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A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae) Cladistics (IF 4.727) Pub Date : 2020-12-26 Liping Yan; Eliana Buenaventura; Thomas Pape; Sujatha Narayanan Kutty; Keith M. Bayless; Dong Zhang
The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life‐history, we inferred a backbone phylogeny based on transcriptomic
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Burrowing into the forest: Phylogeny of the Asian forest scorpions (Scorpionidae: Heterometrinae) and the evolution of ecomorphotypes Cladistics (IF 4.727) Pub Date : 2020-12-24 Stephanie F. Loria; Lorenzo Prendini
Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) are distributed across South and Southeast Asia. All are fossorial, constructing burrows under stones or in open ground, in habitats differing in precipitation and vegetation cover, from rainforests and tropical deciduous forests to savanna and scrubland. The systematics of these scorpions has long been confused due to
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Marimbondos: systematics, biogeography, and evolution of social behaviour of neotropical swarm‐founding wasps (Hymenoptera: Vespidae: Epiponini) Cladistics (IF 4.727) Pub Date : 2020-12-19 Fernando B. Noll; Marjorie da Silva; Raduan A. Soleman; Rogério B. Lopes; Yuri C. Grandinete; Eduardo A. B. Almeida; John W. Wenzel; James M. Carpenter
Neotropical swarm‐founding wasps are divided into 19 genera in the tribe Epiponini (Vespidae, Polistinae). They display extensive variation in several colony‐level traits that make them an attractive model system for reconstructing the evolution of social phenotypes, including caste dimorphism and nest architecture. Epiponini has been upheld as a solid monophyletic group in most phylogenetic analyses
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Analysis of endemism of world arthropod distribution data supports biogeographic regions and many established subdivisions Cladistics (IF 4.727) Pub Date : 2020-12-19 Jonathan Liria; Claudia A. Szumik; Pablo A. Goloboff
We analyzed 769 242 occurrence records for 115 424 species of terrestrial arthropods, from three biodiversity repositories (Global Biodiversity Information Facility (GBIF), Natural History Museum, London, and “Sistema de Informação Distribuído para Coleções Biológicas” (SpeciesLink)), to test the use of global‐scale data points for quantitative assessments of areas of endemism. The data include Insecta
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Total‐evidence backbone phylogeny of Aleocharinae (Coleoptera: Staphylinidae) Cladistics (IF 4.727) Pub Date : 2020-12-18 Igor Orlov; Richard A.B. Leschen; Dagmara Żyła; Alexey Solodovnikov
Phylogenetic studies of Aleocharinae rove beetles, arguably one of the least known and the largest insect lineages, are compromised by its enormous taxonomic diversity. DNA, a powerful resource for phylogenetics, is not available for numerous extant aleocharine species. We provide a broad comparative morphological study of Aleocharinae to frame molecular datasets for total‐evidence analyses. Using
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Total evidence and sensitivity phylogenetic analyses of egg‐brooding frogs (Anura: Hemiphractidae) Cladistics (IF 4.727) Pub Date : 2020-12-17 Lourdes Y. Echevarría; Ignacio De la Riva; Pablo J. Venegas; Fernando J.M. Rojas‐Runjaic; Iuri R. Dias; Santiago Castroviejo‐Fisher
We study the phylogenetic relationships of egg‐brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell‐shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids
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Two centuries of distribution data: detection of areas of endemism for the Brazilian angiosperms Cladistics (IF 4.727) Pub Date : 2020-12-14 Janaína Gomes‐da‐Silva; Rafaela Campostrini Forzza
Brazil has high levels of biodiversity and has received strong criticism for the increasing country‐wide deforestation that threatens it. Although a significant percentage of land area in Brazil is protected, the areas are insufficient and unevenly distributed. Many studies have contributed to the biogeographical knowledge of Brazilian flora, but no endemicity analysis (EA) has been conducted including
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Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae) Cladistics (IF 4.727) Pub Date : 2020-11-26 Jean‐Yves Rasplus; Lillian Jennifer Rodriguez; Laure Sauné; Yang‐Qiong Peng; Anthony Bain; Finn Kjellberg; Rhett D. Harrison; Rodrigo A.S. Pereira; Rosichon Ubaidillah; Christine Tollon‐Cordet; Mathieu Gautier; Jean‐Pierre Rossi; Astrid Cruaud
Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction‐site‐associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase
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Molecular phylogeny and trait evolution of Madeiran land snails: radiation of the Geomitrini (Stylommatophora: Helicoidea: Geomitridae) Cladistics (IF 4.727) Pub Date : 2020-10-29 Alissa Brozzo; Josef Harl; Willy De Mattia; Dinarte Teixeira; Frank Walther; Klaus Groh; Barna Páll‐Gergely; Matthias Glaubrecht; Bernhard Hausdorf; Marco T. Neiber
The Geomitrini is the most species‐rich group of land snails in the Madeiran Archipelago. The phylogeny of the group is reconstructed based on mitochondrial and nuclear genetic markers. The timing of diversification, the colonisation history of the islands of the Madeiran Archipelago and the evolution of characters of the dart apparatus are studied. The results of the phylogenetic analyses confirm
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Phenotypic characters of static homology increase phylogenetic stability under direct optimization of otherwise dynamic homology characters Cladistics (IF 4.727) Pub Date : 2020-10-29 Samuli Lehtonen
Direct optimization of unaligned sequence characters provides a natural framework to explore the sensitivity of phylogenetic hypotheses to variation in analytical parameters. Phenotypic data, when combined into such analyses, are typically analyzed with static homology correspondences unlike the dynamic homology sequence data. Static homology characters may be expected to constrain the direct optimization
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Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae) Cladistics (IF 4.727) Pub Date : 2020-11-20 Xuankun Li; Luisa C. Teasdale; Keith M. Bayless; Allan G. Ellis; Brian M. Wiegmann; Carlos José E. Lamas; Christine L. Lambkin; Neal L. Evenhuis; James A. Nicholls; Diana Hartley; Seunggwan Shin; Michelle Trautwein; Andreas Zwick; Bryan D. Lessard; David K. Yeates
Bombyliidae is a very species‐rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present‐day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were
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Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family‐level relationships Cladistics (IF 4.727) Pub Date : 2020-11-09 Jorge R. Flores; Alexander C. Bippus; Guillermo M. Suárez; Jaakko Hyvönen
In recent years, the use of extensive molecular and morphological datasets has clarified the phylogenetic relationships among the orders of complex thalloid liverworts (Marchantiidae). However, previous studies excluded extinct taxa; thereby, undersampling the actual taxonomic diversity of the group. Here, we conducted a total‐evidence analysis of Marchantiidae incorporating fossils. The combined dataset
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Phylogeny of Lithobiidae Newport, 1844, with emphasis on the megadiverse genus Lithobius Leach, 1814 (Myriapoda, Chilopoda) Cladistics (IF 4.727) Pub Date : 2020-11-04 Anne‐Sarah Ganske; Varpu Vahtera; László Dányi; Gregory D. Edgecombe; Nesrine Akkari
Phylogenetic analyses based on molecular and morphological data were conducted to shed light on relationships within the mostly Palaearctic/Oriental centipede family Lithobiidae, with a particular focus on the Palaearctic genus Lithobius Leach, 1814 (Lithobiidae, Lithobiomorpha), which contains >500 species and subspecies. Previous studies based on morphological data resolved Lithobius as nonmonophyletic
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Phylogenetic relationships and revised classification of the true bug infraorder Dipsocoromorpha (Insecta: Hemiptera: Heteroptera) Cladistics (IF 4.727) Pub Date : 2020-11-04 Alexander Knyshov; Christiane Weirauch; Rochelle Hoey‐Chamberlain
Currently comprising only about 430 species, Dipsocoromorpha or minute litter bugs are one of the small infraorders of Heteroptera. They are classified into five morphologically distinct families––Ceratocombidae, Dipsocoridae, Hypsipterygidae, Schizopteridae and Stemmocryptidae––but relationships among and within these families are poorly understood owing to the lack of phylogenetic studies. A phylogenetic
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Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web Cladistics (IF 4.727) Pub Date : 2020-10-29 Robert J. Kallal; Siddharth S. Kulkarni; Dimitar Dimitrov; Ligia R. Benavides; Miquel A. Arnedo; Gonzalo Giribet; Gustavo Hormiga
