scholarly journals Total evidence analysis of the phylogenetic relationships of Lycosoidea spiders (Araneae, Entelegynae)

2015 ◽  
Vol 29 (2) ◽  
pp. 124 ◽  
Author(s):  
Daniele Polotow ◽  
Anthea Carmichael ◽  
Charles E. Griswold
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Total Evidence ◽  
Base Pairs ◽  
New Family ◽  
Senior Synonym ◽  
Evidence Analysis ◽  
High Support

Phylogenetic relationships within the superfamily Lycosoidea are investigated through the coding and analysis of character data derived from morphology, behaviour and DNA sequences. In total, 61 terminal taxa were studied, representing most of the major groups of the RTA-clade (i.e. spiders that have a retrolateral tibial apophysis on the male palp). Parsimony and model-based approaches were used, and several support values, partitions and implied weighting schemes were explored to assess clade stability. The morphological–behavioural matrix comprised 96 characters, and four gene fragments were used: 28S (~737 base pairs), actin (~371 base pairs), COI (~630 base pairs) and H3 (~354 base pairs). Major conclusions of the phylogenetic analysis include: the concept of Lycosoidea is restricted to seven families: Lycosidae, Pisauridae, Ctenidae, Psechridae, Thomisidae, Oxyopidae (but Ctenidae and Pisauridae are not monophyletic) and also Trechaleidae (not included in the analysis); the monophyly of the ‘Oval Calamistrum clade’ (OC-clade) appears to be unequivocal, with high support, and encompassing the Lycosoidea plus the relimited Zoropsidae and the proposed new family Udubidae (fam. nov.); Zoropsidae is considered as senior synonym of Tengellidae and Zorocratidae (syn. nov.); Viridasiinae (rank nov.) is raised from subfamily to family rank, excluded from the Ctenidae and placed in Dionycha. Our quantitative phylogenetic analysis confirms the synonymy of Halidae with Pisauridae. The grate-shaped tapetum appears independently at least three times and has a complex evolutionary history, with several reversions.

Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)

Zootaxa ◽  
2012 ◽  
Vol 3315 (1) ◽  
pp. 1 ◽  
Author(s):  
FERNANDO LOBO ◽  
CRISTIAN ABDALA ◽  
SOLEDAD VALDECANTOS
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Diversity ◽  
Color Pattern ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Set ◽  
The North ◽  
South Central ◽  
Evidence Analysis ◽  
La Rioja

With 36 species and at least nine potentially independent lineages (not formally described yet) occurring mostly in theAndes and adjacent Patagonia and Puna plateau areas, Phymaturus lizards represent one of the most endemic vertebrategroups of the arid southwestern region of South America. Phylogenetic relationships among species of Phymaturus areinferred using mainly a morphological data set of 206 characters. Also available sequences of mitochondrial DNA for sev-en terminals were added for a total evidence analysis. Most information is included in the discrete characters block; mostcharacters involve color pattern, osteology and squamation. Continuous characters were taken from body proportions,squamation and skeletons. Among morphological data, binary polymorphic characters were analyzed applying the scaledcoding criteria. Continuous characters were entered in the analysis using standardized ranges, a method that allows a sim-ple optimization to estimate distances/costs avoiding the arbitrary coding as discrete characters. For our parsimony anal-yses we chose the implied weights method, which underweights homoplastic characters. Several runs were madeanalyzing all the information combined and also separating morphological from molecular datasets. Binary polymor-phisms were also analyzed as missing data. All characters affected by sexual dimorphism were analyzed separating thesexes; female information was more congruent with the total evidence analysis. Characters involving continuous and poly-morphic information are relevant for searching and building phylogenetic hypotheses in Phymaturus. There exists signif-icant congruence between the molecular information analyzed in this study and previous published analyses. Within bothmain clades of Phymaturus, northern subgroups are those more recently originated during the genus diversification. Spe-cies belonging to the puna subclade of the palluma group are arranged in two natural groups, one distributed in the north(Catamarca and La Rioja provinces), and the other in the south, La Rioja and San Juan provinces. Within the patagonicusgroup, the majority of the species are arranged in a south-central Chubut clade, eastern-central Chubut clade, central Rio Negro clade and a Payunia clade.

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

scholarly journals Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)

2017 ◽  
Vol 91 (4) ◽  
pp. 815-828 ◽  
Author(s):  
Selina R. Cole
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Major Group ◽  
Higher Taxa ◽  
Morphologic Evolution ◽  
Phylogenetic Framework ◽  
Selection For

AbstractThe subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.

scholarly journals Taxonomic Studies of Some often Over-Looked Diaporthomycetidae and Sordariomycetidae

2021 ◽  
Author(s):  
Huang Shi-Ke ◽  
Kevin D. Hyde ◽  
Ausana Mapook ◽  
Sajeewa S.N. Maharachchikumbura ◽  
D. Jayarama Bhat ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Type Species ◽  
New Genus ◽  
Molecular Data ◽  
New Combinations ◽  
Number Of Species ◽  
New Family ◽  
Taxonomic Studies

