Systematic Biology最新文献_第2页

On the Mkv Model with Among-Character Rate Variation 特征间速率变化的Mkv模型

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-16 DOI: 10.1093/sysbio/syaf038

Alessio Capobianco, Sebastian Höhna

{"title":"On the Mkv Model with Among-Character Rate Variation","authors":"Alessio Capobianco, Sebastian Höhna","doi":"10.1093/sysbio/syaf038","DOIUrl":"https://doi.org/10.1093/sysbio/syaf038","url":null,"abstract":"Models used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model—which introduces an acquisition bias correction for sampling only characters that are observed to be variable—and for models of among-character rate variation (ACRV), routinely applied by researchers to relax the equal-rates assumption of Mkv. However, the interaction between variable character acquisition bias and ACRV has never been explored before. We demonstrate that there are two distinct approaches to condition the likelihood on variable characters when there is ACRV, and we call them joint and marginal acquisition bias. Far from being just a trivial mathematical detail, we show that the way in which the variable character conditional likelihood is calculated results in different assumptions about how rate variation is distributed in morphological datasets. Simulations demonstrate that tree length and amount of ACRV in the data are systematically biased when conditioning on variable characters differently from how the data was simulated. Moreover, an empirical case study with extant and extinct taxa reveals a potential impact not only on the estimation of branch lengths, but also of phylogenetic relationships. We recommend the use of the marginal acquisition bias approach for morphological datasets modeled with ACRV. Finally, we urge developers of phylogenetic software to clarify which acquisition bias correction is implemented for both estimation and simulation, and we discuss the implications of our findings on modeling variable characters for the future of morphological phylogenetics.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"33 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144066939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Batesian Mimicry Converges Towards Inaccuracy in Myrmecomorphic Spiders 蜘蛛的贝叶斯拟态趋近于不准确

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-16 DOI: 10.1093/sysbio/syaf037

Michael B J Kelly, Shahan Derkarabetian, Donald James McLean, Ryan Shofner, Cristian J Grismado, Charles R Haddad, Gerasimos Cassis, Gonzalo Giribet, Marie E Herberstein, Jonas O Wolff

{"title":"Batesian Mimicry Converges Towards Inaccuracy in Myrmecomorphic Spiders","authors":"Michael B J Kelly, Shahan Derkarabetian, Donald James McLean, Ryan Shofner, Cristian J Grismado, Charles R Haddad, Gerasimos Cassis, Gonzalo Giribet, Marie E Herberstein, Jonas O Wolff","doi":"10.1093/sysbio/syaf037","DOIUrl":"https://doi.org/10.1093/sysbio/syaf037","url":null,"abstract":"Batesian mimicry is an impressive example of convergent evolution driven by predation. However, the observation that many mimics only superficially resemble their models despite strong selective pressures is an apparent paradox. Here, we tested the ‘perfecting hypothesis’, that posits that inaccurate mimicry may represent a transitional stage at the macro-evolutionary scale by performing the hereto largest phylogenetic analysis (in terms of the number of taxa and genetic data) of ant-mimicking spiders across two speciose but independent clades, the jumping spider tribe Myrmarachnini (Salticidae) and the sac spider sub-family Castianeirinae (Corinnidae). We found that accurate ant mimicry evolved in a gradual process in both clades, by an integration of compound traits contributing to the ant-like habitus with each trait evolving at different speeds. Accurate states were highly unstable at the macro-evolutionary scale likely because strong expression of some of these traits comes with high fitness costs. Instead, the inferred global optimum of mimicry expression was at an inaccurate state. This result reverses the onus of explanation from inaccurate mimicry to explaining the exceptional evolution and maintenance of accurate mimicry and highlights that the evolution of Batesian mimicry is ruled by multiple conflicting selective pressures.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"18 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144097490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

phyddle: software for exploring phylogenetic models with deep learning Phyddle：用深度学习探索系统发育模型的软件

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-14 DOI: 10.1093/sysbio/syaf036

