Corticioid fungi: a cladistic study of a paraphyletic group

1995 ◽  
Vol 73 (S1) ◽  
pp. 843-852 ◽  
Author(s):  
Erast Parmasto
Keyword(s):  
Key Words ◽  
Majority Rule ◽  
Cladistic Analysis ◽  
Fungal Taxonomy ◽  
Parsimony Analysis ◽  
Corticioid Fungi ◽  
Consensus Trees ◽  
Representative Species ◽  
Paraphyletic Group ◽  
Cladistic Analyses

Cladistic analyses were used to assess monophyly for genera of corticioid fungi (Hymenomycetes, Basidiomycota). Based on parsimony analysis, many genera were found to be paraphyletic; to recognize only monophyletic taxa, 50 genera have been synonymized and 142 presumably monophyletic genera retained for further analysis. Over 12 000 equally parsimonious trees are possible for the 142 taxa. Although consensus trees leave much of the phylogeny unresolved, more than 10 monophyletic groups can be distinguished based on 95% majority-rule consensus, including the families Atheliaceae, Botryobasidiaceae, Hericiaceae (syn.: Gloeocystidiellaceae), Peniophoraceae (syn.: Stereaceae), Schizophyllaceae (syn.: Meruliaceae) and Xenasmataceae. The use of representative species in cladistic analysis is not recommended. To avoid the use of paraphyletic genera (and unnecessary nomenclatural changes), robust taxonomic systems are needed which avoid unnecessary splitting. Key words: fungal taxonomy, Hymenomycetes, Corticiaceae, classification.

The phylogenetic relationships of the anaerobic chytridiomycetous gut fungi (Neocallimasticaceae) and the Chytridiomycota. II. Cladistic analysis of structural data and description of Neocallimasticales ord.nov.

1993 ◽  
Vol 71 (3) ◽  
pp. 393-407 ◽  
Author(s):  
Jinliang Li ◽  
I. Brent Heath ◽  
Laurence Packer
Keyword(s):  
Key Words ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Structural Data ◽  
Monophyletic Group ◽  
Rrna Sequence ◽  
Cladistic Analyses

We investigated the phylogenetic relationships of the Chytridiomycota and the chytridiomycetous gut fungi with a cladistic analysis of 42 morphological, ultrastructural, and mitotic characters for 38 taxa using both maximum parsimony and distance algorithms. Our analyses show that there are three major clades within the Chytridiomycota: the gut fungi, the Blastocladiales, and the Spizellomycetales–Chytridiales–Monoblepharidales. Consequently, we elevated the gut fungi to the order Neocallimasticales ord.nov. Our results suggest that a modified Chytridiales, including the Monoblepharidales, is a monophyletic group. In contrast the Spizellomycetales are paraphyletic because the Chytridiales arose within them. The separation of the traditional Chytridiales into two orders is thus doubtful. Although the Blastocladiales are closer to members of the Spizellomycetales than the Chytridiales, the cladistic analyses of both structural and rRNA sequence data do not support the idea that the Blastocladiales were derived from the Spizellomycetales. We suggest emendations to the classification of the Chytridiomycota and note which groupings require further analysis. Our phylogeny for the currently recognized species of gut fungi is inconsistent with the existing classification. Nonetheless, pending further investigations, we prefer to retain the existing, easily defined genera for which a key is provided. Key words: Chytridiomycota, rumen fungi, phylogeny, morphology, ultrastructure, mitosis.

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.

The phylogenetic position of the tuatara, Sphenodon (Sphenodontida, Amniota), as indicated by cladistic analysis of the ultrastructure of spermatozoa

1992 ◽  
Vol 335 (1274) ◽  
pp. 207-219 ◽  
Keyword(s):  
Cladistic Analysis ◽  
Sister Group ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
Usual Concept ◽  
Cladistic Analyses ◽  
Relationship Of

Sphenodon has traditionally been regarded as a little changed survivor of the Permo-Triassic thecodont or eosuchian ‘stem reptiles’ but has alternatively been placed in the Lepidosauria as the plesiomorphic or even apomorphic sister-taxon of the squamates. A cladistic analysis of 16 characters from spermatozoal ultrastructure of Sphenodon and other amniotes unequivocally confirms its exceedingly primitive status. The analysis suggests that monotremes are the sister-group of birds; squamates form the sister-group of a bird + monotreme clade while the three sister-groups successively below the bird + monotreme + squa- mate assemblage are the caiman, the tuatara and the outgroup (turtles). The monotreme + bird couplet, supports the concept of the Haemothermia, but can only be regarded heuristically. The usual concept of mammals as a synapsid-derived outgroup of all other extant amniotes is not substantiated spermatologically. All cladistic analyses made, and a separate consideration of apomorphies, indicate that Sphenodon is spermatologically the most primitive amniote, excepting the Chelonia. It is advanced (apomorphic) for the amniotes in only two of the 16 spermatozoal characters considered. A close, sister-group relationship of Sphenodon with squamates is not endorsed.

