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Phylogenetic dating with confidence intervals using mean path lengths
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A phylogenetic subclade analysis of range sizes of endemic

Confidence intervals on stratigraphic ering plants: APG II. Botanical Journal of the Linnean Society 141: 399– ranges can thus be calculated for fossils that are abundant and 436. widely distributed.

Phylogenetic dating with confidence intervals using mean path lengths
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Phylogenetic dating with confidence intervals using mean

We also tried the mean path length method using the PATH program (MPL; Britton, 2002; Britton et al., 2002). MPL tolerates zero-length branches but requires a strictly bifurcating tree with branch lengths in terms of whole numbers of substitutions, observed or expected (corrected).

Phylogenetic dating with confidence intervals using mean path lengths
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Бремер, Коре — Википедия

Phylogenetic dating with confidence intervals using mean path-lengths. Molecular phylogenetics and evolution 24: 58-65. Lundberg, J. & Bremer, K. 2003. A phylogenetic study of the order Asterales using one large morphological and three molecular data sets. …

Phylogenetic dating with confidence intervals using mean path lengths
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Molecular Phylogenetic Dating of Asterid Flowering Plants

An exciting recent development is the merging of phylogenetics and genomics. Phylogenetic hypotheses have become the framework for the choice of organisms in genomic analyses, and more and more molecular biologists are using phylogenetic trees to guide their sampling of taxa for comparative research. This trend will continue.

Phylogenetic dating with confidence intervals using mean path lengths
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Коре Бремер — Вікіпедія

To generate ultrametric trees, we used the mean path length (MPL) method implemented in APE . We generated interval estimates for these divergence dates by conducting the same molecular date correction technique using the upper and lower limits from the 95% Bayesian HPDs of the BS, EV, and REV reconstructions.

Phylogenetic dating with confidence intervals using mean path lengths
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Molecular dating of phylogenies by likelihood methods: A

‘Tip-dating’ promises a conceptual advance, integrating fossil species among their living relatives using molecular/morphological datasets and evolutionary models. Fossil species of known age establish calibration directly, and their phylogenetic uncertainty is accommodated through the co-estimation of time and topology.

Phylogenetic dating with confidence intervals using mean path lengths
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Kåre Bremer - Wikispecies

Abstract Phylogenetic interrelationships among all 18 families of Poales were assessed by cladistic analysis of chloroplast DNA rbcL and atpB sequences from 65 species. These relationships help in elucidating the evolution of grasses and the grass spikelet. Phylogenetic dating with confidence intervals using mean path-lengths. Mol. Phyl

Phylogenetic dating with confidence intervals using mean path lengths
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Reconstructing the Evolutionary History of Transposable

Phylogenetic dating with confidence intervals using mean path-lengths. Molecular phylogenetics and evolution 24: 58-65. Molecular phylogenetic dating of asterid flowering plants shows Early Cretaceous diversification. Systematic Biology 53: 496-505. Dating phylogenetically basal eudicots using /rbc/L sequences and multiple reference

Phylogenetic dating with confidence intervals using mean path lengths
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The Role of Phylogenetics in Comparative Genetics | Plant

In most cases, the estimates from BEAST2 were more uncertain with credible intervals that were wider than the confidence intervals from LSD. We investigated two aspects of phylogenetic data that can affect estimates of evolutionary rates; the topological uncertainty and the degree of clocklike variation.

Phylogenetic dating with confidence intervals using mean path lengths
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The Role of Phylogenetics in Comparative Genetics

Background. Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates.

Phylogenetic dating with confidence intervals using mean path lengths
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How to Summarize Estimates of Ancestral Divergence Times

This multichotomous phylogeny was resolved to a dichotomous tree using “multi2di” function in “ape” package. Then, the molecular dating of the tree was employed by the mean path length method (Britton et al., 2002). To account for uncertainties, I resolved the multichotomous tree and carried out the dating of divergence time for 100 times.