Michael J Landis, Ammon Thompson

{"title":"phyddle: software for exploring phylogenetic models with deep learning","authors":"Michael J Landis, Ammon Thompson","doi":"10.1093/sysbio/syaf036","DOIUrl":"https://doi.org/10.1093/sysbio/syaf036","url":null,"abstract":"Phylogenies contain a wealth of information about the evolutionary history and process that gave rise to the diversity of life. This information can be extracted by fitting phylogenetic models to trees. However, many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, pipeline-based software for performing phylogenetic modeling tasks on trees using likelihood-free deep learning approaches. phyddle has a flexible command-line interface, making it easy to integrate deep learning approaches for phylogenetics into research workflows. phyddle coordinates modeling tasks through five pipeline analysis steps (Simulate, Format, Train, Estimate, and Plot) that transform raw phylogenetic datasets as input into numerical and visual model-based output. We conduct three experiments to compare the accuracy of likelihood-based inferences against deep learning-based inferences obtained through phyddle. Benchmarks show that phyddle accurately performs the inference tasks for which it was designed, such as estimating macroevolutionary parameters, selecting among continuous trait evolution models, and passing coverage tests for epidemiological models, even for models that lack tractable likelihoods. Learn more about phyddle at https://phyddle.org.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"13 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unravelling the Effects of Ecology and Evolutionary History in the Phenotypic Convergence of Fishes. 揭示生态学和进化历史对鱼类表型趋同的影响。

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-13 DOI: 10.1093/sysbio/syaf034

Jennifer R Hodge,Danielle S Adams,Keiffer L Williams,Laura R V Alencar,Benjamin Camper,Olivier Larouche,Mason A Thurman,Katerina Zapfe,Samantha A Price

{"title":"Unravelling the Effects of Ecology and Evolutionary History in the Phenotypic Convergence of Fishes.","authors":"Jennifer R Hodge,Danielle S Adams,Keiffer L Williams,Laura R V Alencar,Benjamin Camper,Olivier Larouche,Mason A Thurman,Katerina Zapfe,Samantha A Price","doi":"10.1093/sysbio/syaf034","DOIUrl":"https://doi.org/10.1093/sysbio/syaf034","url":null,"abstract":"Understanding the ecological drivers and limitations of adaptive convergence is a fundamental challenge. Here, we explore how adaptive convergence of planktivorous fishes has been influenced by multiple ecological factors, evolutionary history, and chance. Using ecomorphological data for over 1600 marine species, we integrate pattern-based metrics of convergence with evolutionary model fitting to test whether phenotypic similarities among specialist planktivores exceed expectations under null models and whether ecology, evolutionary history, or their combined effects best explain trait evolution. We find that planktivores are significantly more similar in phenotype than expected. Traits with functional relevance for prey detection and capture, such as eye diameter and lower jaw length, are strongly convergent, while general body size and shape are constrained by deep divisions between clades where the effects of evolutionary history are most pronounced. Since not all traits undergo strong selection toward a convergent ecomorph, their evolutionary trajectories have not entirely overcome ancestral differences in the multivariate trait space, resulting in a specific form of convergence termed conservatism. We show how adaptive responses to feeding ecology intertwine with other ecological pressures (i.e., light environment) and historical contingency to shape fish phenotype evolution over deep time, offering key insights into the generality of phenotypic evolution.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"1 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River. 超保守基因的系统基因组和种群基因组分析揭示了刚果河Lamprologine慈鲷的深聚结和渐入形多样化模式。

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-13 DOI: 10.1093/sysbio/syaf032

Fernando Alda,S Elizabeth Alter,Naoko P Kurata,Prosanta Chakrabarty,Melanie L J Stiassny

{"title":"Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River.","authors":"Fernando Alda,S Elizabeth Alter,Naoko P Kurata,Prosanta Chakrabarty,Melanie L J Stiassny","doi":"10.1093/sysbio/syaf032","DOIUrl":"https://doi.org/10.1093/sysbio/syaf032","url":null,"abstract":"Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutionary history has been difficult to untangle with previous datasets, particularly with regard to river-dwelling lineages in the genus Lamprologus. This clade notably includes the only known blind and depigmented cichlid, L. lethops. Here, we reconstructed the evolutionary, population, and biogeographic history of a Lamprologus clade from the Congo River by leveraging genomic data and sampling over 50 lamprologine species from the entire Lake Tanganyika radiation. This study provides the most comprehensive species-level coverage to date of the riverine taxa within this lacustrine-origin clade. We found that in the mid-late Pliocene, two lineages of Lake Tanganyika lamprologines independently colonized the Congo River, where they subsequently hybridized and diversified, forming the current monophyletic group of riverine Lamprologus. Our estimates for divergence time and introgression align with the region's geological history and suggest rapid speciation in Lamprologus species from the Congo River marked by rapids-driven vicariance and water level fluctuations, and repeated episodes of secondary contact and reticulation. As a result of our analyses, we propose the taxonomic restriction of the genus Lamprologus to Congo River taxa only. The complex evolutionary history of this group-characterized by introgressive hybridization followed by a rapid series of isolation and reconnection-illustrates the multifaceted dynamics of speciation that have shaped the rich biodiversity of this region. [African cichlids; Congo River; diversification; hybridization; Lamprologini; phylogenomics; UCEs; ultraconserved elements].","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"44 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution 研究同源基因树冲突和解释趋同性状进化的新工具

