Cladistics最新文献

{"title":"On the effect of measures for comparing trees on the representation of treespace.","authors":"Pablo A Goloboff, Martín E Morales","doi":"10.1111/cla.12614","DOIUrl":"https://doi.org/10.1111/cla.12614","url":null,"abstract":"<p><p>The multidimensional space determined by distances between trees (as measured with various methods) is often reduced and projected with multidimensional scaling to visually represent the differences between trees in the possible \"treespace\". This paper discusses the influence of 18 alternative measures of distance on mapping the treespace for all possible trees (or a large sample thereof) when trees of different degrees of resolution are included. Measures of distance appropriate for such mapping are expected to produce (hyper)spherical mappings, with resolved trees in the outer layer, less resolved trees in inner layers and the bush situated in the middle of the diagram. Measures of tree comparison that rescale the values by the observed (rather than potential) resolution produce an inversion of such an arrangement, with less resolved trees in the outer layers. Additionally, some measures are shown to be strongly influenced by tree shape, so that trees of certain shapes end up being situated at specific depths of the diagram (which may become so distorted as to not even look like a hypersphere).</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789366","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":"A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting.","authors":"Markus Grams, Ambrosio Torres, Christian S Wirkner, Stefan Richter","doi":"10.1111/cla.12611","DOIUrl":"https://doi.org/10.1111/cla.12611","url":null,"abstract":"<p><p>Using a new character matrix composed of revised matrices of previous analyses and new morphological findings, the phylogeny of Malacostraca (Pancrustacea) is analysed anew with 207 characters for 35 terminal taxa across all recognized orders. Particular emphasis was placed on methodological versatility, including different degrees of implied weighting and one of the first applications of methods recently developed in TNT (with the xl inks-command) for considering character dependencies. With >67% of ontological dependencies our character matrix offers a perfect opportunity for putting this new methodology to the test. In particular, we can demonstrate the significant impact of character dependencies and conclusively argue the usefulness of \"xlinks\" (or the consideration of character dependencies in general). Furthermore, the multimethod framework also enables a comparative evaluation of established and new approaches, and the resulting cladograms thereof. Although our various results leave many questions about the phylogeny of Malacostraca unanswered, clear support is emerging for some monophyla, whereas some surprising findings give reason for methodological reflection. Also, the necessity for an increased attention in terms of taxon sampling and additional character examinations in certain groups becomes obvious. We herein provide (i) an R-function for automatically translating the character dependency syntax proposed by Grams and Richter (Cladistics, 2023, 39, 437) into xlinks-commands for TNT; and (ii) a TNT-script for analysing a character matrix successively under various k-values for implied weighting.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781771","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":"Phylogenetic analysis and biogeography of Scolia (Hymenoptera, Scoliidae, Scoliinae): implications for the classification and origin of Scoliini.","authors":"Ivan Fernandes Golfetti, Marjorie da Silva, Eduardo Fernando Dos Santos, Fernando Barbosa Noll","doi":"10.1111/cla.12612","DOIUrl":"https://doi.org/10.1111/cla.12612","url":null,"abstract":"<p><p>Scoliidae is a commonly found cosmopolitan family and currently one of the most neglected taxa within Hymenoptera. As expected, information on the members of this group is scarce and extremely outdated, especially when it comes to their phylogenetic relationships. The genus Scolia Fabricius, 1755 includes species that do not present diagnostic characters used to identify the other genera of Scoliini, and so it can be considered a \"dumping ground group\". Seeking to better understand the evolutionary history and, consequently, the morphological variation in \"New World\" Scolia species, the phylogenetic relationships among all species from the Neotropical and Nearctic Regions and their biogeography are analysed for the first time. For this, 104 morphological characters are proposed from males and females of 45 species. The phylogenetic analysis points to the monophyly of the \"New World\" species, and the biogeographical analysis indicates that the \"New World\" species originated from a Palaearctic ancestor, through a dispersal event to the Nearctic Region. Considering the taxonomic history and phylogenetic relationships obtained, aiming to initially resolve a part of the chaotic taxonomic situation of Scolia and its subgenera, here we proposed that the subgenus Discolia should be restricted exclusively to the \"New World\" and the species from the \"Old World\" should no longer be treated as Discolia, being considered as members of Scolia s.s. Additionally, Hesperoscolia should be considered a junior synonym of Discolia. Furthermore, the phylogenetic analysis confirms the monophyly of most Scoliini genera included in it.