Systematic Wood Anatomy of Cornaceae and Allies

IAWA Journal ◽  
1998 ◽  
Vol 19 (1) ◽  
pp. 43-97 ◽  
Author(s):  
S. Noshiro ◽  
P. Baas
Keyword(s):  
Wood Anatomy ◽  
Cladistic Analysis ◽  
The Other ◽  
Infrageneric Classification ◽  
Diversity Pattern ◽  
Quantitative Characters ◽  
Cladistic Analyses ◽  
Trees And Shrubs ◽  
Remarkable Agreement

The wood anatomy of Comaceae, Alangiaceae, Garryaceae, and Nyssaceae constituting the Comales in the sense of Cronquist (1981, 1988) is described in great detail and subjected to a cladistic analysis. A microscopic identification key to the woods studied is given. The alliance includes seventeen genera, mostly of trees and shrubs, very rarely herbs. Although wood anatomically fairly homogeneous, variation exists in both qualitative and quantitative characters. Some of the latter show distinct latitudinal trends within individual genera, and character states have only been recognised taking their latitudinal dependencies into account. The character states ultimately recognised in these continuously varying quantitative characters coincide with intergeneric or intersectional gaps. The cladistic analysis based on a datamatrix with twentyone characters (Table 3) and using Cereidiphyllum, Daphniphyllum, and Hamamelis as outgroups yielded a strict consensus tree with a quadrichotomy with two monophyletic clades, Hydrangea panieulata (a representative of the closely allied Hydrangeaceae) and Daphniphyllum (Fig. 81). One weakly supported clade includes Alangium, Camptotheea, Cornus, Curtisia, Davidia, Diplopanax, Mastixia, and Nyssa without any robust lineages among them. The other genera, Aralidium, Aueuba, Corokia, Garrya, Griselinia, Helwingia, Melanophylla and Toricellia, constitute a second, well-supported clade. Two Hydrangea taxa included in the analysis nest in the second clade and a basal branching respectively. The wood anatomical diversity pattern thus supports a family concept of Comaceae including Cornus, Curtisia, Diplopanax, Mastixia, Alangiaceae, and Nyssaceae, and exclusion of the genera in the other clade. There is remarkable agreement between some of these wood anatomical r~sults and recent cladistic analyses of rbcL sequences by Xiang and co-workers. The infrageneric classification of Cornus, Alangium and Nyssa is also discussed.

Before the floras—Monographs

1998 ◽  
Vol 11 (2) ◽  
pp. 243 ◽  
Author(s):  
James W. Grimes
Keyword(s):  
Cladistic Analysis ◽  
Basic Data ◽  
Rigorous Analysis ◽  
Species Definition ◽  
Cladistic Analyses ◽  
Applied Biology ◽  
Major Consideration

The proposal is made that writing of national or regional floras is premature, and that systematic resources should be directed toward the preparation of monographs with cladistic analyses. This proposal results from one major consideration: that the preparation of floras does not require rigorous analysis of species definition and delimitation, and therefore the basic data (i.e. the species circumscriptions) are more unreliable than that in monographs. Furthermore, contrary to some published arguments, the data in floras are not presented and summarised in a format compatible with other areas of comparative and applied biology, whereas it is otherwise in a monograph with cladistic analysis. This proposition is based on the author’s experience in preparing both monographs and floristic treatments.

Dysponetus joeli sp. nov. (Polychaeta: Chrysopetalidae) from the north-east Atlantic, with a cladistic analysis of the genus and a key to species

2012 ◽  
Vol 92 (5) ◽  
pp. 989-996
Author(s):  
Frederic Olivier ◽  
Paulo Lana ◽  
Veronica Oliveira ◽  
Tim Worsfold
Keyword(s):  
Morphological Traits ◽  
Cladistic Analysis ◽  
English Channel ◽  
Unique Combination ◽  
Parsimony Analysis ◽  
Key To Species ◽  
East Atlantic ◽  
The Third ◽  
North East ◽  
The North

