Linguistic homoplasy and phylogeny reconstruction. The cases of Lezgian and Tsezic languages (North Caucasus)

2017 ◽  
Vol 51 (s38) ◽  
Author(s):  
Alexei S. Kassian
Keyword(s):  
Phylogeny Reconstruction ◽  
Neighbor Joining ◽  
North Caucasus ◽  
Input Matrix ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Bayesian Mcmc ◽  
Phylogenetic Methods ◽  
Network Method ◽  
Ancestral Character States

AbstractThis paper deals with the problem of linguistic homoplasy (parallel or backward development), how it can be detected, what kinds of linguistic homoplasy can be distinguished and which varieties of the phenomenon are the most deleterious for the reconstruction of language phylogeny. It is proposed that language phylogeny reconstruction should consist of two main stages. Firstly, a strict consensus tree should be built on the basis of high-quality input data elaborated with the help of the main phylogenetic methods (such as Neighbor-joining, Bayesian MCMC, and Maximum parsimony), and ancestral character states, allowing us to reveal a certain number of homoplastic characters. Secondly, after the detected instances of homoplasy are eliminated from the input matrix, the consensus tree is to be compiled again. It is expected that after homoplastic optimization it will be possible to better resolve individual “problem clades”, and generally the homoplasy-optimized phylogeny should be more robust than the tree constructed initially. The proposed procedure is tested on the 110-item Swadesh wordlists of the Lezgian and Tsezic groups. The Lezgian and Tsezic results generally support theoretical expectations. The MLN (minimal lateral network) method, currently implemented in the LingPy software, is a helpful tool for the detection of linguistic homoplasy.

Application of the matK gene sequences to grass systematics

1996 ◽  
Vol 74 (1) ◽  
pp. 125-134 ◽  
Author(s):  
Hongping Liang ◽  
Khidir W. Hilu
Keyword(s):  
Dna Sequence ◽  
Neighbor Joining ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Dna Mutations ◽  
Monophyletic Lineage ◽  
The Family ◽  
Basal Clade ◽  
Matk Gene ◽  
Insight Into

The 3′ region of the matK gene from 17 species, representing 13 tribes and six subfamilies of the Poaceae, is used to investigate the potential of the gene in addressing systematic questions in the family. The aligned sequences were analyzed by the Wagner parsimony methods using PAUP and PHYLIP and by the neighbor-joining method. Out of the 583 bp sequenced, 30% were variable and 14.9% were informative. The strict consensus tree, rooted by Joinvillea (Joinvilleaceae), showed well-resolved major clades that represent the grass subfamilies. The bambusoid Phyllostachys appeared as a basal clade in the family. Oryza diverged either before or after the Pooideae in the parsimony and neighbor-joining methods, respectively. The three members of the Pooideae grouped in a monophyletic lineage in both analyses. Arundo (Arundinoideae) was basal to the subfamilies Panicoideae and Chloridoideae. Analysis of the various types of DNA mutations underscores the potential of the matK gene in providing insight into grass systematic and evolution. Keywords: matK, Poaceae, grasses, phylogeny, chloroplast, DNA sequence.

A cladistic analysis of the Old World species of Lotus L. (Fabaceae: Loteae)

2000 ◽  
Vol 78 (3) ◽  
pp. 351-360 ◽  
Author(s):  
Ana M Arambarri
Keyword(s):  
Cladistic Analysis ◽  
Morphological Characters ◽  
Comparison Method ◽  
Data Matrix ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
World Species ◽  
Old World ◽  
Species Phylogeny ◽  
The World

The diagnostic characters of the genus Lotus L. are a claw with a thickened infolded margin, diadelphous stamens, and a style hardened from the base. This genus contains about 100 species that are distributed throughout the world. To investigate the phylogeny of the Old World species of Lotus, subgenus Edentolotus, sections Krokeria, Xantholotus, and Erythrolotus, a cladistic analysis was performed using 31 morphological characters. To test the phylogenetic relationships among species of Lotus-Edentolotus and Dorycnium, Pedrosia, and Tetragonolobus, these taxa were included as part of the ingroup. The polarity of the characters was based on the outgroup comparison method, using Anthyllis as one outgroup and Tripodion as another. The analysis with Anthyllis as outgroup yielded eight equally parsimonious trees (with all characters equally weighted), each with 62 steps, a consistency index of 0.53, and a retention index of 0.75. All trees (including the strict consensus tree from the eight initial trees) showed that genus Lotus, subgenus Edentolotus, and sections Xantholotus and Erythrolotus are polyphyletic, with only section Krokeria appearing as monophyletic. On the other hand, the groups of species Lotus angustissimus, Lotus corniculatus, Lotus creticus, and Lotus peregrinus are monophyletic. Identical results were derived from the data matrix using Tripodion as the outgroup. Results are compared with previous cytogenetic and biochemical evidence.Key words: cladistic analysis, Fabaceae, Loteae, Lotus, Old World species, phylogeny.