Phylogenetic dating with confidence intervals using mean path lengths
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chronoMPL function | R Documentation

Molecular phylogenetic dating is now rapidly gaining attention, and recently several papers have appeared dealing with age estimates of groups of flowering plants (e.g., Bremer and Gustafsson, 1997; Phylogenetic dating with confidence intervals using mean path-lengths.

Phylogenetic dating with confidence intervals using mean path lengths
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Dating Tips for Divergence-Time Estimation: Trends in Genetics

A thorough phylogenetic analysis, evaluating alternative alignments, exon versus intron boundaries, using different phylogenetic methods, and obtaining estimates of internal support, may take several weeks or more, and this should not be considered an unreasonable investment of time.

Phylogenetic dating with confidence intervals using mean path lengths
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Phylogenetic dating with confidence intervals using mean

Both the BA and the WS are representative for two important aspects of contact heterogeneity. Networks generated by the BA model have both a large variance in the degree distribution as well as short mean path lengths. Networks generated by the WS model have …

Phylogenetic dating with confidence intervals using mean path lengths
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Bayesian random local clocks, or one rate to rule them all

2007 britton et al.—divergence times in large phylogenetic trees 745 a) b) figure 3. Phylograms of the 200+ eudicot (a) and the reduced eudicot (b) data sets. Fossil constrained nodes are marked with absolute age in million years.

Phylogenetic dating with confidence intervals using mean path lengths
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Origin and diversification of living cycads: a cautionary

The multichotomies of the tree are resolved using R package “ape” , and the dating of divergence time is done using the mean path length method . Negative branch lengths have occurred after molecular dating but do influence the inference of phylogenetic signal test. 3. Results and Discussion 3.1.

Phylogenetic dating with confidence intervals using mean path lengths
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Bengt Oxelman | University of Gothenburg - Academia.edu

Molecular Dating With Mean Path Lengths. This function estimates the node ages of a tree using the mean path lengths method of Britton et al. (2002). The branch lengths of the input tree are interpreted as (mean) numbers of substitutions.

Phylogenetic dating with confidence intervals using mean path lengths
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age of major monocot groups inferred from 800+rbcL

Phylogenetic dating with confidence intervals using mean path-lengths. Molecular phylogenetics and evolution 24: 58-65. Molecular phylogenetic dating of asterid flowering plants shows Early Cretaceous diversification. Systematic Biology 53: 496-505. Dating phylogenetically basal eudicots using /rbc/L sequences and multiple reference

Phylogenetic dating with confidence intervals using mean path lengths
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GitHub - thkuo/treedater: Scalable relaxed clock

The mean path length (MPL) method, a simple method for dating nodes in a phylogenetic tree, is presented. For small trees the age estimates and corresponding confidence intervals, calibrated with fossil data, can be calculated by hand, and for larger trees a computer program gives the results instantaneously (a Pascal program is available upon request).

Phylogenetic dating with confidence intervals using mean path lengths
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Package repository for r :: Anaconda Cloud

Estimating divergence times in large phylogenetic trees by Tom Britton, Cajsa Lisa Anderson, David Jacquet, Samuel Lundqvist and Kåre Bremer, in Systematic Biology 56:5, pp 741 - 752 . Britton, T., B. Oxelman, A. Vinnersten, and K. Bremer. 2002. Phylogenetic dating …

Phylogenetic dating with confidence intervals using mean path lengths
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Dating phylogenetically basal eudicots using rbcL

Phylogenetic dating with confidence intervals using mean path lengths For small trees the age estimates and corresponding confidence intervals, calibrated with fossil data, can be calculated by hand, and for larger trees a computer program gives the results instantaneously (a Pascal program is …

Phylogenetic dating with confidence intervals using mean path lengths
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Relaxed molecular clocks for dating historical plant

Phylogenetic dating with confidence intervals using mean path-lengths. Molecular phylogenetics and evolution 24: 58–65. Lundberg, J. & Bremer, K. 2003. A phylogenetic study of the order Asterales using one large morphological and three molecular data sets. …

Phylogenetic dating with confidence intervals using mean path lengths
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Ben Bolker | Collaborator | R Documentation

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and

Phylogenetic dating with confidence intervals using mean path lengths
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Phylogenetic dating with confidence intervals using mean

treedater. treedater fits a strict or relaxed molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry. The calendar time of each sample must be specified (possibly with bounds of uncertainty) and the length of the sequences used to estimate the tree.