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-08 DOI: 10.1093/sysbio/syaf028

Holly M Robertson, Joseph F Walker, Edwige Moyroud

{"title":"CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution","authors":"Holly M Robertson, Joseph F Walker, Edwige Moyroud","doi":"10.1093/sysbio/syaf028","DOIUrl":"https://doi.org/10.1093/sysbio/syaf028","url":null,"abstract":"Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analysing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"27 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade 跨越狭窄接触带的渗入形成了非洲鸟类进化进化的基因组景观

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-07 DOI: 10.1093/sysbio/syaf033

Loïs Rancilhac, Stacey G de Souza, Sifiso M Lukhele, Matteo Sebastianelli, Bridget O Ogolowa, Michaella Moysi, Christos Nikiforou, Tsyon Asfaw, Colleen T Downs, Alan Brelsford, Bridgett M vonHoldt, Alexander N G Kirschel

{"title":"Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade","authors":"Loïs Rancilhac, Stacey G de Souza, Sifiso M Lukhele, Matteo Sebastianelli, Bridget O Ogolowa, Michaella Moysi, Christos Nikiforou, Tsyon Asfaw, Colleen T Downs, Alan Brelsford, Bridgett M vonHoldt, Alexander N G Kirschel","doi":"10.1093/sysbio/syaf033","DOIUrl":"https://doi.org/10.1093/sysbio/syaf033","url":null,"abstract":"Genomic analyses of hybrid zones provide excellent opportunities to investigate the consequences of introgression in nature. In combination with phylogenomics analyses, hybrid zone studies may illuminate the role of ancient and contemporary gene flow in shaping variation of phylogenetic signals across the genome, but this avenue has not been explored yet. We combined phylogenomic and geographic cline analyses in a Pogoniulus tinkerbird clade to determine whether contemporary introgression through hybrid zones contributes to gene-tree heterogeneity across the species ranges. We found diverse phylogenetic signals across the genome with the most common topologies supporting monophyly among taxa connected by secondary contact zones. Remarkably, these systematic conflicts were also recovered when selecting only individuals from each taxon's core range. Using analyses of derived allele sharing and “recombination aware” phylogenomics, we found that introgression shapes gene-tree heterogeneity, and the species tree most likely supports monophyletic red-fronted tinkerbirds, as recovered in previous reconstructions based on mitochondrial DNA. Furthermore, by fitting geographic clines across two secondary contact zones, we found that introgression rates were lower in genomic regions supporting the putative species tree compared to those supporting the two taxa in contact as monophyletic. This demonstrates that introgression through narrow contact zones shapes gene-tree heterogeneity even in allopatric populations. Finally, we did not find evidence that mitochondria-interacting nuclear genes acted as barrier loci. Our results show that species can withstand important amounts of introgression while maintaining their phenotypic integrity and ecological separation, raising questions regarding the genomic architecture of adaptation and barriers to gene flow.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"119 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Estimating Genome-wide Phylogenies Using Probabilistic Topic Modeling 利用概率主题模型估计全基因组系统发育

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-05 DOI: 10.1093/sysbio/syaf015

Marzieh Khodaei, Scott V Edwards, Peter Beerli

{"title":"Estimating Genome-wide Phylogenies Using Probabilistic Topic Modeling","authors":"Marzieh Khodaei, Scott V Edwards, Peter Beerli","doi":"10.1093/sysbio/syaf015","DOIUrl":"https://doi.org/10.1093/sysbio/syaf015","url":null,"abstract":"Methods for rapidly inferring the evolutionary history of species or populations with, genome-wide data are progressing, but computational constraints still limit our abilities in, this area. We developed an alignment-free method to infer genome-wide phylogenies and, implemented it in the Python package TopicContml. The method uses probabilistic, topic modeling (specifically, Latent Dirichlet Allocation or LDA) to extract ‘topic’, frequencies from k-mers, which are derived from multilocus DNA sequences. These, extracted frequencies then serve as an input for the program Contml in the PHYLIP, package, which is used to generate a species tree. We evaluated the performance of, TopicContml on simulated datasets with gaps and three biological datasets: (1) 14 DNA, sequence loci from two Australian bird species distributed across nine populations, (2), 5162 loci from 80 mammal species, and (3) raw, unaligned, non-orthologous PacBio, sequences from 12 bird species. We also assessed the uncertainty of the estimated, relationships among clades using a bootstrap procedure. Our empirical results and, simulated data suggest that our method is efficient and statistically robust.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"50 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PickMe: Sample selection for species tree reconstruction using coalescent weighted quartets PickMe：使用聚结加权四重奏进行物种树重建的样本选择