Phylogenetic relationships among families of the order Anomopoda (Crustacea, Branchiopoda, Cladocera)

Zootaxa ◽  
2004 ◽  
Vol 760 (1) ◽  
pp. 1 ◽  
Author(s):  
LOURDES M.A. ELMOOR-LOUREIRO
Keyword(s):  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Trunk Limbs ◽  
Trunk Limb

The phylogenetic relationships among families of the Order Anomopoda (Crustacea, Branchiopoda, Cladocera) were investigated through a cladistic analysis including 93 characters and 37 terminal taxa (2 as outgroups). The strict consensus tree supported the monophyly of the Anomopoda and its families, and indicated the existence of two main clades: (Moinidae+Daphniidae) and (Dumontidae (Ilyocryptidae+Bosminidae+Radopoda)). The later clade was supported by trunk limb characters, probably related to life associated with the bottom or with macrophytes (lifestyle lost in Bosminidae, but still visible in some of its trunk limbs). Within the Radopoda, the Eurycercoidea was monophyletic, but the monophyly of the Macrothricoidea was not supported.

Larval morphology of the Palaearctic genera Deronectes Sharp and Scarodytes Gozis (Coleoptera: Dytiscidae: Hydroporinae), with implications for the phylogeny of the Deronectes-group of genera

1999 ◽  
Vol 30 (2) ◽  
pp. 173-195 ◽  
Author(s):  
Lars Hendrich ◽  
Yves Alarie ◽  
Anders N. Nilsson
Keyword(s):  
Phylogenetic Analysis ◽  
Sister Group ◽  
Larval Morphology ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Larval Instars ◽  
Monophyletic Origin ◽  
First Instar ◽  
Statistical Support

AbstractDescription of larval instars of Deronectes depressicollis Rosenhauer 1856, D. lareynii (Fair-maire 1858), D. latus (Stephens 1829), D. aubei (Mulsant 1843), and Scarodytes halensis (Fabricius 1787) is presented including a detailed chaetotaxic and porotaxic analysis of the cephalic capsule, head appendages, legs, last abdominal scgment and urogomphi. A phylogenetic analysis of 14 genera of the tribe Hydroporini, based on 22 larval characteristics was conducted with Hennig86. Three of the branches of the strict consensus tree have a statistical support greater than 60% according to the Parsimony Jackknifer. One of the supported clades is Antiporus Sharp + Nebrioporus Régimbart + Neonectes J. Balfour-Browne + Oreodytes Seidlitz + Stictotarsus Zimmermann + Scarodytes Gozis, of which the sister-group is the genus Deronectes Sharp. Consequently larval characters, in contrast to adult characters support the inclusion of Antiporus, Neonectes and Oreodytes in the Deronectes-group of genera. All members of this clade are characterized by: (i) presence of an occipital suture in first instar, (ii) presence of a constriction at level of occipital suture, (iii) absence of maxillary cardo, and (iv) insertion of the primary seta MX I on the maxillary stipes. Scarodytes is postulated to share a monophyletic origin with Nebrioporus, Stictotarsus, and Antiporus based on (i) the presence of natatory setae on femora, tibiae, and tarsi and (ii) the shape of the urogomphomere I which is more than 3.10 times longer than urogomphomere 2.

scholarly journals An experimental study comparing linguistic phylogenetic reconstruction methods

Diachronica ◽  
2013 ◽  
Vol 30 (2) ◽  
pp. 143-170 ◽  
Author(s):  
François Barbançon ◽  
Steven N. Evans ◽  
Luay Nakhleh ◽  
Don Ringe ◽  
Tandy Warnow
Keyword(s):  
Experimental Study ◽  
Simulation Study ◽  
Maximum Parsimony ◽  
Phylogenetic Reconstruction ◽  
Phylogeny Reconstruction ◽  
Neighbor Joining ◽  
Reconstruction Methods

This paper reports a simulation study comparing and evaluating the performance of different linguistic phylogeny reconstruction methods on model datasets for which the true trees are known. UPGMA performed least well, then (in ascending order) neighbor joining, the method of Gray & Atkinson and finally maximum parsimony. Weighting characters greatly improves the accuracy of maximum parsimony and maximum compatibility if the characters with high weights exhibit low homoplasy.