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long‐standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages
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Repeated colonization, adaptive radiation and convergent evolution in the sheet‐weaving spiders (Linyphiidae) of the south Pacific Archipelago of Juan Fernandez Cladistics (IF 4.727) Pub Date : 2020-10-29 Miquel A. Arnedo; Gustavo Hormiga
We report on the colonization and diversification of linyphiid spiders in the Pacific oceanic archipelago of Juan Fernandez. About 50 spider species occur naturally in these islands, most of them endemic and about half of them are linyphiids. Linyphiidae includes no fewer than 15 species of Laminacauda and three of Neomaso (with several additional undescribed species in the latter genus), all of them
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The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae) Cladistics (IF 4.727) Pub Date : 2020-09-13 Victor G.D. Orrico; Taran Grant; Julian Faivovich; Mauricio Rivera‐Correa; Marco A. Rada; Mariana L. Lyra; Carla S. Cassini; Paula H. Valdujo; Walter E. Schargel; Denis J. Machado; Ward C. Wheeler; Cesar Barrio‐Amorós; Daniel Loebmann; Jiří Moravec; Juliana Zina; Mirco Solé; Marcelo J. Sturaro; Pedro L.V. Peloso; Pablo Suarez; Célio F.B. Haddad
The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial
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On the value of Burmese amber for understanding insect evolution: Insights from †Heterobathmilla – an exceptional stem group genus of Strepsiptera (Insecta) Cladistics (IF 4.727) Pub Date : 2020-09-10 Hans Pohl; Benjamin Wipfler; Brendon Boudinot; Rolf Georg Beutel
Burmese amber and amber from other periods and regions became a rich source of new extinct insect species and yielded important insights in insect evolution in the dimension of time. Amber fossils have contributed to the understanding of the phylogeny, biology, and biogeography of insects and other groups, and have also gained great importance for dating molecular trees. Another major potential is
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Dasycerine rove beetles: Cretaceous diversification, phylogeny and historical biogeography (Coleoptera: Staphylinidae: Dasycerinae) Cladistics (IF 4.727) Pub Date : 2020-07-29 Zi‐Wei Yin; Liang Lü; Shûhei Yamamoto; Margaret K. Thayer; Alfred F. Newton; Chen‐Yang Cai
Within the hyperdiverse beetle family Staphylinidae, Dasycerinae is one of the smallest and most cryptic subfamilies, comprising a sole extant genus characterized by a latridiid beetle‐like body form. Little has been known about their early diversification, character evolution, phylogeny and historical biogeography because of limited fossil material and lack of a phylogeny integrating extant and extinct
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Origins of SARS‐CoV‐1 and SARS‐CoV‐2 are often poorly explored in leading publications Cladistics (IF 4.727) Pub Date : 2020-07-30 John Wenzel
In the rush to understand the coronaviruses that threaten human health, authors of many prominent papers have not performed phylogenetic analyses to the standard of the field today. Errors include faulty placement of the root of the phylogeny, outdated methods of reconstruction, poor taxon sampling, inappropriate emphasis on selected functional elements, and inadequate consideration of ambiguity. As
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Epidemiology needs more interdisciplinary teams with expertise in molecular systematics, public health and food safety Cladistics (IF 4.727) Pub Date : 2020-07-30 Marc W. Allard, Eric W. Brown
What are considered fundamental principles within the Willi Hennig Society and published in their journal are not always fully appreciated by many other biological fields that have not been schooled in these disciplines of systematics principles and the reasons for why these principles are important (Wenzel, Cladistics, 2020, in press). Natural history museums and their associated programs have been
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Corrigendum of Zhao et al. (2020): a revised infrageneric classification of Lepisorus (Polypodiaceae) Cladistics (IF 4.727) Pub Date : 2020-07-20 Cun‐Feng Zhao, Ran Wei, Xian‐Chun Zhang
Here, we publish Lepisorus sect. Paragramma (Blume) C.F. Zhao, R. Wei & X.C. Zhang as a combinatio nova to replace the section name in Zhao et al. (2020), which was published as a status nova and turned out to be an invalid name, because we cited an incorrect basionym. A revised infrageneric classification of Lepisorus also is proposed.
