Cladistics最新文献

{"title":"Science and storytelling","authors":"Andrew V. Z. Brower","doi":"10.1111/cla.12569","DOIUrl":"10.1111/cla.12569","url":null,"abstract":"","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 2","pages":"204-207"},"PeriodicalIF":3.6,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139598791","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":"Systematics and character evolution of capitate hydrozoans","authors":"Davide Maggioni,&nbsp;Peter Schuchert,&nbsp;Andrew N. Ostrovsky,&nbsp;Andrea Schiavo,&nbsp;Bert W. Hoeksema,&nbsp;Daniela Pica,&nbsp;Stefano Piraino,&nbsp;Roberto Arrigoni,&nbsp;Davide Seveso,&nbsp;Enrico Montalbetti,&nbsp;Paolo Galli,&nbsp;Simone Montano","doi":"10.1111/cla.12567","DOIUrl":"10.1111/cla.12567","url":null,"abstract":"<p>Capitate hydrozoans are a morphologically and ecologically diverse hydrozoan suborder, currently including about 200 species. Being grouped in two clades, Corynida and Zancleida, these hydrozoans still show a number of taxonomic uncertainties at the species, genus and family levels. Many Capitata species established symbiotic relationships with other benthic organisms, including bryozoans, other cnidarians, molluscs and poriferans, as well as with planktonic dinoflagellates for mixotrophic relationships and with bacteria for thiotrophic ectosymbioses. Our study aimed at providing an updated and comprehensive phylogeny reconstruction of the suborder, at modelling the evolution of selected morphological and ecological characters, and at testing evolutionary relationships between the symbiotic lifestyle and the other characters, by integrating taxonomic, ecological and evolutionary data. The phylogenetic hypotheses here presented shed light on the evolutionary relationships within Capitata, with most families and genera being recovered as monophyletic. The genus <i>Zanclea</i> and family Zancleidae, however, were divided into four divergent clades, requiring the establishment of the new genus <i>Apatizanclea</i> and the new combinations for species in <i>Zanclea</i> and <i>Halocoryne</i> genera. The ancestral state reconstructions revealed that symbiosis arose multiple times in the evolutionary history of the Capitata, and that homoplasy is a common phenomenon in the group. Correlations were found between the evolution of symbiosis and morphological characters, such as the perisarc. Overall, our results highlighted that the use of genetic data and a complete knowledge of the life cycles are strongly needed to disentangle taxonomic and systematic issues in capitate hydrozoans. Finally, the colonization of tropical habitat appears to have influenced the evolution of a symbiotic lifestyle, playing important roles in the evolution of the group.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 2","pages":"107-134"},"PeriodicalIF":3.6,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12567","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138813066","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":"Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage.","authors":"Michal Motyka, Dominik Kusy, Gabriel Biffi, Michael Geiser, Sergey V Kazantsev, Renata Bilkova, Eva Jahodarova, Alfried P Vogler, Ladislav Bocak","doi":"10.1111/cla.12555","DOIUrl":"10.1111/cla.12555","url":null,"abstract":"<p><p>This study addresses the long-standing uncertainty about the internal classification of soldier beetles (Elateroidea: Cantharidae). Four datasets were compiled and analysed: 66 genes for 14 terminals, 15 mtDNA genes for 79 terminals, one mtDNA and two rRNA genes for 217 terminals, and barcodes for 576 terminals. Based on congruent topologies, Chauliognathinae is proposed as a sister to the remaining Cantharidae, followed by the redefined Malthininae (including Tytthonyxini), the paraphyletic \"dysmorphocerine\" lineages (Dysmorphocerinae sensu stricto and Heteromastiginae subfam. nov.), and Silinae + Cantharinae as a terminal clade. The present phylogeny supersedes earlier morphology and short-fragment molecular hypotheses that have not converged on a consensus. Few morphological characters corroborate the DNA-based relationships (see the adults and larval keys). However, morphology-based hypotheses have relied on a few informative characters, and no evidence strongly rejects the preferred molecular topology. The interpretation of morphological characters and uncertain polarity resulting from the high phenotypic disparity of Elateroidea are discussed in detail. The dated phylogeny hypothesizes the earliest split within the Cantharidae in the Berriasian stage (Early Cretaceous, ~141 Myr) and the diversification of most extant subfamilies and tribes already in the Late Cretaceous. The most diverse subfamily, Cantharinae, represents a delayed radiation that started during the Eocene climatic optimum, 55.5 Myr. The late origin of Cantharinae questions the classification of Cretaceous Cantharidae as members of Cantharinae. Instead, the results suggest their deeper rooting after separating from dysmorphocerine lineages and before the node between Cantharinae and Silinae.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"548-570"},"PeriodicalIF":3.9,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10176445","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":"Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies.","authors":"Siddharth Kulkarni, Hannah M Wood, Gustavo Hormiga","doi":"10.1111/cla.12557","DOIUrl":"10.1111/cla.12557","url":null,"abstract":"<p><p>In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"479-532"},"PeriodicalIF":3.