The Phylogeny of Lecanactis (Opegraphaceae)

1997 ◽  
Vol 29 (5) ◽  
pp. 397-414 ◽  
Author(s):  
Anders Tehler ◽  
José M. Egea
Keyword(s):  
Chemical Data ◽  
Successive Approximations ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Weighting Method ◽  
Parsimonious Tree ◽  
Character Weighting

AbstractThe genus Lecanactis, with 24 species, has been phylogenetically analysed using cladistic parsimony methods and support tests. Morphological, anatomical and chemical data were used, comprising 38 characters. Twelve equally most parsimonious trees were obtained. The successive approximations character weighting method gave one most parsimonious tree. The ingroup, Lecanactis, is supported as monophyletic. Although parsimony jackknifing and Bremer support indicate that the trees are poorly supported, some groups are wholly or partly distinguished in both the strict consensus tree, the successive weighting tree and the Jac tree.

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.

Siamosuchus phuphokensis, a new goniopholidid from the Early Cretaceous (ante-Aptian) of northeastern Thailand

2007 ◽  
Vol 178 (3) ◽  
pp. 201-216 ◽  
Author(s):  
Komsorn Lauprasert ◽  
Gilles Cuny ◽  
Eric Buffetaut ◽  
Varavudh Suteethorn ◽  
Kumthorn Thirakhupt
Keyword(s):  
The Other ◽  
New Taxon ◽  
Postcranial Skeleton ◽  
Consensus Tree ◽  
Caudal Part ◽  
Strict Consensus Tree ◽  
The Family ◽  
The Right ◽  
High Median ◽  
Northeastern Thailand

Abstract A new taxon of a broad-snouted goniopholidid, Siamosuchus phuphokensis, gen. et sp. nov., was discovered in the Sao Khua Formation (ante-Aptian), northeastern Thailand. The specimen is described on the basis of an incomplete skeleton showing the premaxillae, maxillae, nasals, left lacrimal, frontal, left jugal, right postorbital, caudal part of the cranial table, most of the right part of the postcranial skeleton, and several heavily sculptured osteoderms. S. phuphokensis is distinguished from the other broad-snouted goniopholidids on the basis of the following characters: penetration of the nasals in the narial border; presence of a robust and high median ridge on the interorbital surface; lateral margin of the frontal forming the medial edge of the orbit; supraoccipital exhibiting a wide pentagonal shape. A phylogenetic analysis using 101 characters for 29 mesoeucrocodylian taxa and 3 outgroup taxa supports the monophyly of the family Goniopholididae. In addition, the Thai specimen forms a clade with the European Goniopholis. Based on our strict consensus tree, the generic name Goniopholis should be restricted to the European forms only.

scholarly journals An appraisal of the phylogenetic relationships of Hypoptopomatini cascudinhos with description of two new genera and three new species (Siluriformes: Loricariidae)

2017 ◽  
Vol 15 (4) ◽  
Author(s):  
Maria Laura S. Delapieve ◽  
Pablo Lehmann A ◽  
Roberto E. Reis
Keyword(s):  
New Species ◽  
New Taxa ◽  
Retention Index ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Data Matrix ◽  
New Genera ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Three New Species

ABSTRACT The discovery of three new taxa of Hypoptotopomatini with ambiguous generic assignment prompted a reanalysis of the phylogenetic relationships of the tribe. The analysis focused on a data matrix of 56 terminals and 107 morphological characters comprising the three new taxa, most species of Hypoptopoma and Otocinclus, and all other species of the tribe. The 162 maximally parsimonious trees of 382 steps, consistency index of 0.41, and retention index of 0.83 were then summarized in a strict consensus tree. The results confirm the monophyly of the Hypoptopomatini, recover four genera as monophyletic (Acestridium, Hypoptopoma, Niobichthys, and Otocinclus), revealed Hypoptopoma and Oxyropsis to be non-monophyletic; and revealed two new genera within Hypoptopomatini. Additionally, Otocinclus was found to be sister to a group with all remaining genera of the tribe; Acestridium and Niobichthys were found to be sister to each other and that clade sister to a group formed by ((Leptotocinclus + Hypoptopoma [part]) + (Nannoxyropsis (Oxyropsis + Hypoptopoma [part]))). Based on this framework, changes to the classification and the taxonomy of the Hypoptopomatini are suggested and the new taxa are described.

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