Cladistics最新文献

{"title":"Accuracy of phylogenetic reconstructions from continuous characters analysed under parsimony and its parametric correlates.","authors":"Victor A Tagliacollo, Mario de Pinna, Junior Chuctaya, Alessio Datovo","doi":"10.1111/cla.12606","DOIUrl":"https://doi.org/10.1111/cla.12606","url":null,"abstract":"<p><p>Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyse this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, our ability to accurately infer relationships from continuous characters is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analysed by parsimony. We sampled 100 empirical trees to simulate 9000 matrices, each containing between 25 and 50 taxa, and 50 and 150 continuous characters evolving under three evolutionary processes: Brownian motion, Ornstein-Uhlenbeck and early burst with variable parametrizations. Our cladogram comparisons revealed that continuous character matrices, when properly coded and analysed by parsimony in TNT, carry phylogenetic signals from which species relationships can be inferred, regardless of the evolutionary models and parameterization schemes. Interestingly, implementing equal weighting or implied weighting with varying penalization strengths against homoplasies did not affect cladogram reconstructions based on continuous characters. Finally, the accuracy of continuous characters in resolving species relationships is skewed towards apical nodes of the recovered trees. Our findings provide general insights of the utility of quantitative traits in cladistics and demonstrate that their effectiveness in estimating shallower nodes is independent of the underlying evolutionary model, parameters and weighting schemes.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cladistic estimates of evolutionary rates focused on palaeontological datasets using TNT","authors":"Diego Pol,&nbsp;Martín D. Ezcurra","doi":"10.1111/cla.12608","DOIUrl":"10.1111/cla.12608","url":null,"abstract":"<p>We describe a protocol for estimating evolutionary rates from phylogenetic trees based on parsimony character optimization. The rate estimation is conducted through a TNT script and the results are analysed in a script for the software environment R. The TNT script allows analysing multiple optimal topologies, considering optimization ambiguity, and alternative time-calibrations or pre-calibrated trees. The R script summarizes estimated rates on a consensus tree and plots the variation of evolutionary rates through time, jointly with the phylogenetic diversity and a new metric (clade completeness index) that measures the distribution of missing data along the tree. We present results for simulated and empirical analyses, and evaluate the impact of missing data and alternative calibration methods in rate estimates. We found that while missing data can lower the nominal values of evolutionary rates, the overall pattern of rate variation through time remained robust. Empirical cases highlight different scenarios, such as datasets in which peaks of evolutionary rates can be coupled or decoupled from diversification dynamics (phylogenetic diversity) and cases in which missing data may influence the variation of estimated evolutionary rates. We conclude with recommendations for using this protocol and interpreting the results of parsimony-based rate estimates.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 1","pages":"28-54"},"PeriodicalIF":3.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Osteology of the appendicular skeleton of Bagualia alba (Dinosauria, Eusauropoda) from the Lower Jurassic of Patagonia and the macroevolutionary history of early eusauropods","authors":"Kevin L. Gomez,&nbsp;Diego Pol,&nbsp;Martín D. Ezcurra,&nbsp;José L. Carballido","doi":"10.1111/cla.12607","DOIUrl":"10.1111/cla.12607","url":null,"abstract":"<p>Since their origin, sauropodomorphs have undergone numerous anatomical changes from small and bipedal early sauropodomorphs towards massive-bodied and quadrupedal sauropods. However, the timing of these changes in the evolution of the group is unclear. Here, we describe the appendicular skeleton of the early diverging eusauropod <i>Bagualia alba</i> from the late Early Jurassic of Patagonia, Argentina, and conduct a morphological disparity analysis based on a phylogenetic dataset of Sauropoda. The results reveal a change in morphospace occupation between the pre-Toarcian and Toarcian–Middle Jurassic sauropodomorphs and between the latter and Late Jurassic forms. The first shift corresponds with the extinction of non-sauropodan sauropodomorphs and the diversification of sauropods, while the second corresponds with the diversification of Neosauropoda and closely related eusauropods (mamenchisaurids, turiasaurians) in the Late Jurassic, leading to a substantial shift and increase in morphological disparity. Finally, we found that body mass is significantly correlated with the first principal coordinate axis of the morphospace in two-thirds of a random sample of optimal trees, which suggests that body size played a role in shaping the evolution of sauropod morphology. In this context, <i>Bagualia</i> provides insights into the evolution of Sauropoda, particularly regarding changes that occurred during the Early to Middle Jurassic.