We describe Dysponetus joeli sp. nov. from shallow maerl habitats in the north-east Atlantic (English Channel and Bay of Biscay). Dysponetus joeli differs from congeneric species by a unique combination of characters, including a large syllid-like pharynx, 2–4 simple serrated neurochaetae (closely similar to notochaetae, but much smaller and more delicate), D-shaped chaetal spines and ventral cirri on the third segment. A phylogenetic parsimony analysis based on morphological traits suggests that Dysponetus is not monophyletic unless it includes the closely related genera Vigtorniella and Pseudodysponetus, which are well delineated inside the dysponetid clade. Chaetal spines seem to be secondarily derived from paleae and to have originated in infaunal dysponetid forms. They should not be considered as plesiomorphic, but as evidence to support the clade made up by Dysponetus–Vigtorniella and Pseudodysponetus as delineated by a phylogenetic analysis.

scholarly journals Majority Does Not Rule: The Trouble with Majority-Rule Consensus Trees

Cladistics ◽  
2005 ◽  
Vol 17 (3) ◽  
pp. 282-284 ◽  
Author(s):  
Michael J. Sharkey ◽  
Jason W. Leathers
Keyword(s):  
Majority Rule ◽  
Consensus Trees

Systematics of the Ordovician trilobites Ischyrotoma and Dimeropygiella, with species from the type Ibexian area, western U.S.A.

2001 ◽  
Vol 75 (5) ◽  
pp. 947-971 ◽  
Author(s):  
Jonathan M. Adrain ◽  
Stephen R. Westrop ◽  
Ed Landing ◽  
Richard A. Fortey
Keyword(s):  
New Species ◽  
Parsimony Analysis ◽  
Field Sampling ◽  
Number Of Species ◽  
Lower Ordovician ◽  
New Material ◽  
Paraphyletic Group

Lower Ordovician sections in the type Ibexian area of western Utah contain a considerably more diverse trilobite fauna than has previously been reported. Reinvestigation of these faunas, based on new field sampling, allows a reassessment of the dimeropygid genera Ischyrotoma Raymond, 1925, and Dimeropygiella Ross, 1951. These taxa have been considered synonyms, but parsimony analysis indicates each is a well supported clade, and they are best recognized as sister genera. The number of species known from Ibex has been doubled, from four to eight, and morphological information is now available for most parts of the exoskeleton. New species include Ischyrotoma juabensis (Juab Formation), I. wahwahensis (Wah Wah Formation), Dimeropygiella fillmorensis (Fillmore Formation), and D. mccormicki (Fillmore Formation). The previously named species Dimeropygiella caudanodosa, D. blanda, and D. ovata are fully revised on the basis of abundant new material. Pseudohystricurus is a paraphyletic group, with species distributed as a basal grade of the Ischyrotoma/Dimeropygiella group.

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.

Larval morphology of Rhantus Dejean, 1833 (Coleoptera: Dytiscidae: Colymbetinae): descriptions of 22 species and phylogenetic considerations

Zootaxa ◽  
2009 ◽  
Vol 2317 (1) ◽  
pp. 1-102 ◽  
Author(s):  
YVES ALARIE ◽  
MARIANO C. MICHAT ◽  
ANDERS N. NILSSON ◽  
MIGUEL ARCHANGELSKY ◽  
LARS HENDRICH
Keyword(s):  
Abdominal Segment ◽  
Strong Support ◽  
Larval Morphology ◽  
Parsimony Analysis ◽  
Larval Instars ◽  
Consensus Trees ◽  
Neotropical Species ◽  
Distinct Lineage ◽  
Similar Character ◽  
Phylogenetic Origin

Descriptions of larval instars of 22 species of Rhantus Dejean, 1833 are presented including a detailed chaetotaxic analysis of the cephalic capsule, head appendages, legs, last abdominal segment and urogomphi. A parsimony analysis including 25 Rhantus species (the 22 species described in this paper + 3 additional ones) from all major zoogeographic regions and representatives of other Colymbetini genera was conducted using the program TNT based on 43 informative larval characteristics. Jackknife values indicate strong support for the monophyly of members of the tribe Colymbetini (Colymbetinae), which is supported by eight synapomorphies. It is postulated that Rhantus is polyphyletic as Rhantus (Nartus) grapii (Gyllenhal, 1908) and R. monteithi Balke, Wewalka, Alarie & Ribera, 2007 occur as more closely related phylogenetically to other genera of the tribe Colymbetini than to the Rhantus species studied. We suggest that the Neotropical species R. orbignyi Balke, 1992, R. antarcticus nahueli Trémouilles, 1984, R. calidus (Fabricius, 1792) and R. validus Sharp, 1882 represent a distinct lineage within the Colymbetini. All these species diverge at the basis of the strict consensus trees prior to all other Colymbetini studied and are characterized by several unique larval character states. Larvae of Palearctic and Nearctic species of Rhantus were found to share similar character states, which is suggestive of a common phylogenetic origin.

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