scholarly journals MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Diep Thi Hoang ◽  
Le Sy Vinh ◽  
Tomáš Flouri ◽  
Alexandros Stamatakis ◽  
Arndt von Haeseler ◽  
...  
Keyword(s):  
Maximum Parsimony ◽  
Maximum Parsimony Tree ◽  
Bootstrap Approximation ◽  
Parsimony Tree ◽  
Tree Inference

Morphological phylogeny of the Australian genera of the bee fly subfamily Bombyliinae (Diptera : Bombyliidae) with description of four new genera

2018 ◽  
Vol 32 (2) ◽  
pp. 319 ◽  
Author(s):  
Xuankun Li ◽  
David K. Yeates
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
Junior Synonym ◽  
Maximum Parsimony Tree ◽  
New Combinations ◽  
New Genera ◽  
Parsimony Tree

Bombyliinae, one of the largest subfamilies of Bombyliidae, including 78 genera assigned to four tribes, is distributed on all continents except Antarctica. Their larvae are parasitoids, and adults are important pollinators. The Australian Bombyliinae currently has 17 described genera and 87 described species. The purpose of this study is to establish the phylogeny of the Australian members of the subfamily Bombyliinae, including the boundaries and relationships of the genera, using morphological characters. One maximum parsimony tree was generated from 83 morphological characters scored for 50 species, representing all recognised genera and some unplaced species that we considered may represent new genera. Phylogenetic analysis recovered the relationships between the recognised Australian genera of Bombyliinae and clarified generic limits. The group comprises five main clades, with the genus Pilosia being sister to the remaining Bombyliinae. On the basis of this analysis, four new genera are described: Lambkinomyia Li & Yeates, gen. nov., Dissodesma Bowden & Li, gen. nov., Nigromyia Li & Yeates, gen. nov. and Robertsmyia Li & Yeates, gen. nov. Ten new species are described: Dissodesma immaculata Li & Yeates, sp. nov., Dissodesma flava Li & Yeates, sp. nov., Dissodesma smarti Li & Yeates, sp. nov., Nigromyia collessi Li & Yeates, sp. nov., Nigromyia crocea Li & Yeates, sp. nov., Nigromyia flavimana Li & Yeates, sp. nov., Nigromyia longistriata Li & Yeates, sp. nov., Nigromyia pantherina Li & Yeates, sp. nov., Nigromyia parva Li & Yeates, sp. nov. and Nigromyia tomentosa Li & Yeates, sp. nov. Two new junior synonyms are identified: Apiformyia is a junior synonym of Eristalopsis and Brychosoma is a junior synonym of Staurostichus. The following new combinations are proposed: from Apiformyia: Eristalopsis australis (Yeates), comb. nov.; from Bombylius: Dissodesma primogenita (Walker) comb. nov.; from Brychosoma: Staurostichus aureolatus (Walker), comb. nov., Staurostichus hilaris (Walker), comb. nov. and Staurostichus pictipennis (Macquart), comb. nov.; from Laurella: Robertsmyia pallidoventris (Roberts), comb. nov.; from Mandella: Lambkinomyia cinctiventris (Roberts), comb. nov., Lambkinomyia flavovillosa (Roberts), comb. nov., Lambkinomyia pallida (Roberts), comb. nov. and Lambkinomyia rubida (Roberts), comb. nov.; and from Meomyia: Mandella australis (Guérin-Méneville), comb. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E4A86A19-4AC3-498C-8BDF-B8B501E5A248

Corrigendum to: Morphological phylogeny of the Australian genera of the bee fly subfamily Bombyliinae (Diptera : Bombyliidae) with description of four new genera

2018 ◽  
Vol 32 (2) ◽  
pp. 504
Author(s):  
Xuankun Li ◽  
David K. Yeates
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
Junior Synonym ◽  
Maximum Parsimony Tree ◽  
New Combinations ◽  
New Genera ◽  
Link Type ◽  
Parsimony Tree