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41174782","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":"Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters","authors":"Pablo A. Goloboff,&nbsp;Jan De Laet","doi":"10.1111/cla.12564","DOIUrl":"10.1111/cla.12564","url":null,"abstract":"<p>This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of transformation costs in some character being higher or lower when other characters have certain states or transformations between states. Character–state reconstructions and evaluation of trees under the assumption of independence may easily lead to ancestral assignments that violate elementary rules of biomechanics, well-established theories relating form and function or ideas about character co-variation. An obvious example is reconstructing an ancestral bird as wingless and flying at the same time; another is reconstructing a protein-coding gene as having a stop codon in some ancestors. If the characters are optimized independently, such chimeric ancestral reconstructions can occur even when no terminal displays the impossible combination of states. A set of conventions (implemented via new TNT commands and options) allows the definition of complex rules of interaction. By recoding groups of characters with proper step–matrix costs (and excluding impossible combinations from the set of permissible states), it is possible to find the ancestral reconstructions that maximize homology (and thus the degree to which similarities can be explained by common ancestry), within the constraints imposed by the rules specified by the user. We expect that considerations of biomechanics, functional morphology and natural history will be a source of many theories on possible character dependences, and that the present implementation will encourage users to take the possibility of character dependences into account in their phylogenetic analyses.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 3","pages":"209-241"},"PeriodicalIF":3.6,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138446914","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":"Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity","authors":"Mei-Zhen Wang,&nbsp;Jing Wu,&nbsp;Sheng-Lu Zhang,&nbsp;Li-Mi Mao,&nbsp;Tetsuo Ohi-Toma,&nbsp;Atsuko Takano,&nbsp;Yong-Hua Zhang,&nbsp;Kenneth M. Cameron,&nbsp;Pan Li","doi":"10.1111/cla.12565","DOIUrl":"10.1111/cla.12565","url":null,"abstract":"<p>Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus <i>Amana</i> (Liliaceae), known as ”East Asian tulips” has a number of cryptic species and a huge genome size (1C = 21.48–57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within <i>Amana</i> are challenging. Here we included all species and 84 populations of <i>Amana</i>, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in <i>Amana</i>. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, <i>Amana polymorpha</i>, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 2","pages":"135-156"},"PeriodicalIF":3.6,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138177803","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":"PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program","authors":"Ward C. Wheeler,&nbsp;Alexander Washburn,&nbsp;Louise M. Crowley","doi":"10.1111/cla.12560","DOIUrl":"10.1111/cla.12560","url":null,"abstract":"<p>We present Phylogenetic Graph (<span>PhyG</span>), an open-source, phylogenetic search tool for diverse data types and graphs, including softwired and hardwired networks, in addition to trees. This allows for analysis of horizontal transfer and hybridization scenarios, as well as the necessary vertical inheritance of trees. <span>PhyG</span> is the successor to <span>POY5</span> in performing combined data tree-alignment with enhancements in heuristic optimality (up to 7% in example data) and execution time (up to a factor of 200). Input data may exhibit a practically unlimited number of character states in qualitative or sequence (aligned and unaligned) types. Novel graph construction and refinement algorithms have been implemented and integrated into a variety of search procedures. Currently, <span>PhyG</span> implements parsimony and No-Common-Mechanism Likelihood optimization.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 1","pages":"97-105"},"PeriodicalIF":3.6,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49684588","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":"Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae)","authors":"Diana Delicado,&nbsp;Torsten Hauffe,&nbsp;Thomas Wilke","doi":"10.1111/cla.12558","DOIUrl":"10.1111/cla.12558","url":null,"abstract":"<p>The fifth mass extinction event (MEE) at the Cretaceous–Palaeogene (K–Pg) boundary 66 million years ago (Ma) led to massive species loss but also triggered the diversification of higher taxa. Five models have been proposed depending on whether this diversification occurred before, during or after the K–Pg boundary and the rate of species accumulation. While the effects of the K–Pg MEE on vertebrate evolution are relatively well understood, the impact on invertebrates, particularly in freshwater ecosystems, remains controversial. One example is the hyperdiverse Hydrobiidae—the most species-rich family of freshwater gastropods. Whereas some studies place its origin in the Jurassic or even Carboniferous, most fossil records postdate the K–Pg event. We therefore used robustly