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711929","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":"Correction to Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage.","authors":"","doi":"10.1111/cla.12613","DOIUrl":"https://doi.org/10.1111/cla.12613","url":null,"abstract":"","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664974","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":"A new phylogeny and classification of the tinamous, volant palaeognathous birds from the Neotropics.","authors":"Sara Bertelli, Francisca Cunha Almeida, Norberto P Giannini","doi":"10.1111/cla.12605","DOIUrl":"https://doi.org/10.1111/cla.12605","url":null,"abstract":"<p><p>The Neotropical Tinamidae is the most diverse family of palaeognathous birds (Neornithes; Palaeognathae). This is the only family with species capable of powered flight, in striking contrast to all the other flightless, large-bodied, both living and recently extinct, palaeognaths. Here we report our latest phylogenetic analysis of tinamous, built on previous comprehensive studies, presently including all 46 currently recognized species. Our goal was to apply all the valid available supraspecific names to the clades recovered, creating new ones as needed. We recovered the traditional major subclades, forest-dwelling vs. open-areas tinamous, with all three currently recognized genera in the former matching the chief groupings, and with two taxa in the latter that do not fit the current classification as per the phylogenetic results. Our analysis of the taxonomic history of tinamid taxa revealed complications chiefly owing to the convoluted history of certain key names, particularly Tinamus. We disentangled the perceived misapplication of Tinamus to various tinamid taxa, concluding that Tinamus Hermann, 1783 is valid and not Tinamus Latham, 1790, with type species soui Hermann, 1783, currently placed in Crypturellus. As a consequence, while the phylogenetic signal is clear, a major taxonomic rearrangement is needed in the forest-dwelling tinamous reassigning species of small forest tinamous (currently in Crypturellus) according to priority to Tinamus Hermann, and former invalid Tinamus Latham to Pezus Spix, 1825. In the open-areas tinamous (Tinamotidinae), we recognize two tribes and the phylogeny also indicated the need for a new genus to be applied to cinerascens, formerly in Nothoprocta; and the synonymy of Taoniscus, as the single species nanus was recovered nested in Nothura. We discuss at length our taxonomic proposal against alternatives; this is particularly complicated owing to a long, unresolved taxonomic history.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634942","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":"Machine learning models accurately predict clades of proteocephalidean tapeworms (Onchoproteocephalidea) based on host and biogeographical data.","authors":"Philippe Vieira Alves, Reinaldo José da Silva, Tomáš Scholz, Alain de Chambrier, José Luis Luque, Anastasiia Duchenko, Daniel Janies, Denis Jacob Machado","doi":"10.1111/cla.12610","DOIUrl":"https://doi.org/10.1111/cla.12610","url":null,"abstract":"<p><p>Proteocephalids are a cosmopolitan and diverse group of tapeworms (Cestoda) that have colonized vertebrate hosts in freshwater and terrestrial environments. Despite the ubiquity of the group, key macroevolutionary processes that have driven the group's evolution have yet to be identified. Here, we review the phylogenetic relationships of proteocephalid tapeworms using publicly available (671) and newly generated (91) nucleotide sequences of the nuclear RNA28S and the mitochondrial MT-CO1 for 537 terminals. The main tree search was carried out under the parsimony optimality criterion, analysing different gene alignments simultaneously. Interestingly, we were not able to recover monophyly of the Proteocephalidae. Additionally, it was difficult to reconcile the tree with host and biogeographical data using traditional character optimization strategies in two dimensions. Therefore, we investigated if host and biogeographical data can be correlated with the parasite clades in a multidimensional space-thus considering multiple layers of information simultaneously. To that end, we used random forests (a class of machine learning models) to test the predictive potential of combined (not individual) host and biogeographical data in the context of the proteocephalid tree. Our resulting models can correctly place 88.85% (on average) of the terminals into eight representative clades. Moreover, we interactively increased the levels of clade perturbation probability and confirmed the expectation that model accuracy negatively correlates with the degree of clade perturbation. Our results show that host and biogeographical data can accurately predict proteocephalid clades in multidimensional space, even though they are difficult to optimize in the parasite tree. These results agree with the assumption that the evolution of proteocephalids is not independent of host and biogeography, and both may provide external support for our tree.