Cladistics最新文献

{"title":"Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae)","authors":"Paola A. Carrasco,&nbsp;Claudia Koch,&nbsp;Felipe G. Grazziotin,&nbsp;Pablo J. Venegas,&nbsp;Juan C. Chaparro,&nbsp;Gustavo J. Scrocchi,&nbsp;David Salazar-Valenzuela,&nbsp;Gerardo C. Leynaud,&nbsp;Camilo I. Mattoni","doi":"10.1111/cla.12522","DOIUrl":"10.1111/cla.12522","url":null,"abstract":"<p>Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers, the most taxon/character comprehensive phylogeny to date. Our analysis includes all genera, morphological data from external morphology, cranial osteology and hemipenial morphology, and DNA sequences from mitochondrial and nuclear genes. We performed analyses with parsimony as an optimality criterion, using different schemes for character weighting. We evaluated the contribution of the different sources of characters to the phylogeny through analyses of reduced datasets and calculation of weighted homoplasy and retention indexes. We performed a morphological character analysis to identify synapomorphies for the main clades. In terms of biogeography, our results support a single colonization event of the Americas by pitvipers, and a cladogenetic event into a Neotropical clade and a North American/Neotropical clade. The results also shed light on the previously unstable position of some taxa, although they could not sufficiently resolve the position of <i>Bothrops lojanus</i>, which may lead to the paraphyly of either <i>Bothrops</i> or <i>Bothrocophias</i>. The morphological character analyses demonstrated that an important phylogenetic signal is contained in characters related to head scalation, the jaws and the dorsum of the skull, and allowed us to detect morphological convergences in external morphology associated with arboreality.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 2","pages":"71-100"},"PeriodicalIF":3.6,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9184944","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":"TNT version 1.6, with a graphical interface for MacOS and Linux, including new routines in parallel","authors":"Pablo A. Goloboff,&nbsp;Martín E. Morales","doi":"10.1111/cla.12524","DOIUrl":"10.1111/cla.12524","url":null,"abstract":"<p>A new graphical user interface (GUI) for the parsimony program TNT is presented that works under the Linux and Mac operating systems, as well as the Cygwin environment (which runs under Windows). The new interface is based on the GIMP Tool Kit, GTK (version 3). Formerly, only Windows versions of TNT had a GUI. The new interface improves upon the existing Windows GUI in several respects. These changes, together with several additions to the program since the publication of version 1.5, warrant a change in minor version, thus moving from version 1.5 to 1.6. Among the most notable improvements are the possibility to access graphical user dialogs by means of simple commands, to easily save trees in SVG format (“Scalable Vector Graphics”) directly from any tree-diagram being displayed, and to manage analyses in parallel (using multiple processors, by means of the PVM system or “Parallel Virtual Machine”), as well as a generally more stable and consistent behaviour. As the binaries for the new version are compiled as native 64-bit applications, this removes the limitations for accessing large amounts of memory in the previous GUI Windows interface (which is a 32-bit application).</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 2","pages":"144-153"},"PeriodicalIF":3.6,"publicationDate":"2023-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9178260","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":"Phylogenomics and systematics of Entomobryoidea (Collembola): marker design, phylogeny and classification","authors":"Nerivania Nunes Godeiro,&nbsp;Yinhuan Ding,&nbsp;Nikolas Gioia Cipola,&nbsp;Sopark Jantarit,&nbsp;Bruno Cavalcante Bellini,&nbsp;Feng Zhang","doi":"10.1111/cla.12521","DOIUrl":"10.1111/cla.12521","url":null,"abstract":"<p>Entomobryoidea has been the focus of phylogenetic studies in recent years owing to a divergence between morphological and genetic data. Recent phylogenies have converged on the sister relationship of Orchesellidae with the remaining Entomobryoidea, and on the non-monophyly of the traditional Paronellidae and Entomobryidae, but still lack resolution. Known molecular phylogenies of the superfamily differ greatly between mitogenomic and multilocus markers. For this reason, we designed universal single-copy orthologue (USCO) and ultraconserved element (UCE) marker sets specific for Entomobryoidea, based on 11 genome assemblies. Upon the newly designed 3406 USCOs and 4030 UCEs, we analysed 34 species covering all Entomobryoidea families and major subfamilies. New data for 26 species were mined from whole-genome sequencing. Phylogenetic inference confirmed the Orchesellidae as an independent family and the Entomobryinae remained the most puzzling taxon gathering scaled and unscaled lineages of both traditional Entomobryidae and Paronellidae. To accommodate <i>Paronellides</i>, <i>Zhuqinia</i> and related genera, Paronellidinae subfam. nov. is proposed within Entomobryidae. The sampled representatives of Paronellinae were recovered as the sister group of (Seirinae+Lepidocyrtinae), suggesting that reduction on the dorsal macrochaetotaxy and trunk sensillar pattern may have occurred independently within the Lepidocyrtinae and Paronellinae or represent their symplesiomorphy posteriorly modified in the Seirinae. The current systematics of the superfamily are revised here, with Entomobryidae now comprising six subfamilies, including all taxa with smooth dens. Our data also point out that all the main events of cladogenesis of the families and subfamilies of Entomobryoidea occurred during the Jurassic. Our genome-scale phylogenomics provides a complete, reliable example for systematics of Entomobryoidea, as well as other invertebrates in the big data era.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 2","pages":"101-115"},"PeriodicalIF":3.6,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9189346","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":"Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude","authors":"Kamil Hupało,&nbsp;Denis Copilaș-Ciocianu,&nbsp;Florian Leese,&nbsp;Martina Weiss","doi":"10.1111/cla.12520","DOIUrl":"10.1111/cla.12520","url":null,"abstract":"<p>DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within <i>Echinogammarus sicilianus</i>. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence = 1.8–20.3%), co-occurring in syntopy at two-thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co-occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI-based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 2","pages":"129-143"},"PeriodicalIF":3.6,"publicationDate":"2022-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12520","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9549745","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":"The oldest Gondwanan fossil of Leiinae (Diptera, Mycetophilidae): Phylogenetic and evolutionary implications","authors":"Dalton de Souza Amorim,&nbsp;Sarah Siqueira Oliveira,&nbsp;Daniel Dias Dornelas do Carmo,&nbsp;Guilherme Cunha Ribeiro","doi":"10.1111/cla.12519","DOIUrl":"10.1111/cla.12519","url":null,"abstract":"<p>A fossil Mycetophilidae from the Aptian Crato Formation—<i>Cretomanota gondwanica</i> gen. nov., sp. nov.—is described, which is the first mycetophilid from the Crato Formation and corresponds to the oldest known fossil leiine and only the second Gondwanan fossil mycetophilid described so far. <i>Cretomanota gondwanica</i> and both species of <i>Alavamanota</i> Blagoderov and Arillo were added as terminals to the data matrix of a general phylogenetic analysis of the Mycetophilidae, and both fit into the Leiinae. <i>Alavamanota</i> is monophyletic, sister to the clade composed by <i>Cretomanota</i> and the extant genus <i>Manota</i> Williston. The biology of the extant members of this fungivorous family corroborates the reconstruction of the Crato palaeoenvironment as including woodlands with humid habitats and microhabitats. The presence of a Cretaceous member of the tribe Manotini at low latitudes in South America reinforces the hypothesis that the clade with all manotines except <i>Leiella</i> Edwards corresponds to a Lower Cretaceous offshoot from a group in southern Gondwana expanding its distribution to more northern areas into the Gondwana and into Laurasia.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 1","pages":"43-57"},"PeriodicalIF":3.6,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9183452","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":"When phylogenetics met biogeography: Willi Hennig, Lars Brundin and the roots of phylogenetic and cladistic biogeography","authors":"Juan J. Morrone","doi":"10.1111/cla.12517","DOIUrl":"10.1111/cla.12517","url":null,"abstract":"<p>Willi Hennig's (Beitr. Ent. 1960, 10, 15) <i>Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem</i> applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to <i>a posteriori</i> methods of cladistic biogeography is erroneous and should be avoided.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 1","pages":"58-69"},"PeriodicalIF":3.6,"publicationDate":"2022-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12517","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9188669","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":"Molecular phylogeny of the tropical wandering spiders (Araneae, Ctenidae) and the evolution of eye conformation in the RTA clade","authors":"Nicolas A. Hazzi,&nbsp;Gustavo Hormiga","doi":"10.1111/cla.12518","DOIUrl":"10.1111/cla.12518","url":null,"abstract":"<p>Tropical wandering spiders (Ctenidae) are a diverse group of cursorial predators with its greatest species richness in the tropics. Traditionally, Ctenidae are diagnosed based on the presence of eight eyes arranged in three rows (a 2–4–2 pattern). We present a molecular phylogeny of Ctenidae, including for the first time representatives of all of its subfamilies. The molecular phylogeny was inferred using five nuclear (histone H3, 28S, 18S, Actin and ITS-2) and four mitochondrial (NADH, COI, 12S and 16S) markers. The final matrix includes 259 terminals, 103 of which belong to Ctenidae and represent 28 of the current 49 described genera. We estimated divergence times by including fossils as calibration points and biogeographic events, and used the phylogenetic hypothesis obtained to reconstruct the evolution of the eye conformation in the retrolateral tibial apophysis (RTA) clade. Ctenidae and its main lineages originated during the Paleocene–Eocene and have diversified in the tropics since then. However, in some analyses Ctenidae was recovered as polyphyletic as the genus <i>Ancylometes</i> Bertkau, 1880 was placed as sister to Oxyopidae. Except for Acantheinae, in which the type genus <i>Acantheis</i> Thorell, 1891 is placed inside Cteninae, the four recognized subfamilies of Ctenidae are monophyletic in most analyses. The ancestral reconstruction of the ocular conformation in the retrolateral tibial apophysis clade suggests that the ocular pattern of Ctenidae has evolved convergently seven times and that it has originated from ocular conformations of two rows of four eyes (4–4) and the ocular pattern of lycosids (4–2–2). We also synonymize the monotypic genus <i>Parabatinga</i> Polotov &amp; Brescovit, 2009 with <i>Centroctenus</i> Mello-Leitão, 1929. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework offered by the molecular phylogenetic results of the study.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 1","pages":"18-42"},"PeriodicalIF":3.6,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9175671","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":"Issue Information","authors":"","doi":"10.1176/rcp2.1050","DOIUrl":"https://doi.org/10.1176/rcp2.1050","url":null,"abstract":"","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47927992","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":"Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents","authors":"Andrea Dalmasso,&nbsp;Pablo Peláez-Campomanes,&nbsp;Raquel López-Antoñanzas","doi":"10.1111/cla.12516","DOIUrl":"10.1111/cla.12516","url":null,"abstract":"<p>Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"38 6","pages":"702-710"},"PeriodicalIF":3.6,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10632679","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":"Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex","authors":"Anthony I. Cognato,&nbsp;William Taft,&nbsp;Rachel K. Osborn,&nbsp;Daniel Rubinoff","doi":"10.1111/cla.12515","DOIUrl":"10.1111/cla.12515","url":null,"abstract":"Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi‐gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting that it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"39 1","pages":"1-17"},"PeriodicalIF":3.6,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12515","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9532489","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}