Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot

Cladistics ◽  
2021 ◽  
Author(s):  
Pablo A. Goloboff ◽  
Santiago A. Catalano ◽  
Ambrosio Torres
Keyword(s):  
Parsimony Analysis

EFFECTS OF RANDOMLY AND NON-RANDOMLY DISTRIBUTED MISSING DATA IN SUPPORT VALUES OF BAYESIAN AND PARSIMONY ANALYSIS

2016 ◽  
Author(s):  
Diego Pol ◽  
◽  
Alfredo Holley
Keyword(s):  
Missing Data ◽  
Parsimony Analysis

Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)

Cladistics ◽  
2021 ◽  
Author(s):  
Ambrosio Torres ◽  
Pablo A. Goloboff ◽  
Santiago A. Catalano
Keyword(s):  
New Technology ◽  
Parsimony Analysis ◽  
Tree Analysis

scholarly journals The hobo Transposable Element Excises and Has Related Elements in Tephritid Species

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1339-1347
Author(s):  
Alfred M Handler ◽  
Sheilachu P Gomez
Keyword(s):  
Drosophila Melanogaster ◽  
Ceratitis Capitata ◽  
Bactrocera Dorsalis ◽  
Parsimony Analysis ◽  
Wild Type ◽  
Anastrepha Suspensa ◽  
Tephritid Species ◽  
Mutant Strains ◽  
Almost All ◽  
Horizontal Transfers

Abstract Function of the Drosophila melanogaster hobo transposon in tephritid species was tested in transient embryonic excision assays. Wild-type and mutant strains of Anastrepha suspensa, Bactrocera dorsalis, B. cucurbitae, Ceratitis capitata, and Toxotrypana curvicauda all supported hobo excision or deletion both in the presence and absence of co-injected hobo transposase, indicating a permissive state for hobo mobility and the existence of endogenous systems capable of mobilizing hobo. In several strains hobo helper reduced excision. Excision depended on hobo sequences in the indicator plasmid, though almost all excisions were imprecise and the mobilizing systems appear mechanistically different from hobo. hobe-related sequences were identified in all species except T. curvicauda. Parsimony analysis yielded a subgroup including the B. cucurbitae and C. capitata sequences along with hobo and Hermes, and a separate, more divergent subgroup including the A. suspensa and B. dorsalis sequences. All of the sequences exist as multiple genomic elements, and a deleted form of the B. cucurbitae element exists in B. dorsalis. The hobo-related sequences are probably members of the hAT transposon family with some evolving from distant ancestor elements, while others may have originated from more recent horizontal transfers.

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 Detection of areas of endemism on two spatial scales using Parsimony Analysis of Endemicity (PAE): the Neotropical region and the Atlantic Forest

2008 ◽  
Vol 8 (4) ◽  
pp. 33-42 ◽  
Author(s):  
Mário Sérgio Sigrist ◽  
Claudio José Barros de Carvalho
Keyword(s):  
Atlantic Forest ◽  
Spatial Scales ◽  
Distribution Patterns ◽  
Neotropical Region ◽  
Conservation Priorities ◽  
Parsimony Analysis ◽  
Areas Of Endemism ◽  
Endemic Areas ◽  
Analysis Scale ◽  
Parsimony Analysis Of Endemicity

An important biological challenge today is the conservation of biodiversity. Biogeography, the study of the distribution patterns of organisms, is an important tool for this challenge. Endemism, the co-occurrence of several species unique to the same area, has important implications for the preservation of biodiversity, since many areas of endemism are also areas with large human impact. More rigorously defined, areas of endemism are historical units of distributional congruence of monophyletic taxa. These areas often assumed to be due to nonrandom historical events that favored conditions associated with high rates of speciation. Thus, understanding endemism and the delimitation of endemic areas has important implications for conservation. Today, most studies delimit areas of endemism by superimposing maps of distribution for various species. This approach suffers from arbitrary delimitations, however, when a great distributional data is used. In this paper we used the method of Parsimony Analysis of Endemicity (PAE) based on georeferenced quadrats in order to delimit areas of endemism. This modality of the method is important due to its testable nature and can also be used to infer area relationships. We applied the method to raw distributional data from 19 unrelated taxa to delimit general patterns of endemism in the Neotropical Region and in the Atlantic forest domain using different grid scales. Neotropical areas found are comprised over the Panama region, northern Andean region and the Atlantic forest. Atlantic forest showed a major division into two distinct components (northern x southern). Endemic areas delimited using smaller scale grids on the Atlantic forest should be considered for conservation priorities once they showed endemism at regional and local scales. The results were also compared to other studies using different taxa and methods. Finally, some considerations on the analysis scale and future perspectives of the method are presented.

scholarly journals Parsimony analysis of endemicity of enchodontoid fishes from the Cenomanian

2007 ◽  
Author(s):  
Hilda Maria Andrade da SILVA ◽  
Valéria GALLO
Keyword(s):  
Parsimony Analysis ◽  
Parsimony Analysis Of Endemicity

Bird distributional patterns support biogeographical histories and are associated with bioclimatic units in the Atlantic Forest, Brazil

Zootaxa ◽  
2017 ◽  
Vol 4337 (2) ◽  
pp. 223 ◽  
Author(s):  
CRISTIANO DE SANTANA CARVALHO ◽  
NAYLA FÁBIA FERREIRA DO NASCIMENTO ◽  
HELDER F. P. DE ARAUJO
Keyword(s):  
Multivariate Analysis ◽  
Atlantic Forest ◽  
Analysis Of Variance ◽  
Forest Birds ◽  
Distributional Pattern ◽  
Parsimony Analysis ◽  
Multivariate Analysis Of Variance ◽  
Distributional Patterns ◽  
Parsimony Analysis Of Endemicity

Rivers as barriers to dispersal and past forest refugia are two of the hypotheses proposed to explain the patterns of biodiversity in the Atlantic Forest. It has recently been shown that possible past refugia correspond to bioclimatically different regions, so we tested whether patterns of shared distribution of bird taxa in the Atlantic Forest are 1) limited by the Doce and São Francisco rivers or 2) associated with the bioclimatically different southern and northeastern regions. We catalogued lists of forest birds from 45 locations, 36 in the Atlantic forest and nine in Amazon, and used parsimony analysis of endemicity to identify groups of shared taxa. We also compared differences between these groups by permutational multivariate analysis of variance and identified the species that best supported the resulting groups. The results showed that the distribution of forest birds is divided into two main regions in the Atlantic Forest, the first with more southern localities and the second with northeastern localities. This distributional pattern is not delimited by riverbanks, but it may be associated with bioclimatic units, surrogated by altitude, that maintain current environmental differences between two main regions on Atlantic Forest and may be related to phylogenetic histories of taxa supporting the two groups. 

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.

scholarly journals On the Three-Taxon Approach to Parsimony Analysis

Cladistics ◽  
1998 ◽  
Vol 14 (4) ◽  
pp. 363-381 ◽  
Author(s):  
Jan Laet ◽  
Erik Smets
Keyword(s):  
Parsimony Analysis
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