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The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps Chalcidoidea生命灌木:微小黄蜂大规模辐射的进化史。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-11-02 DOI: 10.1111/cla.12561
Astrid Cruaud, Jean-Yves Rasplus, Junxia Zhang, Roger Burks, Gérard Delvare, Lucian Fusu, Alex Gumovsky, John T. Huber, Petr Janšta, Mircea-Dan Mitroiu, John S. Noyes, Simon van Noort, Austin Baker, Julie Böhmová, Hannes Baur, Bonnie B. Blaimer, Seán G. Brady, Kristýna Bubeníková, Marguerite Chartois, Robert S. Copeland, Natalie Dale-Skey Papilloud, Ana Dal Molin, Chrysalyn Dominguez, Marco Gebiola, Emilio Guerrieri, Robert L. Kresslein, Lars Krogmann, Emily Lemmon, Elizabeth A. Murray, Sabine Nidelet, José Luis Nieves-Aldrey, Ryan K. Perry, Ralph S. Peters, Andrew Polaszek, Laure Sauné, Javier Torréns, Serguei Triapitsyn, Ekaterina V. Tselikh, Matthew Yoder, Alan R. Lemmon, James B. Woolley, John M. Heraty
{"title":"The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps","authors":"Astrid Cruaud,&nbsp;Jean-Yves Rasplus,&nbsp;Junxia Zhang,&nbsp;Roger Burks,&nbsp;Gérard Delvare,&nbsp;Lucian Fusu,&nbsp;Alex Gumovsky,&nbsp;John T. Huber,&nbsp;Petr Janšta,&nbsp;Mircea-Dan Mitroiu,&nbsp;John S. Noyes,&nbsp;Simon van Noort,&nbsp;Austin Baker,&nbsp;Julie Böhmová,&nbsp;Hannes Baur,&nbsp;Bonnie B. Blaimer,&nbsp;Seán G. Brady,&nbsp;Kristýna Bubeníková,&nbsp;Marguerite Chartois,&nbsp;Robert S. Copeland,&nbsp;Natalie Dale-Skey Papilloud,&nbsp;Ana Dal Molin,&nbsp;Chrysalyn Dominguez,&nbsp;Marco Gebiola,&nbsp;Emilio Guerrieri,&nbsp;Robert L. Kresslein,&nbsp;Lars Krogmann,&nbsp;Emily Lemmon,&nbsp;Elizabeth A. Murray,&nbsp;Sabine Nidelet,&nbsp;José Luis Nieves-Aldrey,&nbsp;Ryan K. Perry,&nbsp;Ralph S. Peters,&nbsp;Andrew Polaszek,&nbsp;Laure Sauné,&nbsp;Javier Torréns,&nbsp;Serguei Triapitsyn,&nbsp;Ekaterina V. Tselikh,&nbsp;Matthew Yoder,&nbsp;Alan R. Lemmon,&nbsp;James B. Woolley,&nbsp;John M. Heraty","doi":"10.1111/cla.12561","DOIUrl":"10.1111/cla.12561","url":null,"abstract":"<p>Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, &gt;95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the “Angiosperm Terrestrial Revolution”. Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3–180.5 Ma) and a crown age of 162.2 Ma (153.9–169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 1","pages":"34-63"},"PeriodicalIF":3.6,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71428728","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}
引用次数: 0
PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program 系统发育图(PhyG)是一个新的系统发育图搜索和优化程序。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-10-19 DOI: 10.1111/cla.12560
Ward C. Wheeler, Alexander Washburn, Louise M. Crowley
{"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}
引用次数: 0
Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships 鲎科(Diptera:Calyptratae:Oestroidea)的系统发育基因组分析:理解亚科关系的转录组方法。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-10-13 DOI: 10.1111/cla.12562
Letícia Chiara Baldassio de Paula, Rodrigo de Vilhena Perez Dios, Filipe Macedo Gudin, Marcelo Domingos de Santis, Deivys Moises Alvarez-Garcia, Manuel Antunes Júnior, Beatriz Vieira Freire, Fernando Portella de Luna Marques, Daniel José Galafasse Lahr, Silvio Shigueo Nihei
{"title":"Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships","authors":"Letícia Chiara Baldassio de Paula,&nbsp;Rodrigo de Vilhena Perez Dios,&nbsp;Filipe Macedo Gudin,&nbsp;Marcelo Domingos de Santis,&nbsp;Deivys Moises Alvarez-Garcia,&nbsp;Manuel Antunes Júnior,&nbsp;Beatriz Vieira Freire,&nbsp;Fernando Portella de Luna Marques,&nbsp;Daniel José Galafasse Lahr,&nbsp;Silvio Shigueo Nihei","doi":"10.1111/cla.12562","DOIUrl":"10.1111/cla.12562","url":null,"abstract":"<p>Tachinidae is the second most species-rich family of Diptera. It comprises four subfamilies, and all of its members have parasitoid habits. We present the first phylogenomic analysis of Tachinidae using transcriptomic data, based on 30 species. We constructed four datasets: three using translated data at the amino acid level (100% coverage, with 106 single-copy protein-coding genes; 75% coverage, with 1359 genes; and 50% coverage, with 1942 genes). The trees were estimated by analysing four matrices using maximum likelihood and maximum parsimony inferences, and only minor differences were found among them. Overall, our topologies are well resolved, with high node support. Polleniidae is corroborated as a sister group to Tachinidae. Within Tachinidae, our results confirm the hypothesis (Phasiinae + Dexiinae) + (Tachininae + Exoristinae). Phasiinae, Dexiinae and Exoristinae are recovered as monophyletic, and Tachininae as polyphyletic. Once again, the tribe Myiophasiini (Tachininae) composes a fifth lineage, clade sister to all the remaining Tachinidae. The Neotropical tribe Iceliini, formerly in Tachininae, is recovered within Exoristinae, sister to Winthemiini. In general, our results are congruent with recent phylogenetic studies that include tachinids, with the important confirmation of the subfamilial relationships and the existence of a fifth lineage of Tachinidae.