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 1","pages":"70-103"},"PeriodicalIF":3.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting the phylogeny of royal ferns (Osmundales) through the lens of character dependence and restudied fossil taxa questions existing family and subfamily concepts","authors":"María José Urrea,&nbsp;Agustina Yañez,&nbsp;Jorge R. Flores","doi":"10.1111/cla.12602","DOIUrl":"10.1111/cla.12602","url":null,"abstract":"<p>The royal ferns (Osmundales) are a morphologically diverse group of leptosporangiate ferns, the fossil record of which dates back to the Permian. Despite there being numerous described permineralized species, the phylogenetic relationships between extinct species remain contentious. Although several analytical approaches have been applied to infer well-resolved phylogenetic hypotheses—even methods that are arguably conceived to be better at dealing with data conflict and uncertainty, many taxa have not been assigned to specific taxonomic categories. Here, we evaluate the phylogenetic affinities in Osmundales by reanalysing a dataset comprising an extensive taxon sampling of fossil Osmundalean rhizomes. The impact of both character dependence and weighting characters against homoplasy on the inferred topologies is also evaluated. Our analyses cast doubts on the monophyly of Osmundaceae and Guaireaceae. Subfamily Itopsidemoideae was rendered monophyletic when inferences were conducted by considering character dependence and downweighting characters. The subfamily Osmundoideae was retrieved monophyletic only under one concavity value and using character dependence while the remaining subfamilies included fossils with uncertain affinities within Osmundales. The position of <i>Osmundacaulis</i>, for instance, was recovered as a sister taxon to guaireoid fossils. To recover the monophyly of the categories below the subfamily level, incorporating character dependence and/or weighting against homoplasy was necessary. Consistent with previous studies, multiple taxa were unstable, leaving their phylogenetic affinities unclear. Our analyses underline the impact of accounting for both character dependence and weighting against homoplasy, especially when considering the contribution of missing data to observed homoplasy. Ultimately, these considerations yield markedly different topologies that imply contrasting classification schemes, highlighting the complexity inherent in resolving the evolutionary history of royal ferns.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 1","pages":"55-69"},"PeriodicalIF":3.9,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[genus]_[species]; Presenting phylogenies to facilitate synthesis.","authors":"Douglas Chesters, Silas Bossert, Michael C Orr","doi":"10.1111/cla.12601","DOIUrl":"https://doi.org/10.1111/cla.12601","url":null,"abstract":"<p><p>Each published phylogeny is a potential contribution to the synthesis of the Tree of Life and countless downstream projects. Steps are needed for fully synthesizable science, but only a minority of studies achieve these. We here review the range of phylogenetic presentation and note aspects that hinder further analysis. We provide simple suggestions on publication that would greatly enhance utilizability, and propose a formal grammar for phylogeny terminal format. We suggest that each published phylogeny should be accompanied by at minimum the single preferred result in machine readable tree (e.g. Newick) form in the supplement, a simple task fulfilled by fewer than half of studies. Further, the tree should be clear from the file name and extension; the orientation (rooted or unrooted) should match the figures; terminals labels should include genus and species IDs; underscores should separate strings within-field (instead of white spaces); and if other informational fields are added these should be separated by a unique delimiting character (we suggest multiple underscores or the vertical pipe character, |) and ordered consistently. These requirements are largely independent of phylogenetic study aims, while we note other requirements for synthesis (e.g. removal of species repeats and uninformative terminals) that are not necessarily the responsibility of authors. Machine readable trees show greater variation in terminal formatting than typical phylogeny images (owing presumably to greater scrutiny of the latter), and thus are complex and laborious to parse. Since the majority of existing studies have provided only images, we additionally review typical variation in plotting style, information that will be necessary for developing the automated phylogeny transcription tools needed for their eventual inclusion in the Tree of Life.