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Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae) Cladistics (IF 4.727) Pub Date : 2020-07-14 Chase H. Smith; John M. Pfeiffer; Nathan A. Johnson
Freshwater mussels are a species‐rich group with biodiversity patterns strongly shaped by a life history strategy that includes an obligate parasitic larval stage. In this study, we set out to reconstruct the life history evolution and systematics in a clade of freshwater mussels adapted to parasitizing a molluscivorous host fish. Anchored hybrid enrichment and ancestral character reconstruction revealed
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Genomics‐based re‐examination of the taxonomy and phylogeny of human and simian Mastadenoviruses: an evolving whole genomes approach, revealing putative zoonosis, anthroponosis, and amphizoonosis Cladistics (IF 4.727) Pub Date : 2020-07-14 June Kang, Ashrafali Mohamed Ismail, Shoaleh Dehghan, Jaya Rajaiya, Marc W. Allard, Haw Chuan Lim, David W. Dyer, James Chodosh, Donald Seto
With the advent of high‐resolution and cost‐effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics‐based re‐evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines
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Sweet or salty? The origin of freshwater gastrotrichs (Gastrotricha, Chaetonotida) revealed by molecular phylogenetic analysis Cladistics (IF 4.727) Pub Date : 2020-07-06 Małgorzata Kolicka; Miroslawa Dabert; Ziemowit Olszanowski; Jacek Dabert
Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based
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Ultra‐Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea) Cladistics (IF 4.727) Pub Date : 2020-04-20 Astrid Cruaud; Gérard Delvare; Sabine Nidelet; Laure Sauné; Sujeevan Ratnasingham; Marguerite Chartois; Bonnie B. Blaimer; Michael Gates; Seán G. Brady; Sariana Faure; Simon van Noort; Jean‐Pierre Rossi; Jean‐Yves Rasplus
Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the
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Genetic capitalism and stabilizing selection of antimicrobial resistance genotypes in Escherichia coli Cladistics (IF 4.727) Pub Date : 2020-06-29 Colby T. Ford, Gabriel Lopez Zenarosa, Kevin B. Smith, David C. Brown, John Williams, Daniel Janies
Antimicrobial resistance (AMR) in pathogenic strains of bacteria, such as Escherichia coli (E. coli), adversely impacts personal and public health. In this study, we examine competing hypotheses for the evolution of AMR including (i) ‘genetic capitalism’ in which genotypes that confer antibiotic resistance are gained and not often lost in lineages, and (ii) ‘stabilizing selection’ in which genotypes
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Total‐evidence analysis of an undescribed fauna: resolving the evolution and classification of Australia’s golden trapdoor spiders (Idiopidae: Arbanitinae: Euoplini) Cladistics (IF 4.727) Pub Date : 2020-06-17 Jeremy D. Wilson; Robert J. Raven; Daniel J. Schmidt; Jane M. Hughes; Michael G. Rix
In the trapdoor spider genus Euoplos Rainbow & Pulleine (tribe Euoplini), it was discovered recently that two divergent lineages occur in sympatry in eastern Australia. This challenged the monogeneric classification of the tribe and, in combination with inadequate taxonomic descriptions of some species, precluded comprehensive taxonomic revision. To resolve these issues, we conducted a total‐evidence
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A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns Cladistics (IF 4.727) Pub Date : 2020-06-17 Marybel Soto Gomez; Qianshi Lin; Eduardo da Silva Leal; Timothy J. Gallaher; David Scherberich; Constantijn B. Mennes; Selena Y. Smith; Sean W. Graham
We used a bi‐organellar phylogenomic approach to address higher‐order relationships in Pandanales, including the first molecular phylogenetic study of the panama‐hat family, Cyclanthaceae. Our genus‐level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses
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Phylogeny and evolution of Mesozoic and extant lineages of Histeridae (Coleoptera), with discovery of a new subfamily Antigracilinae from the Lower Cretaceous Cladistics (IF 4.727) Pub Date : 2020-06-14 Yu‐Lingzi Zhou; Michael S. Caterino; Dong Ren; Adam Ślipiński
In order to place a newly discovered species Antigracilus costatus gen. sp. n. from the Lower Cretaceous Yixian Formation (China) and to assess previously unplaced fossil taxa, we investigated the relationships of extant and extinct lineages of Histeridae based on three data sets: (i) 69 morphological characters belonging to 48 taxa (representing all 11 subfamilies and 15 of 17 tribes of modern Histeridae);
