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501 results for “Phylogenetic tree”
Figure 4 in Amplified fragment length polymorphisms, the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics
Figure 4. Reconstruction of shell shape and size based on weighted (above branches) and unweighted (below branches) branch lengths. The inset shows the tree shape based on COI sequence data evolved into the AFLP tree topology. Node numbers are in italic; size is expressed as centroid size; the colour of the centroid size values indicates shape changes.
Figure 2. Phylogenetic tree resulting from a in Host specialization and species diversity in the genus Stylops (Strepsiptera: Stylopidae), revealed by molecular phylogenetic analysis
Figure 2. Phylogenetic tree resulting from a Bayesian analysis of the partial sequence from the mitochondrial NADH gene. The names of the host Andrena bees are indicated with every Stylops voucher number. The posterior probabilities are given before the slash; the bootstrap values from the maximum-likelihood (ML) analysis are given after the slash. Posterior probability values lower than 0.9, and bootstrap values lower than 50, are considered as unsupported and are thus replaced by an asterisk (*); incongruent nodes between the two analyses are indicated by a dash (-). Branch support is omitted at the nodes that were unsupported in both the Bayesian and the ML analyses.
Figure 3. Phylogenetic tree resulting from a in Host specialization and species diversity in the genus Stylops (Strepsiptera: Stylopidae), revealed by molecular phylogenetic analysis
Figure 3. Phylogenetic tree resulting from a Bayesian analysis of the partial sequence from the nuclear EF1 gene. Names of host Andrena bees are indicated at every Stylops voucher number. The names of the host Andrena bees are indicated with every Stylops voucher number. The posterior probabilities are given before the slash; the bootstrap values from the maximum-likelihood (ML) analysis are given after the slash. Posterior probability values lower than 0.9, and bootstrap values lower than 50, are considered as unsupported and thus replaced by an asterisk (*); incongruent nodes between the two analyses are indicated by a dash (-). Branch support is omitted at the nodes that were unsupported in both the Bayesian and the ML analyses.
Figure 8. A summary tree showing 52 in Deciphering the diversity and history of New World nightjars (Aves: Caprimulgidae) using molecular phylogenetics
Figure 8. A summary tree showing 52 New World nightjar species using the taxonomy recommended in this study. Also shown are 15 Old World species. Maximum-likelihood (ML) and maximum-parsimony (MP) bootstrap scores are displayed above and below the nodes.
Figure 15. Bayesian tree inferred from D2-D3 in Phylogenetic relationships within the superfamily Desmodoroidea (Nematoda: Desmodorida), with descriptions of two new and one known species
Figure 15. Bayesian tree inferred from D2-D3 of LSU sequences under the general time-reversible (GTR) + proportion of invariable sites (I) + gamma distribution (G) model. Posterior probability (left) and bootstrap values (right) greater than or equal to 75% are given on appropriate clades. Taxa belonging to the Draconematidae and Epsilonematidae are shown in blue and red, respectively. The scale stands for substitutions per site.
Figure 10. The most parsimonious tree that resulted from the phylogenetic analysis, with 509 in The cranial morphology of the temnospondyl Australerpeton cosgriffi (Tetrapoda: Stereospondyli) from the Middle-Late Permian of Paraná Basin and the phylogenetic relationships of Rhinesuchidae
Figure 10. The most parsimonious tree that resulted from the phylogenetic analysis, with 509 steps, depicting the position of Australerpeton cosgriffi. Decay indices (Bremer support) with values above 1 are given below the nodes. Bootstrap percentages are given after the Bremer support values (ins) for clades with values above 50%.
Figure 5. Preferred single tree resulting from the analysis under implied weights with concavity constant k in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics
Figure 5. Preferred single tree resulting from the analysis under implied weights with concavity constant k = 100. Clade support is indicated above (Bremer support values) and below [symmetric resampling values; only significant values (over 50%) are presented] branches. Sensitivity plots ('Navajo rugs') indicate the recovery of the nodes in the analysis under implied weights with different values of k (black squares indicate monophyly; white squares indicate nonmonophyly).
Figure 6. Preferred single tree resulting from analyses under implied weights with concavity constant k in Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics
Figure 6. Preferred single tree resulting from analyses under implied weights with concavity constant k = 100, 60, and 30, and equivalent to one of the most parsimonious trees recovered in the analysis with equal weights and continuous characters. Images on the tree represent the morphological congruence of the clades with the structures pictured (pedipalps and spermathecae). The genus Mayazomus is clearly separated from Rowlandius by the presence of robust pedipalps and trochanters with apical process; the clade (Mayazomus yaax + Mayazomus estor) is supported by the rounded distal margin of the pedipalp femur; the clade (Mayazomus loobil + Mayazomus infernalis) is supported by the presence of a patella curved in a 'U'-shape; and spermathecae with lobes slender and subequal in length; the clade (Mayazomus aluxe + Mayazomus kaamuul) is supported by setae Fv1 and Fv2 located distally and projected, with spermathecal lateral lobes reduced and wider than medial lobes.
