An optimized algorithm to find maximum parsimonious tree using PrimeNucleotide based approach

2014 ◽  
Author(s):  
Rasif Ajwad ◽  
Syed Nayem Hossain ◽  
Golam Mostaeen ◽  
M. A. Mottalib
Keyword(s):  
Parsimonious Tree

Systematic studies in Paniceae (Poaceae): Homopholis and Whalleya gen. et sp. nov.

2000 ◽  
Vol 13 (3) ◽  
pp. 437 ◽  
Author(s):  
Karen E. Wills ◽  
R. D. B. Whalley ◽  
Jeremy J. Bruhl
Keyword(s):  
Sister Group ◽  
The Other ◽  
Sister Species ◽  
Parsimonious Tree ◽  
The Third ◽  
Putative Species ◽  
Anatomical Data ◽  
Cladistic Analyses

The taxonomy ofHomopholis C.E.Hubb. is revised, and anew genus Whalleya K.E.Wills & J.J.Bruhl isdescribed. Relationships among the known species ofHomopholis (H. belsonii C.E.Hubb.,H. proluta F.Muell., and a putative species,H. sp. nov.), and the relationships betweenHomopholis and other genera within the Paniceae were investigated. Morphological and anatomical data forHomopholis and selected species ofDigitaria and Panicum were analysed phenetically and cladistically. The value and contribution ofcharacters to the findings were assessed. In the phenetic analyses, threedistinct clusters of species were formed. The first cluster includedDigitaria coenicola (F.Muell.) Hughes,D. divaricatissima (R.Br.) Hughes andD. papposa (R.Br.) P.Beauv.; the second,Panicum effusum R.Br.,P. queenslandicum Domin var.queenslandicum and P. simileDomin; and the third, H. sp. nov.,H. proluta, H. belsonii andP. subxerophilum Domin. Specimens ofH. belsonii noticeably separated from the other threespecies. For the cladistic analyses, species ofEntolasia and Thyridolepis were used as outgroup taxa. One most parsimonious tree was produced.Homopholis belsonii was well supported as the most basalmember of the ingroup. The three species ofDigitariaformed a well-supported clade.Panicum effusum, P. queenslandicumvar. queenslandicum and P. simileformed a well-supported clade, and were the sister group toEntolasia marginata (R.Br.) Hughes andE. stricta (R.Br.) Hughes.Panicum subxerophilum was in a clade (=Whalleya) with H. sp. nov. andH. proluta, with P. subxerophilumand H. proluta as sister species.

A new Xenungulata (Mammalia) from the Paleocene of Patagonia, Argentina

2008 ◽  
Vol 82 (2) ◽  
pp. 329-335 ◽  
Author(s):  
Javier N. Gelfo ◽  
Guillermo M. López ◽  
Mariano Bond
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Phylogenetic Relationship ◽  
New Taxon ◽  
Parsimonious Tree ◽  
Late Paleocene ◽  
Direct Association ◽  
Mammalian Faunas ◽  
New Form ◽  
Preliminary Phylogenetic Analysis

A new form of Xenungulata Paula Couto, 1952 from red levels of the Peñas Coloradas Formation in a locality near Puerto Visser (45°17'S, 67°01'W), Chubut province, Argentina, is represented by a fragmentary left jaw with the m3 (MPEF-PV 1871). Notoetayoa gargantuai n. gen. and n. sp. is the first ever found in direct association with Carodnia feruglioi Simpson, 1935a which characterizes the incompletely known homonymous zone of the late Paleocene of Patagonia. A preliminary phylogenetic analysis, including representatives of “Condylarthra,” Litopterna, Notoungulata, Pyrotheria, Xenungulata and Astrapotheria, plus the characters that could be scored in the new taxon, was performed using TNT software. A single most parsimonious tree was obtained. Notoetayoa gargantuai has a closer phylogenetic relationship with the Xenungulate Etayoa bacatensis Villarroel, 1987 from the ?middle Paleocene of Colombia than with any other Tertiary ungulate group of South America. Notoetayoa gargantuai fills an important gap in the knowledge of the mammalian faunas from the Paleocene of Patagonia, particularly of the poorly known pre-Itaborian times.