Bombyliinae, one of the largest subfamilies of Bombyliidae, including 78 genera assigned to four tribes, is distributed on all continents except Antarctica. Their larvae are parasitoids, and adults are important pollinators. The Australian Bombyliinae currently has 17 described genera and 87 described species. The purpose of this study is to establish the phylogeny of the Australian members of the subfamily Bombyliinae, including the boundaries and relationships of the genera, using morphological characters. One maximum parsimony tree was generated from 83 morphological characters scored for 50 species, representing all recognised genera and some unplaced species that we considered may represent new genera. Phylogenetic analysis recovered the relationships between the recognised Australian genera of Bombyliinae and clarified generic limits. The group comprises five main clades, with the genus Pilosia being sister to the remaining Bombyliinae. On the basis of this analysis, four new genera are described: Lambkinomyia Li & Yeates, gen. nov., Dissodesma Bowden & Li, gen. nov., Nigromyia Li & Yeates, gen. nov. and Robertsmyia Li & Yeates, gen. nov. Ten new species are described: Dissodesma immaculata Li & Yeates, sp. nov., Dissodesma flava Li & Yeates, sp. nov., Dissodesma smarti Li & Yeates, sp. nov., Nigromyia collessi Li & Yeates, sp. nov., Nigromyia crocea Li & Yeates, sp. nov., Nigromyia flavimana Li & Yeates, sp. nov., Nigromyia longistriata Li & Yeates, sp. nov., Nigromyia pantherina Li & Yeates, sp. nov., Nigromyia parva Li & Yeates, sp. nov. and Nigromyia tomentosa Li & Yeates, sp. nov. Two new junior synonyms are identified: Apiformyia is a junior synonym of Eristalopsis and Brychosoma is a junior synonym of Staurostichus. The following new combinations are proposed: from Apiformyia: Eristalopsis australis (Yeates), comb. nov.; from Bombylius: Dissodesma primogenita (Walker) comb. nov.; from Brychosoma: Staurostichus aureolatus (Walker), comb. nov., Staurostichus hilaris (Walker), comb. nov. and Staurostichus pictipennis (Macquart), comb. nov.; from Laurella: Robertsmyia pallidoventris (Roberts), comb. nov.; from Mandella: Lambkinomyia cinctiventris (Roberts), comb. nov., Lambkinomyia flavovillosa (Roberts), comb. nov., Lambkinomyia pallida (Roberts), comb. nov. and Lambkinomyia rubida (Roberts), comb. nov.; and from Meomyia: Mandella australis (Guérin-Méneville), comb. nov. <a ext-link-type=

From Dampier to DNA: the 300-year-old mystery of the identity and proposed allopolyploid origin of Conostylis stylidioides (Haemodoraceae)

2001 ◽  
Vol 49 (5) ◽  
pp. 611 ◽  
Author(s):  
Siegfried L. Krauss ◽  
Stephen D. Hopper
Keyword(s):  
Genetic Variation ◽  
Maximum Parsimony ◽  
Hybrid Origin ◽  
Maximum Parsimony Tree ◽  
Aflp Data ◽  
Parsimony Tree ◽  
Different Populations ◽  
Current Species ◽  
Origin Hypothesis ◽  
Hybridisation Event

The tetraploid Conostylis stylidioides (n= 16) has been proposed to be a stabilised hybrid between the diploid (n = 8) species C. prolifera and C. candicans because of morphological and geographical intermediacy, as well as a polyploid chromosome number. To test this hybrid-origin hypothesis, we used the DNA-fingerprinting technique amplified fragment length polymorphism (AFLP) and measured genetic variation within these taxa, as well as the putative outgroups C. robusta and C. aculeata. One AFLP primer pair generated 192 dominant markers for 36 samples from these species, of which 189 were polymorphic. Polymorphism within populations was uniformly high for all species, with 66–86% of all fragments polymorphic and estimates of heterozygosity ranging from 0.36 to 0.41. Ordination, UPGMA and maximum parsimony analyses of these genetic data consistently clustered species, supporting the current species’ level taxonomy. The intermediate placement of C. stylidioides between C. proliferaand C. candicans on the maximum parsimony tree supports the hybrid-origin hypothesis, although other interpretations are possible. The phenetic results for AFLP data, in which C. stylidioides is not strictly intermediate between C. prolifera and C. candicans, are either concordant with recent research suggesting that rapid intra- and inter-genomic rearrangements occur with the origin of polyploid taxa, or indicate an ancient hybridisation event. While our results do not reject the hybrid origin hypothesis, the extremely high levels of genetic variation detected with AFLP within these populations, in combination with extensive genomic reorganisation with the origin of C. stylidioides and the possibility of independent origins for different populations, make it difficult to confidently exclude other scenarios.