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Body size and evolutionary rate analyses reveal complex evolutionary history of Alvarezsauria","authors":"Jorge Gustavo Meso,&nbsp;Diego Pol,&nbsp;Luis Chiappe,&nbsp;Zichuan Qin,&nbsp;Ignacio Díaz-Martínez,&nbsp;Federico Gianechini,&nbsp;Sebastián Apesteguía,&nbsp;Peter J. Makovicky,&nbsp;Michael Pittman","doi":"10.1111/cla.12600","DOIUrl":"10.1111/cla.12600","url":null,"abstract":"<p>Some of the smallest examples of dinosaurian body size are from alvarezsaurians, an enigmatic group of maniraptoran coelurosaurians with a peculiar combination of anatomical features unique among theropods. Despite the large number of alvarezsaurian species described worldwide and the increased understanding this has provided, the body-size macroevolution of alvarezsaurians has received little attention. Here we reconstruct and analyse directional trends of alvarezsaurian body-size evolution through an integrated analysis of body mass, ontogenetic age, and morphological rate data enabled by a comprehensively revised phylogeny. Our analyses identify four periods of high morphological rate evolution (Bathonian–Callovian, Hauterivian–early Berriasian, early Cenomanian, and late Cenomanian–Turonian) that we link to the key effects of animal body-size changes for the first time, including morphological novelty, structural reduction and simplification, elevated homoplasy, and behavioral changes associated with miniaturization. In doing so, this study provides a holistic example of miniaturization in a Mesozoic vertebrate group that offers a framework for other detailed studies of animal body-size evolution, including in more disparate groups.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 1","pages":"135-155"},"PeriodicalIF":3.9,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12600","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incomplete barriers to heterospecific mating among Somatochlora species (Odonata: Corduliidae) as revealed in multi-gene phylogenies","authors":"Jordy Hernandez,&nbsp;Anthony I. Cognato","doi":"10.1111/cla.12599","DOIUrl":"10.1111/cla.12599","url":null,"abstract":"<p>Mating between species occurs within many insect orders. The result of heterospecific mating depends upon the effectiveness of pre- and post-reproductive barriers. Incomplete reproductive barriers lead to introgression of DNA into one species or both. Intricate genital morphology among dragonflies provides little assurance of species specificity given that heterospecific mating or mating attempts have been observed among many species. The genetic consequence is unknown for many heterospecific matings. For example, <i>Somatochlora</i> species mating and genetic exchange have been hypothesized based on observational records and individuals with hybrid morphology. We investigate the potential of heterospecific mating between North American <i>Somatochlora</i> species as inferred from multi-gene phylogenies. We used mitochondrial genes (<i>COI</i> and <i>ND3</i>) and nuclear genes (<i>EF1-α</i> and <i>ITS2</i>) to construct phylogenies using maximum parsimony. Observation of non-monophyletic mtDNA lineages but monophyletic nDNA lineages between <i>Somatochlora</i> sister-species would indicate mtDNA introgression and suggest heterospecific matings. Our results highlighted three instances of non-monophyly of mtDNA clades in the following groups: (i) <i>S. hineana</i> + <i>S. tenebrosa</i>; (ii) <i>S. kennedyi</i> + <i>S. forcipata</i> + <i>S. franklini</i>; and (iii) <i>S. calverti</i> + <i>S. provocan</i>s + <i>S. filosa</i>. Analysis of partitioned Bremer support indicates that mtDNA <i>COI</i> largely contributed to the non-monophyly of these species, thus suggesting mtDNA introgression resulting from heterospecific matings. Additionally, the topology resulting from the combined data analysis was concordant with previous taxonomic understanding of <i>Somatochlora</i> species groups. These multi-gene phylogenies of North American <i>Somatochlora</i> are the first, providing a foundation for future ecological and evolution studies and knowledge for effective decision-making and public policy, which is especially important for the endangered species, <i>S. hineana</i>.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 6","pages":"598-617"},"PeriodicalIF":3.9,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rethinking spatial history: envisioning a mechanistic historical biogeography","authors":"Eduardo D. Schultz,&nbsp;Joel Cracraft","doi":"10.1111/cla.12598","DOIUrl":"10.1111/cla.12598","url":null,"abstract":"<p>Historical biogeography is the study of geographic distributions of taxa through space and time. Over the last 50 years, several methods have been proposed to reconstruct these histories. However, despite their particularities, conceptually they have been most often derived from the reconstruction of area relationships. Here we advocate that area cladograms lack explanatory power and that biogeography needs to move towards a more mechanistic approach. We discuss the ontological problems related to areas of endemism and their validity as biogeographic units. Specifically, we propose that areas of endemism are not discrete historical entities and that area-based analyses are inappropriate for analytical biogeography. Instead, we suggest that biogeographic analyses should focus on those spatial–geographic elements that cause diversification, namely barriers. We discuss how barriers have more discrete boundaries in space and time than do areas of endemism, which allows the identification of homologous units and the recovery of vicariant events. Reconstructing the history of vicariant events results in a better understanding of spatial evolution within a biota because barrier formation is the relevant causal mechanism of diversification. We end by acknowledging the largely ignored views of Peter Hovenkamp and his conceptual contributions to developing a mechanistic biogeography.