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-05 DOI: 10.1093/sysbio/syaf017

Joseph Rusinko, Yu Cai, Allison Crysler, Katherine Thompson, Julien Boutte, Mark Fishbein, Shannon C K Straub

{"title":"PickMe: Sample selection for species tree reconstruction using coalescent weighted quartets","authors":"Joseph Rusinko, Yu Cai, Allison Crysler, Katherine Thompson, Julien Boutte, Mark Fishbein, Shannon C K Straub","doi":"10.1093/sysbio/syaf017","DOIUrl":"https://doi.org/10.1093/sysbio/syaf017","url":null,"abstract":"After collecting large data sets for phylogenomics studies, researchers must decide which, genes or samples to include when reconstructing a species tree. Incomplete or unreliable, data sets make the empiricist’s decision more difficult. Researchers rely on ad hoc, strategies to maximize sampling while ensuring sufficient data for accurate inferences. An, algorithm called PickMe formalizes the sample selection process, assuming that the, samples evolved under the Tree Multispecies Coalescent model. We propose a Bayesian, framework for selecting samples for species tree analysis. Given a collection of gene trees, we compute a posterior probability for each quartet, describing the likelihood that the, species tree displays this topology. From this, we assign individual samples reliability, scores computed as the average of a scaled version of the posterior probabilities. PickMe, uses these weights to recommend which samples to include in a species tree analysis., Analysis of simulated data showed that including the samples suggested by Pickme, produced species trees closer to the true species trees than both unfiltered data sets and, data sets with ad hoc gene occupancy cut-offs applied. To further illustrate the efficacy of, this tool, we apply PickMe to gene trees generated from target capture data from, milkweeds. PickMe indicates more samples could have reliably been included in a previous, milkweed phylogenomic analysis than the authors analyzed without access to a formal, methodology for sample selection. Using simulated and empirical data, we also compare, PickMe to existing sample selection methods. Inclusion of PickMe will enhance, phylogenomics data analysis pipelines by providing a formal structure for sample selection.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"29 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary Tempo, Supertaxa and Living Fossils 进化速度，超级分类群和活化石

IF 6.5 1区生物学

Systematic Biology Pub Date : 2025-05-05 DOI: 10.1093/sysbio/syaf020

Graham E Budd, Richard P Mann

{"title":"Evolutionary Tempo, Supertaxa and Living Fossils","authors":"Graham E Budd, Richard P Mann","doi":"10.1093/sysbio/syaf020","DOIUrl":"https://doi.org/10.1093/sysbio/syaf020","url":null,"abstract":"A relationship between the rate of molecular change and diversification has long been, discussed, on both theoretical and empirical grounds. However, the effect on our, understanding of evolutionary patterns is yet to be fully explored. Here we develop a new, model, the Covariant Evolutionary Tempo (CET) model, with the aim of integrating, patterns of diversification and molecular evolution within a framework of a continuously, changing ‘tempo’ variable that acts as a master control for molecular, morphological and, diversification rates. Importantly, tempo itself is treated as being variable at a rate, proportional to its own value. This model predicts that diversity is dominated by a small, number of extremely large clades at any historical epoch including the present; that these, large clades are expected to be characterised by explosive early radiations accompanied by, elevated rates of molecular evolution; and that extant organisms are likely to have evolved, from species with unusually fast evolutionary rates. Under such a model, the amount of, molecular change along a particular lineage is essentially independent of its height, which, weakens the molecular clock hypothesis. Finally, our model explains the existence of ‘living, fossil’ sister groups to large clades that are species poor and exhibit slow rates of, morphological and molecular change. Our results demonstrate that the observed historical, patterns of evolution can be modelled without invoking special evolutionary mechanisms or, innovations that are unique to specific times or taxa, even when they are highly, non-uniform","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"25 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0