Cladistics最新文献

{"title":"Phylogenetic reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes.","authors":"Katarzyna Krawczyk, Mateusz Maździarz, Łukasz Paukszto, Marcin Nobis, Jakub Sawicki","doi":"10.1111/cla.12618","DOIUrl":"https://doi.org/10.1111/cla.12618","url":null,"abstract":"<p><p>Compared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial genome fragments can be valuable for both molecular species identification and phylogenetic analysis in grasses of the tribe Stipeae. To explore this potential, we first assembled the complete mitochondrial genome of Nassella tenuissima-the first fully described mitogenome in Stipeae-which served as a reference for selecting 29 aligned mitochondrial genome fragments totalling 139 680 bp. These fragments were then analysed across 49 representatives of the tribe, including 43 Stipa species and six other taxa. The mitochondrial fragments achieved a species discrimination efficiency of 75%, slightly exceeding the 71% efficiency observed for plastid super-barcodes. Additionally, comparative phylogenetic analyses using plastid and mitochondrial genomes underscored the utility of mitochondrial data in resolving phylogenetic relationships within Stipeae. Our findings provide a valuable resource for future research in transcriptomics, comparative genomics, phylogenomics and phylogeography of grasses.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175528","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":"Areas of endemism of semiaquatic bugs (Hemiptera: Gerromorpha): an approach to the biogeographic regionalization of Colombia.","authors":"Irina Morales, Patricia Mondragón-F, Ximena A Galindo-Malagón, Jorge D Mercado-Gómez","doi":"10.1111/cla.12616","DOIUrl":"https://doi.org/10.1111/cla.12616","url":null,"abstract":"<p><p>Areas of endemism, defined by the congruence of the distribution of two or more taxa that are only found in that specific area, are considered an important input for biogeographic regionalization and determining priority areas for conservation. Herein we inferred the areas of endemism of Gerromorpha and their representation within the current protected areas system of Colombia. We analyzed 480 records of 69 species of semiaquatic bugs (Hemiptera - Gerromorpha) using the NDM/VNDM and three different grid sizes. We identified eight areas of endemism and 15 endemic species belonging to the genera Altavelia, Hydrometra, Oiovelia, Microvelia, Platygerris, Potamobates, Rhagovelia, Rheumatobates, Stridulivelia, Telmatometropsis and Veloidea. We identified five consensus areas. The endemism patterns of Gerromorpha from smaller units within the biogeographic provinces proposed by Morrone (Zootaxa 2014, 3782, 1-110). Rather, they form smaller units within provinces, similar to those found in vertebrates, suggesting the existence of biogeographic districts and therefore the need for a new classification. Only six of the 15 endemic species are protected under the current protected areas system. Defining Gerromorpha AEs constitutes a first step to infer the biogeographic history and the evolutionary processes that influence the distribution of semiaquatic bugs in Colombia and guide actions for their conservation.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144121408","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":"The limits of phylogenetic analysis: identifying analytical hallucinations.","authors":"Ward C Wheeler","doi":"10.1111/cla.12617","DOIUrl":"https://doi.org/10.1111/cla.12617","url":null,"abstract":"<p><p>Phylogenetic analysis strives to construct graphs, such as trees or networks, that encapsulate the historical structure of a set of terminal taxa. This process is based on comparative character data and an optimality criterion by which these graphs are evaluated. Whether there is structure in the data or not, phylogenetic analytical methods will produce a collection of heuristically optimal graphs. The question examined here is how to determine when a data set, or components of a data set, possess sufficient shared information to yield results founded in historical phylogenetic structure, and where \"hallucinatory\" patterns are conjured from a lack of information. A method is described to identify mutually analysable data components based on shared information and to distinguish them from components that cannot be meaningfully analysed.