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 1","pages":"64-81"},"PeriodicalIF":3.6,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41219303","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}
引用次数: 0
Toward transparent taxonomy: an interactive web-tool for evaluating competing taxonomic arrangements 走向透明分类法:一个用于评估相互竞争的分类安排的交互式网络工具。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-10-12 DOI: 10.1111/cla.12563
Oksana V. Vernygora, Felix A. H. Sperling, Julian R. Dupuis
{"title":"Toward transparent taxonomy: an interactive web-tool for evaluating competing taxonomic arrangements","authors":"Oksana V. Vernygora,&nbsp;Felix A. H. Sperling,&nbsp;Julian R. Dupuis","doi":"10.1111/cla.12563","DOIUrl":"10.1111/cla.12563","url":null,"abstract":"<p>Informative and consistent taxonomy above the species level is essential to communication about evolution, biodiversity and conservation, and yet the practice of taxonomy is considered opaque and subjective by non-taxonomist scientists and the public alike. While various proposals have tried to make the basis for the ranking and inclusiveness of taxa more transparent and objective, widespread adoption of these ideas has lagged. Here, we present TaxonomR, an interactive online decision-support tool to evaluate alternative taxonomic classifications. This tool implements an approach that quantifies the criteria commonly used in taxonomic treatments and allows the user to interactively manipulate weightings for different criteria to compare scores for taxonomic groupings under those weights. We use the butterfly taxon <i>Argynnis</i> to demonstrate how different weightings applied to common taxonomic criteria result in fundamentally different genus-level classifications that are predominantly used in different continents and geographic regions. These differences are objectively compared and quantified using TaxonomR to evaluate the kinds of criteria that have been emphasized in earlier classifications, and the nature of the support for current alternative taxonomic arrangements. The main role of TaxonomR is to make taxonomic decisions transparent via an explicit prioritization scheme. TaxonomR is not a prescriptive application. Rather, it aims to be a tool for facilitating our understanding of alternative taxonomic classifications that can, in turn, potentially support global harmony in biodiversity assessments through evidence-based discussion and community-wide resolution of historically entrenched taxonomic tensions.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 2","pages":"181-191"},"PeriodicalIF":3.6,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41219304","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}
引用次数: 0
Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea) 大规模的基因组数据揭示了猫头鹰蛾(夜蛾总科)的系统发育和进化。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-10-03 DOI: 10.1111/cla.12559
Xuankun Li, Jesse W. Breinholt, Jose I. Martinez, Kevin Keegan, Emily A. Ellis, Nicholas T. Homziak, Andreas Zwick, Caroline G. Storer, Duane McKenna, Akito Y. Kawahara
{"title":"Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea)","authors":"Xuankun Li,&nbsp;Jesse W. Breinholt,&nbsp;Jose I. Martinez,&nbsp;Kevin Keegan,&nbsp;Emily A. Ellis,&nbsp;Nicholas T. Homziak,&nbsp;Andreas Zwick,&nbsp;Caroline G. Storer,&nbsp;Duane McKenna,&nbsp;Akito Y. Kawahara","doi":"10.1111/cla.12559","DOIUrl":"10.1111/cla.12559","url":null,"abstract":"<p>The owlet moths (Noctuoidea; ~43–45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"40 1","pages":"21-33"},"PeriodicalIF":3.6,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151667","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}
引用次数: 0
Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae) 第五次大灭绝事件引发了最大的淡水腹足类(腹足纲:Truncatelloidea: Hydrobiidae)家族的多样化。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-09-15 DOI: 10.1111/cla.12558
Diana Delicado, Torsten Hauffe, Thomas Wilke
{"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}
引用次数: 0
