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58 results for “dated phylogeny”
Data from: Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of nuclear RAG1 gene
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Data from: Dated plant phylogenies resolve Neogene climate and landscape evolution in the Cape Floristic Region
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Data from: Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation
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Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data
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Figure 3 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 3 Undated 18S–26S nuclear DNA repeat region BEAST 2 phylogeny of Pennantia, under the Birth-Death model. The tree was rooted to make P. cunninghamii sister to the other species of Pennantia, in accordance with the chloroplast DNA tree and the ITS tree of Keeling et al. (2004). Node posterior probability is shown next to the corresponding node. The sequences downloaded from GenBank have their accession number in round brackets; the others were generated from the samples used in this study.
Supplementary material 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
BEAST2 and RAxML files
Figure 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 2 Dated chloroplast DNA BEAST 2 phylogeny of Pennantia, under the Birth-Death model. Mean node age and 95% HPD (in My) is given in the table embedded in the figure under the corresponding letter code. 95% HPD is also represented by blue bars. All node posterior probabilities are equal to 1 except if indicated otherwise. The calibrated nodes (see text) are indicated by red dots.
Supplementary material 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figs S1–S5; Tables S1–S3
Figure 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 1 General distribution of the four Pennantia species. TKI = Three Kings Islands. Generated in QGIS 3.0.1 from Google Satellite data obtained through the XYZ Tiles tool (https://mt1.google.com/vt/lyrs=s&x={x}&y={y}&z={z}).
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.
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 6 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models
Figure 6. Estimated rate multipliers for homoplasy-based partitions in each model.
Data from: Molecular phylogeny and dating reveal a terrestrial origin in the early Carboniferous for ascaridoid nematodes
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Data from: Dating phylogenies with sequentially sampled tips
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Data from: Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae
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Figure 3 in Total-evidence dating and morphological partitioning: a novel approach to understand the phylogeny and biogeography of augochlorine bees (Hymenoptera: Apoidea)
Figure 3. Time-calibrated consensus tree and ancestral range estimation for Augochlorini bees. Pie charts on nodes represent ancestral range estimation under the highest likelihood of DIVALIKE. The nodes with alternative ancestral range reconstructions are indicated by b for BAYAREALIKE analysis. Reconstructions of South America uplands of A, Palaeocene; B, Late Eocene and C, Miocene, based on Lundberg et al. (1998) and Aceñolaza (2000) (uplands in grey); D, endemism areas used herein. Absolute time scale presented in millions of years. P = Pliocene, Q = Quaternary
Fig. 1 a Dated phylogeny and ancestral area reconstruction for 147 in Against all odds: reconstructing the evolutionary history of Scrophularia (Scrophulariaceae) despite high levels of incongruence and reticulate evolution
Fig. 1 a Dated phylogeny and ancestral area reconstruction for 147 Scrophularia species, on a majority-rule consensus tree obtained from Bayesian analysis of combined plastid trnQ-rps16 intergenic spacer and trnL-trnF region alongside coded indels. Branches indicate levels of support, based on posterior probabilities (PP) and plotted bootstrap support values (BS) from Maximum Likelihood optimization; bold PP ≥ 95 or BS ≥ 85, semi-bold PP ≥ 90 or BS ≥ 75, thin PP <90/BS <75. Seven additional nodes only supported by ML (BS ≥ 50) were added manually but not incorporated into further analyses. Gray bars on the right denote Clades 1–18 and main species groups as discussed in the text. An arrow indicates the position of the Himalayan-Tibetan endemic genus Oreosolen. Single accessions displaying hard incongruence among (2ISP-coded) nuclear and plastid trees are marked in bold; Clades 7 and 5 (excluding S. chlorantha; plus S. cryptophila) as a whole are also hardly incongruent. The occurrence of large indels as defined in Table 2 is indicated next to each accession with the respective length type number;
Figure 9 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models
Figure 9. Bayesian chronogram for the best-fitting dating model (FBD_TK02_TIP). Shaded bars depict uncertainty in estimates of node and tip ages. Main sloth clades are named on the right.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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