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Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Evaluating country-scale irrigation demand through parsimonious agro-hydrological modeling
<p>WaterCROPv2 is an advanced agro-hydrological model designed to estimate irrigation<br>water demand at a national scale by effectively balancing hydrological accuracy with manageable data<br>requirements. Building on the original WaterCROPv1 model, WaterCROPv2 incorporates several<br>significant enhancements, including hourly computation, rainwater canopy interception, soil-dependent5<br>leakage dynamics, and daily evapotranspiration trends based on localized meteorological data.</p> <p>WaterCROPv2 was used to assess mean irrigation water demand for maize from 2005<br>to 2015, illustrating its potential as a decision-support tool for policymakers. </p>
Supplementary Data: MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation
<p>Supplementary Data<br> MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation<br> Submitted to BMC Evolutionary Biology</p> <p>This record contains PANDIT based dataset and TreeBASE dataset (Nguyen et al. 2015) which are analyzed by different bootstrap methods in the study "MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation". The PANDIT based dataset (compressed in file data_pandit.tar.gz) is used to benchmark the accuracy of bootstrap estimates. The TreeBASE dataset (compressed in file data_treebase.tar.gz) is used to benchmark computing times and capability of finding the best-known MP scores. </p> <p>After being uncompressed, the PANDIT based dataset comprises two subdirectories corresponding to the simulated DNA and AA MSAs. They were generated by Seq-Gen (Rambaut and Grass 1997), where the model parameters and true tree were inferred from the original MSAs downloaded from the PANDIT database (Whelan et al. 2006).</p> <ul> <li>Inside "dna" subdirectory, there are 6,207 numbered directories corresponding to 6,207 DNA MSAs. Note that the numbering of these directories is not consecutive because we excluded MSAs where TNT or PAUP* runs did not finish. In each numbered directory N, there are three files: (1) data.N contains the simulated MSA in PHYLIP format; (2) model.N contains the best-fit model detected from the corresponding original MSA; (3) tree.N contains the tree (in Newick format) inferred from the corresponding original MSA. tree.N and model.N are used by Seq-Gen to simulate the MSA in data.N.</li> <li>The "aa" subdirectory is organized similarly for 6,165 AA MSAs.</li> </ul> <p>After being uncompressed, the TreeBASE dataset comprises 115 files corresponding to 115 MSAs. There are:</p> <ul> <li>70 DNA MSAs in PHYLIP format. These files follow the naming scheme dna_[number of sequences]_[number of sites].phy.</li> <li>45 protein MSAs in PHYLIP format. These files follow the naming scheme prot_[number of sequences]_[number of sites].phy.<br> </li> </ul>
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers> 50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. The letter A corresponds to a clade referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–3 and 5–6.
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers> 50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. Letters A and B correspond to clades referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–2 and 4–6.
Figure 126. Parsimony phylogeny. Part B in Revision of the northern South American species of Mortoniella Ulmer 1906 (Trichoptera: Glossosomatidae: Protoptilinae)*
Figure 126. Parsimony phylogeny. Part B (above).
Figure 126. Parsimony phylogeny. Part A in Revision of the northern South American species of Mortoniella Ulmer 1906 (Trichoptera: Glossosomatidae: Protoptilinae)*
Figure 126. Parsimony phylogeny. Part A (above). Part B continues on the next page.
Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approaches
Open the record for dataset details and reuse information.
FIGURE 1. The strict consensus tree resulting from the parsimony analysis I in Taxonomy and evolution of asymmetric male genitalia in the subgenus Ashima Chen (Diptera: Drosophilidae: Phortica Schiner), with descriptions of seven new species
FIGURE 1. The strict consensus tree resulting from the parsimony analysis I (PAUP* v4.0a166) of the data matrix of 40 spp. × 66 morphological characters (Appendix 1) for the genus Phortica (especially focusing on the subgenus Ashima). Synapomorphies (solid circle: nonhomoplastic; open circle: homoplastic) inferred from both ACCTRAN and DELTRAN character optimization are indicated on each internal branch along with support values (bootstrap frequency %).
