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FIG. 12 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)
FIG. 12. Phylogenetic relationships of Rhinella recovered in one of the most parsimonious trees from the total evidence analysis with TNT considering gaps as a fifth state (length 25,399 steps). The clades and species groups shown are those recognized in this study. Part 2 of 4. The R . marina Clade (2): the ghost introgressed mitochondrion and the R . crucifer and R . marina Groups. Black circles indicate nodes that collapse in the strict consensus. Values around nodes are parsimony jackknife frequencies (frequency differences value [above]/ absolute [below]). An asterisk (*) indicates 100% jackknife support. Clades lacking references have <25% frequency difference values or <50% jackknife absolute frequencies. Lower left inset shows the entire cladogram with present view marked in white. Abbreviations: MtG, mitochondrial genome; NuG, nuclear genome.
FIG. 7 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)
FIG. 7. Musculature of the dorsal surface of the hand and forearm: A, B. Rhinella paraguas CD 870. C, D. R . dorbignyi MACN 39350. A. First muscular layer: m. extensor digitorum; the m. extensor carpi ulnaris is also shown. Elements figured: 1, m. extensor digitorum and the m. extensor carpi ulnaris (head from humerus): common tendon of origin; 2, m. extensor digitorum; 3, m. extensor digitorum: slip to the dorsal surface of the m. extensor brevis superficialis digiti IV (both muscles attaches to the metacarpophalangeal joint of digit IV via a common tendon); 4, m. extensor digitorum: slip to metacarpal V; 5, m. extensor carpi ulnaris: head from humerus; 6, m. extensor carpi ulnaris (head from humerus): tendon of insertion. B. Second muscular layer: m. abductor pollicis longus and mm. extensores breves superficiales; the head from radioulna of the m. extensor carpi ulnaris is also shown (the head from humerus was removed). Elements figured: 1, m. extensor carpi ulnaris (head from radioulna): fleshy origin; 2, m. extensor carpi ulnaris: head from radioula; 3, m. extensor carpi ulnaris (heads from humerus and radioulna): common tendon of insertion on distal carpal 3-4-5; 4, m. abductor pollicis longus; 5, m. extensor indicis brevis superficialis: slip from radiale; 6, m. extensor indicis brevis superficialis: slip from ulnare; 7, m. extensor brevis superficialis digiti III; 8, m. extensor brevis superficialis digiti IV: slips from ulnare and distal carpal 3-4-5; 9, m. extensor brevis superficialis digiti V. C. First muscular layer: m. extensor digitorum; the m. extensor carpi ulnaris is also shown. Elements figured: 1, m. extensor digitorum and m. extensor carpi ulnaris (head from humerus): common tendon of origin; 2, m. extensor digitorum; 3, m. extensor digitorum: slip to the dorsal surface of the m. extensor brevis superficialis digiti IV (both muscles attaches to the metacarpophalangeal joint of digit IV via a common tendon); 4, m. extensor digitorum: slip to metacarpal V; 5, m. extensor carpi ulnaris: head from humerus; 6, m. extensor carpi ulnaris: tendon of insertion. D. Second muscular layer: m. abductor pollicis longus and mm. extensores breves superficiales; the head from radioulna of the m. extensor carpi ulnaris is also shown (the head from humerus was removed). Elements figured: 1, m. extensor carpi ulnaris (head from radioulna): tendon of origin; 2, m. extensor carpi ulnaris: head from radioulna; 3, m. extensor carpi ulnaris (heads from humerus and radioulna): common tendon of insertion on distal carpal 3-4-5; 4, m. abductor pollicis longus; 5, m. extensor indicis brevis superficialis: slip from ulnare inserting on metacarpal II (in common with the m. abductor pollicis longus); 6, m. extensor indicis brevis superficialis: slip from ulnare inserting on metacarpophalangeal joint; 7, m. extensor brevis superficialis digiti III: slips from ulnare and distal carpal 3-4-5; 8, m. extensor brevis superficialis digiti IV: slip from distal carpal 3-4-5; 9, m. extensor brevis superficialis digiti V. Characters figured: char. 46.1, presence of the head from radioulna of the m. extensor carpi ulnaris; char. 47.0, fleshy origin of the head from radioulna of the m. extensor carpi ulnaris; char. 47.1, origin via a flat tendon of the head from radioulna of the m. extensor carpi ulnaris. Scale bars = 1 mm.
FIG. 4 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)
FIG. 4. Skulls (lateral view of the anterior region) showing the orientation of alary process of the premaxilla in relation to the anterior margin of the premaxilla (premaxilla in gray): A, Nannophryne cophotis KU 218525 (char. 13.0; species not included in this study; B, R . crucifer KU 93112 (char. 13.1); C, R . sp. margaritifera Group (char. 13.2). All the figures redrawn and slightly modified from Pramuk (2006). The voucher number provided for the specimen of the R . sp. margaritifera Group was erroneously stated in Pramuk's (2006) figures according to the information provided in appendix 1 of that publication and in VertNet database (http://portal.vertnet.org/).