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Exploring the phylogeny of the marattialean ferns Cladistics (IF 4.727) Pub Date : 2020-05-26 Samuli Lehtonen; Péter Poczai; Gaurav Sablok; Jaakko Hyvönen; Dirk N. Karger; Jorge Flores
The eusporangiate marattialean ferns represent an ancient radiation with a rich fossil record but limited modern diversity in the tropics. The long evolutionary history without close extant relatives has confounded studies of the phylogenetic origin, rooting and timing of marattialean ferns. Here we present new complete plastid genomes of six marattialean species and compiled a plastid genome dataset
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A dated phylogeny of Lardizabalaceae reveals an unusual long‐distance dispersal across the Pacific Ocean and the rapid rise of East Asian subtropical evergreen broadleaved forests in the late Miocene Cladistics (IF 4.727) Pub Date : 2020-04-07 Wei Wang; Xiao‐Guo Xiang; Kun‐Li Xiang; Rosa del C. Ortiz; Florian Jabbour; Zhi‐Duan Chen
Temperate South American–Asian disjunct distributions are the most unusual in organisms, and challenging to explain. Here, we address the origin of this unusual disjunction in Lardizabalaceae using explicit models and molecular data. The family (c.40 species distributed in ten genera) also provides an opportunity to explore the historical assembly of East Asian subtropical evergreen broadleaved forests
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Cretaceous and Eocene fossils of the rare extant genus Synneuron Lundstrom (Diptera: Canthyloscledidae): evidence of a true Pangean clade Cladistics (IF 4.727) Pub Date : 2020-03-29 Dalton de Souza Amorim, Dale E. Greenwalt
The first two fossil species of the canthyloscelid genus Synneuron are described based on compression wings. Synneuron eomontana sp. nov. is described from the Middle Eocene Coal Creek Member of the Kishenehn Formation, in the USA, and Synneuron jelli sp. nov. is described from the Lower Cretaceous Koonwarra Fossil Bed of the Korumburra Group, in Australia. The wings are illustrated and compared to
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The phylogeny of the Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini) Cladistics (IF 4.727) Pub Date : 2020-03-27 Boris L. Blotto; Mariana L. Lyra; Monica C.S. Cardoso; Miguel Trefaut Rodrigues; Iuri R. Dias; Euvaldo Marciano‐Jr; Francisco Dal Vechio; Victor G.D. Orrico; Reuber A. Brandão; Clodoaldo Lopes de Assis; Amanda S.F. Lantyer‐Silva; Mike G. Rutherford; Giussepe Gagliardi‐Urrutia; Mirco Solé; Diego Baldo; Ivan Nunes; Rodrigo Cajade; Ambrosio Torres; Taran Grant; Karl‐Heinz Jungfer; Helio R. da Silva; Célio
The South American and West Indian Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini) include 85 species. These are notably diverse in morphology (e.g. disparate levels of cranial hyperossification) and life history (e.g. different reproductive modes, chemical defences), have a wide distribution, and occupy habitats from the tropical rainforests to semiarid scrubland. In this paper, we present
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Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects Cladistics (IF 4.727) Pub Date : 2020-03-13 Fabien L. Condamine, André Nel, Philippe Grandcolas, Frédéric Legendre
Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass‐extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites
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Monophyletic classification and information content Cladistics (IF 4.727) Pub Date : 2020-03-01 James E. Hayden
The connection between monophyly and efficient taxonomic diagnoses is elaborated. The inefficiency of nonmonophyletic groups is shown by reconstructing data matrices from hierarchical sets of diagnoses that are derived from apomorphies and read in order from highest to lowest rank. The practice of diagnosing nonmonophyletic groups either results in omitting data, resulting in errors in reconstructed
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Evolutionary relationships of the ancient fern lineage the adder's tongues (Ophioglossaceae) with description of Sahashia gen. nov Cladistics (IF 4.727) Pub Date : 2020-01-17 Liang Zhang, Xue‐Ping Fan, Sahanat Petchsri, Lin Zhou, Rossarin Pollawatn, Xin Zhang, Xin‐Mao Zhou, Ngan Thi Lu, Ralf Knapp, Sahut Chantanaorrapint, Ponpipat Limpanasittichai, Hang Sun, Xin‐Fen Gao, Li‐Bing Zhang
