scholarly journals Phylogeny and systematics of the lichen family Gomphillaceae (Ostropales) inferred from cladistic analysis of phenotype data

2005 ◽  
Vol 37 (2) ◽  
pp. 123-170 ◽  
Author(s):  
Robert LÜCKING ◽  
Emmanuël SÉRUSIAUX ◽  
Antonín VĚZDA
Keyword(s):  
Cladistic Analysis ◽  
Data Matrix ◽  
Consistency Index ◽  
Parsimony Analysis ◽  
Phenotype Data ◽  
The Family ◽  
Character Weighting ◽  
High Level ◽  
Family Classification

The phylogeny of the lichen family Gomphillaceae sensu Vězda & Poelt was reconstructed by parsimony analysis of a phenotype data matrix including ecological, thallus, apothecial, and hyphophore characters. Two hundred and twenty-eight taxa and 209 characters, grouped into ecology (14), thallus (45), apothecia (83), and hyphophores (67), were included in the analysis. Gyalidea hyalinescens (Asterothyriaceae) was used as outgroup. Because of the high level of homoplasy (consistency index of all-taxa tree without character weighting CI=0·12), and the resulting uncertainty (generally low support) with respect to group topologies, we accepted both monophyletic clades and paraphyletic grades and only rejected previously proposed classifications if the taxon in question appeared polyphyletic, or if segregate taxa were characterized by functionally independent apomorphies and/or by evidence of radiation. Thus, the following 19 genera (synonyms in brackets) are accepted as a result of this study: Actinoplaca (segregate of Echinoplaca; isidioid hyphophores), Aderkomyces (Psathyromyces; segregate of Tricharia; white setae, hyphal excipulum), Aplanocalenia (segregate of Calenia; immersed applanate apothecia), Arthotheliopsis (Phallomyces; segregate of Echinoplaca; smooth thallus, differentiated diahyphae), Aulaxina (Lochomyces; carbonized apothecia, bristle-shaped hyphophores with palmate diahyphae on prothallus), Calenia (Bullatina; zeorine apothecia, acute to bristle-shaped hyphophores with moniliform diahyphae), Caleniopsis (thick white thallus with dark prothallus, zeorine apothecia, bristle-shaped hyphophores with palmate diahyphae on prothallus), Diploschistella (segregate of Gyalideopsis; immersed apothecia), Echinoplaca (Spinomyces, Sporocybomyces; crystalline thallus, acute to bristle-shaped hyphophores with moniliform or derived diahyphae), Ferraroa (segregate of Gyalideopsis; campylidioid hyphophores), Gomphillus (vertically elongate apothecia, filiform ascospores), Gyalectidium (Tauromyces; zeorine apothecia, squamiform hyphophores), Gyalideopsis (Epilithia, Microlychnus, Microspatha; chiefly biatorine apothecia, setiform or flabellate hyphophores), Hippocrepidea (applanate apothecia, squamiform hyphophores with strongly derived diahyphae), Jamesiella (segregate of Gyalideopsis; isidioid hyphophores), Lithogyalideopsis (segregate of Gyalideopsis; lecideine apothecia, bristleshaped hyphophores with palmate diahyphae), Paratricharia (black setae, partly carbonized apothecia with columella), Rubrotricha (segregate of Tricharia; red-brown setae, hyphal excipulum), and Tricharia (Microxyphiomyces, Setomyces; black setae, proso- or paraplectenchymatous excipulum). The following taxa and combinations are introduced: Actinoplaca gemmifera comb. nov. [Echinoplaca gemmifera], Aderkomyces albostrigosus comb. nov. (Tricharia albostrigosa), A. armatus comb. nov. (T. armata), A. carneoalbus comb. nov. (T. carneoalba), A. cretaceus comb. nov. (T. cretacea), A. cubanus comb. nov. (T. cubana), A. deslooveri comb. nov. (T. deslooveri), A. dilatatus comb. nov. (T. dilatata), A. fumosus comb. nov. (T. fumosa), A. heterellus comb. nov. (Arthonia heterella; Lopadium membranula; Echinoplaca affinis), A. guatemalensis comb. nov. (T. guatemalensis), A. lobulimarginatus sp. nov., A. microcarpus comb. nov. (T. microcarpa), A. microtrichus comb. nov. (T. microtricha), A. papilliferus comb. nov. (T. papillifera), A. planicarpus comb. nov. (T. planicarpa), A. planus comb. nov. (T. plana), A. purulhensis comb. nov. (T. purulhensis), A. ramiferus comb. nov. (T. ramifera), A. subalbostrigosus comb. nov. (T. subalbostrigosa), A. subplanus comb. nov. (T. subplana), A. testaceus comb. nov. (T. testacea), A. verruciferus comb. nov. (T. verrucifera), A. verrucosus comb. nov. (T. verrucosa), Aplanocalenia gen. nov., A. inconspicua comb. nov. (Heterothecium inconspicuum; Calenia inconspicua), Arthotheliopsis serusiauxii comb. nov. (Echinoplaca serusiauxii), A. tricharioides comb. nov. (E. tricharioides), Caleniopsis aggregata comb. nov. (Calenia aggregata), C. conspersa comb. nov. (Thelotrema conspersa; Calenia conspersa), Diploschistella lithophila comb. nov. (Gyalideopsis lithophila), D. solorinellaeformis comb. nov. (G. solorinellaeformis), D. trapperi comb. nov. (G. trapperi), Echinoplaca macgregorii comb. nov. (Arthonia macgregorii), Ferraroa gen. nov., Ferraroa hyalina comb. nov. (Gyalideopsis hyalina), Gyalideopsis brevipilosa comb. nov. (Tricharia brevipilosa), G. buckei nom. nov. (Tricharia vezdae), G. cristata comb. nov. (Epilithia cristata), G. glauca comb. nov. (Microspatha glauca), G. puertoricensis sp. nov., Jamesiella gen. nov., J. anastomosans comb. nov. (Gyalideopsis anastomosans), J. perlucida comb. nov. (G. perlucida), J. scotica comb. nov. (G. scotica), Lithogyalideopsis gen. nov., L. aterrima comb. nov. (Gyalideopsis aterrima), L. poeltii comb. nov. (G. poeltii), L. vivantii comb. nov. (G. vivantii), L. zeylandica comb. nov. (G. zeylandica), Rubrotricha gen. nov., R. helminthospora comb. nov. (Tricharia helminthospora), R. subhelminthospora sp. nov., Tricharia atrocarpa sp. nov., and Tricharia variratae sp. nov. A key is presented to all genera of Gomphillaceae, and a synopsis of the family classification, with all presently known species, is provided.

