Evolution最新文献

{"title":"Correlated evolution of categorical characters under a simple model.","authors":"Michael C Grundler","doi":"10.1093/evolut/qpae166","DOIUrl":"https://doi.org/10.1093/evolut/qpae166","url":null,"abstract":"<p><p>I describe a simple model for quantifying the strength of association between two categorical characters evolving on a phylogenetic tree. The model can be used to estimate a correlation statistic that asks whether or not the two characters tend to change at the same time (positive correlation) or at different times (no correlation). This is different than asking if changes in one character are associated with a particular state in another character, which has been the focus of most prior tests for phylogenetic correlation in categorical characters. Analyses of simulated data indicate that positive correlations can be accurately estimated over a range of different tree sizes and phylogenetic signals.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686482","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":"Selection on sporulation strategies in a metapopulation can lead to coexistence.","authors":"Stephen R Proulx, Taom Sakal, Zach Reitz, Kelly Thomasson","doi":"10.1093/evolut/qpae161","DOIUrl":"https://doi.org/10.1093/evolut/qpae161","url":null,"abstract":"<p><p>In constant environments the coexistence of similar species or genotypes is generally limited. In a metapopulation context, however, types that utilize the same resource but are distributed along a competition-colonization trade-off, can coexist. Much thought in this area focuses on a generic trade-off between within-deme competitive ability and between-deme dispersal ability. We point out that the sporulation program in yeasts and other microbes can create a natural trade-off such that strains which initiate sporulation at higher rates suffer in terms of within-deme competition but benefit in terms of between deme dispersal. We develop metapopulation models where the within- deme behavior follows chemostat dynamics. We first show that the rate of sporulation determines the colonization ability of the strain, with colonization ability increasing with sporulation rate up to a point. Metapopulation stability of a single strain exists in a defined range of sporulation rates. We then use pairwise invasability plots to show that coexistence of strains with different sporulation rates generally occurs, but that the set of sporulation rates that can potentially coexist is smaller than the set that allows for stable metapopulations. We extend our pairwise results to show how a continuous set of strains can coexist and verify our conclusions with numerical calculations and stochastic simulations. Our results show that stable variation in sporulation rates is expected under a wide range of ecological conditions.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686582","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":"Hill-Robertson interference may bias the inference of fitness effects of new mutations in highly selfing species.","authors":"Austin Daigle, Parul Johri","doi":"10.1093/evolut/qpae168","DOIUrl":"https://doi.org/10.1093/evolut/qpae168","url":null,"abstract":"<p><p>The accurate estimation of the distribution of fitness effects (DFE) of new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed for DFE inference using the site frequency spectrum of putatively neutral and selected sites, their applicability in species with diverse life history traits and complex demographic scenarios is not well understood. Selfing is common among eukaryotic species and can lead to decreased effective recombination rates, increasing the effects of selection at linked sites, including interference between selected alleles. We employ forward simulations to investigate the limitations of current DFE estimation approaches in the presence of selfing and other model violations, such as linkage, departures from semidominance, population structure, and uneven sampling. We find that distortions of the site frequency spectrum due to Hill-Robertson interference in highly selfing populations lead to mis-inference of the deleterious DFE of new mutations. Specifically, when inferring the distribution of selection coefficients, there is an overestimation of nearly neutral and strongly deleterious mutations and an underestimation of mildly deleterious mutations when interference between selected alleles is pervasive. In addition, the presence of cryptic population structure with low rates of migration and uneven sampling across subpopulations leads to the false inference of a deleterious DFE skewed towards effectively neutral/mildly deleterious mutations. Finally, the proportion of adaptive substitutions estimated at high rates of selfing is substantially overestimated. Our observations apply broadly to species and genomic regions with little/no recombination and where interference might be pervasive.