scholarly journals A phylogenetic analysis of the genus Pleurothallis, with emphasis on Pleurothallis subsection Macrophyllae-Fasciculatae, using nuclear ITS and chloroplast DNA sequencing

Lankesteriana ◽  
2011 ◽  
Vol 11 (3) ◽  
Author(s):  
M. Wilson ◽  
C. Belle ◽  
A. Dang ◽  
P. Hannan ◽  
C. Kenyon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Preliminary Data ◽  
Plastid Dna ◽  
Maximum Parsimony Tree ◽  
Its Sequencing ◽  
Phylogenetic Studies ◽  
Parsimony Tree ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Expanded Concept

Several revisions of the genus Pleurothallis have been proposed. Luer has proposed that Pleurothallis species in subgenus Scopula be segregated into the genera Colombiana and Ancipitia. Szlachetko and Margonska (2001) proposed the genus Zosterophyllanthos for Pleurothallis subsection Macrophyllae-Fasciculatae. As an alternative, Luer (2005) proposed the genus Acronia by uniting Pleurothallis subsection Macrophyllae-Fasciculatae with subsections Acroniae and Amphygiae. The molecular phylogenetic studies by Pridgeon and Chase (2001), however, suggested that these taxonomic revisions might not be justified. We report here a more detailed phylogenetic analysis of the genus Pleurothallis, with emphasis on subsection Macrophyllae-Fasciculatae, with data primarily from nuclear ITS sequencing, supplemented with preliminary data from plastid DNA (rpoB2, rpoC1, and ycf1) sequencing. Some initial, tentative conclusions can be drawn. In the strict consensus maximum-parsimony tree of ITS data, many of the clades collapse, leaving a polytomy with a single, highly supported node that tentatively could be used to delimit the genus Pleurothallis. Such a tree would argue for an expanded concept of the genus Pleurothallis, in which the groups Ancipitia, Colombiana, and Acronia/Zosterophyllanthos, if shown to be monophyletic, are relegated to subgenera. 

scholarly journals A central limit theorem for the parsimony length of trees

1996 ◽  
Vol 28 (04) ◽  
pp. 1051-1071 ◽  
Author(s):  
Mike Steel ◽  
Larry Goldstein ◽  
Michael S. Waterman
Keyword(s):  
Central Limit Theorem ◽  
Limit Theorem ◽  
Central Limit ◽  
Large Deviation ◽  
Null Model ◽  
Independent Random Variables ◽  
Minimum Length ◽  
Maximum Parsimony Tree ◽  
Parsimony Tree ◽  
Mean And Variance

In phylogenetic analysis it is useful to study the distribution of the parsimony length of a tree under the null model, by which the leaves are independently assigned letters according to prescribed probabilities. Except in one special case, this distribution is difficult to describe exactly. Here we analyze this distribution by providing a recursive and readily computable description, establishing large deviation bounds for the parsimony length of a fixed tree on a single site and for the minimum length (maximum parsimony) tree over several sites. We also show that, under very general conditions, the former distribution converges asymptotically to the normal, thereby settling a recent conjecture. Furthermore, we show how the mean and variance of this distribution can be efficiently calculated. The proof of normality requires a number of new and recent results, as the parsimony length is not directly expressible as a sum of independent random variables, and so normality does not follow immediately from a standard central limit theorem.

scholarly journals Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA

2020 ◽  
Vol 7 (3) ◽  
pp. 35-44
Author(s):  
Fakhar -i-Abbas ◽  
Fakhar -i-Abbas ◽  
Fakhra Nazir ◽  
Fida Muhammad Khan
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Taxonomy ◽  
Columba Livia ◽  
Taxonomic Diversity ◽  
Coi Gene ◽  
Maximum Parsimony Tree ◽  
Maximum Likelihood Tree ◽  
Wide Range ◽  
Parsimony Tree

