ArticlePDF Available

MrModeltest V2. Program Distributed by the Author

Authors:
Johan Nylander at Swedish Museum of Natural History
Johan Nylander
Download full-text PDF
Read full-text
Download citation
Content uploaded by Johan Nylander
Author content
All content in this area was uploaded by Johan Nylander on Oct 31, 2016
Content may be subject to copyright.
MrModeltest2
C program for selecting DNA substitution models using PAUP* (http://paup.csit.fsu.edu)
MrModeltest 2.3 README, May 22 2008
MrModeltest 2.3 by Johan A. A. Nylander, Dept. Systematic Zoology, EBC, Uppsala University, Sweden.
Orignal code by David Posada, U. Vigo, Spain.
E-mail: jnylander @ users.sourceforge.net
Description
For performing hierarchical likelihood ratio tests and calculating approximate AIC and/or very approximate
AICc values of the nucleotide substitution models currently implemented in both PAUP*4 and MrBayes v3.
Version 2.3 also does some model averaging of the parameter estimates obtained by PAUP.
MrModeltest 2.3 is a modified version of David Posada’s Modeltest 3.6 (see Modeltest homepage). “Modified
version” means that it was rewritten to compare 24 instead of 56 models of nucleotide substitution (basically
a Modeltest version 1.0). On the other hand, all of the 24 models can be implemented in MrBayes version
3. Furthermore, MrModeltest uses (by default) four different hierarchies for the likelihood ratio tests. The
hierarchies are described in detail in Posada, D. and K. A. Crandall. 2001. Selecting the best-fit model
of nucleotide substitution. Systematic Biology, 50:580-601 (Fig. 4a-d). The hierarchies implemented in
MrModeltest are also depicted in the files ‘hLRT1.jpg’, ‘hLRT2.jpg’, ‘hLRT3.jpg’, and ‘hLRT4.jpg’.
Suggested reference
Nylander, J. A. A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre,
Uppsala University.
Quick instructions
Installing the pre-build program on Windows or MacOSX
1.
Find the appropriate binary file for your operating system (in the ‘bin’ folder) and use directly (see
Running MrModeltest2 below) or, preferrably, copy it to a location included in your PATH.
Note: The windows version is compiled and tested on Win XP.
Installing from source (on UNIX/MacOSX)
1. cd into the distribution src directory:
cd MrModeltest2/src
2. Compile by typing (try ‘make -f Makefile.MACOSX’ if ‘make’ fails on the Mac):
make
3.
The binary file ‘mrmodeltest2’ can then be run in the same directory or be moved somewhere on your
system where you have access to it (i.e., in your PATH).
Before using MrModeltest2
1. Execute your data file in PAUP*.
1
2.
Execute the file ‘MrModelblock’ in PAUP*. A file called ‘mrmodel.scores’ will appear in the current
directory.
3. This file is the input for MrModeltest2.
Running MrModeltest2
MrModeltest2 does not have a graphical user interface. Therefore, UNIX/Win/MacOSX users need to open
a terminal (“Console”,“DOS window”) and type:
mrmodeltest2 < mrmodel.scores > out
The results are written in the ‘out’ file.
Note: If mrmodeltest2 is not in your PATH, you can try to run the program by first cd in to the same
directory where the binary and the mrmodel.scores are located and then type:
./mrmodeltest2 < mrmodel.scores > out
Disclaimer
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General
Public License as published by the Free Software Foundation; either version 2 of the License, or (at your
option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received
a copy of the GNU General Public License along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
2
... ML analyses were implemented with RAxML-HPC v8.2.10, and 1000 rapid bootstrap replicates were performed; GTRGAMMA was set by default as the selected model [44]. For BI analyses, the most appropriate substitution models were selected by MrModeltest v2.3 under the Akaike information criterion (AIC) [45]. BI analyses were conducted using MrBayes v3.2.7 [46]. ...
New Contributions on Species Diversity of Genus Hydnum and Lentaria s.l. in China
Article
Full-text available
  • Nov 2024
  • J. Fungi
Southwest China is extremely rich in fungal resources, and a large number of new taxa have been discovered in recent years. In the present study, we examined 26 specimens of the genera Hydnum and Lentaria sensu lato, most of which were obtained in Yunnan Province. Through ITS-nrLSU-tef1 phylogenetic analysis, combined with morphological studies and geographic analyses, five new species were described, viz. H. cremeum (奶油齿菌), H. flavoquamosum (黄鳞齿菌), H. roseoalbum (粉白齿菌), H. roseotangerinum (粉橙齿菌), and L. subalpina (亚高山木瑚菌). Furthermore, we also supplied new information on some known species, including host plants and new distribution records. We re-examined the holotype sequences of two known taxa, H. flabellatum and H. pallidomarginatum, treating H. flabellatum as a synonym of H. pallidomarginatum. Additionally, a key to Lentaria s.l. in China was provided.