FIGURE 36. Maximum parsimony tree for cytochrome b in Two new species of oak gall wasps from Turkey (Hymenoptera: Cynipidae Cynipini)
FIGURE 36. Maximum parsimony tree for cytochrome b sequences indicating the relationships of Cynips izzetbaysali sp. nov. and Callirhytis afion, sp. nov. to other Cynipini species. GenBank Accession number for each species used in the analysis is given with the species names. Two new species included in the analysis are coloured in red. Numbers above nodes indicate posterior probability support values.
Data from: Using parsimony-guided tree proposals to accelerate convergence in Bayesian phylogenetic inference
<p>Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as `convergence') and in estimating the correct proportions of the different types of them (known as `mixing'). Here, we introduce a new class of moves, which propose trees based on their parsimony scores. The proposal distribution derived from the parsimony scores is a quickly computable albeit rough approximation of the conditional posterior distribution over candidate trees. We demonstrate with simulations that parsimony-guided moves correctly sample the uniform distribution of topologies from the prior. We then evaluate their performance against standard moves using six challenging empirical datasets, for which we were able to obtain accurate reference estimates of the posterior using long MCMC runs, a mix of topology proposals, and Metropolis coupling. On these datasets, ranging in size from 357 to 934 taxa and from 1,740 to 5,681 sites, we find that single chains using parsimony-guided moves usually converge an order of magnitude faster than chains using standard moves. They also exhibit better mixing, that is, they cover the most probable trees more quickly. Our results show that tree moves based on quick and dirty estimates of the posterior probability can significantly outperform standard moves. Future research will have to show to what extent the performance of such moves can be improved further by finding better ways of approximating the posterior probability, taking the trade-off between accuracy and speed into account.</p>
Data from: Taxonomic reassessment of Clevosaurus latidens Fraser, 1993 (Lepidosauria, Rhynchocephalia) and rhynchocephalian phylogeny based on parsimony and Bayesian inference
The Late Triassic rhynchocephalian Clevosaurus latidens Fraser, 1993 is known from the fissure deposits of Cromhall Quarry, England. Many studies have questioned its referral to the genus Clevosaurus and some phylogenetic analyses suggest a close relationship with herbivorous rhynchocephalians. We reexamine the type specimens and referred material of C. latidens to elucidate its taxonomic identity. Additionally, we provide new phylogenetic analyses of the Rhynchocephalia using both parsimony and Bayesian approaches. Our taxonomic review and both phylogenetic analyses reveal that C. latidens is not referable to Clevosaurus, but represents a new genus. We reassess C. latidens and provide an amended diagnosis for the new genus Fraserosphenodon gen. nov. Both parsimony and Bayesian analyses recover similar topologies and we propose formal names for two higher clades within Rhynchocephalia: Eusphenodontia and Neosphenodontia.
FIGURE 8. Single most parsimonious tree obtained for Chilicola s in Revision and phylogenetic analysis of Chilicola sensu stricto (Hymenoptera: Colletidae) with the description of a new species
FIGURE 8. Single most parsimonious tree obtained for Chilicola s. str. Support values are shown (GC value/frequency slope/Bremer support). Length: 100, CI: 62, RI: 67. The secondary sexual expansion of the male hind tibia has been mapped onto the phylogeny (blue branch without preapical concavity; red branches with preapical concavity).
FIGURE 8. Single most parsimonious tree for 28SD2 in A new species of Gonatocerus (Hymenoptera: Mymaridae) parasitic on proconiine sharpshooters (Hemiptera: Cicadellidae) in the New World
FIGURE 8. Single most parsimonious tree for 28SD2 (length 396, c.i. 0.75, r.i. 0.77). Bootstrap values indicated above or beside branches.
