bModelTest: Bayesian phylogenetic site model averaging and model comparison

AbstractBackground:Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates of uncertainty and being able to incorporate different sources of information based on formal principles. Bayesian phylogenetic analyses are popular for interpreting nucleotide sequence data, however for such studies one needs to specify a site model and associated substitution model. Often, the parameters of the site model is of no interest and an ad-hoc or additional likelihood based analysis is used to select a single site model.Results:bModelTest allows for a Bayesian approach to inferring and marginalizing site models in a phylogenetic analysis. It is based on trans-dimensional Markov chain Monte Carlo (MCMC) proposals that allow switching between substitution models as well as estimating the posterior probability for gamma-distributed rate heterogeneity a proportion of invariable sites and unequal base frequencies. The model can be used with the full set of time-reversible models on nucleotides, but we also introduce and demonstrate the use of two subsets of time-reversible substitution models.Conclusion:With the new method the site model can be inferred (and marginalized) during the MCMC analysis and does not need to be pre-determined, as is now often the case in practice, by likelihood-based methods. The method is implemented in the bModelTest package of the popular BEAST 2 software, which is open source, licensed under the GNU Lesser General Public License and allows joint site model and tree inference under a wide range of models.

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OBAMA: OBAMA for Bayesian amino-acid model averaging

PeerJ ◽

10.7717/peerj.9460 ◽

2020 ◽

Vol 8 ◽

pp. e9460

Author(s):

Remco R. Bouckaert

Keyword(s):

Amino Acid ◽

Model Uncertainty ◽

Ad Hoc ◽

Model Averaging ◽

Rate Heterogeneity ◽

Bayesian Analyses ◽

Site Model ◽

Wide Range ◽

Substitution Models ◽

Tree Inference

Background Bayesian analyses offer many benefits for phylogenetic, and have been popular for analysis of amino acid alignments. It is necessary to specify a substitution and site model for such analyses, and often an ad hoc, or likelihood based method is employed for choosing these models that are typically of no interest to the analysis overall. Methods We present a method called OBAMA that averages over substitution models and site models, thus letting the data inform model choices and taking model uncertainty into account. It uses trans-dimensional Markov Chain Monte Carlo (MCMC) proposals to switch between various empirical substitution models for amino acids such as Dayhoff, WAG, and JTT. Furthermore, it switches base frequencies from these substitution models or use base frequencies estimated based on the alignment. Finally, it switches between using gamma rate heterogeneity or not, and between using a proportion of invariable sites or not. Results We show that the model performs well in a simulation study. By using appropriate priors, we demonstrate both proportion of invariable sites and the shape parameter for gamma rate heterogeneity can be estimated. The OBAMA method allows taking in account model uncertainty, thus reducing bias in phylogenetic estimates. The method is implemented in the OBAMA package in BEAST 2, which is open source licensed under LGPL and allows joint tree inference under a wide range of models.

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An Assessment of the Molecular Diversity of Ticks and Tick-Borne Microorganisms of Small Ruminants in Pakistan

Microorganisms ◽

10.3390/microorganisms8091428 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1428 ◽

Cited By ~ 1

Author(s):

Abdul Ghafar ◽

Adil Khan ◽

Alejandro Cabezas-Cruz ◽

Charles G. Gauci ◽

Sadaf Niaz ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Strong Support ◽

Small Ruminants ◽

Ixodid Ticks ◽

Nucleotide Sequence Data ◽

Health Significance ◽

Second Internal Transcribed Spacer ◽

Theileria Spp

This study investigated ticks and tick-borne microorganisms of small ruminants from five districts of the Federally Administered Tribal Area (FATA) of Pakistan. Morphological (n = 104) and molecular (n = 54) characterization of the ticks revealed the presence of six ixodid ticks: Rhipicephalus (Rh.) haemaphysaloides, Rh. microplus, Rh. turanicus, Haemaphysalis (Hs.) punctata, Hs. sulcata and Hyalomma anatolicum. Phylogenetic analyses of nucleotide sequence data for two mitochondrial (16S and cytochrome c oxidase 1) and one nuclear (second internal transcribed spacer) DNA regions provided strong support for the grouping of the six tick species identified in this study. Microfluidic real-time PCR, employing multiple pre-validated nuclear and mitochondrial genetic markers, detected 11 potential pathogens and endosymbionts in 72.2% of the ticks (n = 54) tested. Rickettsia (R.) massiliae was the most common pathogen found (42.6% of ticks) followed by Theileria spp. (33.3%), Anaplasma (A.) ovis and R. slovaca (25.9% each). Anaplasma centrale, A. marginale, Ehrlichia spp., R. aeschlimannii, R. conorii and endosymbionts (Francisella- and Coxiella-like) were detected at much lower rates (1.9–22.2%) in ticks. Ticks from goats (83.9%) carried significantly higher microorganisms than those from sheep (56.5%). This study demonstrates that ticks of small ruminants from the FATA are carrying multiple microorganisms of veterinary and medical health significance and provides the basis for future investigations of ticks and tick-borne diseases of animals and humans in this and neighboring regions.