Abstract Sordariomycetes is an earlier and one of the widely distributed class of Ascomycota. The class was initially classified based on morphology in having inoperculate and unitunicate asci. With the development of DNA based phylogenetic analysis, several undetermined or polyphyletic members of Sordariomycetes were reclassified. However, not all species belonging to this class have been sequenced and analyzed. There are a number of species, especially those old and poorly studied ones which have never been sequenced before and not even recollected again for further taxonomic verification. One of the main objective in this study is to revise and update the taxonomy of several well-known old and poorly studied species whose classification are still obscure. Herein, we re-examined the type materials and/or authentic specimens together to explore 74 relatively poorly-studied genera, which mainly belong to Boliniales, Calosphaeriales, Chaetosphaeriales, Jobellisiales, and Sordariales classified under Diaporthomycetidae and Sordariomycetidae. We provide descriptions, notes, figures and/or drawings and discussed their phylogenetic relationships. As a result, the monotypic Jobellisiales is transferred from Hypocreomycetidae to Diaporthomycetidae. Based on phylogenetic analysis, the polyphyletic Lasiosphaeriaceae is divided into five families, Bombardiaceae (Apodospora, Bombardia, Bombardioidea and Fimetariella), Lasiosphaeriaceae (Anopodium, Bellojisia, Corylomyces, Lasiosphaeria, Mammaria and Zopfiella), Lasiosphaeridaceae (Lasiosphaeris), Strattoniaceae (Strattonia) and Zygospermellaceae (Episternus and Zygospermella). In addition, a new family Neoschizotheciaceae is established based on Neoschizothecium. Analysis of the type species of Boothiella, Stellatospora, Sulcatistroma and Tengiomyces placed them in Sordariaceae, Chaetomiaceae, Hypocreales and Coronophorales, respectively. We classify the genera lacking molecular data based on their morphology and expect them to be recollected; that is, Kacosphaeria in Calosphaeriales; Arnium, Biconiosporella, Camptosphaeria, Diffractella, Emblemospora, Eosphaeria, Periamphispora, Ramophialophora, Synaptospora and Tripterosporella in Sordariales; Conidiotheca in Sordariomycetes; Copromyces, Effetia, Endophragmiella and Tulipispora are accommodated in Ascomycota. Besides, we establish a new genus Neoschizothecium based on phylogenetic analysis. New combinations proposed include: Camaropella amorpha, Cam. microspora, Cam. plana, Cladorrhinum grandiusculum, Cla. leucotrichum, Cla. terricola, Cla. olerum, Helminthosphaeria plumbea, Immersiella hirta, Jugulospora minor, Lasiosphaeris arenicola, Neoschizothecium aloides, Neo. carpinicola, Neo. conicum, Neo. curvisporum, Neo. fimbriatum, Neo. glutinans, Neo. inaequale, Neo. minicaudum, Neo. selenosporum, Neo. tetrasporum, Neurospora autosteira, Podospora brunnescens, P. flexuosa, P. jamaicensis, P. hamata, P. macrospora, P. spinosa, Strattonia petrogale and Triangularia microsclerotigena, T. nannopodalis, T. praecox, T. samala, T. tarvisina, T. unicaudata, T. yaeyamensis. New epithets are proposed for Apiorhynchostoma apiosporum and Podospora dacryoidea.

Phylogenetic analysis of the rumen ciliate family Ophryoscolecidae based on 18S ribosomal RNA sequences, with new sequences fromDiplodinium,Eudiplodinium, andOphryoscolex

1997 ◽  
Vol 75 (6) ◽  
pp. 963-970 ◽  
Author(s):  
André-Denis G. Wright ◽  
Denis H. Lynn
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Small Subunit ◽  
Base Pairs ◽  
Rna Sequences ◽  
Ribosomal Rna Sequences ◽  
The Family

Phylogenetic relationships within the largest family of entodiniomorphid rumen ciliates, the Ophryoscolecidae, were inferred from comparisons of small-subunit ribosomal RNA gene sequences. These included three new sequences from Diplodinium dentatum (1638 base pairs (bp)), Eudiplodinium maggii (1637 bp), and Ophryoscolex purkynjei (1636 bp). Using morphological characters, Lubinsky constructed a cladogram of the Ophryoscolecidae, and on the basis of his analysis, he divided the family into three subfamilies (Entodiniinae, Diplodiniinae, Ophryoscolecinae) to reflect his "natural" groupings (G. Lubinsky. 1957. Can. J. Zool. 35: 141 – 159). Our cladistic analysis, based on the limited morphological and ultrastructural data available, indicates that there are no synapomorphies supporting the Diplodiniinae sensu Lubinsky. However, based upon the six 18S sequences for the Ophryoscolecidae, the rumen ciliates are monophyletic and fall into three distinct groups corresponding to Lubinsky's subfamilial division of the family. Our molecular analysis shows Entodinium to be the earliest branching rumen ciliate (subfamily Entodiniinae) and Eudiplodinium, not Diplodiium, branching first among the diplodiniines.