scholarly journals Phylogenetic relationships within the Pylochelidae (Decapoda: Anomura: Paguroidea): A cladistic analysis based on morphological characters

Zootaxa ◽  
2009 ◽  
Vol 2022 (1) ◽  
pp. 1-14 ◽  
Author(s):  
RAFAEL LEMAITRE ◽  
PATSY A. MCLAUGHLIN ◽  
ULF SORHANNUS
Keyword(s):  
Hermit Crab ◽  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Data Matrix ◽  
Parsimony Analysis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
The Family

Phylogenetic relationships within the “symmetrical” hermit crab family Pylochelidae were analyzed for 41 of the 45 species and subspecies currently considered valid. In the analyses, 78 morphological characters comprised the data matrix and the outgroup consisted of Thalassina anomala, a member of the Thalassinidae, and Munida quadrispina, a member of the Galatheidae. A poorly resolved strict consensus tree was obtained from a heuristic parsimony analysis of unweighted and unordered characters, which showed the family Pylochelidae and the subfamilies Pylochelinae and Pomatochelinae to be monophyletic taxa – the latter two groups had the highest Bremer support values. Additionally, while the subgenus Pylocheles (Pylocheles) was strongly supported, the subgenera Xylocheles, and Bathycheles were not. More fully resolved trees were obtained when using implied weighting, which recognized the monotypic subfamilies Parapylochelinae, Cancellochelinae and Mixtopagurinae. The subfamily Trizochelinae was found to have four distinct clades and several ambiguously placed taxa.

