Evolution Letters最新文献

{"title":"<i>k</i>-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species.","authors":"Miles D Roberts, Emily B Josephs","doi":"10.1093/evlett/qraf011","DOIUrl":"10.1093/evlett/qraf011","url":null,"abstract":"<p><p>A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was noted by Richard Lewontin in 1974 and reaffirmed by later studies, the slope of the population size-diversity relationship in nature is much weaker than expected under neutral theory. We hypothesize that one contributor to this paradox is that current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads to a reference genome underestimate levels of genetic diversity in many species. As a first step to testing this idea, we calculated nucleotide diversity ( <math><mi>π</mi></math> ) and <math><mi>k</mi></math> -mer-based metrics of genetic diversity across 112 plant species, amounting to over 205 terabases of DNA sequencing data from 27,488 individuals. After excluding 14 species with low coverage or no variant sites called, we compared how different diversity metrics correlated with proxies of population size that account for both range size and population density variation across species. We found that our population size proxies scaled anywhere from about 3 to over 20 times faster with <math><mi>k</mi></math> -mer diversity than nucleotide diversity after adjusting for evolutionary history, mating system, life cycle habit, cultivation status, and invasiveness. The relationship between <math><mi>k</mi></math> -mer diversity and population size proxies also remains significant after correcting for genome size, whereas the analogous relationship for nucleotide diversity does not. These results are consistent with the possibility that variation not captured by common SNP-based analyses explains part of Lewontin's paradox in plants, but larger scale pangenomic studies are needed to definitively address this question.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 4","pages":"434-445"},"PeriodicalIF":3.7,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diverging <i>Arabidopsis</i> populations quickly accumulate pollen-acting genetic incompatibilities.","authors":"Christopher Condon, Fantin Carpentier, Marie Tabourin, Natalia Wozniak, Margarita Takou, Christelle Blassiau, Vinod Kumar, Björn Pietzenuk, Rémi Habert, Juliette De Meaux, Ute Krämer, Camille Roux, Russell Corbett-Detig, Vincent Castric","doi":"10.1093/evlett/qraf013","DOIUrl":"10.1093/evlett/qraf013","url":null,"abstract":"<p><p>The process by which species diverge from one another, gradually accumulate genetic incompatibilities, and eventually reach full-fledged reproductive isolation is a key question in evolutionary biology. However, the nature of reproductive barriers, the pace at which they accumulate, and their genomic distribution remain poorly documented. The disruption of co-adapted epistatic interactions in hybrids and the accumulation of selfish genetic elements are proposed contributors to this process, and can lead to the distortion of the Mendelian segregation of the affected loci across the genome. In this study we detect and quantify segregation distortion across the genomes of crosses produced from a diverse sampling of <i>Arabidopsis lyrata</i> and <i>A. halleri</i> populations, 2 species at the early stages of speciation and that can still interbreed. We observe no distortion loci in crosses with geographically and genetically similar parents, but both their frequency of occurrence and their magnitude become highly variable in more distant crosses. We also observe that distorter loci evolve rapidly, as they occur not only in interspecific hybrids, but also in intraspecific hybrids produced by crossing individuals from 2 isolated regions. Finally, we identify both genome-wide nonindependence and 2 specific genomic regions on different chromosomes where opposite distortion effects are repeatedly observed across multiple F1 individuals, suggesting negative epistasis is a major contributor to the evolution of hybrid segregation distortion. Our study demonstrates that pollen-acting segregation distortion is ubiquitous, and may contribute not only to the ongoing reproductive isolation between <i>A. halleri</i> and <i>A. lyrata</i>, but also between recently diverged populations of the same species.