View
... Two runs were established, each consisting of four chains, with sampling from the posterior distribution occurring every 100 generations. The default values for all other parameters were maintained and complemented in MrModeltest 2.3 [79]. Bayesian analysis of the combined nuclear dataset (28S + TEF1 + RPB2) was run for 40 million generations, and the average deviation of split frequencies was 0.003331. ...
Pseudophylloporus Gen. nov. and Rubroleccinum Gen. nov., Two New Genera Revealed by Morphological and Phylogenetic Evidences in the Family Boletaceae from Subtropical China
Article
Full-text available
  • Nov 2024
  • J. Fungi
Boletaceae, the largest and most diverse family of Boletales (Agaricomycetes and Basidiomycota), is both ecologically and economically important. Although many taxa have been described in China, the diversity of the family still remains incompletely understood. In the present study, Pseudophylloporus baishanzuensis gen. nov., sp. nov. and Rubroleccinum latisporus gen. nov., sp. nov. are proposed based on morphological and molecular phylogenetic analyses. These findings contribute to a deeper understanding of the diversity within the Boletaceae family.
View
... Since we did not detect any conflicting clades between these analyses, the individual sequence alignments were concatenated into two final alignments (deposited in TreeBASE, study number 31694) and subjected to phylogenetic analyses. Partitions, for which we assumed rate heterogeneity, were evaluated using MrModeltest v. 2.4 (Nylander 2004) to determine the best partitioning scheme for our datasets and to select the best-fit models under Akaike information criteria. ...
Re-evaluation of Ceratostomella and Xylomelasma with introduction of two new species (Sordariomycetes)
Article
Full-text available
  • Nov 2024
In this study, we assessed the phylogenetic relationships among members of Ceratostomella and the morphologically similar genus Xylomelasma, currently classified within the Sordariomycetes. Our phylogenetic analyses, utilising three and five gene markers, revealed that species from these two genera are congeneric, supporting the transfer of Xylomelasma to Ceratostomella. Consequently, we propose two new combinations: C. sordidacomb. nov. and C. novae-zelandiaecomb. nov. In addition, we identified two cryptic species within the C. sordida species complex, which are described as C. cryptasp. nov. and C. melanosporasp. nov. Traditional micromorphological characters have proven insufficient for differentiating these new species; however, they are clearly distinguishable by molecular data, particularly using the internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) of the nuclear rRNA cistron, and genes encoding the second largest subunit of RNA polymerase II (rpb2), and translation elongation factor 1-α (tef1-α) as primary and secondary barcodes. This study provides new insights into the morphological characteristics of Ceratostomella, identifying the ascogenous system as an important diagnostic trait at the generic level, which distinguishes Ceratostomella from morphologically similar fungi. Ceratostomella is currently recognised with eight species. We also investigated the relationship between Ceratostomella and the closely related Barbatosphaeria. The lack of statistical support in the Maximum likelihood analysis is discussed and the inclusion of Ceratostomella in Barbatosphaeriaceae is not supported. Ceratostomella is accepted as a genus incertae sedis, while Barbatosphaeriaceae remains a monotypic family. The global diversity of Ceratostomella is inferred from metabarcoding data and published field observations. Biogeographic analysis indicates that members of Ceratostomella are widespread, found in soil and decaying wood, as well as in air, dust, roots, shoots, and water across temperate, subtropical and tropical regions in both the Northern and Southern Hemispheres. We are concurrently publishing whole-genome analyses of three ex-type strains of Ceratostomella, i.e. C. crypta, C. melanospora and C. sordida. This effort aims to establish a new standard for high-quality taxonomic studies, which, in accordance with current trends, should incorporate whole-genome sequencing data for future research and application. Our findings underscore the importance of integrating morphological, biogeographic and molecular data for accurate species delineation and highlight the complexity within the genus Ceratostomella.
View
... The ITS, LSU, TEF, ACT and RPB1 sequences were analysed individually and jointly. The optimal evolutionary model for each partition was determined and included in the analysis using MrModelTest v.2.3 (Nylander 2004). Phylogenetic history was reconstructed using Maximum Likelihood (ML) algorithm with RaxML-HPC2 on XSEDE 8.2.12 (Stamatakis 2014;Zhao et al. 2024) and Bayesian Inference (BI) algorithm with MrBayes 3.2.7a ...