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Confusion surrounding Didymosphaeria—phylogenetic and morphological evidence suggest Didymosphaeriaceae is not a distinct family

Phytotaxa ◽

10.11646/phytotaxa.176.1.12 ◽

2014 ◽

Vol 176 (1) ◽

pp. 102 ◽

Cited By ~ 21

Author(s):

HIRAN A. ARIYAWANSA ◽

ERIO CAMPORESI ◽

KASUN M. THAMBUGALA ◽

AUSANA MAPOOK ◽

JI-CHUAN KANG ◽

...

Keyword(s):

New Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Morphological Evidence ◽

Nucleotide Sequence Data ◽

The Family ◽

Family Based ◽

Phylogenetic Lineages ◽

A New Species

Didymosphaeriaceae is a ubiquitous fungal family that is reported to include saprobic, endophytic and pathogenic species associated with a wide variety of substrates. The family is characterized by 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci. In recent treatments Appendispora, Didymosphaeria, Roussoella, Phaeodothis and Verruculina were placed in the family. The aim of the present study is to delineate phylogenetic lineages within Didymosphaeriaceae and allied genera. A new species, Didymosphaeria rubi-ulmifolii, was isolated and identified based on morphological characters and phylogenetic analyses of partial 18S nrDNA and 28S nrDNA nucleotide sequence data. Didymosphaeria rubi-ulmifolii clustered with Montagnulaceae as a separate genus, while two putative strains (HKUCC 5834 and CMW 22186) of D. futilis from GenBank clustered with Cucurbitariaceae and Didymellaceae, respectively. The new species is characterized by immersed to slightly erumpent ascomata immersed under a clypeus, a peridium with compressed cells of textura intricata, long trabeculate pseudoparaphyses, anastomosing mostly above the asci and brown, 1-septate ascospores with granulate ornamentation. Phylogenetic analysis in combination with morphology and a review of literature show that Appendispora, Phaeodothis, Roussoella and Verruculina should be excluded from the family. Phaeodothis belongs in Montagnulaceae, Verruculina in Testudinaceae, while Appendispora and Roussoella belong in Roussoellaceae. The position of Didymosphaeriaceae as a distinct family, based on 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci is doubtful. Fresh collections of more Didymosphaeria strains are needed for epitypification and to obtain sequence data to establish if this family can be maintained.

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A Re-Examination of Generic Concepts of Baeomycetoid Lichens Based on Phylogenetic Analyses of Nuclear ssu and Lsu Ribosomal Dna

The Lichenologist ◽

10.1006/lich.1999.0230 ◽

1999 ◽

Vol 31 (5) ◽

pp. 409-418 ◽

Cited By ~ 10

Author(s):

Jamie L. Platt ◽

Joseph W. Spatafora

Keyword(s):

Ribosomal Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Small Subunit ◽

Lsu Rdna ◽

Character State ◽

Nucleotide Sequence Data ◽

Lichen Symbiosis ◽

Data Support

AbstractThe lichen symbiosis has evolved several times within the fungal kingdom, although the total number of lichenization events leading to extant taxa is still unclear. Two lichenized families, the Icmadophilaceae and Baeomycetaceae have been classified in the Helotiales. Because the Helotiales are predominantly nonlichenized, this suggests that these families represent independent evolutionary episodes of lichenization from the Lecanorales. As a first step towards understanding the evolution of the lichen symbiosis within this order, we tested recent hypotheses concerning the segregation of lichen genera between the two lichen families. Specifically, we used phylogenetic analyses of nucleotide sequence data from nuclear small-subunit and large-subunit ribosomal DNA to test the morphology-based hypotheses that Dibaeis is a distinct genus from Baeomyces and that Dibaeis is a member of the Icmadophilaceae rather than the Baeomycetaceae. Phylogenetic analyses of nuclear SSU rDNA and combined SSU and LSU rDNA data support the hypothesis that Dibaeis is more closely related to IcmadophUa than it is to Baeomyces. Therefore, these data support the resurrection of Dibaeis from its previous synonymy with Baeomyces based on the characters of ascocarp colour and ascus morphology. The recognition of two distinct genera is also consistent with character state distribution of unique lichen acids.