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675335","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":"Brain-body co-evolution in incipient versus established primate species - evaluating Simpson's \"most important distinction\".","authors":"Folmer Bokma, Masahito Tsuboi, Nils Chr Stenseth","doi":"10.1093/evolut/qpae167","DOIUrl":"10.1093/evolut/qpae167","url":null,"abstract":"<p><p>Are differences between species the long-term consequence of microevolution within species, or does speciation involve fundamentally different processes? We analyzed brain and body sizes of present-day primate species using a novel phylogenetic comparative method that decomposes the phenotypic covariance of these traits into speciational and anagenetic components. We estimated that approximately half of speciation events are accompanied by accelerated phenotypic change. Equivalent in magnitude to approximately 7 million years of gradual microevolution, such speciational changes in brain and body size account for about 58% of the phenotypic variation among extant species. Interestingly, speciational changes in brain and body size appear significantly less correlated (r≈0.83) than gradual, microevolutionary changes in these same traits (r≈0.97). This indicates that the strong allometric constraint that dictates microevolution in brain and body sizes is relaxed at speciation events. These results suggest that phenotypic evolution is not only accelerated during speciation, but also involves events that seldomly occur at microevolutionary timescales.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667129","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":"Weak integration allows novel fin shapes and spurs locomotor diversity in reef fishes.","authors":"Darien R Satterfield, Bernice Yin, Sky Jung, Samantha Hodges-Lisk, Dylan K Wainwright, Michael D Burns, Peter C Wainwright","doi":"10.1093/evolut/qpae165","DOIUrl":"10.1093/evolut/qpae165","url":null,"abstract":"<p><p>In complex functional systems composed of many traits, selection for specialized function can induce trait evolution by acting directly on individual components within the system, or indirectly through networks of trait integration. However, strong integration can also hinder diversification into regions of trait space that are not aligned with axes of covariation among traits. As a result, non-independence among traits may limit capacity for functional expansion. We explore this dynamic in the evolution of fin shapes in 106 species from 38 families of coral reef fishes, a polyphyletic assemblage that shows exceptional diversity in locomotor function. Despite strong shared developmental pathways and expectations of a strong match between form and function, we find that species that share swimming mode show substantial disparity in fin shape, and preferred swimming mode is a poor predictor of fin shape. The evolution of fin shape is weakly integrated across the four functionally dominant fins in swimming (the pectoral, caudal, dorsal, and anal fins) and integration is weakened as derived swimming modes evolve. The weak integration among fins in the ancestral locomotor condition provides a primary axis of diversification while allowing for substantial off-axis diversification via independent trait responses to selection. However, the evolution of novel locomotor modes coincides with a loss of integrated axes of covariation among fins. Our study highlights the need for additional work on the functional consequences of fin shape in fishes and impact of evolutionary integration on functions other than locomotion.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667148","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":"Juvenile and total reproductive values for sexual reproduction under any genetic system.","authors":"Petri Rautiala, Jussi Lehtonen","doi":"10.1093/evolut/qpae163","DOIUrl":"https://doi.org/10.1093/evolut/qpae163","url":null,"abstract":"<p><p>Reproductive value (RV) is the expected contribution of genes by an individual or class of individuals to the gene pool in the distant future, and it plays a crucial role in understanding adaptation in long-term evolution. Class RVs are linked to the genetic system and to life history: for diploid genetics, Grafen derived expressions for relative RVs of female and male juveniles, and for the absolute RVs of all females and of all males. Subsequently, Gardner presented a derivation for relative RVs of juvenile females and males under haplodiploidy. Here we generalise these results to any genetic system for biparental sexual reproduction, such that RV is explicitly linked to parameters of the genetic system and life history. The earlier results by Grafen and Gardner arise as special cases. Finally, we derive expressions for absolute juvenile and total reproductive values of both sexes under any genetic system.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646632","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":"Correction to: Making sense of recent models of the \"sheltering\" hypothesis for recombination arrest between sex chromosomes.","authors":"","doi":"10.1093/evolut/qpae153","DOIUrl":"https://doi.org/10.1093/evolut/qpae153","url":null,"abstract":"","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644245","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":"Whole-genome sequencing confirms multiple species of Galapagos giant tortoises.","authors":"Stephen J Gaughran, Rachel Gray, Alexander Ochoa, Menna Jones, Nicole Fusco, Joshua M Miller, Nikos Poulakakis, Kevin de Queiroz, Adalgisa Caccone, Evelyn L Jensen","doi":"10.1093/evolut/qpae164","DOIUrl":"https://doi.org/10.1093/evolut/qpae164","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with most analyses supporting 13 species. There is mixed support for the species status of taxa living on the same island, with some methods delimiting them as separate species and others suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. Our study provides insight into the complex process of speciation on islands, which is urgently needed given the threatened status of island species