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 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. 

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

scholarly journals A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans

2020 ◽  
Vol 12 (2) ◽  
pp. 3906-3916 ◽  
Author(s):  
James F Fleming ◽  
Roberto Feuda ◽  
Nicholas W Roberts ◽  
Davide Pisani
Keyword(s):  
Phylogenetic Signal ◽  
Single Gene ◽  
G Protein Coupled Receptors ◽  
Data Sets ◽  
Gene Trees ◽  
Tree Reconstruction ◽  
Phylogenetic Information ◽  
Novel Approach ◽  
Gene Data ◽  
G Protein Coupled

Abstract Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.

DISTANCE-BASED PHYLOGENETIC ALGORITHMS: NEW INSIGHTS AND APPLICATIONS

2010 ◽  
Vol 20 (supp01) ◽  
pp. 1511-1532 ◽  
Author(s):  
S. POMPEI ◽  
E. CAGLIOTI ◽  
V. LORETO ◽  
F. TRIA
Keyword(s):  
Horizontal Transfer ◽  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction ◽  
Local Property ◽  
Reconstruction Algorithms ◽  
Reconstruction Methods ◽  
Tree Length ◽  
Point Condition ◽  
Generative Algorithms ◽  
The One

Phylogenetic methods have recently been rediscovered in several interesting areas among which immunodynamics, epidemiology and many branches of evolutionary dynamics. In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence, a divergence arises between the true evolutionary distances and the distances between pairs of taxa as inferred from the available data, making the phylogenetic reconstruction a challenging problem. Mathematically this divergence translates in the non-additivity of the actual distances between taxa and the quest for new algorithms able to efficiently cope with these effects is wide open. In distance-based reconstruction methods, two properties of additive distances were extensively exploited as antagonist criteria to drive phylogeny reconstruction: on the one hand a local property of quartets, i.e. sets of four taxa in a tree, the four-point condition; on the other hand, a recently proposed formula that allows to write the tree length as a function of the distances between taxa, the Pauplin's formula. A deeper comprehension of the effects of the non-additivity on the inspiring principles of the existing reconstruction algorithms is thus of paramount importance. In this paper we present a comparative analysis of the performances of the most important distance-based phylogenetic algorithms. We focus in particular on the dependence of their performances on two main sources of non-additivity: back-mutation processes and horizontal transfer processes. The comparison is carried out in the framework of a set of generative algorithms for phylogenies that incorporate non-additivity in a tunable way.

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.

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=

scholarly journals Fast-evolving alignment sites are highly informative for reconstructions of deep Tree of Life phylogenies

2019 ◽  
Author(s):  
L. Thibério Rangel ◽  
Gregory P. Fournier
Keyword(s):  
Signal To Noise Ratio ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Tree Of Life ◽  
Signal To Noise ◽  
Fast Analysis ◽  
Substantial Impact ◽  
Substitution Saturation ◽  
Noise Ratio

AbstractThe trimming of fast-evolving sites, often known as “slow-fast” analysis, is broadly used in microbial phylogenetic reconstruction under assumption that fast-evolving sites do not retain accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here we show that, contrary to this assumption, even the fastest evolving sites, present in conserved proteins often used in Tree of Life studies, contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site specific substitution-rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we additionally show that both slow-and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.Significance StatementIt is common practice among comprehensive microbial phylogenetic studies to trim fast-evolving sites from the source alignment in the expectation to increase the signal to noise ratio. Here we show that despite fast-evolving sites being more sensitive to parameter misspecifications than mid-rate evolving sites, such sensitivity is comparable, if not smaller, than what we observe among slow-evolving sites. Through the use of both empirical and simulated datasets we also show that, besides the lack of evidences regarding the noisy nature of fast-evolving sites, such sites are of core importance for the reliable the reconstruction of short-branched bipartitions. Such points are exemplified by the variations in the Eukarya+Archaea Tree of Life when subjective alignment trimming strategies are employed.

scholarly journals IgEvolution: clonal analysis of antibody repertoires

2019 ◽  
Author(s):  
Yana Safonova ◽  
Pavel A. Pevzner
Keyword(s):  
Binding Sites ◽  
Clonal Analysis ◽  
Reconstruction Algorithms ◽  
Tree Reconstruction ◽  
New Approach ◽  
Clonal Development ◽  
Antibody Repertoires ◽  
Complementarity Determining Regions ◽  
Independent Tasks

AbstractConstructing antibody repertoires is an important error-correcting step in analyzing immunosequencing datasets that is important for reconstructing evolutionary (clonal) development of antibodies. However, the state-of-the-art repertoire construction tools typically miss low-abundance antibodies that often represent internal nodes in clonal trees and are crucially important for clonal tree reconstruction. Thus, although repertoire construction is a prerequisite for follow up clonal tree reconstruction, the existing repertoire reconstruction algorithms are not well suited for this task. Since clonal analysis has the potential to reveal errors in the constructed repertoires and contribute to constructing more accurate repertoires, we advocate a tree-guided construction of antibody repertoires that combines error correction and clonal reconstruction as interconnected (rather than independent) tasks. We developed the IgEvolution algorithm for simultaneous repertoire and clonal tree reconstruction and applied it for analyzing multiple immunosequencing datasets representing antigen-specific immune responses. We demonstrate that analysis of clonal trees reveals highly mutable positions that correlate with antigen-binding sites and light-chain contacts in crystallized antibody-antigen complexes. We further demonstrate that this analysis leads to a new approach for identifying complementarity determining regions (CDRs) in antibodies.

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.

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