time-calibrated multi-locus phylogenies of &gt;400 species representing &gt;100 hydrobiid genera to unravel its evolutionary history and patterns of diversification. We found that the family started diversifying shortly after the K–Pg boundary (∼60 Ma; 95% highest posterior density 52–69 Ma). Lineage richness gradually increased to the present and phylogenetic diversity until ∼25 Ma. These findings suggest that diversification was not initially driven by ecological opportunity. Combining the two criteria of timing and rate of diversification, a soft-explosive diversification model of aquatic vertebrates best fits the patterns observed. We also show that most higher hydrobiid taxa (i.e. subfamilies) diversified from the Middle Oligocene to Middle Miocene (i.e. 12–28 Ma). Two of the 15 major clades delimited are described here as new subfamilies (i.e. Bullaregiinae n. subfam. and Pontobelgrandiellinae n. subfam.), whose members are restricted to subterranean waters. Our results are an important contribution to understanding how the fifth MEE has shaped evolution and patterns of biodiversity in continental aquatic systems. Given the high extinction risks faced by many hydrobiids today, they also emphasise the need to study the biodiversity of vulnerable ecosystems.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 1","pages":"82-96"},"PeriodicalIF":3.6,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12558","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10609982","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":"Wing pattern diversity in Eunica butterflies (Nymphalidae: Biblidinae): phylogenetic analysis implies decoupled adaptive trends in dorsal sexual dimorphism and ventral eyespot evolution","authors":"Ivonne J. Garzón-Orduña,&nbsp;Karina Lucas Silva-Brandão,&nbsp;Keith Willmott,&nbsp;André V. L. Freitas,&nbsp;Niklas Wahlberg,&nbsp;Andrew V. Z. Brower","doi":"10.1111/cla.12556","DOIUrl":"10.1111/cla.12556","url":null,"abstract":"<p>Butterfly eyespots are wing patterns reminiscent of vertebrate eyes, formed by concentric rings of contrastingly coloured scales. Eyespots are usually located close to the wing margin and often regarded as the single most conspicuous pattern element of butterfly wing colour displays. Recent efforts to understand the processes involved in the formation of eyespots have been driven mainly by evo-devo approaches focused on model species. However, patterns of change implied by phylogenetic relationships can also inform hypotheses about the underlying developmental mechanisms associated with the formation or disappearance of eyespots, and the limits of phenotypic diversity occurring in nature. Here we present a combined evidence phylogenetic hypothesis for the genus <i>Eunica</i>, a prominent member of diverse Neotropical butterfly communities, that features notable variation among species in eyespot patterns on the ventral hind wing surface. The data matrix consists of one mitochondrial gene region (COI), four nuclear gene regions (GAPDH, RPS5, EF1a and Wingless) and 68 morphological characters. A combined cladistic analysis with all the characters concatenated produced a single most parsimonious tree that, although fully resolved, includes many nodes with modest branch support. The phylogenetic hypothesis presented corroborates a previously proposed morphological trend leading to the loss of eyespots, together with an increase in the size of the conserved eyespots, relative to outgroup taxa. Furthermore, wing colour pattern dimorphism and the presence of androconia suggest that the most remarkable instances of sexual dimorphism are present in the species of <i>Eunica</i> with the most derived eyespot patterns, and are in most cases accompanied by autapomorphic combinations of scent scales and “hair pencils”. We discuss natural and sexual selection as potential adaptive explanations for dorsal and ventral wing patterns.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 1","pages":"1-20"},"PeriodicalIF":3.6,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12556","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10298694","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":"Much ado about nothing: inapplicable data as insertion–deletion events","authors":"Ward C. Wheeler","doi":"10.1111/cla.12553","DOIUrl":"10.1111/cla.12553","url":null,"abstract":"<p>The treatment of inapplicable characters has proved especially vexing to systematists. Investigators have wrestled with alternative coding scenarios to capture both the presence and absence of a feature, and its variation when present, in a reasonable manner. Three basic issues have presented themselves: (i) impossible states at internal nodes; (ii) action at a distance among disparate parts of the tree; and (iii) “secondary” (i.e. aspect variation) characters overwhelming “primary” (i.e. character presence/absence) patterns in grouping taxa. Multiple methods have been proposed to deal with these issues in the context of standard character coding with varying levels of complexity. Here, I show that these issues can be dealt with in a direct fashion by treating presence/absence not as a character, but as insertion/deletion of a character with all its potential variation. This approach removes these three problems in simple, straightforward manner.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"475-478"},"PeriodicalIF":3.6,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10313929","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}