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060004","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":"Morphological data, phylogenomics and recalcitrant nodes.","authors":"Rob DeSalle, Michael Tessler","doi":"10.1111/cla.12615","DOIUrl":"https://doi.org/10.1111/cla.12615","url":null,"abstract":"<p><p>In this paper we examine the relative contribution of information to nodes in a phylogenomic analysis combined with morphological datasets. We examine the behaviour of branch support metrics using the partitioned Bremer support (PBS) and its likelihood counterpart partitioned likelihood support (PLS). These metrics measure the contribution of a data partition to a node in question, and can be easily computed for likelihood and parsimony. Specifically, we assess the ratios of support values for morphological data to molecular data at this recalcitrant node. We find that there is a strong linear correlation between this ratio with the weight of the weaker partition where a flip (the flip weight) in topology ensues. This linear relationship allows us to estimate the amount of morphological data it will take to flip a phylogenomic hypothesis. For the datasets we use in this study flip weights are surprisingly small.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006520","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":"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,&nbsp;Ambrosio Torres,&nbsp;Christian S. Wirkner,&nbsp;Stefan Richter","doi":"10.1111/cla.12611","DOIUrl":"10.1111/cla.12611","url":null,"abstract":"<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 xlinks-command) for considering character dependencies. With &gt;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 <i>R</i>-function for automatically translating the character dependency syntax proposed by Grams and Richter (<i>Cladistics</i>, 2023, 39, 437) into xlinks-commands for TNT; and (ii) a TNT-script for analysing a character matrix successively under various <i>k</i>-values for implied weighting.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 3","pages":"283-303"},"PeriodicalIF":3.9,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12611","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":"OA","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,&nbsp;Marjorie da Silva,&nbsp;Eduardo Fernando Dos Santos,&nbsp;Fernando Barbosa Noll","doi":"10.1111/cla.12612","DOIUrl":"10.1111/cla.12612","url":null,"abstract":"<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 <i>Scolia</i> 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” <i>Scolia</i> 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 <i>Scolia</i> and its subgenera, here we proposed that the subgenus <i>Discolia</i> should be restricted exclusively to the “New World” and the species from the “Old World” should no longer be treated as <i>Discolia</i>, being considered as members of <i>Scolia</i> s.s<i>.</i> Additionally, <i>Hesperoscolia</i> should be considered a junior synonym of <i>Discolia</i>. Furthermore, the phylogenetic analysis confirms the monophyly of most Scoliini genera included in it.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 3","pages":"304-320"},"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":"10.1111/cla.12613","url":null,"abstract":"<p>Citation: Motyka, M., Kusy, D., Biffi, G., Geiser, M., Kazantsev, S.V., Bilkova, R., Jahodarova, E., Vogler, A.P. &amp; Bocak, L. (2023) Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage. Cladistics, 39 (6), 1–23. doi: https://doi.org/10.1111/cla.12555</p><p>The affiliation ‘a’ incorrectly states: “^aLaboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, 779 00 Olomouc, Slechtitelu 27, Czech Republic;”</p><p>This should have read:</p><p>“^aCzech Advanced Technology Research Institute, Palacký University, 779 00 Olomouc, Slechtitelu 27, Czech Republic;”</p><p>We apologize for this error.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 3","pages":"321"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12613","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":"OA","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,&nbsp;Francisca Cunha Almeida,&nbsp;Norberto P. Giannini","doi":"10.1111/cla.12605","DOIUrl":"10.1111/cla.12605","url":null,"abstract":"<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 <i>Tinamus</i>. We disentangled the perceived misapplication of <i>Tinamus</i> to various tinamid taxa, concluding that <i>Tinamus</i> Hermann, 1783 is valid and not <i>Tinamus</i> Latham, 1790, with type species <i>soui</i> Hermann, 1783, currently placed in <i>Crypturellus</i>. 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 <i>Crypturellus</i>) according to priority to <i>Tinamus</i> Hermann, and former invalid <i>Tinamus</i> Latham to <i>Pezus</i> 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 <i>cinerascens</i>, formerly in <i>Nothoprocta</i>; and the synonymy of <i>Taoniscus</i>, as the single species <i>nanus</i> was recovered nested in <i>Nothura</i>. 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":"41 3","pages":"239-263"},"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,&nbsp;Reinaldo José da Silva,&nbsp;Tomáš Scholz,&nbsp;Alain de Chambrier,&nbsp;José Luis Luque,&nbsp;Anastasiia Duchenko,&nbsp;Daniel Janies,&nbsp;Denis Jacob Machado","doi":"10.1111/cla.12610","DOIUrl":"10.1111/cla.12610","url":null,"abstract":"<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":"41 3","pages":"264-282"},"PeriodicalIF":3.9,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12610","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}