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FIGURE 4 in Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan
FIGURE 4. Coniochaeta acaciae (holotype TASM 6103) a, b. Ascomata on the substrate. c, d. Vertical section of ascoma. e. Section of peridium (in water). f. Section of peridium (in 5% KOH). g. Ostiole. h. Setae. i. Ascus apex in Congo Red. j–l. Ascospores (arrow heads show germ slits in l). m–o. Asci. Scale bars: a=500 μm, b=200 μm, c,d=100 μm, e–h=20 μm, i=10 μm, j–o=5 μm.
FIGURE 1 in Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan
FIGURE 1. Maximum likelihood tree revealed by RAxML from an analysis of the LSU rDNA matrix of Coniochaeta, showing the phylogenetic position of C. acaciae and C. coluteae. MP, ML bootstrap supports (≥50%) and Bayesian posterior probabilities (≥0.9PP) support are given above or below the branches respectively. The tree was rooted with Chaetosphaeria garethjonesii (MFLUCC 15-1012) and C. jonesii (MFLUCC 15-1015). New species proposed in this study are indicated in red, and type strains are in boldface.
Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
Data from: Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models
Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene transfer and gene duplication. Among these, deep coalescence is usually quantified as the number of extra lineages and has been studied as the principal source of discordance among gene trees, while the other processes that could contribute to gene tree discordance have not been fully explored. This is an important issue for hybridization because interspecific gene flow is well documented and widespread across many plant and animal groups. Here, we propose a new way to detect gene flow when ILS is present that evaluates the likelihood of different models with various levels of gene flow, by comparing the expected gene tree discordance, using the number of extra lineages. This approach consists of proposing a model, simulating a set of gene trees to infer a distribution of expected extra lineages given the model, and calculating a likelihood function by comparing the fit of the real gene trees to the simulated distribution. To count extra lineages, the gene tree is first reconciled within the species tree, and for a given species tree branch the number of gene lineages minus one is counted. We develop a set of R functions to parallelize software to allow simulations, and to compare hypotheses via a likelihood ratio test to evaluate the presence of gene flow when ILS is present, in a fast and simple way. Our results show high accuracy under very challenging scenarios of high impact of ILS and low gene flow levels, even using a modest dataset of five to ten loci and five to ten individuals per species. We present a powerful and fast method to detect hybridization in presence of ILS. We discuss its advantage with large dataset (such as genomic scale), and also identifies possible issues that should be explored with more complex models in future studies.
Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.
Figure 7. Mitochondrial DNA gene tree estimated for Acanthocercus atricollis using a in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 7. Mitochondrial DNA gene tree estimated for Acanthocercus atricollis using a portion of the 16S gene. The support for branches from BI and ML are shown on each branch, respectively. The *BEAST species tree is shown in the top left with posterior probability values on branches.
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Shanxi province, China
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Shanxi province, China
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 2. The tree represents a 50 in A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes
FIGURE 2. The tree represents a 50% majority rule consensus of the Bayesian topology (numbers represent the posterior probability of the clades), with bootstrap values from MP and ML mapped onto the topology. MP, ML, and Bayesian analyses produced similar topologies (MP: TL = 12,869, consistency index CI = 0.2372, retention index RI = 0.4450; ML: Ln Likelihood = -54309.4503) with differences mostly on nodes with low bootstrap support. The numbers on branches are MP and ML bootstrap values and posterior probabilities from Bayesian analysis, respectively. Asterisks indicate a bootstrap value of 100% for MP and ML and 1.0 for Bayesian analysis. Nodes with less than 50% bootstrap value are marked with an X if the clade had less than 50% support in any of the MP, ML, or Bayesian analyses.
Figure 1. Bayesian COI gene tree for 51 in Integrative taxonomy of the primitively segmented spider genus Ganthela (Araneae: Mesothelae: Liphistiidae): DNA barcoding gap agrees with morphology
Figure 1. Bayesian COI gene tree for 51 terminals of Ganthela, with the results of five different species delimitation approaches, in addition to morphology (see legend). Numbers above branches show posterior probability and bootstrap supports, and values below branches show mean intraspecific (black) and interspecific genetic distances (red), calculated as Kimura two-parameter (K2P)/p-distance. Species names and locality group terminals (for specimen codes, see Table 1) according to consensus results of species delimitation approaches.
Figure 7 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 7. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific: A–H, ventral, dorsal, lateral, and anterior views of complete specimens, CP 2616, 786–836 m depth; A–D, paratype, IB-2013-2; E–H, holotype, IB-2013-1. I, dorsal view of complete specimen, with very long, thin pedicle, paratype, CP 2616, 786–836 m depth, IB- 2013-3. Scale bars: 5 mm.
Figure 6 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 6. rDNA tree of taxa with modified long loops. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2694 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of 15 in-group and three rhynchonellide out-group taxa. Potentially misaligned and gapped sites (5%) were pruned by GBlocks. Several backbone nodes received very low bootstrap support and the tree has been redrawn by hand to remove them, leaving no effective resolution of relationships between the in-group superfamilies represented in this alignment. The sequence for Argyrotheca (JH97) was used with the permission of Dr J. Hoffman.