As an ancient lineage of ferns, Ophioglossaceae are evolutionarily among the most fascinating because they have the highest chromosome count of any known organism as well as the presence of sporophores, subterranean gametophytes, eusporangiate sporangia without annuli, and endophytic fungi. Previous studies have produced conflicting results, identifyingsome lineages with unresolved relationships, and
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A species‐level total evidence phylogeny of the microteiid lizard family Alopoglossidae (Squamata: Gymnophthalmoidea) Cladistics (IF 4.727) Pub Date : 2020-01-13 Cristian Hernández Morales, Marcelo J. Sturaro, Pedro M. Sales Nunes, Sebastian Lotzkat, Pedro L.V. Peloso
Alopoglossidae is a family of Neotropical lizards composed of 23 species allocated in two genera (Alopoglossus and Ptychoglossus). There is a lack of knowledge about the phylogenetic relationships and systematics of this family. Published phylogenies that include alopoglossid species have very low taxon coverage within the family, and are usually based on limited character sampling. Considering these
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Divergence and support among slightly suboptimal likelihood gene trees Cladistics (IF 4.727) Pub Date : 2019-11-13 Mark P. Simmons, John Kessenich
Contemporary phylogenomic studies frequently incorporate two‐step coalescent analyses wherein the first step is to infer individual‐gene trees, generally using maximum‐likelihood implemented in the popular programs PhyML or RAxML. Four concerns with this approach are that these programs only present a single fully resolved gene tree to the user despite potential for ambiguous support, insufficient
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Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea Cladistics (IF 4.727) Pub Date : 2019-11-13 Katrin Braun, Fanny Leubner, Thomas Stach
With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently
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Morphological phylogeny of the Tegulinae (Mollusca: Vetigastropoda) reinforces a Turbinidae position Cladistics (IF 4.727) Pub Date : 2019-11-12 Ana Paula Dornellas, Diogo Ribeiro Couto, Luiz Ricardo L. Simone
A cladistic analysis of the Tegulinae (Turbinidae) is presented using 132 morphological characters and 41 taxa. Tegulinae is recovered and is sister to Prisogaster niger (Prisogasterinae) within the family Turbinidae. This scenario, with Tegulinae as a subfamily within Turbinidae, corroborates with the most molecular analyses. Tegulinae comprises >40 extant species, belonging to eight genera. Morphological
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Backbone phylogeny of Lepisorus (Polypodiaceae) and a novel infrageneric classification based on the total evidence from plastid and morphological data Cladistics (IF 4.727) Pub Date : 2019-09-25 Cun‐Feng Zhao, Ran Wei, Xian‐Chun Zhang, Qiao‐Ping Xiang
The fern genus Lepisorus represents one of the most complicated and controversial lineages in Polypodiaceae, with about 80 species which have been classified into several separate genera, and is notorious for its taxonomic difficulty. Despite progress in recent phylogenetic studies of the family Polypodiaceae involving Lepisorus and its allies, the deep phylogenetic relationship within this group of
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Evolution of endemic and sylvatic lineages of dengue virus Cladistics (IF 4.727) Pub Date : 2019-09-19 Lambodhar Damodaran, Adriano de Bernardi Schneider, Shi Chen, Daniel Janies
Recent disease outbreaks have raised awareness of tropical pathogens, especially mosquito‐borne viruses. Dengue virus (DENV) is a widely studied mammalian pathogen transmitted by various species of mosquito in the genus Aedes, especially Aedes aegypti and Aedes albopictus. The prevailing view of the research community is that endemic viral lineages that cause epidemics of DENV in humans have emerged
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To be biased or to be Neotropical: systematic reassessment of a megadiverse lineage of rove‐beetles (Philonthina, Staphylinini, Staphylininae) Cladistics (IF 4.727) Pub Date : 2019-08-12 Mariana Raquel Chani‐Posse, José Manuel Ramírez‐Salamanca
