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17 results for “time-scaling”
Data from: How to date a crocodile – estimation of neosuchian clade ages and a comparison of four time-scaling methods
<p>Clade ages within the crocodylomorph clade Neosuchia have long been debated. Molecular and morphological studies have yielded remarkably divergent results. Despite recent advances, there has been no comprehensive relative comparison of the major time calibration methods available to estimate clade ages based on morphological data. We used four methods (cal3, Extended Hedman [EH], smoothed Ghost-Lineage-Analysis [sGLA] and the Fossilised Birth-Death model [FBD]) to date clade ages derived from a published crocodylomorph supertree and a new neosuchian phylogeny. All time-scaling methods applied here agree on the origination of Neosuchia during the Late Triassic/Early Jurassic, and the presence of the major extant eusuchian groups (Crocodyloidea, Gavialoidea, Alligatoroidea, and Caimaininae) by the end of the Late Cretaceous. The number of distinct lineages present before the K/Pg boundary is less certain, with support for two competing scenarios in which Crocodylinae, Tomistominae and Diplocynodontinae either: 1) diverged from other eusuchian lineages before the K/Pg boundary; or 2) evolved during a 'burst' of diversification after the K/Pg event. Cal3 and FBD are identified as the most suitable methods for time-scaling phylogenetic trees dominated by fossil taxa. Extended Hedman estimates are substantially older than the others, with larger standard deviations and a strong vulnerability to taxon sampling and topological changes. sGLA has similar problems and cannot be recommended either. We conclude that a detailed understanding of phylogenetic relationships, tree reconstruction methods, and good taxonomic coverage (in particular the inclusion of the oldest taxon in each clade) is essential when evaluating the results of such dating analyses.</p>
Data from: How to date a crocodile – estimation of neosuchian clade ages and a comparison of four time-scaling methods
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Data from: Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites
Reconstructing the tree of life involves more than identifying relationships among lineages; it also entails accurately estimating when lineages diverged. Paleontologists typically scale cladograms to time a posteriori by direct reference to first appearances of taxa in the stratigraphic record. Some approaches use probabilistic models of branching, extinction, and sampling processes to date samples of trees, such as the recently developed cal3 method, which stochastically draws divergence dates given a set of rates for those processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study that documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the data set make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor–descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor–descendant sequences, but cal3 suggests greater support for budding cladogenesis than anagenesis. This case study demonstrates the potential and wide applicability of the cal3 method and the benefits afforded by choosing cal3 over simpler a posteriori time-scaling approaches.
Identification of hidden population structure in time-scaled phylogenies
Population structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome <i>Neisseria gonorrhoeae</i> sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.
Figure 2 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 2. ALIGROOVE analysis for the datasets considering the third codon positions and RNA. The mean similarity score between sequences is represented by a coloured square, based on ALIGROOVE scores from minus one, indicating a large difference in sequence composition from the remainder of the dataset (red coloration), to plus one, indicating similarity to all other comparisons (blue coloration). Species of Vermileonidae are circled in red.
Figure 5. Chronogram for Brachycera. A in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 5. Chronogram for Brachycera. A chronogram is the Bayesian topology resulting from analysis of the AP12R dataset. Branches have been separated by different colours (same as Fig. 4). Species of Vermileonidae are marked with a red asterisk. The numbers close to the branching points are the mean age. The bar through each node shows the time interval that contains 95% of the probability for the node age.
Figure 4 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 4. Phylogenetic relationships among major lineages of the lower Brachycera inferred from the AP12R dataset. Numbers close to the branching points are Bayesian posterior probabilities expressed as percentages. Relevant taxonomic groups and branches have been separated by different colours.
Figure 3 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 3. Comparison of non-synonymous substitution rate (Ka; for detailed data, see Supporting Information, Table S7). Overall data, including all sampled species, are shown, with infraorder, superfamily or family membership as indicated.
Data from: Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites
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Identification of hidden population structure in time-scaled phylogenies
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Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa
1.) Applying phylogeny-based analyses of trait evolution and diversification in the fossil record generally involves transforming an unscaled cladogram into a phylogeny scaled to geologic time. Current methods produce single time-scaled phylogenies with artificial zero-length branches and no indication of the uncertainty in the temporal relationships. 2.) Here I present a stochastic algorithm for time-scaling phylogenies of fossil taxa by randomly sampling node ages from a constrained distribution, with the ultimate goal of producing large samples of time-scaled phylogenies for a given dataset as the basis for phylogeny-based analyses. I describe how this stochastic approach can be extended to consider potential ancestral relationships and resolve polytomies. 3) The stochastic selection of node ages in this algorithm is weighted by the probability density of the total inferable unobserved evolutionary history at single divergence events in a tree, a distribution dependent on rates of branching, extinction and sampling in the fossil record. 4) The combined time-scaling method must be calibrated with explicit estimates of three rates: branching, extinction and sampling, and thus is named the cal3 time-scaling method, included in the R library paleotree. I test the time-scaling capabilities of the cal3 and older time-scaling methods in simulations. cal3 produces samples of time-scaled trees that better bracket the uncertainty in the true node ages than existing time-scaling methods. This is true even in simulations under a 'terminal-taxon' model of differentiation that violates many of the assumptions of the cal3 method. 5) The cal3 method provides a new approach for time-scaling paleontological cladograms, calibrated to estimated sampling and diversification rates, allowing for better estimates of uncertainty in the phylogenetic time-scaling. The cal3 method is robust to relaxation of at least some model assumptions. Additional work is needed to analyze the impact of time-scaling approaches on macroevolutionary analyses and to integrate time-scaling with phylogenetic inference.
Figure 1 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 1. Boxplot of length of each protein-coding gene.
Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record
Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic "cal3" time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.
Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record
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Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa
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Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria
<p>A phylogenetic framework provides the necessary evolutionary context for studies of comparative anatomy, life history, behavior, biogeography, systematics, and conservation. Time-scaled phylogenetic analyses require researchers to include calibration ages which are used to fit a model that transforms tree branch lengths into units of time. The inclusion of multiple calibration ages (if they are available) is a best practice that brings all the available evidence to bear on the temporal model. While selecting the appropriate ages of calibrating fossil taxa is obviously important, perhaps more relevant is where those calibrations are applied in the tree. A misattributed fossil calibrator (e.g., using a stem-taxon to set a minimum age on a tipward crown-node) can severely distort the results. Our aim is to provide a summary of fossil calibrators that can be used in molecular phylogenetic assessments of Afrotheria. The literature that documents these fossils, and discusses their ages and affiliations, is somewhat scattered. Included in this contribution are the oldest extinct species that are (in our opinion) securely attributable to stem lineages of afrotherian clades. Each informs a minimum age for the adjacent rootward tree node. We then assemble a large DNA supermatrix that includes 32 genes and 39 afrotherian genera – including recently extinct elephants and sea-cows. A time-scaled phylogenetic estimate is derived from this dataset with explicit inclusion of fossil taxa in the analysis.</p>
Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.