FIG. 3 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)
FIG. 3. Skulls (lateral view of the anterior region) showing the relation between the anterior margin of the nasal (black arrow) and the dorsal margin of the alary process of the premaxilla (gray arrow): A, Rhinella yanachaga MSM 24509 (char. 12.0), B, R . amabilis KU 124587 (char. 12.1), C, Schismaderma carens USNM 153380 (char. 12.2). Panels A and B redrawn from Lehr et al. (2007) and Pramuk (2006), respectively. Black arrows indicate the anterior margin of the nasal, gray arrows indicate the dorsal margin of the alary process.
Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating
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Data from: Integrating deep learning derived morphological traits and molecular data for total-evidence phylogenetics: lessons from digitized collections
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A total evidence approach justifies taxonomic splitting of the endangered Pecos Gambusia into three species
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Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses
<p>Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth <em>Bradypus</em> is consistently recovered as a megatherioid, and <em>Choloepus</em> as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae", whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an <em>a posteriori</em> removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models, and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.</p>
Bayesian total-evidence inference resolves the position of the ant genus Phaulomyrma (Hymenoptera, Formicidae)
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Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses
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Data and scripts from: Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of anostomid fishes
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Data from: But the clock, tick-tock: The preeminence of relaxed clock models in total-evidence dated phylogenetics
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Fig. 2 in Total evidence phylogenetic analysis and reclassification of Euschistus Dallas within Carpocorini (Hemiptera: Pentatomidae: Pentatominae)
Fig. 2. Bayesian inference consensus tree based on the analysis of four molecular markers and morphological characters for 23 species of Euschistus and related carpocorines. Numbers in circles near branches refer to clades discussed in the text. Numbers close to nodes are Bayesian posterior probabilities (PPs) and maximum likelihood bootstrap support (BS), respectively. Only nodal support above PP = 0.5 or BS = 50 is displayed ('–' indicates no support). The fast track depicts morphological features for ease of recognition of species within the specified clades. [Colour figure can be viewed at wileyonlinelibrary.com].
Fig. 1 in Total evidence phylogenetic analysis and reclassification of Euschistus Dallas within Carpocorini (Hemiptera: Pentatomidae: Pentatominae)
Fig. 1. Bayesian inference consensus tree based on the analysis of four molecular markers and morphological characters for 32 species of Euschistus and related carpocorines. Numbers in circles above branches refer to clade numbers discussed in the text. Numbers close to nodes are Bayesian posterior probabilities (PPs)/maximum likelihood bootstrap support (BS), respectively. Only nodal support above PP = 0.5 or BS = 50 is displayed ('–' indicates no support for that clade). Habitus photos of representative species of Euschistus Dallas and other Carpocorini's genera. [Colour figure can be viewed at wileyonlinelibrary.com].
A total-evidence dated phylogeny of Echinoidea combining phylogenomic and paleontological data
<p>Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of unidscovered evolutionary history of the crown in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two.</p>
Figure 18 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)
Figure 18. Dorsal fin of Insperanos nattereri, MZUSP 5429, 138.7 mm SL. DFS: dorsal fin stay, DR: distal radial, MR: medial radial, Ns: neural spine, PR: proximal radial, Sn: supraneural.
Figure 16 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)
Figure 16. Pectoral fin of Anostomoides nattereri, MZUSP 5429, 138.7 mm SL, in lateral view (A) and in detail in medial view (B, C). Co: coracoid, Cl: cleithrum, Dr: distal radial, Exs: extrascapular, Msc: mesocoracoid, Pcl 1-3: postcleithra 1-3, Pr: proximal radials, Pt: posttemporal, Scl: supracleithrum.
Figure 20 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)
Figure 20. Caudal fin of Insperanos nattereri, MZUSP 5429, 138.7 mm SL. Ep1–3: epural s1–3; H1-6: hipurals 1–6; Hs: haemal spine; Mnp: modified neural process, Ns: neural spine, Opc: opisthural cartilage, Ph: parhypural, Un1–2: uroneurals 1–2, Us: urostyle.
Figure 5 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)
Figure 5. Cranium of Anostomoides nattereri in (A) dorsal and (B) ventral views, MZUSP 5429, 138.7 mm SL. Bl: Baudelot ligament, Boc: basioccipital, C1-4: centra 1–4, CLA: claustrum, Epo: epiotic, Exo: exoccipital, Fro: frontal, In: intercalar, Let: lateral ethmoid, LpC2: lateral process of centrum 2, Mes: mesethmoid, Os: os suspensorium, Osph: orbitosphenoid, Par: parietal, Pro: prootic, Pto: pterotic, Psph: parasphenoid, Ptsph: pterosphenoid, Rb4: rib of vertebra 4, SOc: supraoccipital, Sph: sphenotic, Tr: tripus, Vom: vomer.
Figure 12 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)
Figure 12. Summarized phylogenetic relationships of the Anostomidae and selected outgroup Characiformes, based on a node and tip calibrated Bayesian Inference analysis of combined data from morphology (158 characters) and six gene sequences (COI, Cytb, Myh6, Rag1, Rag2, 16S). See Supporting Information (Fig. S1) for the cladogram including the complete set of terminals.
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