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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
Biogeographic–tectonic calibration of 14 nodes in a butterfly timetree 蝴蝶时间表中14个节点的生物地理构造定标
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-06-06 DOI: 10.1111/cla.12537
Michael Heads, John R. Grehan, John Nielsen, Brian Patrick
{"title":"Biogeographic–tectonic calibration of 14 nodes in a butterfly timetree","authors":"Michael Heads,&nbsp;John R. Grehan,&nbsp;John Nielsen,&nbsp;Brian Patrick","doi":"10.1111/cla.12537","DOIUrl":"10.1111/cla.12537","url":null,"abstract":"<p>The butterfly subtribe Coenonymphina (Nymphalidae: Satyrinae) comprises four main clades found, respectively, in (1) the Solomon Islands, (2) Australasia, (3) NW South America and (4) Laurasia, with a phylogeny: 1 (2 (3 + 4)). In assessing biogeographic evolution in the group we rejected the conversion of fossil-calibrated clade ages to likely maximum clade ages by the imposition of arbitrary priors. Instead, we used biogeographic–tectonic calibration, with fossil-calibrated ages accepted as minima. Previous studies have used this approach to date single nodes (phylogenetic–biogeographic breaks) in a group, but we extended the methodology to date multiple nodes. Within the Coenonymphina as a whole, 14 nodes coincide spatially with ten major tectonic events. In addition, the phylogenetic sequence of these nodes conforms to the chronological sequence of the tectonic events, consistent with a vicariance origin of the clades. Dating of the spatially coincident tectonic features provides a timescale for the vicariance events. The tectonic events are: pre-drift intracontinental rifting between India and Australia (150 Ma); seafloor spreading at the margins of the growing Pacific plate, and between North and South America (140 Ma); magmatism flare-up along the SW Pacific Whitsunday Volcanic Province–Median Batholith (130 Ma); a change from extension in the Clarence basin, eastern Australia, to uplift of the Great Dividing Range (114 Ma); Pamir Mountains uplift, foreland basin dynamics and high eustatic sea-levels leading to marine transgression of the proto-Paratethys Ocean eastward to Central Asia and Xinjiang (100 Ma); predrift rifting and seafloor spreading west of New Caledonia (100–50 Ma); sinistral strike-slip displacement along the proto-Alpine fault, New Zealand (100–80 Ma); thrust faulting in the Longmen Shan and foreland basin dynamics around the Sichuan Basin (85 Ma); pre-drift rifting in the Coral Sea basin (85 Ma); and dextral displacement on the Alpine fault (20 Ma).</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 4","pages":"293-336"},"PeriodicalIF":3.6,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9889588","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
Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae) 分子系统发育、分化时间、生物地理学和寄主植物使用趋势在农业上重要的tortricid部落Grapholitini(鳞翅目:Tortricidae:Olethrutinae)。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-05-20 DOI: 10.1111/cla.12543
Gui-Lin Hu, John Brown, Maria Heikkilä, Leif Aarvik, Marko Mutanen
{"title":"Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae)","authors":"Gui-Lin Hu,&nbsp;John Brown,&nbsp;Maria Heikkilä,&nbsp;Leif Aarvik,&nbsp;Marko Mutanen","doi":"10.1111/cla.12543","DOIUrl":"10.1111/cla.12543","url":null,"abstract":"<p>The leaf-roller moth tribe Grapholitini comprises about 1200 described species and contains numerous notorious pests of fruits and seeds. The phylogeny of the tribe has been little studied using contemporary methods, and the monophyly of several genera remains questionable. In order to provide a more robust phylogenetic framework for the group, we conducted a multiple-gene phylogenetic analysis of 104 species representing 27 genera of Grapholitini and 29 outgroup species. Divergence time, ancestral area, and host plant usage were also inferred to explore evolutionary trends in the tribe. Our analyses indicate that <i>Larisa</i> and <i>Corticivora</i>, traditionally assigned to Grapholitini, are best excluded from the tribe. After removal of these two genera, the tribe is found to be monophyletic, represented by two major lineages—a <i>Dichrorampha</i> clade and a <i>Cydia</i> clade, the latter of which can be divided into seven generic groups. The genus <i>Grapholita</i> was found to be polyphyletic, comprising three different clades, and we propose three genera to accommodate these groups: <i>Grapholita</i> (sensu stricto), <i>Aspila</i> (formerly a subgenus of <i>Grapholita</i>) and <i>Ephippiphora</i> (formerly considered a synonym of <i>Grapholita</i>). We summarize each generic group, including related genera not included in our analysis, providing morphological, pheromone and food plant characters that support particular branches within the molecular hypotheses. Biogeographical analyses indicate that Grapholitini probably originated in the Nearctic, Afrotropical and Neotropical regions in the Lutetian of the middle Eocene (ca. 44.3 Ma). Our results also indicate that most groups in Grapholitini originated from Fabaceae-feeding monophagous or oligophagous ancestors, and that host plant shifts probably promoted species diversification within the tribe.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"359-381"},"PeriodicalIF":3.6,"publicationDate":"2023-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12543","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217778","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
Himalayan upliftment and Shiwalik succession act as a cradle for divergence in Bengal monitor lizard Varanus bengalensis (Reptilia: Varanidae) in India 喜马拉雅山脉的隆起和排灯节的演替是印度孟加拉巨蜥Varanus bengalensis(爬行纲:Varanidae)分化的摇篮。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-05-18 DOI: 10.1111/cla.12542
Kumudani Bala Gautam, Ajit Kumar, Abhijit Das, Sandeep Kumar Gupta
{"title":"Himalayan upliftment and Shiwalik succession act as a cradle for divergence in Bengal monitor lizard Varanus bengalensis (Reptilia: Varanidae) in India","authors":"Kumudani Bala Gautam,&nbsp;Ajit Kumar,&nbsp;Abhijit Das,&nbsp;Sandeep Kumar Gupta","doi":"10.1111/cla.12542","DOIUrl":"10.1111/cla.12542","url":null,"abstract":"<p>The Himalayan foothills and associated environment are well-known for driving the rapid diversification of many species and the formation of biodiversity hotspots. The effects of environmental change since the Miocene have accelerated species diversification, and hence are useful for studying population genetic structure, and evolutionary relationships via genetic approaches. To date, the effects of climatic fluctuations on the biogeography of large-bodied lizards have not been assessed comprehensively. Herein, we examine the diversification of <i>Varanus bengalensis</i>, focusing on its genetic structure to provide insights into how landscape structure and climatic fluctuations have shaped species differentiation. We confirm the existence of two distinct lineages within <i>V. bengalensis</i> distributed across the Himalayan foothills and the remainder of mainland India. Divergence analyses revealed the split between the Himalayan foothills and the remainder of the mainland lineages of <i>V. bengalensis</i> in the mid-Pliocene ~3.06 Ma, potentially as a consequence of the Siwalik broadening and climatic fluctuations across the Himalayan foothills. The results suggest recognition of a new lineage of <i>V. bengalensis</i> from the Himalayan foothills as a distinctive evolutionarily significant unit.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"382-397"},"PeriodicalIF":3.6,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10216453","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
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses 利用系统发育学联合分析的整体成功解析来量化基因树与多面体之间的一致性。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-04-25 DOI: 10.1111/cla.12540
Mark P. Simmons, Pablo A. Goloboff, Ben C. Stöver, Mark S. Springer, John Gatesy
{"title":"Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses","authors":"Mark P. Simmons,&nbsp;Pablo A. Goloboff,&nbsp;Ben C. Stöver,&nbsp;Mark S. Springer,&nbsp;John Gatesy","doi":"10.1111/cla.12540","DOIUrl":"10.1111/cla.12540","url":null,"abstract":"<p>Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-tree branches with 0% approximate-likelihood-ratio-test (SH-like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (<span>congsort</span>), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson–Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene-tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent-tree clades that contradicted concatenation-tree clades were generally less robust to gene-tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene-tree clades (0% SH-like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony-based analyses) for improving quantification of gene-tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene-tree-estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"418-436"},"PeriodicalIF":3.6,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12540","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217731","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