around the world. Las tortugas gigantes de las Galápagos son endémicas del Archipiélago de Galápagos, donde se encuentran como poblaciones aisladas. Aunque estas poblaciones se consideran distinguibles en cuanto a morfología, comportamiento y genética, la divergencia reciente de estos taxones hace que su estatus como especies sea controvertido. Aquí aplicamos métodos de coalescencia de especies múltiples con datos de resecuenciación de genomas completos de 38 tortugas de los 13 taxones existentes para evaluar el sustento de la delimitación de estos taxones como especies. En contraste con estudios previos basados únicamente en el tiempo de divergencia, encontramos evidencia sólida para rechazar la hipótesis de que todas las tortugas gigantes de las Galápagos pertenecen a una sola especie. En cambio, una interpretación conservadora de los resultados basados en modelos y divergencia indica que estos taxones forman un complejo de especies que consiste de un mínimo de 9 especies, con la mayoría de los análisis respaldando la existencia de 13 especies. Hay sustento mixto para designar como especies a los taxones que habitan la misma isla, con algunos métodos delimitándolos como especies y otros sugiriendo la existencia de poblaciones múltiples de una sola especie por isla. Estos resultados dejan en claro que los taxones de tortugas gigantes de las Galápagos representan diferentes etapas del proceso de especiación, con algunos taxones más avanzados en ese proceso evolutivo que otros. Nuestro estudio ofrece una perspectiva sobre el com","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644249","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":"Convergent evolution in shape in European lineages of gobies.","authors":"Jasna Vukić, Kristina Beatrix Bílá, Tereza Soukupová, Marcelo Kovačić, Radek Šanda, Lukáš Kratochvíl","doi":"10.1093/evolut/qpae162","DOIUrl":"https://doi.org/10.1093/evolut/qpae162","url":null,"abstract":"<p><p>During their radiation, certain groups of animals evolved significant phenotypic disparity (morphological diversity), enabling them to thrive in diverse environments. Adaptations to the same type of environment can lead to convergent evolution in function and morphology. However, well-documented examples in repeated adaptations of teleost fishes to different habitats, which are not primarily related to trophic specialization, are still scarce. Gobies are a remarkable fish group, exhibiting a great species diversity, morphological variability, and extraordinary ability to colonize very different environments. A variety of lifestyles and body forms evolved also in European lineages of gobies. We conducted two-dimensional geometric morphometric and phylomorphospace analyses in European lineages of gobies and evaluated the extent of convergent evolution in shape associated with adaptation to various habitats. Our analyses revealed the change in shape along the nektonic-cryptobenthic axis, from very slender head and body to stout body and wide head. We showed convergent evolution related to mode of locomotion in the given habitat in four ecological groups: nektonic, hyperbenthic, cryptobenthic and freshwater gobies. Gobies, therefore, emerge as a highly diversified lineage with unique lifestyle variations, offering invaluable insights into filling of ecomorphological space and mechanisms of adaptation to various aquatic environments with distinct locomotion requirements.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616641","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":"Asymmetrical hybridization and environmental factors influence the spatial genetic structure of a killifish hybrid zone.","authors":"Andrew L Hardy, Michelle R Gaither, Katie E Lotterhos, Samuel Greaves, Kyra Jean Cipolla, Emily V Kerns, Andres Prieto Trujillo, Matthew R Gilg","doi":"10.1093/evolut/qpae160","DOIUrl":"https://doi.org/10.1093/evolut/qpae160","url":null,"abstract":"<p><p>Hybridization offers insight into speciation and the forces that maintain barriers to reproduction, and hybrid zones provide excellent opportunities to test how environment shapes barriers to reproduction and hybrid fitness. A hybrid zone between the killifish, Fundulus heteroclitus and F. grandis, had been identified in northeastern Florida, although the spatial structure and parameters that affect the distribution of the two species remain unknown. The present study aimed to determine the fine-scale spatial genetic patterns of the hybrid zone to test the hypothesis that species ranges are influenced by changes in dominant vegetation, and to determine how differences in reproductive barriers between the two species influence the observed patterns. The area of overlap between the two species spanned ~37 km and showed a mosaic pattern of hybridization, suggesting the spatial structure of the hybrid zone is largely influenced by the environment. Environmental association analysis, however, suggested that while dominant vegetation had a significant influence on the spatial structure of the hybrid zone, a combination of environmental factors was driving the observed patterns. Hybridization tended to be rare at sites where F. heteroclitus was the more abundant species, suggesting that differences in preference for conspecifics can lead to differences in rates of introgression into parental taxa and likely result in a range-shift as opposed to adaptation in the face of climate change.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603782","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}