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568738","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 backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes","authors":"Xin-Jie Jin,&nbsp;Yan Yu,&nbsp;Han-Yang Lin,&nbsp;Feng-Luan Liu,&nbsp;Hai-feng Wang,&nbsp;Qing Ma,&nbsp;Yang Chen,&nbsp;Yong-Hua Zhang,&nbsp;Pan Li","doi":"10.1111/cla.12604","DOIUrl":"10.1111/cla.12604","url":null,"abstract":"<p>The angiosperm tribe of Elsholtzieae (Lamiaceae) is characterized by complex inflorescences and has notable medicinal and economic significance. Relationships within Elsholtzieae, including the monophyly of <i>Elsholtzia</i> and <i>Keiskea</i>, and relationships among <i>Mosla</i>, <i>Keiskea</i> and <i>Perilla</i>, remain uncertain, hindering insights into inflorescence evolution within the tribe. Using hybridization capture sequencing and deep genome skimming data analysis, we reconstruct a phylogeny of Elsholtzieae using 279 orthologous nuclear loci from 56 species. We evaluated uncertainty among relationships using concatenation, coalescent and network approaches. Using a time-calibrated phylogeny, we reconstructed ancestral inflorescence traits to elucidate the patterns in their evolution within the tribe. Our analyses consistently support the paraphyly of the genus <i>Elsholtzia</i>. Phylogenetic network analyses, confirmed by PhyloNetworks and SplitsTree, showed reticulation events among the major lineages of Elsholtzieae. The unstable polyphyly of <i>Keiskea</i> observed in ASTRAL (accurate species tree algorithm), ML (maximum likelihood) and MP (maximum parsimony) analyses may be related to introgression from <i>Perilla</i> and <i>Mosla</i>. Based on the analyses of phylogenetic trees within Elsholtzieae, the evolutionary trajectory of inflorescences demonstrates a pattern of diversification, with specialization as one aspect of this process. Elsholtzieae support the hypothesis that compressed inflorescences evolved from larger and more complex ancestral forms through successive compressions of the inflorescence axis. Additionally, certain lineages within the tribe display a trend towards simplified inflorescences, characterized by a reduction in the number of florets. This highlights both the specialization and the diversity in the evolution of inflorescence structures within the tribe.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 2","pages":"157-176"},"PeriodicalIF":3.9,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450854","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":"“Dark taxonomy”: A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment","authors":"Rudolf Meier,&nbsp;Amrita Srivathsan,&nbsp;Sarah Siqueira Oliveira,&nbsp;Maria Isabel P.A. Balbi,&nbsp;Yuchen Ang,&nbsp;Darren Yeo,&nbsp;Jostein Kjærandsen,&nbsp;Dalton de Souza Amorim","doi":"10.1111/cla.12609","DOIUrl":"10.1111/cla.12609","url":null,"abstract":"<p>We are entering the sixth mass extinction with little data for “dark taxa”, although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call “dark taxonomy”. It addresses (i) taxonomic impediments, (ii) the lack of biodiversity baselines and (iii) the low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is reduced by delimiting species based on two types of data. We furthermore show that dark taxonomy can yield important biodiversity baseline data by using samples obtained with biomonitoring traps. Lastly, we argue that the impact of revisionary research can be improved by publishing two papers addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapore's fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (<i>N</i> = 1454) contains 120 species, of which 115 are new to science, thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of Molecular Operational Taxonomic Units (MOTUs) before “LIT” (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we next analysed a second batch of 1493 specimens and found that &gt;97% belonged to the 120 species delimited based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs, i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that “dark taxonomy” can quickly ready a large unknown taxon for biomonitoring.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 2","pages":"223-238"},"PeriodicalIF":3.9,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434206","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":"Phylogenetic minimum description length: an optimality criterion based on algorithmic complexity","authors":"Ward C. Wheeler,&nbsp;Andres Varón","doi":"10.1111/cla.12603","DOIUrl":"10.1111/cla.12603","url":null,"abstract":"<p>Phylogenetic minimum description length (PMDL) is proposed as an optimality criterion for phylogenetic analysis. PMDL is based on algorithmic (Kolmogorov) information and the minimum description length principle. This criterion generates natural weighting functions (i.e. not being externally specified) for a diversity of phylogenetic graph, data and model types. PMDL is a generalized criterion that converges on existing forms of inference (i.e. parsimony, likelihood, Bayesian) in specific circumstances. Furthermore, as opposed to existing criteria, PMDL includes graph complexity allowing for the competition of hypotheses with myriad types of phylogenetic graphs (e.g. trees, networks, forests). Owing to its compound nature, PMDL allows for analytical model choice along with phylogenetic graph hypothesis while avoiding over-parameterization. Although uncomputable, heuristic methods are presented for the calculation of upper bounds on the algorithmic information content of a phylogenetic hypothesis. Examples are presented demonstrating the approach.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 2","pages":"193-211"},"PeriodicalIF":3.9,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434208","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":"Accuracy of phylogenetic reconstructions from continuous characters analysed under parsimony and its parametric correlates","authors":"Victor A. Tagliacollo,&nbsp;Mario de Pinna,&nbsp;Junior Chuctaya,&nbsp;Alessio Datovo","doi":"10.1111/cla.12606","DOIUrl":"10.1111/cla.12606","url":null,"abstract":"<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":"41 2","pages":"212-222"},"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}