Figure 1. Bayesian tree inferred from the 18S in A molecular analysis of the phylogenetic position of the suborder Cavernicola within the Tricladida (Platyhelminthes), with the description of a new species of stygobiont flatworm from Benin
Figure 1. Bayesian tree inferred from the 18S rDNA sequences showing the relationship of the new Novomitchellia species to other Tricladida species included in this analysis. Maximum likelihood (ML) yielded the same topology. Asterisks at nodes indicate posterior probabilities = 1/bootstrap values> 75% obtained respectively in the ML and Bayesian inference analyses. Scale bar: number of substitutions per nucleotide position.
Figures 5–6. Optimal trees obtained under Bayesian analyses. Fig. 5. Mkv model. Fig. 6 in Phylogenetic analysis of Micrathena and Chaetacis spiders (Araneae: Araneidae) reveals multiple origins of extreme sexual size dimorphism and long abdominal spines
Figures 5–6. Optimal trees obtained under Bayesian analyses. Fig. 5. Mkv model. Fig. 6. MkvG model. Posterior probabilities values are indicated below branches.
Figures 3–4. Optimal trees obtained under parsimony analyses. Fig. 3 in Phylogenetic analysis of Micrathena and Chaetacis spiders (Araneae: Araneidae) reveals multiple origins of extreme sexual size dimorphism and long abdominal spines
Figures 3–4. Optimal trees obtained under parsimony analyses. Fig. 3. Unweighted analysis [length = 575.3; consistency index (CI) = 0.305; retention index (RI) = 0.693]. Fig. 4. Implied weighted analysis (k = 5; length = 579.718; fit = 105; CI = 0.303; RI = 0.689). Bremer supports and symmetric resampling values are indicated below and above branches, respectively. Symmetric resampling values are given in frequency differences (GC; Goloboff et al., 2003).
FIGURE 2. The Bayesian phylogenetic tree from trnL-F in Primulina cataractarum sp. nov. (Gesneriaceae) from limestone landform in Southern Hunan, China
FIGURE 2. The Bayesian phylogenetic tree from trnL-F sequence data with BI posterior probability/MP bootstrap support values (>0.5 or 50%) shown above and below the corresponding branches. * indicates the new species.
FIGURE 3. Phylogenetic tree inferred from maximum likelihood methods using 70 in Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China
FIGURE 3. Phylogenetic tree inferred from maximum likelihood methods using 70 protein-coding genes from the complete chloroplast genome sequences of Tigridiopalma longmenensis and other 15 species of Melastomataceae. The numbers beside the node indicate the bootstrap percentages (%) after 5000 replications of bootstrap sampling.
What is the current extent of our systematic knowledge? A case study in synthesizing phylogenetic data for building large trees to advance phylogenetic research in Orobanchaceae
To date, no comprehensive phylogenetic analyses have been conducted in Orobanchaceae that include both a wide generic sampling and a large sampling of species. Here, we utilize a recently developed set of tools for synthesizing publicly available data, and apply these to assess where the gaps in our phylogenetic knowledge exist in the angiosperm clade Orobanchaceae. We then use the resulting timetree to investigate diversification dynamics in this clade of mostly parasitic plants. We used the PyPHLAWD pipeline and RAxML to assemble a supermatrix of >900 species and construct a comprehensive phylogenetic hypothesis of Orobanchaceae. Divergence times were estimated with penalized likelihood from a 'congruified' set of secondary calibrations, and diversification dynamics were investigated in both trait-independent and trait-dependent (parasitic habit) contexts with BAMM and HiSSE. We sampled 39.8% of described species from 80 of 108 genera, representing all eight primary clades of Orobanchaceae. Relationships and divergence time estimates were similar to previous, clade-specific studies; however, eight genera were recovered as non-monophyletic, and will require focused systematic attention. Ours is first Orobanchaceae wide study to use model based approach to assess diversification dynamics in the parasitic lineage. Our results reveal elevated diversification rates associated with hemiparasitic habit, and holoparasitic habit was revealed to be an absorbing state, meaning that lineages within Orobanchaceae tend towards a reduction in photosynthetic towards hemiparasitism and finally holoparasitism. Using a synthetic phylogenetic hypothesis in conjunction with a unified taxonomic framework, we are able to understand where our taxonomic and phylogenetic knowledge is incomplete or conflicting, and we predict that this approach will aid in identifying where to focus future systematic efforts in any clade of interest. For Orobanchaceae, our phylogeny reflects the most recent taxonomy, and provides a new, comprehensive temporal framework for the clade that can serve as a stepping-stone for future macroevolutionary studies.