FIGURE 9. Single most parsimonious tree for 28SD2, ITS1, ITS2 in A new species of Gonatocerus (Hymenoptera: Mymaridae) parasitic on proconiine sharpshooters (Hemiptera: Cicadellidae) in the New World
FIGURE 9. Single most parsimonious tree for 28SD2, ITS1, ITS2, COI and COII (length 885, c.i. 0.76, r.i. 0.83); outgroups pruned from tree. Bootstrap values indicated above branches. Table presents unambiguous base substitutions (minimum number) for branches numbered on tree in boldface.
FIGURE 4. Maximum parsimony cladogram depicting phylogenetic relationships among 11 isolates representing 4 in First record of Hexaglandula corynosoma (Travassos, 1915) Petrochenko, 1958 (Acanthocephala: Polymorphidae) in intermediate and definitive hosts in Mexico
FIGURE 4. Maximum parsimony cladogram depicting phylogenetic relationships among 11 isolates representing 4 species of polymorphids. Numbers in internodes represent bootstrap support values for the Neighbor-Joining and Parsimony analyses, respectively. * = Cystacanth of Hexaglandula corynosoma.
FIGURE 58. Maximum parsimony strict consensus tree. Bootstrap proportions from 1000 in Taxonomic revision and phylogeny of the ant genus Prenolepis (Hymenoptera: Formicidae)
FIGURE 58. Maximum parsimony strict consensus tree. Bootstrap proportions from 1000 replicates are presented along the branches.
FIGURE 3. Maximum parsimony phylogenetic relationships with the taxon Pituna poranga removed. Heuristic search with 50 in Description of a new annual rivulid killifish genus from Venezuela
FIGURE 3. Maximum parsimony phylogenetic relationships with the taxon Pituna poranga removed. Heuristic search with 50 random additions and TBR branch swapping resulted in a single most parsimonious topology of 5706 steps. Numbers above nodes are bootstrap values based on 2000 pseudoreplicates (25 random additions each); only values over 50 are reported. Numbers below branches are Bremer support indices which are equivalent to unreversed synapomorphies.
FIGURE 2. Maximum parsimony phylogenetic hypothesis. Heuristic search with 50 in Description of a new annual rivulid killifish genus from Venezuela
FIGURE 2. Maximum parsimony phylogenetic hypothesis. Heuristic search with 50 random additions and TBR branch swapping resulted in a single most parsimonious topology of 6206 steps. Numbers above nodes are bootstrap values based on 2000 pseudoreplicates (25 random additions each); only values over 50 are reported. Numbers below branches are Bremer support indices which are equivalent to unreversed synapomorphies.
FIGURE 6 in The nomenclatural status of the nomina of amphibians and reptiles created by Garsault (1764), with a parsimonious solution to an old nomenclatural problem regarding the genus Bufo (Amphibia, Anura), comments on the taxonomy of this genus, and comments on some nomina created by Laurenti (1768)
FIGURE 6. Reproduction of part of the tree of anurans in Van Bocxlaer et al. (2009: 3) including their BUFONIDAE. The specific nomina are those used by these authors, whereas the generic nomina in the column on the right are those supported here, either for genera or subgenera (see text for details). Bidirectional arrows point to reported cases of successful hybridization resulting in adult specimens: (1) between Bufo bufo and Bufo viridis (Hemmer & Böhme 1974; Duda 2008); (2) between Bufo calamita and Bufo viridis (Flindt & Hemmer 1967; Hemmer 1973; Schlyter et al. 1991); (3) between Bufo terrestris and Bufo valliceps (Blair 1941; Moore 1955) and between Bufo fowleri and Bufo valliceps (Blair in Moore 1955); (4) between Bufo bufo and Bufo woodhousii (Blair 1972: 420). The larger grey rectangle includes all the species that must be maintained in the genus Bufo according to these data if the crossability criterion of Dubois (1988a-b, 2004c) is implemented. The darker grey rectangles includes species that could be placed in two distinct genera if the only reported case between Bufo bufo and Bufo woodhousii proved to be in error; in this latter case, several genera should be recognized for the species remaining in the lighter grey area. See text for explanations.
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