Evolution最新文献

{"title":"Molecular Characterization and Cophylogenetic Relationships between Crassicauda spp. (Nematoda: Spirurida) and Cetaceans of the Northwest Atlantic.","authors":"Jacquelyn M Salguero, Sebrina P Brooks, Tiffany F Keenan, D Ann Pabst, William A McLellan, D Wilson Freshwater, Julia C Buck","doi":"10.1093/evolut/qpag164","DOIUrl":"https://doi.org/10.1093/evolut/qpag164","url":null,"abstract":"<p><p>The evolutionary trajectory of helminth parasites of the genus Crassicauda (Nematoda: Spirurida) is thought to be tightly linked with that of their cetacean hosts. However, due to limitations in sampling these giant (some > 3 meters) worms, their diversity and evolutionary relationships remain poorly understood. In this study, we (1) identify Crassicauda species infecting cetacean hosts from the Northwest Atlantic using the mitochondrial cytochrome c oxidase subunit 1, and nuclear internal transcribed spacer 2 and small subunit ribosomal RNA genes; (2) evaluate the phylogenetic relationships among our specimens, augmented with homologous sequences from GenBank, and (3) characterize host-parasite cophylogenetic structure using distance- and event-based methods. Phylogenetic analyses resolved 11 parasite species infecting 15 cetacean species, revealing cryptic and underreported diversity. Distance-based methods detected significant cophylogenetic signal between parasite and host phylogenies, while event-based analyses detected phylogenetic incongruence. This combination supports a complex evolutionary scenario in which Crassicauda lineages colonized and speciated alongside cetaceans, particularly pelagic species within the family Delphinidae, and diversified within odontocetes. Together, these results provide insight into the mosaic of evolutionary processes that shaped the genus Crassicauda and their cetacean hosts, with implications for monitoring health and disease in marine mammal populations.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Robust model comparison and tests of interactions in phylogenetic path analysis: Revisiting \"Why are telomeres the length they are?\" (Benson et al. 2025).","authors":"Alejandro Gonzalez-Voyer, Iker Bargas-Galarraga, Achaz von Hardenberg","doi":"10.1093/evolut/qpag171","DOIUrl":"https://doi.org/10.1093/evolut/qpag171","url":null,"abstract":"<p><p>We discuss robust model comparison in phylogenetic path analysis and how to incorporate interactions in path analysis with d-separation. We revisit a study by Benson et al. (2025) to highlight the importance of carefully evaluating the causal models being compared to avoid erroneous conclusions. Our results show that there are biologically plausible models, not previously considered, that outperform those in the original study leading to quite different biological conclusions. We also use this work to demonstrate, using empirical data, how interactions can be incorporated in path analyses, and highlight how their presence affects the conditional independencies that must be tested for the model to be considered a plausible causal model. Our commentary highlights the importance of rigorously evaluating model space and verifying both the implied conditional independencies as well as the robustness of the assumed causal effects.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How sex shapes transcriptome evolution in the songbird brain.","authors":"Isaac Miller-Crews, Sara E Lipshutz, Ben Fulton, Jason Bertram, Matthew W Hahn, Kimberly A Rosvall","doi":"10.1093/evolut/qpag168","DOIUrl":"10.1093/evolut/qpag168","url":null,"abstract":"<p><p>Sex differences have long captivated scientists, yet the evolutionary rate of change in sex-biased gene expression has not been directly quantified. To address this issue, we introduce new options in CAGEE (Computational Analysis of Gene Expression Evolution), specifically unbounded Brownian motion and variable evolutionary rates among genes. We applied these features to brain transcriptomes of ten songbird species, half of which convergently evolved obligate cavity-nesting, an element of reproductive ecology linked to sex-specific changes in competitive behavior. We find that the degree of sex-bias - measured as male:female expression ratio for each gene - evolves twice as fast on the Z chromosome versus autosomes, but Z gene expression does not evolve at different rates among sexes. Most Z-linked genes are male-biased in their expression, but not all. These sex-balanced genes are not skewed in their rate of evolution, contrary to the hypothesis that some genes experience selection for balance and consequently evolve more slowly. Finally, the degree of sex-bias in gene expression evolves more quickly along obligate-cavity nesting lineages, suggesting that sex-specific selection may shape the evolution of brain sex differences, or lack thereof. Together, these results provide new insights into the interplay between sex and gene expression evolution.