A phylogeny of the family Fanniidae Schnabl (Insecta:Diptera:Calyptratae) based on adult morphological characters, with special reference to the Austral species of the genus Fannia

2008 ◽  
Vol 22 (5) ◽  
pp. 563 ◽  
Author(s):  
M. C. Domínguez ◽  
S. A. Roig-Juñent
Keyword(s):  
Cladistic Analysis ◽  
Morphological Characters ◽  
External Morphology ◽  
Phylogenetic Position ◽  
Phylogenetic Hypothesis ◽  
Parsimony Analysis ◽  
Male And Female ◽  
Southern South America ◽  
The Family ◽  
Species Groups

The present study proposed a phylogenetic hypothesis of the family Fanniidae based on a cladistic analysis using characters from adult external morphology and female and male terminalia. The main purpose of this study was to clarify the phylogenetic position of newly described or poorly known species, mostly from southern South America, the Neotropics, Africa, Australia and New Zealand. In total, 151 characters from adult male and female external morphology and terminalia were scored for 78 species of Fanniidae. Ten continuous characters were included and analysed as such. Three genera of Fanniidae and all the species-groups and subgroups proposed for the genus Fannia, except for the admirabilis-group and the setifer-subgroup were included as terminal taxa. An heuristic parsimony analysis under implied weights was performed. The analysis recovered the monophyly of the Fanniidae and the genus Fannia, as well as the monophyly of several species-groups within Fannia. Male and female external morphological characters were, in general, highly homoplasious, whereas characters from male terminalia showed low level of homoplasy and provided resolution at suprageneric nodes and species-groups.

Microscleres and gemmoscleres as phylogenetic signals in Spongillida: phylogeny and biogeography of the genus Metania Gray, 1867 (Porifera, Metaniidae)

2015 ◽  
Vol 29 (4) ◽  
pp. 369 ◽  
Author(s):  
Cristiana Castello-Branco ◽  
Adolfo Ricardo Calor ◽  
Carla Menegola
Keyword(s):  
Current Distribution ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Parsimony Analysis ◽  
Freshwater Sponge ◽  
The Family

The genus Metania comprises 11 species of freshwater sponge that are distributed circumtropically: five are Neotropical, three Afrotropical, two Oriental and one Australian. Here we infer the phylogeny of the genus Metania and examine the processes that lead to the current biogeographic distribution using cladistic analysis. One matrix with 26 morphological characters was analysed using the TNT software, and resulted in two most parsimonious cladograms (strict consensus). Our results support monophyly of Metania due to two characters unique to the genus: presence of acanthoxeas and presence of spines in the shaft of the gemmoscleres. Also, the genera Drulia and Houssayella were synonymised with Metania. The family Metaniidae – allocated in the recently proposed order Spongillida – now contains three genera: Acalle Gray, 1867, Metania Gray, 1867 and Corvomeyenia Weltner, 1913. Brooks parsimony analysis of Metania resulted in a single area cladogram showing a Gondwanan pattern: (Neartic (Australian (Oriental (Afrotropical, Neotropical)))) and thus the current distribution is explained by the breakup of Gondwana.

A first cladistic analysis of Antarctoperlinae (Plecoptera: Gripopterygidae) and a new micropterous species from Patagonia

2020 ◽  
Vol 190 (3) ◽  
pp. 771-787
Author(s):  
Pablo Pessacq ◽  
Tácio Duarte ◽  
Luis B Epele
Keyword(s):  
New Species ◽  
South America ◽  
Southern Hemisphere ◽  
Molecular Analysis ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Data Matrix ◽  
Phylogenetic Position ◽  
Type Series ◽  
The Family