Figure 2. Case 2 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 2. Case 2: Cancellothyridoid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2810 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 30 in-group and three rhynchonellide out-group taxa. Gblocks was used to prune potentially misaligned and gap sites (18% were discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Four taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon.
Figure 5 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 5. Laqueoidea rDNA tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2882 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of seven laqueoid in-group and six terebratulide out-group taxa. The small number of potentially misaligned and gap sites were not removed. The failure of the two Kingenoids to form a clade may be caused by limited sequence data rather than by misclassification.
Figure 9 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 9. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific, SEM micrographs; A, B, ventral valve, station CP 2556, 741–791 m depth, IB-2013-7; A, transverse section of the entire shell showing the primary layer (pri) underlain by the fibrous secondary layer (sec), passing into the prismatic tertiary layer (ter); B, section of the shell showing primary (pri), secondary (sec), and tertiary (ter) layers; a puncta with a radiating brush is also visible; C, D, dorsal valve, CP 2557, 800–923 m depth, IB-2013-5; C, latero-oblique view of internal surface, showing the incurved valve margin built of densely arranged sheets of secondary fibres (left) and prisms of tertiary layer (right); D, internal surface showing discrete units of prisms and very small punctae (arrows). E, F, Kanakythyris pachyrhynchos Laurin, 1997, cruise NORFOLK 2, Norfolk Ridge, station DW 2136, 402–410 m depth; E, transverse section of the entire shell; F, internal surface with discrete units of prisms. Scale bars: A, C, D, E, F, 50 μm, B, 20 μm.
Figure 4. Laqueoidea cox1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 4. Laqueoidea cox1 tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 1218 nucleotides of aligned sequences of the cox1 mitochondrial gene from 14 laqueoid in-group and six terebratulide out-group taxa. The sequences were aligned with no gaps. Nodes with no bootstrap support value attached are considered to be unsupported (bootstrap <50%) and may be collapsed.
Figure 3. Case 3 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 3. Case 3: Dyscolioid and Terebratuloid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 3427 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 19 in-group and three rhynchonellide out-group taxa. Pruned of potentially misaligned and gap sites by hand (7% discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Nine taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon. These results validate the placement of Ebiscothyris, Dallithyris, and Dyscolia, each of which is represented by LSU alone.
Dataset from: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
<p>This repository contains the datasets, code, and results for:</p> <p>Roberts et al. Resolving marine-freshwater transitions by diatoms through a fog of gene tree discordance.</p> <p>CONTACT INFORMATION:</p> <p>Andrew J. Alverson<br> University of Arkansas<br> aja [at] uark [dot] edu</p> <p>Wade R. Roberts<br> University of Arkansas<br> wader [at] uark [dot] edu</p> <p>TAXON LABEL INFORMATION:</p> <p>Genomes have strain ID before genus_species (e.g., CCMP332_Cyclotella_cryptica)<br> Transcriptomes have genus_species before strain ID (e.g., Cyclotella_nana_AJA048-54)</p> <p><br> DATA AND DIRECTORY OVERVIEW:</p> <p>Voucher images of diatom strains collected:</p> <ul> <li>voucher-images.tgz</li> </ul> <p>OrthoFinder output:</p> <ul> <li>orthofinder.zip</li> </ul> <p>Predicted proteomes and coding sequences for each strain:</p> <ul> <li>proteomes.zip</li> <li>coding-sequences.zip</li> </ul> <p>Workflow for phylogenomic dataset assembly and species tree analyses:</p> <ul> <li>phylogenomic-workflow.html</li> <li>phylogenomic-workflow.md</li> <li>phylogenomic-workflow.pdf</li> </ul> <p>Fasta files, alignments, and gene trees for each ortholog:</p> <ul> <li>datasets.zip</li> </ul> <p>Concatenated alignments, partition models, and estimated species trees:</p> <ul> <li>species-trees.zip</li> <li>species-trees.nexus</li> </ul> <p>Analyses results and code to plot figures:</p> <ul> <li>analyses-and-plots.zip</li> </ul> <p>Additional scripts and miscellaneous files:</p> <ul> <li>scripts-and-misc.zip</li> </ul> <p>Supplemental Materials for publication:</p> <ul> <li>supplemental-materials.zip</li> </ul> <p> </p>
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A in Hidden in the hills: phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A full tree is available in the Supporting Information (File S1). The scale is in substitutions per site.
Figure 3. The BEAST tree for the reduced dataset using the mean rates and SDs for the individual mitochondrial genes from table 4 in Phylogeny of the microcormorants, with the description of a new genus
Figure 3. The BEAST tree for the reduced dataset using the mean rates and SDs for the individual mitochondrial genes from table 4 in the paper by Pacheco et al. (2011) (scale in Mya). The two African species of microcormorants are labelled as Aflocarbo.
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