Total evidence analysis of the phylogenetic relationships of bandicoots and bilbies (Marsupialia: Peramelemorphia): reassessment of two species and description of a new species

Zootaxa ◽  
2018 ◽  
Vol 4378 (2) ◽  
pp. 224 ◽  
Author(s):  
KENNY J. TRAVOUILLON ◽  
MATTHEW J. PHILLIPS
Keyword(s):  
New Species ◽  
Late Miocene ◽  
Phylogenetic Relationships ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Total Evidence ◽  
Bayesian Analyses ◽  
Early Pliocene ◽  
Evidence Analysis ◽  
A New Species

The phylogenetic relationships of bandicoots and bilbies have been somewhat problematic, with conflicting results between morphological work and molecular data. This conflict makes it difficult to assess the taxonomic status of species and subspecies within this order, and also prevents accurate evolutionary assessments. Here, we present a new total evidence analysis, combining the latest cranio-dental morphological matrix containing both modern and fossil taxa, with molecular data from GenBank. Several subspecies were scored in the morphological dataset to match the molecular data available. Both parsimony and Bayesian analyses were performed, giving similar topologies except for the position of four fossil taxa. Total evidence dating places the peramelemorphian crown origin close to the Oligocene/Miocene boundary, and the radiations of most modern genera beginning in the Late Miocene or Early Pliocene. Our results show that some species and subspecies require taxonomic reassessment, and are revised here. We also describe a new, extinct species from the Nullarbor region. This suggests that the number of recently extinct peramelemorphian species is likely to further increase. 

The continuing challenge of phylogenetic relationships in Terebelliformia (Annelida : Polychaeta)

2013 ◽  
Vol 27 (2) ◽  
pp. 186 ◽  
Author(s):  
João Miguel de Matos Nogueira ◽  
Kirk Fitzhugh ◽  
Pat Hutchings
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Character Evolution ◽  
Type Material ◽  
New Family ◽  
Revised Definitions

A comprehensive phylogenetic analysis of the Terebellidae and related families was undertaken. Type material of all genera of Terebellinae was examined, together with representatives of nearly all genera of remaining Terebellidae subfamilies, and representatives of the families that have been traditionally regarded as being closely related, comprising the Terebelliformia. In total, 85 species were coded using 118 subjects (‘characters’) and 286 subject–predicate relations (‘states’). The results indicate: (1) the paraphyly of Terebellidae by the placements of Trichobranchidae, Ampharetidae, Alvinellidae and Pectinariidae within that clade; (2) the occurrences of Thelepodinae as separate clades, consistent with groups ‘A’ and ‘B’ recognised by Nogueira et al. (2010a); and (3) the monophyly of Polycirrinae and Terebellinae. The previously considered subfamilies of Terebellidae are raised to familial level and a new family is described. Revised definitions are provided for: Terebelliformia, Polycirridae, stat. nov., Telothelepodidae, fam. nov., Terebellidae emend., and Thelepodidae, stat. nov., along with a discussion of character evolution in the Terebellidae.

Phylogenetic relationships among megachiropteran species from the two major islands of the Philippines, deduced from DNA sequences of the cytochrome b gene

2001 ◽  
Vol 79 (9) ◽  
pp. 1671-1677 ◽  
Author(s):  
Severo T Bastian, Jr. ◽  
Kazuaki Tanaka ◽  
Rea Victoria P Anunciado ◽  
Nelson G Natural ◽  
Augusto C Sumalde ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
The Philippines ◽  
Cytochrome B Gene ◽  
Likelihood Methods ◽  
Base Pairs ◽  
Maximum Likelihood Methods ◽  
Pteropus Vampyrus ◽  
Cynopterus Brachyotis

Complete cytochrome b gene sequences (1140 base pairs) in species of Megachiroptera were ascertained in order to deduce their phylogenetic relationships, using samples of Cynopterus brachyotis, Eonycteris spelaea, Ptenochirus jagori, Pteropus vampyrus, and Rousettus amplexicaudatus collected from the islands of Luzon and Mindanao in the Philippines. Genetic divergence between samples of R. amplexicaudatus, E. spelaea, and C. brachyotis was very small. On the other hand, a large genetic distance was detected between species of Megachiroptera. The phylogenetic tree using neighbor-joining, parsimony, and maximum-likelihood methods generated similar topologies, reflecting the evolutionary associations among megachiropteran species. We estimated that Megachiroptera separated from Microchiroptera 50.2 million years ago (MYA), and split further approximately 32.4 MYA, forming three lineages: E. spelaea, R. amplexicaudatus, and P. vampyrus and the P. jagori – C. brachyotis cluster. The third lineage, composed of P. vampyrus and the P. jagori – C. brachyotis cluster, branched out 31.9 MYA. We hypothesize that R. amplexi caudatus diverged from the three members of the subfamily Pteropodinae examined, and its phylogenetic relationship with E. spelaea remains unclear.

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