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 4","pages":"461-472"},"PeriodicalIF":3.7,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary trends in the emergence of skeletal cell types.","authors":"Amor Damatac, Sara Koska, Kristian K Ullrich, Tomislav Domazet-Lošo, Alexander Klimovich, Markéta Kaucká","doi":"10.1093/evlett/qraf012","DOIUrl":"10.1093/evlett/qraf012","url":null,"abstract":"<p><p>Cell types are fundamental functional units of multicellular organisms. The evolutionary emergence of new cell types is underpinned by genetic changes, such as gene co-option and cis-regulatory evolution, that propel the assembly or rewiring of molecular networks and give rise to new cell types with specialized functions. Here, we integrate genomic phylostratigraphy with single-cell transcriptomics to explore the evolutionary trends in the assembly of the skeletal cell type-specific gene expression programs. In particular, we investigate how the emergence of lineage-specific genes contributed to this process. We show that osteoblasts and hypertrophic chondrocytes (HC) express evolutionary younger transcriptomes compared to immature chondrocytes that resemble the ancestral skeletogenic program. We demonstrate that the recruitment of lineage-specific genes resulted in subsequent elaboration and individuation of the ancestral chondrogenic gene expression program, propelling the emergence of osteoblasts and HC. Notably, osteoblasts show significant enrichment of vertebrate-specific genes, while HC is enriched in gnathostome-specific genes. By identifying the functional properties of the recruited genes, coupled with the recently discovered fossil evidence, our study challenges the long-standing view on the evolution of vertebrate skeletal structures by suggesting that endochondral ossification and chondrocyte hypertrophy may have already evolved in the last common ancestors of gnathostomes.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 4","pages":"446-460"},"PeriodicalIF":3.7,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Replicate geographic transects across a hybrid zone reveal parallelism and differences in the genetic architecture of reproductive isolation.","authors":"Georgy Semenov, Haley Kenyon, Erik Funk, William Anderson, Michael McQuillan, Joan Spinelli, Austin Russell, Noel Martinez, Alex Van Huynh, Alana Alexander, Rena Schweizer, Ethan Linck, Zachary Cheviron, Matt Carling, Timothy Roth, Mark Robbins, Amber Rice, Scott Taylor","doi":"10.1093/evlett/qraf009","DOIUrl":"10.1093/evlett/qraf009","url":null,"abstract":"<p><p>Determining the genetic architecture of traits involved in adaptation and speciation is one of the key components of understanding the evolutionary mechanisms behind biological diversification. Hybrid zones provide a unique opportunity to use genetic admixture to identify traits and loci contributing to partial reproductive barriers between taxa. Many studies have focused on the temporal dynamics of hybrid zones, but geographical variation in hybrid zones that span distinct ecological contexts has received less attention. We address this knowledge gap by analyzing hybridization and introgression between black-capped and Carolina chickadees in two geographically remote transects across their extensive hybrid zone, one located in eastern and one in central North America. Previous studies demonstrated that this hybrid zone is moving northward as a result of climate change but is staying consistently narrow due to selection against hybrids. In addition, the hybrid zone is moving ~5× slower in central North America compared to more eastern regions, reflecting continent-wide variation in the rate of climate change. We use whole genome sequencing of 259 individuals to assess whether variation in the rate of hybrid zone movement is reflected in patterns of hybridization and introgression, and which genes and genomic regions show consistently restricted introgression in distinct ecological contexts. Our results highlight substantial similarities between geographically remote transects and reveal large Z-linked chromosomal rearrangements that generate measurable differences in the degree of gene flow between transects. We further use simulations and analyses of climatic data to examine potential factors contributing to continental-scale nuances in selection pressures. We discuss our findings in the context of speciation mechanisms and the importance of sex chromosome inversions in chickadees and other species.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 4","pages":"421-433"},"PeriodicalIF":3.