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39 results for “tree topologies”
Figure 6. A–E in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 6. A–E, Baseodiscus takakurai Gibson, 1995, ICHUM 6308, A, anterior end of body, ventral view; B, middle body region, showing appearance of body markings in differently contracted states; C, juvenile, showing dorsal mottling; D, juvenile, with head viewed ventrolaterally, showing two ocelli; E, transverse section of proboscis; F, Baseodiscus komatsui sp. nov., holotype, NSNM NMNS-Ne 1, entire body. Photos by H. Kajihara (A–E) and H. Komatsu (F).
Figure 2. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 2. A, Eopilidion misakiense gen. et sp. nov., holotype, ICHUM 6303, lateral view, head to the right; B, Oxypolella hiebertae sp. nov., holotype, MIMB 42256; C, Cephalomastax brevis Iwata, 1957, ICHUM 6304; D, E, Valencinura jambio sp. nov., holotype, ICHUM 6305, anterior body fragment (D) and enlargement of intestinal region (E) showing yellowish proboscis (indicated by arrowheads); F, Baseodiscus takakurai Gibson, 1995, ICHUM 6306; G, Baseodiscus profundus sp. nov., holotype, MIMB 42257; H, I, Baseodiscus narusei sp. nov., holotype, ICHUM 6310, anterior end of body, dorsal (H) and ventral (I) views; J, Baseodiscus paracelensis sp. nov., holotype, MIMB 33132; K, Baseodiscus komatsui sp. nov., holotype, NMNS-Ne 1; L, Baseodiscus unicolor Stiasny-Wijnhoff, 1925; M, Baseodiscus giribeti sp. nov., holotype, MCZ IZ-135324; N, Baseodiscus cf. amboinensis (Staub, 1900); O, Baseodiscus hemprichii (Ehrenberg, 1828-1831), specimen from Okinawa, different from any voucher specimens in this study; P, Baseodiscus zebra sp. nov., holotype, RUMF-ZN-00001; Q, Baseodiscus quinquelineatus (Quoy & Gaimard, 1833), ICHUM 6319. Photographs by H. Kajihara (A, C, D, E, F, O), A. V. Chernyshev (B, G, J), T. Naruse (H, I), H. Komatsu (K), G. Giribet (L, M), D. Uyeno (P), and R. Yoshida (Q).
FIGURE 3. Phylogenetic tree topology for the 16S in Description of a new flat gecko (Squamata: Gekkonidae: Afroedura) from Mount Gorongosa, Mozambique
FIGURE 3. Phylogenetic tree topology for the 16S gene (identical for Bayes and ML) using Afroedura hawequensis as outgroup. Support values for posterior probabilities and bootstraps are indicated by circles (PP:>0.95 / ML:>70%): full black circles indicated support by both methods and full open circles indicate no strong support by either method.
FIGURE 2. Neighbour-joining tree topology using Kimura 2 in Redescription of Chimaera ogilbyi (Chimaeriformes; Chimaeridae) from the Indo-Australian region
FIGURE 2. Neighbour-joining tree topology using Kimura 2 Parameter distance based on nucleotide sequence divergence in aligned nucleotide NADH2 sequences for Chimaera ogilbyi and closely related species. Outgroup is represented by Rhinochimaera atlantica and Harriotta raleighana. Sequence labels are based on operational taxonomic units defined in paper. GenBank accession numbers follow sequence labels. Scale bar represents 2% K2P distance.
FIGURE 1. Topology showing the most parsimonious tree obtained from a heuristic search with 1,000 in A new species of Microthyrium from Yunnan, China
FIGURE 1. Topology showing the most parsimonious tree obtained from a heuristic search with 1,000 random taxon additions of the combined dataset of SSU and LSU sequences alignment using PAUP v. 4.0b10. The scale bar shows 10 changes. Bootstrap support values for maximum parsimony (MP) and maximum likelihood (ML) greater than 50% above the nodes. The values below the nodes are Bayesian posterior probabilities above 0.95. Hyphen ("-") indicates a value lower than 50% (BS) or 0.90 (PP). The original isolate numbers are noted after the species names. The tree is rooted to Schismatomma decolorans.
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S rRNA + COI sequence data, demonstrating the evolutionary relationships within the P. sidneyi s.l. species complex. Statistical support for nodes is provided as posterior probability values above nodes (> 0.95 PP) and bootstrap values below nodes (> 75%). An * or # denotes nodal relationships that were not supported (<0.95 PP/ <75%). Potamonautes sidneyi s.s. (clade 3) localities are marked with a dark blue triangle, while P. danielsi (clade 5) localities are marked by an orange square. The two new species, P. karooensis, (clade 2) and P. Ʋalles (clade 4), are marked by a light-blue circle and a green diamond, respectively. Specimens of P. barbarai are confined to clade 1.
FIGURE 4. Seven topologically parsimonious constrained trees retrieved from cladistic analysis using a in On the first Baryonychinae (Theropoda, Spinosauridae) teeth from South America
FIGURE 4. Seven topologically parsimonious constrained trees retrieved from cladistic analysis using a dentition-based data matrix (tree length = 1318; CI = 0.198; RI = 0.466), Bremer support is displayed below each node; LPUFS specimens (bold) are recovered within the Spinosauridae clade. Theropod silhouette from phylopic.org, see acknowledgements.