Classifications in the world's tropics often involve an early and sustained adoption of Holarctic‐based patterns. Such is the case of the megadiverse subtribe Philonthina and its Neotropical (NT) members, for which generic limits are ill‐defined due to an alleged high level of homoplasy. Although a recent total‐evidence study confirmed the monophyly of a NT lineage, most of its species are assigned
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Cladistic analysis of morphological data supports a position for Tegulinae (Mollusca: Vetigastropoda) within Turbinidae Cladistics (IF 4.727) Pub Date : 2019-08-09 Ana Paula Dornellas; Diogo Ribeiro Couto; Luiz Ricardo Simone
A cladistic analysis of the Tegulinae (Turbinidae) is presented using 132 morphological characters and 41 taxa. Tegulinae is recovered and is sister to Prisogaster niger (Prisogasterinae) within the family Turbinidae. This scenario, with Tegulinae as a subfamily within Turbinidae, corroborates most molecular analyses. Tegulinae comprises >40 extant species belonging to eight genera. Morphological studies
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Rexiella, a new name for Rexia S. Stenroos, Pino‐Bodas & Ahti (2018), non Rexia D. A. Casamatta, S. R. Gomez & J. R. Johansen (2006) Cladistics (IF 4.727) Pub Date : 2019-08-06 Soili Stenroos, Raquel Pino‐Bodas, Teuvo Ahti
A new generic name, Rexiella, is published to replace the recently published name Rexia S. Stenroos, Pino‐Bodas and Ahti, which turned out to be an illegitimate later homonym of the cyanobacterial genus Rexia D. A. Casamatta, S. R. Gomez and J. R. Johansen.
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Ronald Brady and the cladists Cladistics (IF 4.727) Pub Date : 2019-07-31 Malte C. Ebach, David M. Williams
Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics––that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that
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A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and evolution of leaf architecture Cladistics (IF 4.727) Pub Date : 2019-07-28 Li‐Yaung Kuo, Yi‐Hang Chang, Yu‐Hsuan Huang, Weston Testo, Atsushi Ebihara, Germinal Rouhan, Luis G. Quintanilla, James E. Watkins, Yao‐Moan Huang, Fay‐Wei Li
The thelypteroid fern genus Stegnogramma s.l. contains around 18–35 species and has a global, cross‐continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive
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Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales Cladistics (IF 4.727) Pub Date : 2019-07-22 Ying Yu, Jun‐Bo Yang, Wen‐Zhang Ma, Silvia Pressel, Hong‐Mei Liu, Yu‐Huan Wu, Harald Schneider
As one of the four main lineages diverging from the early diversification of land plants, the phylogeny of liverworts holds the information about nearly 500 Myr of independent adaptation to changing environments. Thus, resolving the phylogenetic history of liverworts will provide unique insights into the successful diversification of early land plants in terrestrial ecosystems. However, the deep diverging
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Comment on Phylogenetic analyses with four new Cretaceous bristletails reveal inter‐relationships of Archaeognatha and Gondwana origin of Meinertellidae Cladistics (IF 4.727) Pub Date : 2019-07-22 Matteo Montagna
Archaeognatha (Machilida plus †Monura), with ~450 extant species worldwide, represent a key lineage for the understanding of insect evolution. In a recently published phylogenetic analysis on Archaeognatha, based on a total‐evidence approach, a Machilidae key fossil (Gigamachilis triassicus) from the Middle Triassic Lagerstätte of Monte San Giorgio and a representative of †Monura (Dasyleptus triassicus)
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A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae) Cladistics (IF 4.727) Pub Date : 2019-07-11 Ke‐Wang Xu, Liang Zhang, Carl J. Rothfels, Alan R. Smith, Ronald Viane, David Lorence, Kenneth R. Wood, Cheng‐Wei Chen, Ralf Knapp, Lin Zhou, Ngan Thi Lu, Xin‐Mao Zhou, Hong‐Jin Wei, Qiang Fan, Su‐Fang Chen, Daniele Cicuzza, Xin‐Fen Gao, Wen‐Bo Liao, Li‐Bing Zhang
The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4‐trnS
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A comprehensive approach uncovers hidden diversity in freshwater mussels (Bivalvia: Unionidae) with the description of a novel species Cladistics (IF 4.727) Pub Date : 2019-07-02 Kentaro Inoue, John L. Harris, Clinton R. Robertson, Nathan A. Johnson, Charles R. Randklev
Major geological processes have shaped biogeographical patterns of riverine biota. The Edwards Plateau of central Texas, USA, exhibits unique aquatic communities and endemism, including several species of freshwater mussels. Lampsilis bracteata (Gould, 1855) is endemic to the Edwards Plateau region; however, its phylogenetic relationship with other species in the Gulf coastal rivers and Mississippi