Abstract Gripopterygidae is a diverse family of stoneflies, Plecoptera, distributed in the Southern Hemisphere. It has been traditionally divided into five subfamilies, but the monophyly of most of these is not supported by molecular the more comprehensive molecular analysis of the order. To test the monophyly of Antarctoperlinae, and to establish the phylogenetic position of a new Gripopterygidae species, we performed a morphological cladistic analysis including 38 morphological characters and 27 terminal taxa, with representatives of the four subfamilies present in South America and three Austroperlidae. Based on published information, we rooted the tree with Penturoperla barbata, Austroperlidae. As a result, Antarctoperlinae was recovered as polyphyletic, with Vesicaperla kuscheli and Plegoperla punctata, two members of the subfamily, placed outside the clade that includes the nine remaining genera of Antarctoperlinae. Vesicaperla also falls outside the family in previous molecular analysis. Based on this evidence, it should not be placed in Antarctoperlinae. Plegoperla punctata, known only from the type series, possesses many missing entries in our data matrix. Based on this, it seems convenient to maintain its subfamilial placement. In the tree obtained, the potential new species nests together with Pehuenioperla llaima. We thus accept it as a member of Pehuenioperla and describe it as P. microptera sp. nov.

scholarly journals Evolutionary Trends in the Physciaceae

2001 ◽  
Vol 33 (1) ◽  
pp. 25-45 ◽  
Author(s):  
C. Scheidegger ◽  
H. Mayrhofer ◽  
R. Moberg ◽  
A. Tehler
Keyword(s):  
A Priori ◽  
Cladistic Analysis ◽  
Taxonomic Structure ◽  
Lichenized Ascomycetes ◽  
Septum Formation ◽  
Equal Importance ◽  
The Family ◽  
Character Weighting ◽  
Cladistic Analyses ◽  
Developmental Line

AbstractThe current delimitation of the family Physciaceae has been generally accepted since detailed descriptions of ascus characters allowed for a more natural circumscription of lichenized ascomycetes. The generic relations within the family are, however, still controversial and depend on the importance different authors attribute to specific morphological or chemical characteristics. The aim of this paper is to describe ascospore ontogeny and to test the present taxonomic structure of the family against a parsimony-based cladistic analysis, which includes three different scenarios of a priori character weighting. A study of ascospore ontogeny revealed two distinct developmental lines. One line revealed a delayed septum formation, which clearly showed transitions from spores with apical and median thickenings to spores without apical, but still well developed median thickenings, and to spores without any thickenings. In the second developmental line with an early septum formation again taxa with no thickenings, median thickenings, and both median and apical thickenings were found. Although these characters were constant at a species level, median wall thickenings especially varied among otherwise closely related taxa. In the cladistic analyses the current taxonomic structure of the Physciaceae was only obtained after the five character groups, namely morphology and anatomy of the vegetative thallus, conidiomata and conidia, morphology and anatomy of the apothecia, ontogeny of the ascospores, and secondary metabolites of the thallus, were given equal importance, and after a subjective a priori weighting further increased the weight of the three characters ‘conidial shape’, ‘presence of apical thickenings’, and ‘spore septation delayed’. This structure was not supported by a cladistic analysis with equally weighted characters but reflected the biased character weighting of the present day Physdaceae taxonomy. The taxonomic importance of conidial characters and of anatomical and ontogenetical spore characteristics need, therefore, a careful reconsideration in future.

New taxa of the Lygistorrhinidae (Diptera: Sciaroidea) and their implications for a phylogenetic analysis of the family

Zootaxa ◽  
2005 ◽  
Vol 960 (1) ◽  
pp. 1 ◽  
Author(s):  
HEIKKI HIPPA ◽  
INGEGERD MATTSSON ◽  
PEKKA VILKAMAA
Keyword(s):  
Phylogenetic Analysis ◽  
New Taxa ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Characters ◽  
Undescribed Species ◽  
Parsimony Analysis ◽  
The Family ◽  
Outgroup Species ◽  
New Material