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149001510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid male benefit adaptation in response to sex-limitation, mates, and genetic context in Drosophila melanogaster.","authors":"Harshavardhan Thyagarajan, Mindy G Baroody, Imran Sayyed, Joshua A Kowal, Troy Day, Adam K Chippindale","doi":"10.1093/evolut/qpag162","DOIUrl":"https://doi.org/10.1093/evolut/qpag162","url":null,"abstract":"<p><p>Intralocus sexual conflict (IaSC) arises when selection favours different trait values in females and males despite their shared genetic architecture. In the presence of IaSC, sex-limited selection is expected to resolve this conflict by allowing one sex to adapt without constraint from selection acting on the other sex, with intersexual genetic correlations predicted to drive a decline in the fitness of the opposite sex. In a recent study, we found that male-limited (ML) selection produced the predicted decline in female fitness, but male fitness improvement was sensitive to genetic background, suggesting unintended sources of adaptation. Here we dissect these evolutionary responses using a fully factorial assay spanning control-like and selection-like conditions, explicitly accounting for the unusual genetic features of the clone-generator (CG) breeding system and the specialized (CG) females used to enforce male-limited inheritance of nuclear genetic variation. Evolved male fitness increased by more than 100% (relative to controls) when tested with all the features of the CG breeding system. Retaining the CG genetic background while replacing CG females with control females yielded an approximately 66% fitness increase. In a control-like genetic background, male fitness increased by 26% when males competed for the CG females they had potentially adapted to, but only by a marginal 6% otherwise. Despite this strong context dependence, the underlying phenotypic responses were remarkably consistent: selected male improvements were driven by enhanced precopulatory traits; greater attractiveness, reflected in higher mating success and shorter mating latency; while postcopulatory traits, including sperm offense (P2) and fecundity induced in mates, remained unchanged. Intriguingly, evolved males also inflicted substantially less mate harm on CG females, contrary to findings from an earlier ML selection experiment. Together, these findings provide clearer evidence of intralocus sexual conflict, expressed as male-benefit adaptations alongside previously established costs to females, but demonstrate that these adaptations were also shaped by the genetic manipulations and mating context of the experimental design.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149001597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simple a posteriori insertion of fossil tips in molecular phylogenies can improve inferences of continuous trait evolution.","authors":"Lindsey M DeHaan, Graham J Slater, Matt Friedman","doi":"10.1093/evolut/qpag166","DOIUrl":"https://doi.org/10.1093/evolut/qpag166","url":null,"abstract":"<p><p>Integrating neontological and paleontological information improves inferences about the tempo and mode of phenotypic evolution over long timescales. However, outside a few exemplar clades, morphological matrices establishing formal phylogenetic placements of fossils within molecular phylogenies are often lacking, limiting the inclusion of fossil data in macroevolutionary inferences. Informal fossil placements are commonly established through morphological assessment (e.g., as is often the case for node-age calibrations) but determining branch length durations is less straightforward. Using simulations, we compared four contrasting methods of a posteriori fossil insertion and assess their impacts on estimating the tempo and mode of continuous trait evolution. We find that arbitrarily assigning branch lengths to fossil taxa or analytically estimating them using continuous trait data had negligible biases on phenotypic inferences relative to true branch lengths. However, use of minimum fossil branch lengths biased model selection toward an Ornstein-Uhlenbeck process and inflated rate estimates. We find that the inclusion of fossil taxa using our preferred approaches improves support for an early burst when it is the generating model. Applying these methods to a comparative dataset of carangarian fishes (flatfishes, jacks, barracudas, and billfishes) reveals high rates of phenotypic evolution early in the clade's history, a signal forecasted by the fossil record but not shown in extant-only analyses. We conclude that a posteriori insertion of fossils, even with designated rather than inferred branch lengths, can strengthen phenotypic inferences relative to analyses including only living taxa.