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Frequentist Estimation of Coalescence Times From Nucleotide Sequence Data Using a Tree-Based Partition

Genetics ◽

10.1093/genetics/161.1.447 ◽

2002 ◽

Vol 161 (1) ◽

pp. 447-459 ◽

Cited By ~ 5

Author(s):

Hua Tang ◽

David O Siegmund ◽

Peidong Shen ◽

Peter J Oefner ◽

Marcus W Feldman

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Recent Common Ancestor ◽

Point Estimate ◽

Nucleotide Sequence Data ◽

Most Recent Common Ancestor ◽

Y Chromosomes ◽

Wide Range ◽

Nominal Coverage ◽

Biased Estimates

AbstractThis article proposes a method of estimating the time to the most recent common ancestor (TMRCA) of a sample of DNA sequences. The method is based on the molecular clock hypothesis, but avoids assumptions about population structure. Simulations show that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability. We discuss conditions that can lead to biased estimates. Performance of this estimator is compared with existing methods based on the coalescence theory. The method is applied to sequences of Y chromosomes and mtDNAs to estimate the coalescent times of human male and female populations.

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Phylogenetic placement of Iodosphaeriaceae (Xylariales, Ascomycota), designation of an epitype for the type species of Iodosphaeria, I. phyllophila, and description of I. foliicola sp. nov.

Fungal Systematics and Evolution ◽

10.3114/fuse.2021.08.05 ◽

2021 ◽

Author(s):

A.N. Miller ◽

M. Réblová

Keyword(s):

Maximum Likelihood ◽

Type Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Monophyletic Group ◽

Its Sequence ◽

Phylogenetic Placement ◽

Wide Range ◽

Single Genus

The Iodosphaeriaceae is represented by the single genus, Iodosphaeria, which is composed of nine species with superficial, black, globose ascomata covered with long, flexuous, brown hairs projecting from the ascomata in a stellate fashion, unitunicate asci with an amyloid apical ring or ring lacking and ellipsoidal, ellipsoidal-fusiform or allantoid, hyaline, aseptate ascospores. Members of Iodosphaeria are infrequently found worldwide as saprobes on various hosts and a wide range of substrates. Only three species have been sequenced and included in phylogenetic analyses, but the type species, I. phyllophila, lacks sequence data. In order to stabilize the placement of the genus and family, an epitype for the type species was designated after obtaining ITS sequence data and conducting maximum likelihood and Bayesian phylogenetic analyses. Iodosphaeria foliicola occurring on overwintered Alnus sp. leaves is described as new. Five species in the genus form a well-supported monophyletic group, sister to the Pseudosporidesmiaceae in the Xylariales. Selenosporella-like and/or ceratosporium-like synasexual morphs were experimentally verified or found associated with ascomata of seven of the nine accepted species in the genus. Taxa included and excluded from Iodosphaeria are discussed.

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nQMaker: estimating time non-reversible amino acid substitution models

10.1101/2021.10.18.464754 ◽

2021 ◽

Author(s):

Cuong Cao Dang ◽

Bui Quang Minh ◽

Hanon McShea ◽

Joanna Masel ◽

Jennifer Eleanor James ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Sequence Alignments ◽

Biological Reality ◽

Wide Range ◽

Substitution Models ◽

Likelihood Approach ◽

Protein Datasets

Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly known root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.

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How Diverse Is the Genus Wolbachia? Multiple-Gene Sequencing Reveals a Putatively New Wolbachia Supergroup Recovered from Spider Mites (Acari: Tetranychidae)

Applied and Environmental Microbiology ◽

10.1128/aem.01109-08 ◽

2008 ◽

Vol 75 (4) ◽

pp. 1036-1043 ◽

Cited By ~ 121

Author(s):

Vera I. D. Ros ◽

Vicki M. Fleming ◽

Edward J. Feil ◽

Johannes A. J. Breeuwer

Keyword(s):

Spider Mite ◽

Sequence Data ◽

Nematode Species ◽

Mite Species ◽

Rrna Gene ◽

Protein Coding ◽

Nucleotide Sequence Data ◽

Multiple Gene ◽

Wide Range ◽

The 16S Rrna Gene

ABSTRACT At least 20% of all arthropods and some nematode species are infected with intracellular bacteria of the genus Wolbachia. This highly diverse genus has been subdivided into eight “supergroups” (A to H) on the basis of nucleotide sequence data. Here, we report the discovery of a new Wolbachia supergroup recovered from the spider mite species Bryobia species V (Acari: Tetranychidae), based on the sequences of three protein-coding genes (ftsZ, gltA, and groEL) and the 16S rRNA gene. Other tetranychid mites possess supergroup B Wolbachia strains. The discovery of another Wolbachia supergroup expands the known diversity of Wolbachia and emphasizes the high variability of the genus. Our data also clarify the existing supergroup structure and highlight the use of multiple gene sequences for robust phylogenetic analysis. In addition to previous reports of recombination between the arthropod-infecting supergroups A and B, we provide evidence for recombination between the nematode-infecting supergroups C and D. Robust delineation of supergroups is essential for understanding the origin and spread of this common reproductive parasite and for unraveling mechanisms of host adaptation and manipulation across a wide range of hosts.