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting fitness in future climates: insights from temporally replicated field experiments in <i>Arabidopsis thaliana</i>.","authors":"Romain Villoutreix, Nathalie Faure, Cédric Glorieux, Fabrice Roux","doi":"10.1093/evlett/qraf007","DOIUrl":"10.1093/evlett/qraf007","url":null,"abstract":"<p><p>Organisms are already facing climate change. To understand and mitigate the negative effects of climate change on wild and cultivated species, recent research has focused on predicting the fitness of organisms or populations in future climates. The accuracy of these predictions is, however, seldom tested. To test such predictions, we grew a set of 800 genetic families of the annual plant <i>Arabidopsis thaliana</i> in the same field site located in Northern France for 2 consecutive years with contrasted climates. Despite observing, in both years, a clear association between fitness and climatic distance between our field site and the climate of origin of these genetic families, the diverse set of methods we used failed to accurately predict fitness from a year to another. This low accuracy can be explained by the fact that different climatic factors contributed to climate adaptation in different years, which impeded the definition of a meaningful climate descriptor across years. Our results also suggest that populations of <i>A. thaliana</i> from Northern France already suffer from an adaptational lag with respect to climate, and that vegetative growth seems to be a more important trait for climate adaptation than phenology. We discuss the implications of our results for predicting the fitness of wild organisms in future climates and for breeding programs.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 4","pages":"392-407"},"PeriodicalIF":3.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Positive correlations in susceptibility to a diverse panel of viruses across Drosophilidae host species.","authors":"","doi":"10.1093/evlett/qraf010","DOIUrl":"10.1093/evlett/qraf010","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/evlett/qraf002.].</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 3","pages":"379-380"},"PeriodicalIF":3.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Drosophila melanogaster</i> pigmentation demonstrates adaptive phenotypic parallelism over multiple spatiotemporal scales.","authors":"Skyler Berardi, Jessica A Rhodes, Mary Catherine Berner, Sharon I Greenblum, Mark C Bitter, Emily L Behrman, Nicolas J Betancourt, Alan O Bergland, Dmitri A Petrov, Subhash Rajpurohit, Paul Schmidt","doi":"10.1093/evlett/qraf008","DOIUrl":"10.1093/evlett/qraf008","url":null,"abstract":"<p><p>Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in <i>Drosophila melanogaster</i> as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field. We show that <i>D. melanogaster</i> pigmentation evolves as a highly parallel and deterministic response to shared environmental variation across latitude and season in natural North American populations. We then experimentally evolved replicate, genetically diverse fly populations in field mesocosms to remove any confounding effects of demography and/or cryptic structure that may drive patterns in wild populations; we show that pigmentation rapidly responds, in parallel, in fewer than 15 generations. Thus, pigmentation evolves concordantly in response to spatial and temporal climatic axes. We next examined whether phenotypic differentiation was associated with allele frequency change at loci with established links to genetic variance in pigmentation in natural populations. We found that across all spatial and temporal scales, phenotypic patterns were associated with variation at pigmentation-related loci, and the sets of genes we identified at each scale were largely nonoverlapping. Therefore, our findings suggest that parallel phenotypic evolution is associated with distinct components of the polygenic architecture shifting across each environmental axis to produce redundant adaptive patterns.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 4","pages":"408-420"},"PeriodicalIF":3.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Landscape structure as a driver of eco-evolution in host-parasite systems.","authors":"Jhelam N Deshpande, Vasilis Dakos, Oliver Kaltz, Emanuel A Fronhofer","doi":"10.1093/evlett/qraf003","DOIUrl":"10.1093/evlett/qraf003","url":null,"abstract":"<p><p>Spatial network structure of biological systems drives ecology and evolution by distributing organisms and their genes. The ubiquitous host-parasite systems are no exception. However, past theoretical work has largely focused on simple spatial structures, such as grids, hampering the translation of theoretical predictions to real ecosystems. Thus, we develop an eco-evolutionary metapopulation model of host-parasite dynamics where hosts and parasites disperse through realistically complex spatial networks representing major biomes using river-like and terrestrial-like networks. We generate the testable prediction that parasite virulence, or how parasites harm their hosts, peaks at intermediate dispersal values in river-like systems while it increases with increasing dispersal in terrestrial-like systems. In river-like systems, virulence also reaches higher overall values. Moreover, we show that kin selection is the main driver of virulence evolution. Spatial networks generate characteristic patterns of parasite relatedness which drive differential virulence evolution. Finally, we show that accounting for virulence evolution allows us to predict the distribution of key epidemiological variables (e.g., parasite extinction risks) within spatial networks. Our study highlights how eco-evolutionary feedbacks can be understood in light of spatial network structure by linking network topology to classical evolutionary mechanisms such as kin selection.