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Phylogeny and diversification of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha) Cladistics (IF 4.727) Pub Date : 2019-04-29 Zhen Ye, Jakob Damgaard, Huanhuan Yang, Martin B. Hebsgaard, Tom Weir, Wenjun Bu
Climate fluctuations and tectonic reconfigurations associated with environmental changes play large roles in determining patterns of adaptation and diversification, but studies documenting how such drivers have shaped the evolutionary history and diversification dynamics of limnic organisms during the Mesozoic are scarce. Members of the heteropteran infraorder Nepomorpha, or aquatic bugs, are ideal
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Phylogeny of the orb‐weaving spider family Araneidae (Araneae: Araneoidea) Cladistics (IF 4.727) Pub Date : 2019-04-23 Nikolaj Scharff, Jonathan A. Coddington, Todd A. Blackledge, Ingi Agnarsson, Volker W. Framenau, Tamás Szűts, Cheryl Y. Hayashi, Dimitar Dimitrov
We present a new phylogeny of the spider family Araneidae based on five genes (28S, 18S, COI, H3 and 16S) for 158 taxa, identified and mainly sequenced by us. This includes 25 outgroups and 133 araneid ingroups representing the subfamilies Zygiellinae Simon, 1929, Nephilinae Simon, 1894, and the typical araneids, here informally named the “ARA Clade”. The araneid genera analysed here include roughly
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Do phytogeographic patterns reveal biomes or biotic regions? Cladistics (IF 4.727) Pub Date : 2019-04-10 Daniel J. Murphy, Malte C. Ebach, Joseph T. Miller, Shawn W. Laffan, Gerasimos Cassis, Visotheary Ung, Andrew H. Thornhill, Nunzio Kerr, Melinda L. Tursky
We present the largest comparative biogeographical analysis that has complete coverage of Australia's geography (20 phytogeographical subregions), using the most complete published molecular phylogenies to date of large Australian plant clades (Acacia, Banksia and the eucalypts). Two distinct sets of areas within the Australian flora were recovered, using distributional data from the Australasian Virtual
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Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion Cladistics (IF 4.727) Pub Date : 2019-03-25 Pablo A. Goloboff, J. Salvador Arias
A likelihood method that approximates the behaviour of implied weighting is described. This approach provides a likelihood perspective on several aspects of implied weighting, such as guidance for the choice of concavity values, a justification to use different concavities for different numbers of taxa, and a natural basis for extended implied weighting. In this approach, the number of free parameters
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Untangling the Echiniscus Gordian knot: paraphyly of the “arctomys group” (Heterotardigrada: Echiniscidae) Cladistics (IF 4.727) Pub Date : 2019-03-22 Piotr Gąsiorek, Witold Morek, Daniel Stec, Łukasz Michalczyk
The genus Echiniscus C.A.S. Schultze, 1840, one of the earliest established and speciose tardigrade genera, has been hypothesized to be polyphyletic. Moreover, the presence or absence of trunk appendages, the type of cuticular sculpturing and body colour have been argued to hold taxonomic significance at the genus level in Echiniscus‐line taxa. Here, by combining morphological and genetic analyses
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Background knowledge: the assumptions of pattern cladistics Cladistics (IF 4.727) Pub Date : 2019-03-22 Andrew V. Z. Brower
This paper reviews the ontogeny of pattern cladistics from the 1970s and 1980s, rebuts criticisms by contemporary anti‐cladists, and endeavours to clarify persistent misunderstandings about the philosophical foundations of the approach.
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Passive uplift of plant and animal populations during mountain‐building Cladistics (IF 4.727) Pub Date : 2019-03-18 Michael Heads
If a community and its substrate are raised by tectonic uplift, the species present can either die out in the area, survive in situ unchanged, or survive in situ with adaptation and differentiation. The large‐scale passive uplift of plant and animal populations during mountain‐building is accepted in a growing number of studies, but the idea has seldom been examined critically. If passive uplift does
更新日期:2019-03-18