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Sequence, catalytic properties and expression of chicken glutathione-dependent prostaglandin D2 synthase, a novel class Sigma glutathione S-transferase

Biochemical Journal ◽

10.1042/bj3330317 ◽

1998 ◽

Vol 333 (2) ◽

pp. 317-325 ◽

Cited By ~ 53

Author(s):

Anne M. THOMSON ◽

David J. MEYER ◽

John D. HAYES

Keyword(s):

Amino Acid ◽

Nucleotide Sequence ◽

Expressed Sequence Tag ◽

Sequence Data ◽

Cdna Clones ◽

Prostaglandin D2 ◽

Glutathione S Transferase ◽

Nucleotide Sequence Data ◽

Chicken Spleen ◽

Wide Range

The Expressed Sequence Tag database has been screened for cDNA clones encoding prostaglandin D2 synthases (PGDSs) by using a BLAST search with the N-terminal amino acid sequence of rat GSH-dependent PGDS, a class Sigma glutathione S-transferase (GST). This resulted in the identification of a cDNA from chicken spleen containing an insert of approx. 950 bp that encodes a protein of 199 amino acid residues with a predicted molecular mass of 22732 Da. The deduced primary structure of the chicken protein was not only found to possess 70% sequence identity with rat PGDS but it also demonstrated more than 35% identity with class Sigma GSTs from a range of invertebrates. The open reading frame of the chicken cDNA was expressed in Escherichia coli and the purified protein was found to display high PGDS activity. It also catalysed the conjugation of glutathione with a wide range of aryl halides, organic isothiocyanates and α,β-unsaturated carbonyls, and exhibited glutathione peroxidase activity towards cumene hydroperoxide. Like other GSTs, chicken PGDS was found to be inhibited by non-substrate ligands such as Cibacron Blue, haematin and organotin compounds. Western blotting experiments showed that among the organs studied, the expression of PGDS in the female chicken is highest in liver, kidney and intestine, with only small amounts of the enzyme being found in chicken spleen; in contrast, the rat has highest levels of PGDS in the spleen. Collectively, these results show that the structure and function, but not the expression, of the GSH-requiring PGDS is conserved between chicken and rat. The nucleotide sequence data reported in this paper have been submitted to the EMBL, GenBank, GSDB and DDBJ Nucleotide Sequence Databases under the accession number AJ006405.

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Species Diversity of the Pleurostomatid Ciliate Genus Amphileptus (Ciliophora, Haptoria), With Notes on the Taxonomy and Molecular Phylogeny of Three Species

Frontiers in Marine Science ◽

10.3389/fmars.2021.642767 ◽

2021 ◽

Vol 8 ◽

Author(s):

Lei Wu ◽

Jiqiu Li ◽

Alan Warren ◽

Xiaofeng Lin

Keyword(s):

Species Diversity ◽

Sequence Data ◽

Southern China ◽

Phylogenetic Analyses ◽

Phylogenetic Methods ◽

Wide Range ◽

Rdna Sequence Data ◽

Molecular Phylogenetic ◽

Intensive Sampling ◽

High Diversity

Amphileptus is one of the largest genera of pleurostomatid ciliates and its species diversity has been reported in various habitats all over the world. In the present work, we review its biodiversity based on data with reliable morphological records. Our work confirms that there are 50 valid Amphileptus species, some of which have a wide range of salinity adaptability and diverse lifestyles. This genus has a high diversity in China but this might be because of the relatively intensive sampling. Phylogenetic analyses based on SSU rDNA sequence data verify the non-monophyly of the genus Amphileptus. Furthermore, two new and one poorly known Amphileptus species, namely A. shenzhenensis sp. n., A. cocous sp. n., and A. multinucleatusWang, 1934, from coastal habitats of southern China were investigated using morphological and molecular phylogenetic methods. These three species are highly similar based on their contractile vacuoles and macronuclear nodules. However, they can be discriminated by details of their living morphology and somatic kineties. We also propose two new combinations, Amphileptus polymicronuclei (Li, 1990) comb. n. (original combination Hemiophrys polymicronucleiLi, 1990) and Amphileptus salimicus (Burkovsky, 1970b) comb. n. (original combination Hemiophrys salimicaBurkovsky, 1970b).

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