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39 results for “tree topologies”
The implications of incongruence between gene tree and species tree topologies for divergence time estimation
<p>Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.</p>
Decomposition, topology, properties, and graphs of woody crown networks of 15 tree species of Cerrado vegetation
<p>Data of decomposition, topology, properties, and the corresponding graphs of 15 adult tree species of Cerrado vegetation, <em>sensu stricto</em> physiognomy. The woody crown networks (WCN) representations in a bidimensional space were obtained by drawing followed the methodology described by Prado et al. (2020, Prado, C.H.B.A., Trovão, D.M.B.M., Souza, J.P.<strong>,</strong> 2020. A network model for determining the woody crown's decomposition, topology, and properties. Journal of Theoretical Biology, v. 499, p. 110318. https://doi.org/<a href="https://www.x-mol.com/paperRedirect/1258515479077781504">10.1016/j.jtbi.2020.110318</a>.). The branching regions were the nodes, and the woody crown segments connecting the nodes or merely emerging from them were the connectors. Those trees grew under natural conditions in a most common (<em>sensu stricto</em>) physiognomy of Cerrado vegetation, in a reservoir of 86 ha, located at 850 m above sea level in São Carlos city, São Paulo state, Brazil, at 21°58'- 22°00'S and 47°51'-47°52'W. Following the Köppen climatic classification, this region is between Aw and Cwa, a tropical climate with dry winter and wet summer. The rainy season occurs between October-March, and the dry season between April and September. </p>
Fig. 1. Species trees and alternative constraint convergence topologies. H0 in Positive association between PTN polymorphisms and schizophrenia in Northeast Chinese Han population.
Fig. 1. Species trees and alternative constraint convergence topologies. H0 is the well-accepted species tree. H1, H2, and H3 are three alternate echolocator-converged topologies. H1-control, H2-control and H3-control refer to the constraint convergent topologies of representative non-echolocators (cow, hedgehog, and non-echolocating bats).
Fig. 44. Tree topology taken from figure 43 in Freshwater Stingrays Of The Green River Formation Of Wyoming (Early Eocene), With The Description Of A New Genus And Species And An Analysis Of Its Phylogenetic Relationships (Chondrichthyes: Myliobatiformes)
Fig. 44. Tree topology taken from figure 43 (strict consensus tree) with ambiguous characters mapped (numbered as in text and matrix in table 5, unambiguous characters in fig. 43). Some of the characters are ambiguous because they are scored as uncertain in Hexatrygon (characters 4 and 21) and in Myliobatis (character 16); these are displayed conservatively on the tree (i.e., it is not simply assumed that they will be found in these taxa). Other characters have more than one equally parsimonious optimization (characters 3, 20, 32, 43), whereas others are scored as uncertain in the Green River stingrays (characters 12, 22, and 44). The optimization chosen in both of these cases is accelerated transformation, favoring reversals over independent gains. Characters denoted with an asterisk (*) are part of multistate transformation series that have unambiguous character states in figure 43.
The limits of the constant-rate birth-death prior for phylogenetic tree topology inference
<p>Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.</p>
The limits of the constant-rate birth-death prior for phylogenetic tree topology inference
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The implications of incongruence between gene tree and species tree topologies for divergence time estimation
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Decomposition, topology, properties, and graphs of 10 tree species of Caatinga vegetations
<p>Data were obtained from the observation of ten individuals from ten species growing in a semiarid area of Caatinga vegetation under natural conditions in the Northeast of Brazil in Paraiba State, located at the Fazenda Pocinho (7º29'46" S, 35º58'12" W) in the municipality of Barra de Santana, Brazil. The woody crowns were drawn (skeletonized) in the 2-D format as rooted trees resulting in networks with nodes and connectors following the methodology described by Prado et al. (2020, https://doi.org/10.1016/j.jtbi.2020.110318). Skeletonized crowns capture the data of decomposition, topology, and properties.</p>
Decomposition, topology, properties, and graphs of 14 individuals of Cenostigma pyramidale (Tul.) Gagnon & G.P. Lewis, a Caatinga tree species
<p>Data were obtained from the observation of 14 individuals of the tree species <em>Cenostigma pyramidale</em> (Tul.) Gagnon & G.P. Lewis growing in a semiarid area in Caatinga vegetation under natural conditions in the Northeast of Brazil in Paraiba State, located at the Fazenda Pocinho (7º29'46" S, 35º58'12" W) in the municipality of Barra de Santana. The woody crowns were drawn (skeletonized) in the 2-D format as rooted trees resulting in networks with nodes and connectors named woody crown networks. The data of decomposition, topology, and some properties are captured by skeletonized crowns following the methodology described by Prado et al. (2020, <a href="https://doi.org/10.1016/j.jtbi.2020.110318">https://doi.org/10.1016/j.jtbi.2020.110318</a>).</p>
FIGURE 50. Preferred topology with ACCTRAN character optimisations. Strict consensus tree from 7 trees using implied weights K in The new Southeast Asian goblin spider genus Aposphragisma (Araneae, Oonopidae): diversity and phylogeny
FIGURE 50. Preferred topology with ACCTRAN character optimisations. Strict consensus tree from 7 trees using implied weights K=1–5 (L=149, CI=0.63, RI=0.77). Squares show synapomorphic (black) and homoplastic (white) character state changes. Numbers above the squares correspond to the character numbers, those below to character state changes. The ingroup Aposphragisma gen. nov. is marked in shades of grey: species showing completely ornamented sterna in light grey and those possessing sterna with a glabrous middle stripe ('stripe-clade') in dark grey.
