The Deep Coalescence Consensus Tree Problem is Pareto on Clusters

2011 ◽  
pp. 172-183 ◽  
Author(s):  
Harris T. Lin ◽  
J. Gordon Burleigh ◽  
Oliver Eulenstein
Keyword(s):  
Consensus Tree ◽  
Deep Coalescence

Phylogenetic relationships between the genera Aphidius and Lysaphidus (Hymenoptera: Braconidae: Aphidiinae) with description of Aphidius iranicus sp. nov.

2007 ◽  
Vol 139 (3) ◽  
pp. 297-307 ◽  
Author(s):  
Željko Tomanović ◽  
Ehsan Rakhshani ◽  
Petr Starý ◽  
Nickolas G. Kavallieratos ◽  
Ljubiša Ž. Stanisavljević ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Taxonomic Position ◽  
Parsimony Analysis ◽  
Parasitoid Species ◽  
Consensus Tree ◽  
Artemisia Absinthium ◽  
Diagnostic Characters ◽  
Line Drawings ◽  
Generic Status

AbstractWe analyzed the phylogenetic relationships between eight Aphidius Nees and six Lysaphidus Smith species on the basis of 12 morphological characters by parsimony analysis. The consensus tree does not support the generic status of Lysaphidus. Aphidius iranicus, sp. nov., associated with Titanosiphon bellicosum Nevsky on Artemisia absinthium L. from Iran, is described. The new parasitoid species is described and illustrated by line drawings, and its diagnostic characters are discussed. The taxonomic position of the subgenus Tremblayia Tizado and Núñez-Pérez is also considered. Tremblayia and Lysaphidus are newly classified as synonyms of Aphidius. The following new or revised combinations are proposed: Aphidius adelocarinus Smith, comb. rev., A. ramythirus Smith, comb. rev., A. rosaphidis Smith, comb. rev., A. viaticus (Sedlag), comb. nov., A. arvensis (Starý), comb. nov., and A. erysimi (Starý), comb. nov.

Genetic diversity and morphological variability in Polygonum aviculare s.l. (Polygonaceae) of Iran

Phytotaxa ◽  
2015 ◽  
Vol 233 (2) ◽  
pp. 166 ◽  
Author(s):  
Samaneh Mosaferi ◽  
Masoud Sheidai ◽  
Maryam Keshavarzi ◽  
Zahra Noormohammdai
Keyword(s):  
Morphological Variability ◽  
Genetic Data ◽  
Mantel Test ◽  
Gene Exchange ◽  
Consensus Tree ◽  
Polygonum Aviculare ◽  
Molecular Investigation ◽  
Variable Species ◽  
Issr Molecular Markers ◽  
Positive Significant Correlation

A molecular investigation was carried out on the variable species Polygonum aviculare using 109 plants from 12 Iranian populations. ISSR molecular markers were used for genetic study. AMOVA and Gst analyses revealed a high genetic variability both within and among populations. Mantel test showed positive significant correlation between genetic and geographical distance of populations. Structure and K-Means clustering revealed stratification ingenetic characteristics of accessions. Networking and reticulation analyses showed some degree of gene exchange among populations. Consensus tree based on morphological and genetic data separated some of these populations from the others suggesting the existence of new taxa within this species.

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.

scholarly journals Unconstrained Diameters for Deep Coalescence

2017 ◽  
Vol 14 (5) ◽  
pp. 1002-1012 ◽  
Author(s):  
Pawel Gorecki ◽  
Jaroslaw Paszek ◽  
Oliver Eulenstein
Keyword(s):  
Deep Coalescence

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.

Detection of two cryptic taxa in Meristogenys amoropalamus (Amphibia, Ranidae) through nuclear and mitochondrial DNA analyses

Zootaxa ◽  
2008 ◽  
Vol 1843 (1) ◽  
pp. 24 ◽  
Author(s):  
TOMOHIKO SHIMADA ◽  
MASAFUMI MATSUI ◽  
PAUL YAMBUN ◽  
MAKLARIN LAKIM ◽  
MARYATI MOHAMED
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Gene ◽  
Single Species ◽  
Sympatric Species ◽  
12S Rrna ◽  
Dna Analyses ◽  
Deep Coalescence ◽  
Pomc Gene ◽  
Cryptic Taxa ◽  
Rag 1

We identified three distinct sympatric lineages of frogs among specimens previously considered a single species (Meris- togenys amoropalamus Matsui), based on 909 bp of mitochondrial DNA (12S rRNA and cytochrome b). To seek evidence of reproductive isolation between these lineages, we first analyzed a 249-bp fragment of the nuclear proopiomelanocortin (POMC) gene and found five haplotypes, of which two were limited to lineage 1 and three belonged to lineages 3 and 4. In a subsequent phylogenetic analysis of a 1313-bp fragment of nuclear POMC, Rag-1, and rhodopsin, lineage 1 was again distinct, while lineages 3 and 4 could not be differentiated. The results of the nuclear gene analyses suggest that lineage 1 is strongly isolated reproductively from lineages 3 and 4, which are not isolated from each other. This conclusion conforms to groupings based on larval morphology. These results indicate that frogs morphologically identified as M. amoropalamus should be split into two sympatric species, one of which contains two mitochondrial lineages that have presumably been retained via deep coalescence.

Faster Algorithms for Computing the R* Consensus Tree

2014 ◽  
pp. 414-425 ◽  
Author(s):  
Jesper Jansson ◽  
Wing-Kin Sung ◽  
Hoa Vu ◽  
Siu-Ming Yiu
Keyword(s):  
Consensus Tree

An overview of glossiphoniid leech development

2001 ◽  
Vol 79 (2) ◽  
pp. 218-232 ◽  
Author(s):  
David A Weisblat ◽  
Françoise Z Huang
Keyword(s):  
Model Systems ◽  
Model Organisms ◽  
Consensus Tree ◽  
Comparative Development ◽  
Experimental Embryology ◽  
Molecular Studies ◽  
Research Questions ◽  
Per Se ◽  
Molecular Phylogenies ◽  
Development And Evolution

Dramatic advances in understanding the development of selected "model" organisms, coupled with the realization that genes which regulate development are often conserved between diverse taxa, have renewed interest in comparative development and evolution. Recent molecular phylogenies seem to be converging on a new consensus "tree," according to which higher bilaterians fall into three major groups, Deuterostoma, Ecdysozoa, and Lophotrochozoa. Commonly studied model systems for development fall almost exclusively within the first two of these groups. Glossiphoniid leeches (phylum Annelida) offer certain advantages for descriptive and experimental embryology per se, and can also serve to represent the lophotrochozoan clade. We present an overview of the development of glossiphoniid leeches, highlighting some current research questions and the potential for comparative cellular and molecular studies.

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