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.

scholarly journals The systematic position of Gradsteinia andicola Ochyra (Donrichardsiaceae, Bryopsida) : evidence from nrDNA internal transcribed spacer sequences

2000 ◽  
Vol 18 (1) ◽  
pp. 75-85
Author(s):  
Michael Stech ◽  
Jan-Peter Frahm
Keyword(s):  
New Zealand ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Systematic Position ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Tree ◽  
Systematic Relationship ◽  
Parsimony Tree ◽  
Internal Transcribed Spacer Sequences ◽  
Relationship Of

Nuclear ribosomal DNA internal transcribed spacer (ITS) 1/2 sequences of the Colombian endemic Gradsteinia andicola were determined and compared with those of 16 other species of the Hypnales (Amblystegiaceae, Brachytheciaceae, Hypnaceae, Plagiotheciaceae and Rhytidiaceae). In a maximum parsimony tree Gradsteinia andicola belongs to a well supported clade consisting of Amblystegium, Cratoneuron, Cratoneuropsis, Hypnobartlettia and Palustriella, and seems to be closely related to Cratoneuropsis relaxa from New Zealand. Gradsteinia andicola is therefore transferred to Amblystegiaceae, but the genus Gradsteinia is maintained. The systematic relationship of Amblystegiaceae and Donrichardsiaceae is discussed.

Evolutionary and phylogenetic significance of platypus microsatellites conserved in mammalian and other vertebrate genomes

2009 ◽  
Vol 57 (4) ◽  
pp. 175 ◽  
Author(s):  
E. Buschiazzo ◽  
N. J. Gemmell
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Reconstruction ◽  
Theoretical Development ◽  
Maximum Parsimony Tree ◽  
Reconstruction Algorithms ◽  
Phylogenetic Significance ◽  
Microsatellite Data ◽  
Tree Reconstruction ◽  
Opossum Genome ◽  
Parsimony Tree

Building on the recent publication of the first monotreme genome, that of the platypus, and the discovery that many platypus microsatellites are found in the genomes of three mammals (opossum, human, mouse) and two non-mammalian vertebrates (chicken, lizard), we investigated further the evolutionary conservation of microsatellites identified in the monotreme lineage and tested whether the conservation of microsatellites we observe in vertebrates has phylogenetic signal. Most conserved platypus microsatellites (75%) were found in one species, with the platypus sharing many more microsatellites with mammals than with reptiles (83% versus 30%). Within mammals, unexpectedly, many more platypus microsatellites had orthologues in the opossum genome than in that of either human or mouse, which was at odds with the very well supported view that monotremes diverged from a lineage containing both eutherians and marsupials (Theria hypothesis). We investigated the phylogenetic significance of microsatellite conservation through Bayesian and maximum parsimony tree reconstruction using presence/absence data of microsatellite loci conserved in a total of 18 species, including the platypus. Although models of evolution implemented in current phylogenetic reconstruction algorithms are not tailor-made for microsatellite data, we were able to construct vertebrate phylogenies that correspond well to the accepted mammalian phylogeny, with two of our three reconstructions supporting the Theria hypothesis. Our analysis provides ground for new theoretical development in phylogeny-based analyses of conserved microsatellite data.

scholarly journals Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb

2007 ◽  
Vol 57 (3) ◽  
pp. 513-519 ◽  
Author(s):  
Ingrid Groth ◽  
Geok Yuan Annie Tan ◽  
Juan M. González ◽  
Leonila Laiz ◽  
Marc René Carlsohn ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Taxonomic Status ◽  
Maximum Parsimony Tree ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Parsimony Tree ◽  
High Bootstrap

The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Amycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognized Amycolatopsis species. The new isolates formed a branch in the Amycolatopsis 16S rRNA gene sequence tree with Amycolatopsis minnesotensis NRRL B-24435T, but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely related Amycolatopsis species based on a combination of phenotypic properties and from all Amycolatopsis strains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genus Amycolatopsis. The name proposed for this novel species is Amycolatopsis nigrescens sp. nov., with type strain CSC17Ta-90T (=HKI 0330T=DSM 44992T=NRRL B-24473T).

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