Unveiling species diversity within early-diverging fungi from China III: Six new species and a new record of Gongronella (Cunninghamellaceae, Mucoromycota)
Article
Full-text available
  • Nov 2024
Gongronella had accommodated only two species for more than half a century and as many as 17 new species have been described in this genus since 2015. However, no systematic studies were conducted for this genus so far. The distribution, substrate and morphology of all known species in Gongronella are analysed herein. Meanwhile, with the support of phylogenetic and morphological evidence, six new species (G. abortosporangiasp. nov., G. apophysatasp. nov., G. bawanglingensissp. nov., G. inconstanssp. nov., G. pingtangensissp. nov. and G. reniformissp. nov.) are proposed and G. pamphilae is recorded from China for the first time. The phylogenetic tree was constructed using ITS+LSU+TEF+ACT+RPB1 and the results were basically the same as ITS+LSU. All species of Gongronella, except G. namwonensis from fresh water, were isolated from soil. The genus is distributed worldwide, mainly in tropical and subtropical regions. A synoptic key is provided for a total of 24 species (18 species previously published and six species newly described herein), except for G. banzhaoae due to unavailable protologue, type and living culture. No morphologies were described when G. pamphilae was proposed. Thanks to the strains isolated in this study, G. pamphilae is included in the key and reported as a Chinese new record. This is the first comprehensive taxonomy and phylogeny of the genus Gongronella.
View
... The dataset was analyzed independently based on maximum likelihood (ML) and Bayesian (BI) algorithms using RAxML v. 7.0.3 (Stamatakis 2006) and MrBayes v. 3.2.6 (Ronquist et al. (Nylander 2004) to select the best-fit evolutionary model (GTR+I+G) for the data partition. for ML analyses, the default parameters were used, and bootstrap support (BS) was carried out using the rapid bootstrapping algorithm with the automatic halt option. ...
Alternaria youyangensis sp. nov. (Ascomycota: Pleosporaceae) from leaf spot of Fagopyrum esculentum in China
Article
  • Nov 2024
Alternaria is a widely distributed fungal genus as saprophytes, endophytes, and pathogens. An Alternaria species was isolated from the leaf spot of Fagopyrum esculentum in Banxi Town, Youyang County, Chongqing municipality, China. The obtained strains were determined based on morphological characteristics and multi-locus phylogenetic analyses including the internal transcribed spacer (ITS) of the rDNA region, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), translation elongation factor 1-alpha (TEF1), RNA polymerase second largest subunit (RPB2), a major Alternaria allergen (Alt a 1), endopolygalacturonase (EndoPG) and an anonymous region gene (OPA10-2) gene sequences. The results indicate that the present species is a novel species, which is described and illustrated as Alternaria youyangensis sp. nov. in this study.
View
Untangling the morphological and genetic variation of two endemic lizards from the coastal sand dunes of Northeastern Brazil
Article
  • Dec 2024
  • AMPHIBIA-REPTILIA
Studies in the Neotropical region consistently highlight high levels of endemism and biodiversity. However, challenges persist, particularly in uncovering the cryptic diversity among species. Various approaches are needed to address this, including morphological, genetic, and environmental data. This study focused on genetic and morphological variation in three endemic, sympatric lizard species: Tropidurus hygomi , Glaucomastix abaetensis , and Glaucomastix itabaianensis in the coastal sand dunes of Northeastern Brazil. These lizards are confined to sandy Pleistocene-formed environments with limited distribution. While earlier research revealed substantial genetic diversity, gaps remained in distribution sampling, morphological data, and understanding the correlation between this variation and environmental factors. We aimed to identify genetic clusters to assess the alignment of phenotypic differences with these clusters and explore potential relationships between climatic and geographical factors and morphometric variations. We utilized mtDNA data to assess population clusters. Geometric and linear morphometrics were employed to analyze morphological data, which was then correlated with climatic information. Results unveiled genetic and morphological variations signifying the presence of cryptic diversity. Our analyses also highlighted the influence of geography and climate on morphometric variations. These findings underscore hidden diversity and a complex evolutionary history within the confined Pleistocene sand dunes. Further genomic analyses could contribute to comprehending these patterns and enhancing the conservation strategies for these endangered species.