A unified view of homology 同源性的统一观点。
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-04-25 DOI: 10.1111/cla.12541
Igor Ballego-Campos, Stéphani K. V. Bonifácio, Leandro C. S. Assis
{"title":"A unified view of homology","authors":"Igor Ballego-Campos,&nbsp;Stéphani K. V. Bonifácio,&nbsp;Leandro C. S. Assis","doi":"10.1111/cla.12541","DOIUrl":"10.1111/cla.12541","url":null,"abstract":"<p>As it spread through time and into distinct areas of science—from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology—the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of ‘concepts of homology’; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 ‘concepts of homology’ in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller’s five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 5","pages":"398-417"},"PeriodicalIF":3.6,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10219689","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
Splitting one species into 22: an unusual tripling of molecular, morphological, and geographical differentiation in the fern family Didymochlaenaceae (Polypodiales) 将一种分裂为22种:双足蕨科(水螅目)中分子、形态和地理分化的不寻常的三倍
IF 3.6 2区 生物学
Cladistics Pub Date : 2023-04-21 DOI: 10.1111/cla.12539
Hui Shang, Zhi-Qing Xue, Zhen-Long Liang, Michael Kessler, Rossarin Pollawatn, Ngan Thi Lu, Yu-Feng Gu, Xue-Ping Fan, Yun-Hong Tan, Liang Zhang, Xin-Mao Zhou, Xia Wan, Li-Bing Zhang
{"title":"Splitting one species into 22: an unusual tripling of molecular, morphological, and geographical differentiation in the fern family Didymochlaenaceae (Polypodiales)","authors":"Hui Shang,&nbsp;Zhi-Qing Xue,&nbsp;Zhen-Long Liang,&nbsp;Michael Kessler,&nbsp;Rossarin Pollawatn,&nbsp;Ngan Thi Lu,&nbsp;Yu-Feng Gu,&nbsp;Xue-Ping Fan,&nbsp;Yun-Hong Tan,&nbsp;Liang Zhang,&nbsp;Xin-Mao Zhou,&nbsp;Xia Wan,&nbsp;Li-Bing Zhang","doi":"10.1111/cla.12539","DOIUrl":"10.1111/cla.12539","url":null,"abstract":"<p>The pantropical fern genus <i>Didymochlaena</i> (Didymochlaenaceae) has long been considered to contain one species only. Recent studies have resolved this genus/family as either sister to the rest of eupolypods I or as the second branching lineage of eupolypods I, and have shown that this genus is not monospecific, but the exact species diversity is unknown. In this study, a new phylogeny is reconstructed based on an expanded taxon sampling and six molecular markers. Our major results include: (i) <i>Didymochlaena</i> is moderately or weakly supported as sister to the rest of eupolypods I, highlighting the difficulty in resolving the relationships of this important fern lineage in the polypods; (ii) species in <i>Didymochlaena</i> are resolved into a New World clade and an Old World clade, and the latter further into an African clade and an Asian-Pacific clade; (iii) an unusual tripling of molecular, morphological and geographical differentiation in <i>Didymochlaena</i> is detected, suggesting single vicariance or dispersal events in individual regions and no evidence for reversals at all, followed by allopatric speciation at more or less homogeneous rates; (iv) evolution of 18 morphological characters is inferred and two morphological synapomorphies defining the family are recognized—the elliptical sori and fewer than 10 sori per pinnule, the latter never having been suggested before; (v) based on morphological and molecular variation, 22 species in the genus are recognized contrasting with earlier estimates of between one and a few; and (vi) our biogeographical analysis suggests an origin for <i>Didymochlaena</i> in the latest Jurassic–earliest Cretaceous and the initial diversification of the extant lineages in the Miocene—all but one species diverged from their sisters within the last 27 Myr, in most cases associated with allopatric speciation owing to geologic and climatic events, or dispersal.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 4","pages":"273-292"},"PeriodicalIF":3.6,"publicationDate":"2023-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10192184","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
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