Data from: Rethinking refugia: tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day
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Data from: Exact distribution of divergence times from fossil ages and tree topologies
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Data from: Likelihood of tree topologies with fossils and diversification rate estimation
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Data from: Accurate inference of tree topologies from multiple sequence alignments using deep learning
Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several "zones" of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. Here we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate on simulated data, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. While numerous practical challenges remain, these findings suggest that deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.
Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests
1. From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional traits. 2. The objectives of this study were to describe the interaction network topologies of MNs formed between two ectomycorrhizal fungal species, Rhizopogon vesiculosus and R. vinicolor, and interior Douglas-fir trees at the forest stand scale, identify factors leading to this structure and to contrast MN structures between forest plots with xeric versus mesic soil moisture regimes. 3. Tuberculate mycorrhizas were sampled in six 10 × 10 m plots with either xeric or mesic soil moisture regimes. Microsatellite DNA markers were used to identify tree and fungal genotypes isolated from mycorrhizas and for comparison with reference tree boles above-ground. 4. In all six plots, trees and fungal genets were highly interconnected. Size asymmetries between different tree cohorts led to non-random MN topologies, while differences in size and connectivity between Rhizopogon species-specific subnetwork components contributed towards MN nestedness. Large mature trees acted as network hubs with a significantly higher node degree compared to smaller trees. MNs representing trees linked by R. vinicolor genets were mostly nested within larger, more highly connected R. vesiculosus-linked MNs. 5. Attributes of network nodes showed that hub trees were more important to MN topology on xeric than mesic sites, but the emergent structures of MNs were similar in the two soil moisture regimes. 6. Synthesis. This study suggests MNs formed between interior Douglas-fir trees and R. vesiculosus and R. vinicolor genets are resilient to the random loss of participants, and to soil water stress, but may be susceptible to the loss of large trees or fungal genets. Our results regarding the topology of MNs contribute to the understanding of forest stand dynamics and the resilience of forests to stress or disturbance.
Data from: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
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Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests
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Data from: Accurate inference of tree topologies from multiple sequence alignments using deep learning
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FIGURE 7. The phylogenetic tree topology for Urocaridella arabianensis n in Urocaridella arabianensis n. sp., a new Palaemonid shrimp (Crustacea, Decapoda Palaemonidae) from Lakshadweep Islands, India with taxonomic comparison on the genus Urocaridella Borradaile, 1915
FIGURE 7. The phylogenetic tree topology for Urocaridella arabianensis n. sp. with congener species based on COI (A), 16S (B) genes sequences using Bayesian inference (BI)/maximum likelihood (ML) analyses.
FIGURE 8. The phylogenetic tree topology for Urocaridella arabianensis n in Urocaridella arabianensis n. sp., a new Palaemonid shrimp (Crustacea, Decapoda Palaemonidae) from Lakshadweep Islands, India with taxonomic comparison on the genus Urocaridella Borradaile, 1915
FIGURE 8. The phylogenetic tree topology for Urocaridella arabianensis n. sp. with congener species based on 18S (A) and H3 (B) genes sequences using Bayesian inference (BI)/maximum likelihood (ML) analyses.
FIGURE. Phylogram of Tolypocladium generated from Maximum likelihood analysis of ITS, SSU and LSU sequence data. Purpureocillium lilacinum (CBS 284.36) was selected as an outgroup taxon. The tree topology of the ML analysis was similar to the BI. Maximum likelihood bootstrap values greater than 75 and Bayesian posterior probabilities over 0.90 were indicated above the nodes. The scale bar indicates 0.006 changes. The new species was in blue. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Phylogram of Tolypocladium generated from Maximum likelihood analysis of ITS, SSU and LSU sequence data. Purpureocillium lilacinum (CBS 284.36) was selected as an outgroup taxon. The tree topology of the ML analysis was similar to the BI. Maximum likelihood bootstrap values greater than 75 and Bayesian posterior probabilities over 0.90 were indicated above the nodes. The scale bar indicates 0.006 changes. The new species was in blue.
Figure 5. A, topological similarities between gene trees. A in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 5. A, topological similarities between gene trees. A non-metric multidimensional ordination plot, based on the Robinson–Foulds (RF) distance between each pair of genes, is used to visualize the topological similarity among the 208 single gene trees. Pairs of gene trees with similar topologies are closer together in the two-dimensional space. Colours represent RF distances between individual gene trees and the extended majority-rule consensus (MRE) phylogeny. B, identifying optimal subsets of genes with the least topological incongruence. The graph shows the Tree Certainty (TC) values from Salichos & Rokas (2013). Information theory approach using the MRE phylogeny as a reference tree, where higher values represent greater congruency between the gene trees and the MRE tree. The x-axis represents the number of genes sampled, following an iterative procedure beginning with the first two genes in the respective ranking and progressively adding genes according to their order in the list. The five ranking criteria all outperformed random gene orders.
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