View
A banana burrowing nematode, Radopholus similis (Tylenchida: Pratylenchidae), intercepted from aquarium plants from Southeast Asia in Japanese import plant quarantine
Article
Full-text available
  • Jan 2022
A banana burrowing nematode, Radopholus similis (Cobb, 1893) Thorne, 1949, was intercepted in roots of aquarium plants (Anubias sp. and Bucephalandra sp.) imported to Japan from Southeast Asia in import plant inspections in 2018 and 2019. We describe the morphological and molecular characters of seven samples of R. similis. The morphology of seven samples of R. similis were in congruence with those of previous descriptions of this species. The results of the phylogenetic analyses of the ITS rRNA gene and D2-D3 expansion segments of 28S rRNA gene sequences confirmed the species identification and phylogenetic relationship of R. similis with other Radopholus species. In Japanese import plant quarantine, this is the first report of R. similis from Anubias sp. and Bucephalandra sp.
View
Identification of Pseudopestalotiopsis ampullacea as a new pathogen causing tea gray blight in India and its management strategies
Article
Full-text available
  • Nov 2024
Gray blight is a serious threat to the tea [Camellia sinensis (L.) O. Kuntze] production in major tea cultivating countries including India. The disease is caused by Pestalotiopsis-like species. In this study, five isolates of Pseudopestalotiopsis species isolated from symptomatic tea leaf samples in North Bengal, India were investigated. Based on the multi-locus phylogenetic analysis using concatenated sequences of three (ITS, tef-1 alpha, and tub-2) loci, cultural and micromorphological characters, and host association, the fungal isolates were identified as Pseudopestalotiopsis ampullacea F. Liu & L. Cai. The morphological analysis also revealed that the fungal isolates were evidently differentiated from other Pseudopestalotiopsis species. To date, P. ampullacea has not been reported on tea plants in India. Among the five isolates studied, isolate NKT0P03 was randomly selected for pathogenicity tests and its sensitivity to fungicides and microbial antagonists. In pathogenicity test, the isolate showed weak to high virulence reactions on 25 different tea cultivars. The pathogen showed an avirulent reaction on the cultivar TV11. In order to identify an effective management strategy against this new pathogen, synthetic fungicides and microbial biocontrol agents were evaluated in the laboratory. Results revealed that carbendazim + mancozeb, hexaconazole, propiconazole, and valextra were effective fungicides with an 85.1% to 89.8% range of inhibitory activity against P. ampullacea NKT0P03. Among microbial agents, Trichoderma harzianum, T. reesei, T. hamatum, Bacillus subtilis, and Microbacterium barkeri were efficient bioagents against P. ampullacea NKT0P03 with antagonistic activity ranging between 66.6% and 84.2%. Thus, these fungicides and microbial bioagents can be recommended as effective agents for the management of P. ampullacea causing tea gray blight after their field evaluations.
View
Mitogenomic phylogeny and divergence time estimation of Artemia Leach, 1819 (Branchiopoda: Anostraca) with emphasis on parthenogenetic lineages
Preprint
Full-text available
  • Oct 2024
The brine shrimp Artemia , a crustacean adapted to the extreme conditions of hypersaline environments, comprises nine regionally distributed sexual species scattered (island-like) over heterogeneous environments and asexual (parthenogenetic) lineages with different ploidies. Such sexual and asexual interaction within the genus raises questions regarding the origin and time of divergence of both sexual species and asexual lineages, including the persistence of the latter over time, a problem not yet clarified by the use of single mitochondrial and nuclear markers. Based on the complete mitochondrial genome of all species and parthenogenetic lineages, this article first describes the mitogenomic characteristics (nucleotide compositions, genome mapping, codon usage, and tRNA secondary structure) of sexual species and asexual types and, secondly, it provides a comprehensive updated phylogenetic analysis. Molecular dating and geographical evidence suggest that the ancestral. Artemia taxon originated in the Mediterranean area or South America in ca . 33.97 Mya during the Paleogene Period. The mitogenomic comparisons suggest that the common ancestor of diploid and triploid parthenogenetic lineages ( ca . 0.07 Mya) originated from a historical ancestor ( ca. 0.61 Mya) in the Late Pleistocene. Additionally, the common ancestor of tetraploid and pentaploid parthenogenetic lineages ( ca. 0.05 Mya) diverged from a historical maternal ancestor with A. sinica ( ca . 0.96 Mya) in the early Pleistocene. The parthenogenetic lineages do not share a direct ancestor with any sexual species. The Asian clade ancestor diverged more recently ( ca. 14.27 Mya, Middle Miocene). The mitogenomic characteristics, maternal phylogenetic tree, and especially divergence time prove that A. monica and A. franciscana ( time of divergence ) are two biological species.
View
View
ResearchGate has not been able to resolve any references for this publication.