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64 results for “molecular dating”
Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data
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Data from: The impact of the tree prior on molecular dating of data sets containing a mixture of inter- and intraspecies sampling
In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analysed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling.
Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.
Data from: Molecular dating, evolutionary rates, and the age of the grasses
Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a dataset of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae around 51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups.
Data from: Molecular phylogeny and dating reveal a terrestrial origin in the early Carboniferous for ascaridoid nematodes
Ascaridoids are among the commonest groups of zooparasitic nematodes (roundworms) and occur in the alimentary canal of all major vertebrate groups, including man. They have an extremely high diversity and are of major socio-economic importance. However, their evolutionary history remains poorly known. Here we performed a comprehensive phylogenetic analysis of the Ascaridoidea. Our results divided the Ascaridoidea into six monophyletic major clades, i.e. the Heterocheilidae, Acanthocheilidae, Anisakidae, Ascarididae, Toxocaridae and Raphidascarididae, among which the Heterocheilidae, rather than the Acanthocheilidae, represents the sister clade to the remaining ascaridoids. The phylogeny was calibrated using an approach that involves time priors from fossils of the co-evolving hosts, and dates the common ancestor of the Ascaridoidea back to the Early Carboniferous (approximately 360.47–325.27 Ma). The divergence dates and ancestral host types indicated by our study suggest that members of the Ascaridoidea first parasitized terrestrial tetrapods and subsequently extended their host range to elasmobranchs and teleosts. We also propose that the fundamental terrestrial-aquatic switches of these nematodes were affected by changes in sea-level during the Triassic to the Early Cretaceous.
FIGURE 2 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 2 Median-joining network of CR mtDNA sequences. Haplotypes are represented by colored circles (supplementary table S1), with individual colors corresponding to the different lineages. The haplotypes found in the present study are framed, and for those, the size of the circles is proportional to the haplotype frequencies in the sample. Mutations are represented by hatch marks on the lines connecting the haplotypes. Missing or theoretical haplotypes are shown as black dots.
FIGURE 1 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 1 Map of sampling locations. The names and codes of the sampling sites are listed in table 1. Dots on the map represent sampling locations, while river drainages are indicated by different colors, as in the legend. Colored pie charts around the map represent the distribution and frequencies of mitochondrial DNA control region haplotypes per site.
Fig. 6 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 6. Bayesian analyses of macroevolutionary mixtures (BAMM) using the maximum likelihood (ML)
Table 4. Molecular dating and ancestral area reconstruction results for Liphistius using S in Molecular phylogeny, biogeography, and species delimitation of segmented spider genus Liphistius (Araneae: Liphistiidae) in Thailand
<p><b>Table 4.</b> Molecular dating and ancestral area reconstruction results for <i>Liphistius</i> using S-DIVALIKE+J. The letters A–I correspond to geographical locations shown in Figure 4. The notation shows the biogeographic event in the phylogenetic tree (Fig. 4A) includes →: from the parent node to descendent nodes; ^: Sympatric speciation; |: Vicariance.</p><table><tbody><tr><th><b>Diversification events</b></th><th><b>Dates</b></th><th><b>DIVALIKE+J</b></th><th></th><th></th></tr><tr><th></th><th><b>(Mya)</b></th><th><b>Ancestral areas</b></th><th><b>Process</b></th><th><b>Route and probability</b></th></tr></tbody><tbody><tr><th>The most recent common ancestor of Liphistiidae</th><td>100</td><td>BCI 13.60</td><td>Dispersal:0</td><td>BCI→I|BC</td></tr><tr><th>(Fig. 4, number 1)</th><td></td><td>CEI 13.33</td><td>Vicariance:1</td><td>prob:.02</td></tr><tr><th></th><td></td><td>BEI 10.96</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Heptathelinae</th><td>58.43</td><td>I 100</td><td>Dispersal:0</td><td>I→I^I→I| I</td></tr><tr><th></th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>Liphistius</i></th><td>53.61</td><td>BC 14.34</td><td>Dispersal:0</td><td>BC→C|B</td></tr><tr><th>(Fig. 4, number 2)</th><td></td><td>CE 14.05</td><td>Vicariance:1</td><td>prob:.03</td></tr><tr><th></th><td></td><td>C 12.37</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>L. indra</i> + <i>L.