB), Prince Edward Island (PEI), and Nova Scotia (NS), including multiple locations along estuarine gradients within the same river systems. While genetic differentiation was low  between Maritime locations (F_st = 0.012), ADMIXTURE analysis demonstrated spatial structure with cross-validation (CV) error optimized at K = 4 ancestral populations. Oysters from the Bras d'Or Lakes in NS, and Miramichi and Richibucto in NB were characterized by distinct dominant ancestries, whereas populations from Bouctouche and Caraquet in NB, the Foxley, Grand, and Brudenell Rivers on PEI, and Pictou in NS shared a common dominant ancestry. Populations from coastal Cape Breton (Aspy River and Arichat) in NS exhibited mixed ancestry, primarily consisting of Bras d'Or Lake and ‘Gulf’ lineages. Within estuaries, genetic differentiation between upriver and downriver sites was minimal (F_st = 0.002–0.003), suggesting ongoing gene flow along estuarine gradients; however, each estuary contained a subset of SNP loci putatively under selection, indicating potential local adaptation despite high connectivity. Functional annotation of candidate loci identified genes associated with membrane transport, cellular stress response, protein turnover, and metabolic pathways, suggesting that environmental gradients may contribute to adaptive divergence. Ultimately, this reveals a complex genetic landscape and demonstrates that oyster beds in the Maritime provinces have retained genetic structure from both historical transfer activity in the region and local adaptation. The results provide important insights for the conservation, management, and restoration of eastern oyster populations throughout Atlantic Canada.

Understanding the processes that shape biological invasions is essential for predicting the spread and persistence of introduced species, yet these processes remain poorly resolved for many unintentionally introduced plants. We combined genome-wide SNP data, demographic modeling, and climatic niche analyses to investigate the invasion of giant ragweed in South Korea. A total of 419 individuals from 35 introduced populations and 59 individuals from four native North American populations were analyzed. Introduced populations retained high genetic diversity and exhibited weak spatial structure, consistent with extensive human-mediated dispersal. Approximate Bayesian Computation supported a recent invasion within the last ~70 years involving multiple introductions from genetically divergent sources, followed by rapid divergence and severe but transient demographic bottlenecks. Climatic niche analyses revealed substantial overlap between native and introduced ranges but pronounced niche unfilling, indicating that Ambrosia trifida has yet to occupy its full potential climatic niche in South Korea. Together, these results show that repeated introductions, admixture, and anthropogenic dispersal, rather than major climatic niche shifts, have shaped the contemporary invasion. Our findings highlight how integrating population genomics with niche analyses can resolve invasion processes and inform management of rapidly spreading invasive species.

The potato psyllid (Bactericera cockerelli) is a crop pest that serves as a vector for the bacterial pathogen Candidatus Liberibacter solanacearum (CLso), which causes disease in solanaceous and apiaceous crops. This psyllid species carries substantial haplotypic diversity based on mitochondrial cytochrome oxidase 1 (mtCOI) sequences, associated with strong geographic and temporal separation. Using mtCOI sequencing and genomic ddRADseq analysis of 111,587 SNPs across 590 individuals collected from native Solanaceae and cultivated crops at 50 geographically paired sites in California, we show that the previously described haplotype diversity in B. cockerelli may represent at least three genetically distinct cryptic species. These three lineages exhibited extremely high genomic F_ST values across all 13 chromosomes and are strongly partitioned by the host plant. The Northwestern lineage is strictly associated with the native perennial Solanum umbelliferum, while the Western lineage is associated with solanaceous crops, and the Southwestern lineage moves between native and cultivated hosts in desert regions. Hybridization is also rare, suggesting reproductive isolation. SNP and divergence analyses for the obligate bacterial symbiont support conclusions of the host nuclear and mtCOI sequence analyses. We also detected five CLso variants in psyllid samples. The Northwestern lineage housed G, Sumb2, F and B variants, while the Western lineage housed only B and A variants. The largest diversity of CLso variants occurred in coastal regions where psyllid lineages overlap. Exploring the ecology and CLso associations of this potential cryptic species complex provides a foundation for improving biosecurity and management of potato psyllids and CLso pathogens.

Lake whitefish Coregonus clupeaformis abundance has declined throughout most of the Laurentian Great Lakes in North America for two decades. Current management strategies in Lake Erie assume that there is a single stock of lake whitefish that spawns in the West Basin. There is documented lake whitefish spawning activity throughout the lake, leading to questions about locally adapted genetic stocks. Past research on lake whitefish genetic structure in Lake Erie has supported the single-stock hypothesis, but these studies used only neutral genetic markers or contained a limited number of samples that were collected during the spawning season when stocks would be spatially isolated. Using a GT-seq panel, we evaluate the genetic structure of lake whitefish collected from spawning shoals in the West, Central, and East basins of Lake Erie and compare these populations to lake whitefish from Lake Huron. We then investigate evidence of local adaptation and conduct demographic reconstruction using whole-genome sequencing. Our goals were to conclusively quantify intra-lake genetic structure in Lake Erie and determine whether spawning aggregations possess putatively adaptive variants that could be used for genetic stock identification at a sub-lake level. Our analysis supported the single-stock hypothesis in Lake Erie. However, Lake Erie stocks were distinct from neighboring Lake Huron. Whole-genome analysis did not identify any strong evidence of adaptive loci differentiating stocks. Inference of historic effective population size suggests that declines in lake whitefish populations may have caused a genetic bottleneck. Combined, these results indicate that lake whitefish in Lake Erie may have experienced an Allee Effect after population declines, resulting in a loss of population structure and genetic diversity as spawning shoals were recolonized from a common source.

Shifts between population connectivity and isolation shape evolutionary divergence, but their effects remain underexplored in highly mobile taxa. Flying-foxes (Pteropus) are a compelling model to study evolutionary divergence because of their rapid radiation in the island-rich region of the Indo-Australian Archipelago. Here, we investigate the population genetics of the highly mobile flying-foxes Pteropus alecto, P. conspicillatus, P. poliocephalus, and P. scapulatus across large parts of their overlapping ranges in Australia, Indonesia, and New Guinea. Using reduced-representation sequencing of 242 individuals, we examined the extent to which panmixia, isolation-by-distance, and hybridization are prevalent in these lineages. Phylogenetic, principal component, and demographic analyses indicated isolation-by-distance in P. alecto, including an unexpected east–west genetic split between Australian populations, whereas P. conspicillatus showed weak differentiation between Australia and New Guinea, and P. poliocephalus and P. scapulatus were panmictic across Australia. We further found evidence that infrequent hybridization and asymmetric gene flow, predominantly from P. conspicillatus to P. alecto, have shaped these recently diverged species. Although gene flow connected sampled populations along the geographic chain spanning Indonesia, Australia, and New Guinea, our results did not confirm the hypothesis that P. alecto and P. conspicillatus form a ring species. Rather, demographic analyses supported recent secondary contact during the last 14,848–35,856 years after a period of isolation between P. alecto and P. conspicillatus. Together, our findings indicate that long-range connectivity and spatially heterogeneous restrictions on gene flow have shaped the evolution and diversification of flying-foxes.