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448 results for “phylogenetic inference”
Figure 5 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 5. Lateral, dorsal, and ventral views of a tadpole of Scaphiophryne brevis (ZSM 632/2004) showing the typical morphology of the relatively small tadpoles of the Scaphiophryne (Pseudohemisus) type.
Figure 1 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 1. Dorsal and lateral views of tadpoles of Scaphiophryne madagascariensis (stage 35, ZSM 595/2004) (A, B), S. menabensis (stage 35, ZSM 413/2004) (C, D), S. spinosa (stage 29, ZSM 604/2004) (E, F), S. brevis (stage 31, ZSM 618/ 2004) (G, H) and S. calcarata (stage 31, ZSM 410/2004) (I, J). Scale bars represent 5 mm.
Figure 2 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 2. Oral disc (OD), buccal floor (BF) and buccal roof (BR) of tadpoles of Scaphiophryne madagascariensis (OD: ZSM 600/2004; BF, BR: stage 38, ZSM 599/2004) (A–C), S. menabensis (OD: stage 36 BF, BR: stage 36); all from specimens in batch ZSM 413/2004) (D–F), S. spinosa (OD: stage 28, ZSM 616/2004; BF, BR: stage 29, ZSM 612/2004) (G–I), S. brevis (OD: stage 34; BF, BR: stage 31, ZSM 619/2004) (J–L) and S. calcarata (OD: stage 34; BF, BR: stage 32; both from specimens in batch ZSM 410/2004) (M–O). Scale bars are indicated on the images.
Figure 3 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 3. Dorsal and lateral views of tadpoles of Dyscophus insularis (A, B) (stage 34, ZSM 402/2004) and Paradoxophyla palmata (C, D) (stage 37, ZSM 647/2004). Oral disc of D. insularis (E) (stage 36, specimen from batch ZSM 402/2004) and P. palmata (H) (stage 35, ZSM 645/2004). Buccal floor (BF) and buccal roof (BR) of tadpoles of D. insularis (F, G) (stage 38, specimen from batch ZSM 402/2004) and P. palmata (I, J) (stage 37, ZSM 645/2004). Scale bars in A–D represent 5 mm, scale bars for E–J are indicated on the images.
Figure 4 in Comparative larval morphology of Madagascan toadlets of the genus Scaphiophryne: phylogenetic and taxonomic inferences
Figure 4. Dorsal, lateral, and ventral views of a tadpole of Scaphiophryne spinosa (ZSM 606/2004) showing the typical morphology of the relatively large tadpoles of the Scaphiophryne (Scaphiophryne) type.
Figure 2 in Inferring life history from ovipositor morphology in parasitoid wasps using phylogenetic regression and discriminant analysis
Figure 2. Distal part of ovipositor of the four parasitoid species whose life history is unknown, plus a selection of species whose life history is known. The complete ovipositor of the four species is also shown in profile, drawn relative to the width of the head of the species. Species with known life history are as follows (see Tables 1 and 2 for full names and classification). Endoparasitoids: host is exposed – a Aleiodes, b Zele, c Mesoleptus, d Megastylus, e Ophion, f Microgaster; host is leafminer – g Dacnusa, h Sathon; host is under fruit skin – i Pristomerus; host is in decaying fruit – j Asobara; wasp probes for deeply concealed host – k Orgilus, l Rhimphoctona, m Eubazus; host is stem-borer – n Collyria; host is gall-former – o Orthopelma. Ectoparasitoids: wasp probes for deeply concealed host – p Pseudorhyssa, q Stenobracon; host is leaf-miner – r Colastes; wasp bores for deeply concealed host – s Coeloides.
Figure 4 in Inferring life history from ovipositor morphology in parasitoid wasps using phylogenetic regression and discriminant analysis
Figure 4. Plots of biology vs. phylogenetic regression (PR) estimates of biology for the taxa where the biology is known; results from the three best PR models shown. State 0 = taxa are ectoparasitoids and state 1 = taxa are endoparasitoids. Philomacroploea and Mesoleptus, which are wrongly classified with PR, are indicated. The characters used in the models (U, P and H) are explained in Table 3. Estimates are derived as follows: PR (U) = (0.5281 + 0.8821) ¥ (U - 4730). PR (U + P) = 0.5144 + 1.001 ¥ (U - 0.4617) + 0.1531 ¥ (P - 0.1531). PR (U + P + H) = 0.4948 + 0.9818 ¥ (U - 0.4456) + 0.7428 ¥ (P - 0.1571) - 10.17 ¥ (H - 0.0054).
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 3 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 3. The single most-parsimonious tree (L = 951; CI = 0.568; RI = 0.793) obtained from the maximum parsimony analysis of combined (16S + ITS1) sequence dataset. Maximum likelihood analysis produced a largely congruent topology (HKY model; Ln likelihood = - 7034.61154) with the only difference being Pisidium dubium sister to Sphaerium/Musculium clade. Taxonomic names are arranged according to suggested sphaeriinid taxonomy in the present study and five major monophyletic lineages are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups. MP bootstrap values are shown to the left of the slash and decay index values to the right above the branches. Numbers below the branches indicate ML bootstrap values.
Figure 1 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 1. Strict consensus of the four equally most parsimonious trees (L = 526; CI = 0.447; RI = 0.743) obtained from the phylogenetic analysis of sphaeriid mitochondrial 16S rDNA sequences. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 4. Bayesian Inference phylogenetic tree inferred from 1039 in Genetic Relationships of Long-nosed Potoroos Potorous tridactylus (Kerr, 1792) from the Bass Strait Islands, with Notes on the Subspecies Potorous tridactylus benormi Courtney, 1963
Figure 4. Bayesian Inference phylogenetic tree inferred from 1039 bp of concatenated CO1 and ND2 mitochondrial DNA sequence data. Posterior probabilities for major lineages are shown. A similar tree topology was also inferred from Maximum Likelihood.
Figure 3. Maximum Likelihood phylogenetic tree inferred from 695 in Genetic Relationships of Long-nosed Potoroos Potorous tridactylus (Kerr, 1792) from the Bass Strait Islands, with Notes on the Subspecies Potorous tridactylus benormi Courtney, 1963
Figure 3. Maximum Likelihood phylogenetic tree inferred from 695 bp of CO1 mtDNA sequence, including data from the Potorous tridactylus benormi Holotype (AM M.8319) and Paratype (AM M.8373). Bootstrap values for major lineages are shown. A similar tree topology was inferred from Bayesian inference.
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 ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2
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The limits of the constant-rate birth-death prior for phylogenetic tree topology inference
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Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection
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Algebraic invariants for inferring 4-leaf semi-directed phylogenetic networks
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Data and Supplement from: Phylogenetic tree instability after taxon addition: Empirical frequency, predictability, and consequences for online inference
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Site-specific structure and stability constrained substitution models improve phylogenetic inference
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Data from: Accelerating maximum likelihood phylogenetic inference via early stopping to evade (over-)optimization
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