FIGURE 2. Phylogenetic tree concluded using Cyt b in A new species of Acanthodactylus Fitzinger, 1834 (Sauria: Lacertidae) from the Zagros Mountains, Iran
FIGURE 2. Phylogenetic tree concluded using Cyt b gene for Acanthodactylus species. The topologies of BI and ML trees are the same, therefore only the ML tree is shown. Numbers on branches indicate posterior probabilities (above) and bootstrap supports (below). Only values greater than 0.9 (for the former) and 90 (for the latter) are shown.
UCE alignments and phylogenetic trees
<p>Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus <em>Gerrhonotus </em>to compare and contrast species trees inferred using multiple contemporary methods and provide a timeframe for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provide highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in BPP and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of northeastern Mexico, and erected a new genus to better reflect evolutionary history. In sum, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbor substantial unrecognized diversity.</p>
Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development
<p>Background</p> <p><span>Across the Metazoa, similar genetic programs are found in the development of analogous, independently evolved, morphological features. The functional significance of this reuse and the underlying mechanisms of co-option remain unclear. Cephalopods have evolved a highly acute visual system with a cup shaped retina and a novel refractive lens in the anterior, important for a number of sophisticated behaviors including predation, mating and camouflage. Almost nothing is known about the molecular-genetics of lens development in the cephalopod.</span></p> <p><span>Results</span></p> <p><span>Here we identify the co-option of the canonical bilaterian limb pattering program during cephalopod lens development, a functionally unrelated structure. We show radial expression of transcription factors <i>SP6-9/sp1, Dlx/dll, </i><i>Pbx/exd, Meis/hth, </i>and a <i>Prdl</i> homolog in the squid <i>Doryteuthis pealeii</i>, similar to expression required in <i>Drosophila</i> limb development.<i> </i>We assess the role of Wnt signaling in the cephalopod lens, a positive regulator in the developing <i>Drosophila </i>limb, and find the regulatory relationship reversed, with ectopic Wnt signaling leading to lens loss. </span></p> <p><span>Conclusion</span></p> <p><span>This regulatory divergence suggests that duplication of SP6-9 in cephalopods may mediate the co-option of the limb patterning program. Thus our study suggests that the limb network could perform a more universal developmental function in radial pattering and highlights how canonical genetic programs are repurposed in novel structures.</span></p>
FIGURE 2. Phylogenetic tree constructed from a in Plenodomus dezfulensis sp. nov. causing leaf spot of Rapeseed in Iran
FIGURE 2. Phylogenetic tree constructed from a maximum likelihood analysis based on the combined ITS, tub2 and rpb2 sequences of Plenodomus strains. The tree was rooted to other related genera of Didymellaceae. Bootstrap values obtained in maximum likelihood (ML) and maximum parsimony (MP) analyses equal or greater than 50% and Bayesian posterior probability values (BYPP) equal or greater than 0.95 are shown at the nodes, respectively. T letters indicates the ex-type strains.
FIGURE. 2. Most parsimonious tree obtained from the analysis using implied weights, K in A phylogenetic study of the relationships within Mirinae subfamily (Insecta: Heteroptera: Miridae) based on specimens from Northern Iran: Insight into analyses of genera complexes
FIGURE. 2. Most parsimonious tree obtained from the analysis using implied weights, K= 8. Node numbers correspond to nodes in the results section. Filled circles represent non-homoplasious characters, and open circles represent homoplasious characters.
FIGURE 6. Phylogenetic tree for 15 in A new species of the alpheid shrimp genus Salmoneus Holthuis, 1955 (Decapoda: Caridea) from the Seto Inland Sea, Japan
FIGURE 6. Phylogenetic tree for 15 species of Salmoneus and Jengalpheops rufus Anker & Dworschak, 2007 used as an outgroup taxon; obtained by ML analysis of 16S rRNA gene sequences using the TVM + G + I substitution model. The best tree with the highest log likelihood (-1870.53) is shown. Bootstrap supports of greater than 80% are indicated at nodes as percentage values. There was a total of 514 bp in the final dataset trimmed with GBlocks.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.