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 3","pages":"367-378"},"PeriodicalIF":3.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Do the \"big four\" orders of insects comprise evolutionarily significant higher taxa with coherent patterns of selection on protein-coding genes?","authors":"Pierre J Février, Timothy G Barraclough","doi":"10.1093/evlett/qraf005","DOIUrl":"10.1093/evlett/qraf005","url":null,"abstract":"<p><p>Species are often treated as evolutionarily significant units of diversity that reflect patterns of gene flow and selection. In contrast, higher taxa are mostly regarded as convenient labels for levels in the tree of life, which reflect evolutionary history if defined cladistically but are assumed to have no real significance for ongoing evolution. We test the alternative hypothesis that some higher taxa are evolutionarily significant units with coherent patterns of selection on their constituent species. Specifically, we ask whether the big 4 orders of holometabolous insects, namely Coleoptera, Diptera, Hymenoptera, and Lepidoptera, display divergent, but internally conserved patterns of selection acting on protein-coding genes. Analyzing orthologous genes from whole genome sequence data for multiple species per order, we find that, in most genes, selection on roughly one fifth of codons is conserved within each order but differs significantly among orders. The shift is associated with variation in GC content among orders, but primarily at codon 2nd positions hence due to selection rather than mutational or repair bias. Comparison of alternative models assigning different taxonomic levels (either more lumped or divided than orders) shows that best models always specify Hymenoptera and Lepidoptera as coherent units, whereas patterns of selection on protein-coding genes within Coleoptera and especially Diptera are better explained by subdividing them further. We hypothesise that some aspect of the general lifestyle, body plan or genetic makeup of orders (or of nested clades within Coleoptera and Diptera) leads to conserved patterns of selection across protein-coding genes within them, whereas constraints differ among them. The emergence of whole-genome data for broad and deep phylogenetic samples will allow this hypothesis of evolutionarily significant higher taxa versus more evenly dispersed shifts in selection across genes to be tested further.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 3","pages":"355-366"},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Size in the city: morphological differences between city and forest great tits have a genetic basis.","authors":"Barbara M Tomotani, Mika Couweleers, Bram Ten Brinke, Anne Walboom, Kees van Oers, Marcel E Visser","doi":"10.1093/evlett/qraf006","DOIUrl":"10.1093/evlett/qraf006","url":null,"abstract":"<p><p>Animals living in cities are smaller than their conspecifics from rural areas but whether such differences are caused by genetic differences or food constraints remains untested. We performed a multi-generation common garden study where we raised great tits (<i>Parus major</i>), originating from eggs collected from multiple Dutch cities and forests under the same conditions for two generations. Offspring from city birds had a smaller tarsus than forest birds in both generations, demonstrating that these morphological differences are genetic. Next, we tested whether size differences are an adaptation to the low food abundance when offspring are raised in the city. Third-generation birds of both origins were given food amounts mimicking being raised in forests or cities during the second part of their nestling development. While the treatment resulted in birds in the lower feeding frequency treatment to be smaller, city and forest birds responded the same way, suggesting that city birds do not cope better with reduced food availability. Our study shows that the smaller size of urban birds has a genetic basis and is not only caused by a plastic response to restricted resources in the urban environment. Our experiment does not provide evidence that these genetic differences have evolved as an adaptive response to a reduced food availability in cities.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 3","pages":"317-323"},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}