Data from: Likelihood of tree topologies with fossils and diversification rate estimation
Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils). We propose here a method to compute the likelihood of a phylogenetic tree with fossils in which the only considered time information is the fossil ages, and apply it to the estimation of the diversification rates from such data. Since it is required in our computation, we provide a method for determining the probability of a tree topology under the standard diversification model. Testing 21 our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree topology and the fossil dates are almost as accurate as those obtained by taking into account all the data, including the divergence times. Moreover, they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record). We also provide an empirical example composed of 50 Permo-carboniferous eupelycosaur (early synapsid) taxa ranging in age from about 315 Ma (Late Carboniferous) to 270 Ma (shortly after the end of the Early Permian). Our analyses suggest a speciation (cladogenesis, or birth) rate of about 0.1 per lineage and per My, a marginally lower extinction rate, and a considerable hidden paleobiodiversity of early synapsids.
FIGURE 2. Strict consensus tree from the unweighted analysis. The same topology was obtained from 12 in Phylogenetic relationships of the comb-footed spider subfamily Spintharinae (Araneae, Araneoidea, Theridiidae), with generic diagnoses and a key to the genera
FIGURE 2. Strict consensus tree from the unweighted analysis. The same topology was obtained from 12 (PAUP, branch collapsing rule 3) and two (TNT, branch collapsing rule 1) equally most parsimonious trees (spintharine synapomorphies with character numbers above and character states below).
The limits of the constant-rate birth-death prior for phylogenetic tree topology inference
<p>Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.</p>
Figure 1. Calibrated phylogeny for the main avian taxa. Tree topology was obtained from O in Multivariate analysis of neognath skeletal measurements: implications for body mass estimation in Mesozoic birds
Figure 1. Calibrated phylogeny for the main avian taxa. Tree topology was obtained from O'Connor, Chiappe & Bell (2011) and divergence times are based on a 'literal' interpretation of the fossil record from Brockelhurst et al. (2012). Taxa abbreviations: Nth, Neornithes; Orph, Ornithuromorpha; Orn, Ornithothoraces; Orth, Ornithurae; Pyg, Pygostylia.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
Figure 1 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 1. Maximum-likelihood (ML) tree showing the phylogenetic relationships among 41 newly sequenced specimens of pilidiophorans (indicated with solid blue circles). Numbers near nodes are support values, ML bootstrap/Bayesian inference (BI) posterior probability. Nodes with yellow triangles are fully supported, with 100% ML bootstrap and 1.00 BI posterior probability. New species names are indicated in bold. Some nodes were polytomous in the BI tree (indicated by hyphens in place of posterior probability values).
Figure 7. 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 7. A, Baseodiscus narusei sp. nov., holotype, ICHUM 6310, entire body, showing characteristic lateral edges; B, Baseodiscus paracelensis sp. nov., holotype, MIMB 33132, entire body; C, Baseodiscus aff. marmoratus (Bürger, 1890), anterior end of body, ventral view, head to the left; D, E, Baseodiscus ohtsukai sp. nov., holotype, ICHUM, 6327, drawings of anterior end of body viewed dorsally (D) and ventrally (E); F, G, Baseodiscus urgorrii sp. nov., holotype, MCZ IZ-135319, anterior end of body viewed dorsally (F) and ventrolaterally (G). Photos by T. Naruse (A), A. V. Chernyshev (B, C), and G. Giribet (F, G).
Figure 5. Cephalomastax brevis Iwata, 1957, ICHUM 6267. 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 5. Cephalomastax brevis Iwata, 1957, ICHUM 6267. A, anterior fragment in contracted state, lateral view; B, anterior end of body, ventral view; C, transverse section showing proboscis; D, magnification of anterior proboscis musculature (arrowhead, radial muscle fibre); E, transverse section showing rhynchocoel musculature. Photos by H. Kajihara.
Figure 3. 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 3. A, Baseodiscus aff. marmoratus (Bürger, 1890) (voucher DNA, ICHUM 6322); B, Baseodiscus aff. maculosus (Bürger, 1895a) (voucher DNA, ICHUM 6324); C–E, Baseodiscus delineatus (Delle Chiaje, 1822-1829), ICHUM 6326; F, Baseodiscus cf. curtus (Hubrecht, 1879), ICHUM 6328; G, H, Baseodiscus urgorrii sp. nov., holotype, MCZ IZ-135319, entire body (G) and protruding proboscis (indicated by an arrowhead, H); I, Baseodiscus punnetti (Coe, 1904), specimen different from any voucher specimens in this study; J, K, Baseodiscus kakuii sp. nov., holotype, ICHUM 6334, anterior body (J) and
Figure 4. A–C 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 4. A–C, Eopilidion misakiense gen. et sp. nov., holotype, ICHUM 6303, anterior end of body, ventral view, head to the right (A), frontal view (B), squeezed-slide preparation (C); D, Valencinura jambio sp. nov., holotype, ICHUM 6305, anterior end of body, ventral view. Photos by H. Kajihara.
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