Phylogenetic dating with confidence intervals using mean path lengths
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Dating Lineages: Molecular and Paleontological Approaches

The impact of transposable elements (TEs) on genome structure, plasticity, and evolution is still not well understood. ML phylogenetic trees suggest important changes in the molecular evolutionary rates in some branches, most of them Oxelman B, Vinnersten A, Bremer K. Phylogenetic dating with confidence intervals using mean path lengths

Phylogenetic dating with confidence intervals using mean path lengths
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(PDF) The Role of Phylogenetics in Comparative Genetics

Calibration intervals (green), mean time estimates for all programs (from Table 2) and Multidivtime 95% confidence intervals (in parentheses) are shown next to the respective nodes. The size of the circles is approximately proportional to the calibration intervals or 95% confidence intervals.

Phylogenetic dating with confidence intervals using mean path lengths
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A late origin of the extant eukaryotic diversity

Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation.

Phylogenetic dating with confidence intervals using mean path lengths
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Phylogenetic dating with confidence intervals using mean

Abstract. The mean path length (MPL) method, a simple method for dating nodes in a phylogenetic tree, is presented. For small trees the age estimates and corresponding confidence intervals, calibrated with fossil data, can be calculated by hand, and for larger trees a computer program gives the results instantaneously (a Pascal program is available upon request).

Phylogenetic dating with confidence intervals using mean path lengths
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Volume Contents, Molecular Phylogenetics and Evolution

For each phylogeny, we used time‐calibrated branch lengths to estimate the age of each clade in millions of years (MY the mean path length technique was used to make each tree ultrametric (Britton et A. Vinnersten, and K. Bremer. 2002. . Molecular Phylogenetics and

Phylogenetic dating with confidence intervals using mean path lengths
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Rouzic 2013 GBE Reconstructing the Evolutionary History of

The mean path length (MPL) method, a simple method for dating nodes in a phylogenetic tree, is presented. For small trees the age estimates and corresponding confidence intervals, calibrated with

Phylogenetic dating with confidence intervals using mean path lengths
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Rapid diversification and dispersal during periods of

Read "Volume Contents, Molecular Phylogenetics and Evolution" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. Douglas E. Soltis, Chaun zhu Fan, and Pamela S. Soltis Phylogenetic dating with confidence intervals using mean path lengths ° Tom Britton

Phylogenetic dating with confidence intervals using mean path lengths
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Clade Age and Not Diversification Rate Explains Species

Figure 4(a) depicts the Bayesian consensus tree relating these sequences, along with posterior mean branch lengths scaled in real time. To examine rate variation, we color branches by their posterior mean relative rate of nucleotide substitution.

Phylogenetic dating with confidence intervals using mean path lengths
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PATHd8 - UFRC

. Mol. Phylogenet. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Divers. Distribut., 12: 35

Phylogenetic dating with confidence intervals using mean path lengths
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Comparative evolutionary diversity and phylogenetic

MEAN PATH LENGTH (MPL) CALIBRATION OF PHYLOGENY Mean Path Length (MPL) calibration (Britton et al., 2002) was used to transform all molecular phylogenies into ultrametric chronogram. MPL estimates branch lengths using the mean of all branches descending from it, and thus is closer to molecular clock calibration.

Phylogenetic dating with confidence intervals using mean path lengths
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Natural Selection Determines Synonymous Codon Usage

For instance, the mean path lengths method (Britton et al., 2002) provides a test of the molecular clock for each node of the tree. Whether this is a valuable tool for preliminary explorative analyses before running more complex model fitting, with likelihood or Bayesian models, is not yet clear.