</i></th><td>45.51</td><td>C 45.23</td><td>Dispersal:1</td><td>C→CE→C|E</td></tr><tr><th><i>lahu</i> (Fig. 4, number 3)</th><td></td><td>E 38.20</td><td>Vicariance:1</td><td>prob:.45</td></tr><tr><th></th><td></td><td>CE 16.50</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>trang</i> species</th><td>49.61</td><td>B 39.38</td><td>Dispersal:1</td><td>B→DB→D|B</td></tr><tr><th>group + <i>bristowei</i> species group (Fig. 3, number 4)</th><td></td><td>D 30.43</td><td>Vicariance:1</td><td>prob:.30</td></tr><tr><th></th><td></td><td>BD 14.72</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>bristowei</i> spe-</th><td>32.86</td><td>D 75.76</td><td>Dispersal:0</td><td>D→D^D→D|D</td></tr><tr><th>cies group (Fig. 4, number 5)</th><td></td><td>C 21.28</td><td>Vicariance:0</td><td>prob:.55</td></tr><tr><th></th><td></td><td>A 2.02</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>trang</i> species</th><td>46.54</td><td>B 99.88</td><td>Dispersal:0</td><td>B→B^B→B| B</td></tr><tr><th>group (Fig. 4, number 6)</th><td></td><td>A 0.08</td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td>H 0.01</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Sibumasu I</th><td>41.39</td><td>B 100</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>clade (Fig. 4, number 7)</th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Sinbumasu II–</th><td>42.48</td><td>B 99.76</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>IV and Indochina clades (Fig. 4, number 8)</th><td></td><td>A 0.18</td><td>Vicariance:0</td><td>prob:.96</td></tr><tr><th></th><td></td><td>G 0.03</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu II</th><td>30.56</td><td>B 99.91</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>(Fig. 4, number 9)</th><td></td><td>A 0.09</td><td>Vicariance:0</td><td>prob:.97</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu</th><td>38.89</td><td>B 96.03</td><td>Dispersal:1</td><td>B→AB→A|B</td></tr><tr><th>III–IV and Indochina clade (Fig. 4, number 10)</th><td></td><td>A 2.65</td><td>Vicariance:1</td><td>prob:.48</td></tr><tr><th></th><td></td><td>G 0.67</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu III</th><td>31.69</td><td>A 51.95</td><td>Dispersal:0</td><td>A→A^A→A| A</td></tr><tr><th>(Fig. 4, number 11)</th><td></td><td>B 48.05</td><td>Vicariance:0</td><td>prob:.26</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu</th><td>34.81</td><td>B 96.15</td><td>Dispersal:1</td><td>B→BG→B| G</td></tr><tr><th>IV + Indochina clade (Fig. 4, number 12)</th><td></td><td>G 1.94</td><td>Vicariance:1</td><td>prob:.48</td></tr><tr><th></th><td></td><td>H 1.90</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu IV</th><td>17.02</td><td>B 100</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>(Fig. 4, number 13)</th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Indochina</th><td>31.15</td><td>G 50.43</td><td>Dispersal:1</td><td>G→GH→G|H</td></tr><tr><th>clade (Fig. 4, number 14)</th><td></td><td>H 49.38</td><td>Vicariance:1</td><td>prob:.50</td></tr><tr><th></th><td></td><td>D 0.20</td><td>Extinction:0</td><td></td></tr></tbody></table>
FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Total-evidence dated Bayesian tree. Numbers in nodes are posterior probabilities. Red taxa denote the stem group. Red stars show different possible positions of the Early Cretaceous Australian pan- chelid turtles described by Smith (2010) (see Discussion). Concepts and bars in blue are taken from Vlachos et al. (2018). Abbreviations: A, Acanthochelys; BGBU, Beginning of Gondwana breakup; BODP, Beginning of the opening of the Drake Passage; C, Chelus; Ch, Chelodina; Che, Chelidae; Che. +SAec, Chelidae + South American extinct chelids; E, Erymnochelys; EECO, Early Eocene Climatic Optimum; El, Elseya; Elu, Elusor; Em, Emydura; EODP, End of the opening of the Drake Passage; F, Flavemys; H, Hydromedusa; M, Mesoclemmys; My, Myuchelys; Mya, Million years ago; DownloadedOlig., from Brill Oligocene.com; 10/07 OTS/, 2022 → 07:36:56PM via free access
FIGURE 1 Maximum Parsimony phylogenetic analyses. A in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 1 Maximum Parsimony phylogenetic analyses. A: Morphological phylogeny. B: Molecular phylogeny. C: Total-evidence phylogeny. Bootstrap supports are coded in grayscale. Australasian species are shown in red; South American species are shown in green. Abbreviations: A, Acanthochelys; B, Bonapartemys; Ch, Chelodina; El, Elseya; H, Hydromedusa; L, Lomalatachelys; M, Mesoclemmys; Me, Mendozachelys; My, Myuchelys; Pa, Palaeophrynops; Ph, Phrynops; Pl, Platemys; Pr, Prochelidella; Ps, Pseudemydura; Ri, Rionegrochelys; Y, Yaminuechelys. †, extinct taxa.
Data from: Molecular phylogeny and dating reveal a terrestrial origin in the early Carboniferous for ascaridoid nematodes
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Data from: Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record
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Data from: The impact of the tree prior on molecular dating of data sets containing a mixture of inter- and intraspecies sampling
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Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
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Data from: Molecular dating, evolutionary rates, and the age of the grasses
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A molecular staging model for accurately dating the endometrial biopsy [RNA-seq]
GEO Series GSE234354. Homo sapiens. 295 samples. Type: Expression profiling by high throughput sequencing.
Data from: Aster rupestris (Asteraceae, Astereae), a new species from Guizhou, China: Evidence from morphological, molecular and cytological date
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Data from: Aster rupestris (Asteraceae, Astereae), a new species from Guizhou, China: Evidence from morphological, molecular and cytological date
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A molecular staging model for accurately dating the endometrial biopsy
GEO Series GSE234434. Homo sapiens. 585 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing.
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