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148988849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary associations of bill morphology, migration, and feeding ecology in Tyrant flycatchers (Tyrannidae).","authors":"M Emilia Rebollo, Bryam Mateus-Aguilar, Alex E Jahn, Diego T Tuero, Carlos D Cadena, Valentina Gómez-Bahamón","doi":"10.1093/evolut/qpag163","DOIUrl":"https://doi.org/10.1093/evolut/qpag163","url":null,"abstract":"<p><p>Migratory birds experience changes throughout their annual cycle in food availability and diet, which may influence the evolution of feeding morphology. We investigated the evolution of bill morphology in relation to migratory phenotype, diet, and foraging behavior across 386 species of Tyrant flycatchers (Tyrannidae), and among migratory and non-migratory populations of the Fork-tailed Flycatcher (Tyrannus savana). At the interspecific level, bill morphospace extensively overlapped between migrants and non-migrants, with small differences in bill shape but not size. Migrants had deeper and narrower bills at inter- and intraspecific levels. However, this shape difference was not more pronounced between sister species differing in migratory phenotype, suggesting that the changes in migratory phenotypes during speciation were not associated with bill divergence. At the intraspecific level, migratory Fork-tailed Flycatchers also had smaller bills varying according to age but not sex. Across Tyrannidae, species with an invertivore-herbivore diet that do not forage on the ground and understory exhibited wider and shorter bills. Overall, our results suggest a weak but significant association between bill morphology and migratory phenotypes, with additional variation in diet, foraging strata, and age. However, bill morphology appears largely independent of migratory behavior, underscoring a decoupling of migration from foraging‑related morphological constraints.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148976082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Repeated evolution of high elevation occupation in tropical lizards.","authors":"Jhan C Salazar, Adam C Algar, Steven Poe, Jonathan B Losos, Julián A Velasco","doi":"10.1093/evolut/qpag159","DOIUrl":"https://doi.org/10.1093/evolut/qpag159","url":null,"abstract":"<p><p>Since Darwin and Humboldt, researchers have tried to understand how species adapt to different elevations. Tropical reptiles are typically diverse in warm, lowland environments, yet many reptile lineages have colonized high elevation environments on both islands and the mainland. Nonetheless, the frequency with which these environments have been colonized remains unclear. The occurrence of high elevation species on multiple mountain ranges could reflect a single lowland-to-highland transition followed by subsequent divergence into multiple species or, alternatively, could result from more than one colonization event with limited within-lineage diversification. Here, we test these alternatives for anole lizards which, though predominantly found in tropical lowlands, also occupy multiple mountain ranges in Central and South America and the Caribbean. Analyzing extensive climatic and distributional data for 303 species and thermal physiology data (cold tolerance or CTmin) for 64 species, we found that colonization of high-elevation regions has occurred many times in anoles, that the frequency of such occupation is lower than the opposite, and that biogeographic dispersal across mountains and shifts in climatic niche are distributed non-randomly across the phylogeny. Additionally, transitions between lowland and highland habitats do not coincide with shifts in the rate of stochastic trait evolution for either cold tolerance or minimum thermal niche. Instead, highland lineages show stronger selection toward a colder optimum for minimum ambient temperature, consistent with climatic niche conservatism in montane environments. Cold tolerance itself shows no such shift, suggesting a decoupling between the climatic environment lineages experience and the evolution of a physiological trait that should, in principle, track it. Together, these results show that repeated mountain colonization has reshaped climatic niche evolution in Anolis, while physiological cold tolerance has followed a comparatively stable, elevation-independent trajectory.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148944633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic signatures of carotenoid-based color polytypism in Oophaga granulifera (Anura: Dendrobatidae).","authors":"Ariel Rodríguez, Victor Vasquez, Vasiliki Mantzana Oikonomaki, Evan Twomey, Abel Mora-Machado, Daniel Freire Espin, Nicholas I Mundy, Giselle Tamayo-Castillo, Heike Pröhl","doi":"10.1093/evolut/qpag160","DOIUrl":"https://doi.org/10.1093/evolut/qpag160","url":null,"abstract":"<p><p>Aposematic phenotypes advertise their unprofitability to predators by means of colorful warning signals. The Neotropical family Dendrobatidae comprises some of the prime examples of aposematism in amphibians but with pronounced intraspecific variation in some species, particularly in the genus Oophaga. We herein compare the skin spectral reflectance, pigment composition and gene expression of individuals with aposematic (red) and cryptic (green) phenotypes of Oophaga granulifera from Costa Rica. Our findings reveal that accumulation of