Wing pattern diversity in Eunica butterflies (Nymphalidae: Biblidinae): phylogenetic analysis implies decoupled adaptive trends in dorsal sexual dimorphism and ventral eyespot evolution Eunica蝴蝶(蛱蝶科:Biblidinae)翅膀花纹的多样性:系统进化分析表明背侧性二形和腹侧眼斑进化的适应趋势是脱钩的。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-09-15 DOI: 10.1111/cla.12556
Ivonne J. Garzón-Orduña, Karina Lucas Silva-Brandão, Keith Willmott, André V. L. Freitas, Niklas Wahlberg, Andrew V. Z. Brower
{"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}
引用次数: 0
Much ado about nothing: inapplicable data as insertion–deletion events 事与愿违:不适用的数据作为插入-删除事件。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-07-19 DOI: 10.1111/cla.12553
Ward C. Wheeler
{"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}
引用次数: 0
Parsimony optimization of phylogenetic networks 系统发育网络的分析优化。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-07-19 DOI: 10.1111/cla.12552
Ward C. Wheeler, Alexander J. Washburn
{"title":"Parsimony optimization of phylogenetic networks","authors":"Ward C. Wheeler,&nbsp;Alexander J. Washburn","doi":"10.1111/cla.12552","DOIUrl":"10.1111/cla.12552","url":null,"abstract":"<p>An algorithm is described for the optimization of character data (e.g. qualitative, nucleic acid sequence) on softwired phylogenetic networks. The algorithm presented here is an extension of those developed for trees under the parsimony criterion and can form the basis for phylogenetic network search procedures. Although the problem is (in general) an NP-Hard optimization, the resolution-based algorithm we describe here capitalizes on the significant amount of shared structure in sub-graphs containing network edges, reducing the execution time and allowing for the analysis of empirical datasets.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"456-474"},"PeriodicalIF":3.6,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10218799","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}
引用次数: 1
On the four complementary aspects of hierarchical character relationships and their bearing on scoring constraints, expressed in a new syntax for character dependencies 关于层次字符关系的四个互补方面及其对评分约束的影响,用一种新的字符依赖语法表示。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-07-10 DOI: 10.1111/cla.12550
Markus Grams, Stefan Richter
{"title":"On the four complementary aspects of hierarchical character relationships and their bearing on scoring constraints, expressed in a new syntax for character dependencies","authors":"Markus Grams,&nbsp;Stefan Richter","doi":"10.1111/cla.12550","DOIUrl":"10.1111/cla.12550","url":null,"abstract":"<p>Morphological matrices, including the conceptualization of characters and character states and scoring thereof, still are a valuable and necessary tool for phylogenetic analyses. Although they are often seen only as numerically simplified summaries of observations for the purpose of cladistic analyses, they also hold value as collections of ideas, concepts and the current state of knowledge, conveying various hypotheses on character state identity, homology and evolutionary transformations. A common and persistent issue in scoring and analysing morphological matrices is the phenomenon of inapplicable characters (“inapplicables”). Inapplicables result from the ontological dependency (based on hierarchical relationships) between characters. Traditionally handled the same as “missing data”, inapplicables were shown to be problematic in holding the potential to result in unreasonable algorithmic preference for certain cladograms over others. Recently, though, this problem has been solved by approaching parsimony as a maximization of homology rather than a minimization of transformational steps. We herein aim to further improve our theoretical understanding of the underlying hierarchical nature of morphological characters, which causes the phenomenon of ontological dependencies and, thereby, inapplicables. As a result, we present a discussion of various character-dependency scenarios and a new concept of hierarchical character relationships as being composed of four complementary sub-aspects. Building on this, a new syntax for the designation of character dependencies as part of the character statement is proposed, to help identify and apply scoring constraints for manual and automated scoring of morphological character matrices and their cladistic analysis.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"437-455"},"PeriodicalIF":3.6,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12550","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10209100","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}
引用次数: 1
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