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134 results for “Total Evidence”
FIGURE 3 in Total evidence analysis of the phylogenetic relationships of bandicoots and bilbies (Marsupialia: Peramelemorphia): reassessment of two species and description of a new species
FIGURE 3. Results of the morphometric analysis of the Perameles bougainville complex. A, Principal Component Analysis of cranial data; B, Canonical Variate Analysis of cranial data; C, Principal Component Analysis of dental data; D, Canonical Variate Analysis of dental data. Upright rectangles, Perameles bougainville; crosses, Perameles eremiana; diamonds, Perameles myosuros; circle, Perameles arenaria; stars, Perameles notina; triangles, Perameles fasciata; laying rectangles, Perameles papillon sp. nov.
FIGURE 2 in Total evidence analysis of the phylogenetic relationships of bandicoots and bilbies (Marsupialia: Peramelemorphia): reassessment of two species and description of a new species
FIGURE 2. Total evidence Bayesian inference timescale of peramelemorphian evolution. Node and tip calibrations are employed under a fossilized birth-death model, with molecular and morphological relaxed clock models unlinked. Blue bars show 95% highest posterior density intervals for node ages. The outgroup includes Didelphis and eight dasyuromorphians.
Supplementary material 2 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Morphological matrix : Explanation note: Matrix with the 27 terminals and the first 96 characters. The characters that were not coded due to lack of data of the analyzed specimens and/or from literatures sources are coded as "?"; characters that did not apply were coded as "-"; and the polymorphic characters were coded with a "/" between each state it presented.
Supplementary material 1 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
List of morphological characters and coding : Explanation note: List of morphological characters and their respective coding, used in the morphological and total evidence analyses.
Figure 8 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 8. Maximum clade credibility phylogram obtained with Bayesian inference using combined data: morphological matrix without gamete-related characters and molecular data (18S rRNA and 28S rRNA). Values above branches are posterior probabilities supports.
Figure 3 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 3. The four states coded in the present study for the shape of the apophyses for the insertion of the stylet muscles (AISM) (characters 14, 15; Table 2). A State 1: AISM divided in two; B AISM shaped as one ridge; C AISM shaped as two ridges; D AISM shaped as three ridges. The images represent half a buccal tube in lateral view. The arrow in B indicates an apophysis for the insertion of the stylet muscles connecting with the end of the mouth. The rest of the apophyses for the insertion of the stylet muscles connect with the beginning of the buccal tube.
Figure 1 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 1. Eutardigrade peribuccal structures indicated by arrows. A, lamellae (state 1 in Tables 3 and 4); B, papulae (state 3 in Tables 3 and 4); C, lobes.
Figure 7 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 7. Agreement subtree with groups present with all concavities obtained with the Ratchet algorithm for parsimonious analyses using combined data: morphological matrix without gamete-related characters and molecular data (18S rRNA and 28S rRNA). Values above branches are bootstrap supports after 1000 replicates with a k-value of 16. Values under branches are Bremer relative supports with a k-value of 16.
Figure 5. Agreement subtree cladogram obtained with the Ratchet algorithm for parsimonious analyses using the complete morphological matrix without gamete-related characters. Values above branches are bootstrap supports after 1000 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 5. Agreement subtree cladogram obtained with the Ratchet algorithm for parsimonious analyses using the complete morphological matrix without gamete-related characters. Values above branches are bootstrap supports after 1000 replicates; values under branches are Bremer relative supports.
Figure 2 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 2. Different states (from 0 to 5) coded in the present study for the shape of the furcae (character 13; Table 2).
Figure 4 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 4. Different types of claws present amongst eutardigrades (A–N) and in the outgroup Echiniscidae (O). M modified from Pilato (1971). Dotted lines in F and G indicate right angles in Isohypsibius- and Hypsibius-type claws, respectively. Arrows in D and E indicate cuticular bars joining external and internal claws in Dactylobiotus and Macroversum, respectively. Arrows in L indicate claw position. PIII, third pair of legs. PIV, fourth pair of legs.
Data for Field evidence for Asian outflow and fast depletion of total gaseous mercury in the polluted coastal atmosphere
<p>Hourly data of TGM at Tai Mo Shan in Hong Kong</p>
Photographic Evidence on Total Knee Arthroplasty Outcomes
ClinicalTrials.gov study NCT07223359. IPD Sharing: NO. Countries: 1. Publications: 6.
Development, Piloting and Evaluation of an Evidence-based Informed Consent Form for Total Knee Arthroplasty
ClinicalTrials.gov study NCT04669483. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Between spines and molecules: a total evidence phylogeny of the Brazilian endemic genus Encholirium (Pitcairnioideae, Bromeliaceae)
Open the record for dataset details and reuse information.
A total-evidence dated phylogeny of Echinoidea combining phylogenomic and paleontological data
Open the record for dataset details and reuse information.
Mind the outgroup and bare branches in total-evidence dating: a case study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)
<p>Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: "bare-branch attraction", namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.</p>
Data from: Multiple morphological clocks and total-evidence tip-dating in mammals
Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or 'pacemaker'. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.
Data from: Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians)
Here, I combine previously underutilized models and priors to perform more biologically-realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backwards transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for 'asymmetric.' The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical datasets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend towards recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across datasets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological datasets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.
Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4–20% complete) and 68 extant taxa. In both cases we use molecular data from seven markers (about 5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, approximately 309 Ma (95% interval: 291–347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic.
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