keto-carotenoids, xanthophylls, and β-carotene in the skin are responsible for the red aposematic phenotype in this species. Several differentially expressed pigmentation genes, particularly some in the carotenoid metabolism pathway, are strongly associated with the distinction between red and green skin phenotypes. Green frogs also show pronounced up-regulation of the bco1 gene which has been associated to ketocarotenoid-based polymorphisms in other species and represents a strong candidate for additional enzymatic studies. We found no clear candidate ketolase gene but the ketolation enhancer ttc39b was upregulated in the liver of red O. granulifera, aligning with previous studies that underscore the importance of this ancillary gene for keto-carotenoid metabolism. Gene ontology enrichments indicate that, along with the carotenoid metabolism genes, red frogs upregulate the metabolism of amino acids, lipids and the mitochondrial energy production, markedly in the liver but also in the skin. These results suggest a close association between increased keto-carotenoid accumulation and a higher metabolic rate in the red frogs which is congruent with macroevolutionary patterns in the family and behavioral observations in this species.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148944630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic separation of Salish Sea and Pacific outer coast populations of the keystone sea star Pisaster ochraceus.","authors":"Paige J Duffin, Lauren M Schiebelhut, Michael N Dawson, John P Wares","doi":"10.1093/evolut/qpag146","DOIUrl":"https://doi.org/10.1093/evolut/qpag146","url":null,"abstract":"<p><p>Environmental boundaries shape genetic diversity through the interacting effects of geographic distance, local adaptation, and constraints on gene flow. The ochre sea star (Pisaster ochraceus), an intertidal keystone predator, has long been considered to have limited spatial genetic structure along the North American Pacific coast, likely due to its extended larval dispersal period and high potential for gene flow. Here, we characterize spatial genomic variation in Pisaster ochraceus using whole-genome sequencing data from individuals spanning nearly 3000 kilometers of coastline from Alaska to southern California. Analyses of putatively neutral SNPs demonstrate considerable mixing across the latitudinal range, but also reveal substantial structure between outer Pacific coast populations and those within the semi-enclosed Salish Sea, suggesting restricted gene flow and demographic divergence between these regions. Genomic divergence is further supported by evidence of selection, with outlier loci highlighting extended regions of low diversity in the Salish Sea, consistent with recent selective sweeps and potential local adaptation to distinct estuarine conditions. These findings support the role of oceanographic barriers and environmental heterogeneity in shaping population structure in Pisaster ochraceus, challenging earlier expectations of range-wide homogeneity and providing insight into the persistence of this keystone marine species in a rapidly changing world.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence of genome-wide relaxed selection on mildly deleterious mutations in an ancient subterranean catfish.","authors":"Maxime Policarpo, Julien Fumey, Marine Milhes, Céline Bonillo, Alejandra Campos, Max Hidalgo, Sylvie Rétaux, Marc Pouilly, Didier Casane","doi":"10.1093/evolut/qpag158","DOIUrl":"https://doi.org/10.1093/evolut/qpag158","url":null,"abstract":"<p><p>About one hundred subterranean catfish species have been described, resulting from repeated colonization of cave environments by multiple surface lineages. Most cave-dwelling species are found in the Americas, in particular in South America, but a few species also live in Central and North America. Despite the availability of high-quality genome assemblies for two cave species, the Mexican blind catfish Prietella phreatophila and the Colombian blind catfish Trichomycterus rosablanca, genomic approaches to investigate genetic changes associated with subterranean life or to estimate cave colonization times remain largely unexplored. To fill this gap, we additionally sequenced the genomes of four blind and depigmented subterranean catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Two independent molecular dating methods gave congruent ages, indicating that these catfishes colonized subterranean habitats at different times, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes repeatedly and rapidly adapted to subterranean habitats. The oldest cave species, P. phreatophila, appears to have been thriving in the dark for over 3.5 million years. Moreover, a genome-wide analysis of protein-coding genes suggests weaker purifying selection on mildly deleterious mutations in this cavefish than in other catfish lineages, likely reflecting a long-term small effective population size.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148911264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}