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 6","pages":"653-662"},"PeriodicalIF":3.9,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini)","authors":"Kun Yu,&nbsp;Feng Zhang,&nbsp;Yaozhuo Wang,&nbsp;Wayne P. Maddison,&nbsp;Junxia Zhang","doi":"10.1111/cla.12597","DOIUrl":"10.1111/cla.12597","url":null,"abstract":"<p>The <i>Laufeia</i> clade is a peculiar lineage of euophryine jumping spiders showing rapid divergence of male genital structures, especially the embolic complex that directly interacts with female genitalia during sperm transfer. With the rapid growth of species discovery and the perplexing morphology of male genitalia in the <i>Laufeia</i> clade, the controversy in its classification has become a crucial problem. In this study, we applied a phylogenomic approach using ultra-conserved elements data to infer the phylogeny of the <i>Laufeia</i> clade with extensive taxon sampling. A comparative morphological study was performed to evaluate diagnostic characters and understand the evolution of the male embolic complex within the <i>Laufeia</i> clade. The evolution of microhabitats (foliage, tree trunk, rock and surface litter) was also investigated to uncover the potential link between the microhabitat shifts and male embolic complex divergence. The results provide a strongly supported phylogenetic framework and updated generic concepts for the <i>Laufeia</i> clade. The synapomorphies for the updated genera within the <i>Laufeia</i> clade were identified through character mapping on the phylogeny. Ancestral state reconstruction analyses revealed that the Type I embolic complex (characterized by a disc-like embolic disc with a lamina as its outer edge) was ancestral and gradually evolved into the Type II (without lamina of embolic disc, base of embolic complex often modified into a functional “conductor”) and Type III (lacking lamina of embolic disc and base of embolic complex) embolic complex, and that some embolic shapes evolved multiple times independently in different lineages of the <i>Laufeia</i> clade. The shift from foliage-dwelling to tree trunk-dwelling in the common ancestor of the <i>Laufeia</i> clade may have facilitated the divergent evolution of male embolic complex in the <i>Laufeia</i> clade. This study provides a solid foundation for future studies of systematics and evolution of this group.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 6","pages":"618-635"},"PeriodicalIF":3.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant species diversification in the Himalaya–Hengduan Mountains region: an example from an endemic lineage of Pedicularis (Orobanchaceae) in the role of floral specializations and rapid range expansions","authors":"Rong Liu,&nbsp;Wei-Jia Wang,&nbsp;Hong Wang,&nbsp;Richard H. Ree,&nbsp;De-Zhu Li,&nbsp;Wen-Bin Yu","doi":"10.1111/cla.12596","DOIUrl":"10.1111/cla.12596","url":null,"abstract":"<p>The <i>c.</i> 270 endemic species of <i>Pedicularis</i> in the Himalaya–Hengduan Mountains (HHM) region exhibit high diversity in geographic distribution, elevational range and floral morphology. Many of these, including the species with the longest corolla tubes and beaked galeas, are monophyletic and represent a putative <i>in situ</i> radiation. In this study, we focus on the representative Clade 3 within the HHM region. We integrate the plastid phylogeny of this clade with environmental data and species distributions to infer environmental correlates of species diversity. We estimate macroevolutionary rates and reconstructed ancestral states for geographic ranges and corolla traits, and analyse patterns of range overlap and niche evolution to assess drivers of diversification in the HHM region. Our results show that the region from northwest Yunnan to southwest Sichuan is the centre of diversity for this clade of <i>Pedicularis</i>. Rates of diversification are associated with precipitation and multiple environmental factors. Multiple range expansions from the Sanjiang (Three Parallel Rivers) region, followed by allopatric speciation across the HHM region, contributed to early rapid diversification. Corolla traits are not significantly associated with species diversification. This study highlights the importance of integrated evidence for understanding species diversification dynamics and contributes to our understanding of the origins of the remarkable richness of plant species in the HHM region.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 6","pages":"636-652"},"PeriodicalIF":3.9,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}