New Oriental taxa of the Lygistorrhinidae - Blagorrhina gen. n., with B. blagoderovi sp. n. and B. brevicornis sp. n.; Gracilorrhina gracilis gen. n., sp. n.; and Labellorrhina gen. n., with L. grimaldii sp. n. and L. quantula sp. n. are described, and two undescribed species, known only from females, are characterized. Based on this new material, the family is redefined. The phylogeneticrelationships among the taxa of Lygistorrhinidae were studied by parsimony analysis using 43 morphological characters from the adults of 25 ingroup and one outgroup species. The cladistic analysis produced 14 most parsimonious cladograms. The solution obtained suggests unambiguously the following phylogeny: Palaeognoriste Meunier and “Lygistorrhina” asiatica Senior-White are successively sister groups of the rest of the Lygistorrhinidae; there is a clade Labellorrhina + (Gracil- orrhina + (Blagorrhina + ((Seguyola Matile + (Loyugesa Grimaldi & Blagoderov + Matileola Papp))))) with a monophyletic Lygistorrhina Skuse – Probolaeus Williston lineage as sister group. The phylogeny among the latter group remains largely unresolved.

Classification of basal Cucujoidea (Coleoptera:Polyphaga): cladistic analysis, keys and review of new families

2005 ◽  
Vol 19 (1) ◽  
pp. 17 ◽  
Author(s):  
R. A. B. Leschen ◽  
J. F. Lawrence ◽  
S. A. Ślipiński
Keyword(s):  
New Taxa ◽  
Phylogenetic Relationships ◽  
Type Species ◽  
Cladistic Analysis ◽  
Data Matrix ◽  
Family Status ◽  
The Family

Phylogenetic relationships among the basal Cucujoidea were reconstructed by a cladistic analysis of a data matrix consisting of 37 exemplar taxa and 99 adult and larval characters. Eight most parsimonious cladograms provided evidence for the polyphyly of Phloeostichidae, the paraphyly of Cucujoidea (with respect to the placement of Trogossitidae), and the monophyly of Protocucujidae + Sphindidae, Biphyllidae + Erotylidae, Cryptophagidae, Cucujidae + Silvanidae, Propalticidae + Laemophloeidae, and the Nitidulidae groups (Nitidulidae, Smicripidae, and Brachypteridae). The following families are elevated from subfamily to family status: Agapythidae (one genus), Phloeostichidae (four genera; the subfamilies Phloeostichinae and Hymaeinae are supressed), Priasilphidae (three genera), Tasmosalpingidae (one genus), and Myraboliidae (one genus). These families are described in detail and adult and larval keys to all families of Cucujoidea are provided. The genus Bunyastichus, gen. nov. (type species: B. monteithi, sp. nov.) is described in the family Phloeostichidae and the family Priasilphidae is revised with the following new taxa: Chileosilpha, gen. nov. (type species: C. elguetai, sp. nov.), Priasilpha (P. angulata, sp. nov., P. aucklandica, sp. nov., P. bufonia, sp. nov., P. carinata, sp. nov., P. earlyi, sp. nov., and P. embersoni, sp. nov.), Priastichus (P. crowsoni, sp. nov. and P. megathorax, sp. nov.).

A Survey for Predicting Enzyme Family Classes Using Machine Learning Methods

2019 ◽  
Vol 20 (5) ◽  
pp. 540-550 ◽  
Author(s):  
Jiu-Xin Tan ◽  
Hao Lv ◽  
Fang Wang ◽  
Fu-Ying Dao ◽  
Wei Chen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Catalytic Mechanism ◽  
Biological Function ◽  
Learning Methods ◽  
Biochemical Processes ◽  
Machine Learning Methods ◽  
Enzyme Family ◽  
The Family ◽  
Speed Up ◽  
Family Classification

Enzymes are proteins that act as biological catalysts to speed up cellular biochemical processes. According to their main Enzyme Commission (EC) numbers, enzymes are divided into six categories: EC-1: oxidoreductase; EC-2: transferase; EC-3: hydrolase; EC-4: lyase; EC-5: isomerase and EC-6: synthetase. Different enzymes have different biological functions and acting objects. Therefore, knowing which family an enzyme belongs to can help infer its catalytic mechanism and provide information about the relevant biological function. With the large amount of protein sequences influxing into databanks in the post-genomics age, the annotation of the family for an enzyme is very important. Since the experimental methods are cost ineffective, bioinformatics tool will be a great help for accurately classifying the family of the enzymes. In this review, we summarized the application of machine learning methods in the prediction of enzyme family from different aspects. We hope that this review will provide insights and inspirations for the researches on enzyme family classification.