A new species of Lauromacromia (Odonata: Corduliidae) from Southeastern Brazil, with a cladistic analysis of the genus and comments on Neotropical dragonfly biogeography

Zootaxa ◽  
2010 ◽  
Vol 2425 (1) ◽  
pp. 45 ◽  
Author(s):  
ÂNGELO PARISE PINTO ◽  
ALCIMAR DO LAGO CARVALHO
Keyword(s):  
New Species ◽  
Atlantic Forest ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Southeastern Brazil ◽  
Mato Grosso ◽  
Parsimonious Tree ◽  
Male Characters ◽  
Species Groups ◽  
Mato Grosso Do Sul

Lauromacromia melanica sp. nov. from Conceição da Barra municipality, Espírito Santo State, Brazil, is described and illustrated based on two males (both in MNRJ nº 135). The new species is similar to L. picinguaba differing from it mainly by the absence of pale spots on S3–6 and by the ellipsoid shape of metepisternal pale stripe. A key for males of all species of the genus is provided. A cladistic analysis encompassing 43 external morphological male characters carried out in two distinct procedures, the first with all characters unordered and the second with two or three state characters ordered. The unordered analysis generated only one most-parsimonious tree (66 steps of length, CI = 0.69, RI = 0.62). The hypothesis of monophyly of Lauromacromia is supported and includes three groups, one formed by the Atlantic Forest species (L. melanica sp. nov. + L. picinguaba), and another by the Cerrado species (L. flaviae + (L. bedei + L. luismoojeni)), and L. dubitalis, positioned in polytomy with these two groups. The ordered analysis also generated only one most-parsimonious tree (68 steps of length, CI = 0.70, RI = 0.67), which maintained the monophyly of Lauromacromia but L. dubitalis positioned basally as sister-group to the Atlantic Forest + Cerrado species groups. The geographic distribution of Lauromacromia is updated with a new record of L. luismoojeni based on one adult male (Brazil: Mato Grosso do Sul State) and probable first Brazilian records for L. dubitalis (Amazonas and Pará States) based on two larvae. A vicariance hypothesis is proposed to explain spatial evolution of Lauromacromia, and based on current biogeographical classifications we consider Gomphomacromia and Rialla apart from Neotropical biota. Some aspects of biology and ecology of Lauromacromia are also discussed.

scholarly journals Phylogeny of the Tyrant Flycatchers (Tyrannidae) Based on Morphology and Behavior

The Auk ◽  
2002 ◽  
Vol 119 (3) ◽  
pp. 715-734 ◽  
Author(s):  
Jeffrey S. Birdsley
Keyword(s):  
Nasal Septum ◽  
Color Pattern ◽  
The Other ◽  
Behavioral Data ◽  
Plumage Color ◽  
Parsimonious Tree ◽  
And Behavior ◽  
Better Than ◽  
Tyrant Flycatchers

Abstract Previously published morphological and behavioral data for the tyrant flycatchers (Tyrannidae) were reanalyzed using cladistic techniques. Several additional characters, including two putative synapomorphies of the Tyrannidae were incorporated. Nearly all of the ∼100 traditional tyrannid genera were included. Results of the analysis of this set of 68 characters support three previously proposed tyrannid assemblages: the kingbird assemblage and slightly restricted Empidonax and Myiarchus assemblages. Characters of the nasal septum that past workers have considered conservative and phylogenetically informative are supported as synapomorphies of the kingbird and restricted Empidonax assemblages. Several small monophyletic groups of genera are supported. The monophyly of neither the Elaenia assemblage nor the flatbill and tody-tyrant assemblage is supported in any most-parsimonious tree, but such trees are not significantly better than trees supporting their monophyly. A Tyrannidae exclusive of the Cotingidae and Pipridae is monophyletic in some most-parsimonious trees, but not in others in which flatbills and tody-tyrants are basal to a clade containing Cotingidae, Pipridae, and the remaining tyrannid genera. There is some evidence that characters describing plumage color pattern are more homoplasious than the other character suites I examined.

Cladistic analysis of Megachile (Chrysosarus) Mitchell and revalidation of Megachile (Dactylomegachile) Mitchell (Hymenoptera, Megachilidae)

Zootaxa ◽  
2009 ◽  
Vol 2284 (1) ◽  
pp. 48-62 ◽  
Author(s):  
SILVANA DURANTE ◽  
NORA CABRERA
Keyword(s):  
Cladistic Analysis ◽  
Parsimonious Tree ◽  
Adult Morphology ◽  
The Family ◽  
The World ◽  
Tropical Areas

Megachile is the largest genus of the family Megachilidae, being widely distributed throughout temperate and tropical areas of the world. The validity of M. (Chrysosarus) and M. (Dactylomegachile) was investigated based on a cladistic analysis of 63 characters of adult morphology of 14 taxa. The single most parsimonious tree (181 steps, CI=0.60; RI=0.63) resulting from an implied weighting analysis recovered M. (Chrysosarus) and M. (Dactylomegachile) as monophyletic groups. Both subgenera are redescribed and the value of the most frequently used characters in the taxonomy of Megachile is discussed.

Phylogeny, biogeography and description of Ameripassalus, a new Mesoamerican genus of Passalidae (Coleoptera)

2014 ◽  
Vol 28 (2) ◽  
pp. 124 ◽  
Author(s):  
Larry Jimऻnez-Ferbans ◽  
Pedro Reyes-Castillo
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Monophyletic Group ◽  
Parsimonious Tree

Ameripassalus, gen. nov., is described as the first genus of Passalini with a distribution restricted to Mesoamerica. The species include A. guatemalensis (Kaup, 1869), comb. nov. from Passalus Fabricius, A. difficilis, sp. nov. and A. tamaulipensis, sp. nov. from Mexico, and A. jacki, sp. nov. and A. nigritus, sp. nov. from Guatemala. A matrix of 46 morphological characters, including the species from Ameripassalus, gen. nov. and 13 species of the genera Paxillus MacLeay, Ptichopus Kaup, Heliscus Zang, Veturius Kaup, Spasalus Kaup, Passipassalus Fonseca & Reyes-Castillo, Passalus Fabricius and Leptaulax Kaup were analysed. Only a single most parsimonious tree was found; in this Ameripassalus is retrieved as a monophyletic group. Ameripassalus difficilis, sp. nov. is shown as the sister group of the rest of the species in the genus. The species with the southernmost distribution (A. guatemalensis (A. nigritus, sp. nov. + A. jacki, sp. nov.)) form a nested clade within the species with the northernmost distribution. Keys to identify adults of the genera of Passalini and to the species of Ameripassalus are provided.

Building a Twig Phylogeny

2015 ◽  
Vol 77 (2) ◽  
pp. 141-144
Author(s):  
Kathryn M. Flinn
Keyword(s):  
Plant Species ◽  
Woody Plant ◽  
Classroom Activity ◽  
Plant Structure ◽  
Student Collaboration ◽  
Parsimonious Tree ◽  
Woody Plant Species ◽  
Homologous Characters

In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a parsimonious tree based on synapomorphies (shared derived characters). This activity efficiently demonstrates many systematics concepts, including homology, homoplasy (convergence and reversal), polarity, synapomorphy, symplesiomorphy, autapomorphy, polytomy, and parsimony. It also engages students in inquiry, promotes student collaboration, raises awareness of plant structure, and exposes students to the diversity of common local trees.

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 The most parsimonious tree for random data

2014 ◽  
Vol 80 ◽  
pp. 165-168 ◽  
Author(s):  
Mareike Fischer ◽  
Michelle Galla ◽  
Lina Herbst ◽  
Mike Steel
Keyword(s):  
Random Data ◽  
Parsimonious Tree

scholarly journals HCPC: A New Parsimonious Clustering Method based on Hierarchical Characters for Morphological Phylogenetic Reconstruction

2021 ◽  
Author(s):  
Hongwei Feng ◽  
Meng Liu ◽  
Bei Wang ◽  
Jun Feng ◽  
Jian Han ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Simulated Annealing Algorithm ◽  
Phylogenetic Reconstruction ◽  
Poor Performance ◽  
Morphological Data ◽  
Clustering Method ◽  
Parsimonious Tree ◽  
Quantitative Basis ◽  
History Of ◽  
Two Stages

Abstract Background: Phylogenetic trees are reconstructed frequently to provide a better interpretation of the evolutionary history of species. However, most traditional methods ignore the hierarchical relationships among characters and neglect the inapplicable state that frequently exists in the morphological data, resulting in poor performance of the phylogenetic analysis.Results: In this study, we propose a phylogenetic clustering method based on hierarchical characters. Accordingly, we call our method Hierarchical Characters Parsimonious Clustering(HCPC). To combine prior phylogenetic knowledge and treat the inapplicable state more reasonably, two stages are proposed, i.e., Phylogenetic reconstruction and parsimonious tree search. During phylogenetic reconstruction, HCPC is able to infer the shared ancestral relationships among species. For the search of the parsimonious tree, we use a simulated annealing algorithm to heuristically search the phylogenetic tree based on the parsimony criterion. In addition, HCPC combines asymmetric binary relationships and character hierarchies to solve the problem of the ambiguity of the inapplicable state.Conclusion: The experimental results show that the proposed method provides better performance of phylogenetic analysis than existing methods and a scientific and quantitative basis for biologists to study species evolution.

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