Odontopleura (Trilobita, Silurian), and a method of constrained congruency analysis

1990 ◽  
Vol 64 (4) ◽  
pp. 600-614 ◽  
Author(s):  
Jonathan M. Adrain ◽  
Brian D. E. Chatterton
Keyword(s):  
Cladistic Analysis ◽  
Canadian Arctic ◽  
Wide Distribution ◽  
Parsimony Analysis ◽  
Directed Tree ◽  
Shelf Slope ◽  
Major Species ◽  
Species Groups ◽  
The Universe ◽  
A New Species

Odontopleura (Odontopleura) arctica, a new species of odontopleurine trilobite, is described from the Canadian Arctic. A method of cladistic analysis is detailed. Parsimony analysis should be performed treating all characters as unordered. The universe of directed trees implied by the resulting rootless network(s) can then be examined and a preferred tree selected by a criterion of congruency. Namely, the most parsimonious directed tree that accommodates the most congruent arrangement of character-states should be taken as the preferred cladogram. Since this is essentially a general congruency method operating within the constraints of parsimony, it is termed “constrained congruency.” The method is applied to the genus Odontopleura, resulting in the recognition of two major species groups, the nominate subgenus and Sinespinaspis n. subgen. Odontopleura (Ivanopleura) dufrenoyi Barrande is tentatively included in the genus, but considered too poorly known for cladistic analysis. Species assigned to Odontopleura (Odontopleura) include Odontopleura ovata Emmrich, Odontopleura brevigena Chatterton and Perry, Odontopleura (Odontopleura) arctica n. sp., and Diacanthaspis serotina Apollonov. Species assigned to Sinespinaspis n. subgen. include Taemasaspis llandoveryana Šnajdr, Odontopleura greenwoodi Chatterton and Perry, Odontopleura maccallai Chatterton and Perry, and Odontopleura nehedensis Chatterton and Perry. Odontopleura bombini Chatterton and Perry is tentatively placed in synonymy with Odontopleura nehedensis. The genus had a wide distribution throughout the Early and Middle Silurian, due to preferences for deep-water, distal shelf or shelf-slope transition zone habitats.

scholarly journals Implementation of the Family HELP Protocol: A Feasibility Project for a West Texas ICU

Healthcare ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 146
Author(s):  
Rebecca McClay
Keyword(s):  
Strong Support ◽  
Family Intervention ◽  
Successful Implementation ◽  
Positive Perception ◽  
Family Presence ◽  
West Texas ◽  
The Family ◽  
Control And Prevention ◽  
High Level ◽  
Near Future

The purpose of this project was to determine if bedside intensive care unit (ICU) nurse buy-in to the Family Hospital Elder Life Program (HELP) protocol was sufficient to make implementation feasible at one county hospital in West Texas. Surveys were anonymous with ballot box collection being available to the bedside ICU nurses for one week each. Questions were based on literature findings of expected outcomes, identified barriers and facilitators, Calgary Family Intervention Method framework domains, and the Centers for Disease Control and Prevention Framework for program evaluation. Outcome measures were taken from the stated aims of the project and evaluated from paired baseline and summative survey questions. Survey participation was approximately half of nurses employed in the studied ICU. Analysis of the surveys showed a positive perception of family presence decreasing patient delirium symptoms, and a positive perception of the Family HELP protocol. The results described a high perception of family members as partners in care and high intention to implement the Family HELP protocol, indicating strong support of a full implementation of the protocol. The high level of bedside nurse buy-in present in this study has large implications for successful implementation of the Family HELP protocol in the near future, with sustainability and continued use supported by potential inclusion of the task in the electronic health record charting.

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