Data from: Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

Wood HM, Matzke NJ, Gillespie RG, Griswold CE

Date Published: August 20, 2015

DOI: http://dx.doi.org/10.5061/dryad.7231d.2

 

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Title Supp. Fig. 7 analysis ii
Description Analysis (ii). Plots are created from a 20 million generation BEAST analysis performed both with data and with an empty alignment. Plots compare the posterior distribution from an empty alighment (red line) with the posterior distribution when data was included (green line), and for calibrated nodes, with the theoretical prior (blue line). A-D, plots non-calibrated nodes: compares the posterior distribution from an empty alignment with the posterior distribution with data, and shows that the data is influencing the results. E-K, plots calibrated nodes: compares the posterior distribution from an empty alignment, the posterior distribution with data, and the theoretical prior placed on the node. For plots E-J, the expected prior (blue line) matches the observed prior (red line). For plot K, the expected prior does not match the observed prior: this is likely because the youngest soft bound on the root node calibration, which was left intentionally broad in order to not bias the results and to contain the true age of Araneomorphae divergence, overlaps with the oldest soft bound on other node calibrations, which pushes the observed root prior back in time. However, we do not feel this is a problem because the observed prior is still broad, still contains the true age of Araneomorphae divergence, and is still reasonable.
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Title Supp. Fig. 8 analysis v
Description Analysis (v). Plots are created from a 20 million generation BEAST analysis performed both with data and with an empty alignment. Plots compare the posterior distribution from an empty alighment (red line) with the posterior distribution when data was included (green line), and for calibrated nodes, with the theoretical prior (blue line). A-E, plots non-calibrated nodes: compares the posterior distribution from an empty alignment with the posterior distribution with data, and shows that the data is influencing the results. F-K, plots calibrated nodes: compares the posterior distribution from an empty alignment, the posterior distribution with data, and the theoretical prior placed on the node. For plots F-J, the expected prior (blue line) matches the observed prior (red line). For plot K, the expected prior does not match the observed prior: this is likely because the youngest soft bound on the root node calibration, which was left intentionally broad in order to not bias the results and to contain the true age of Araneomorphae divergence, overlaps with the oldest soft bound on other node calibrations, which pushes the observed root prior back in time. However, we do not feel this is a problem because the observed prior is still broad, still contains the true age of Araneomorphae divergence, and is still reasonable.
Download Supp. Fig. 8 analysis v.jpg (1.626 Mb)
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Title analysis_i_CORRECTED_link_tip_dates
Downloaded 1 time
Description BEAST file for analysis (i)
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Title analysis_ii_
Description BEAST file for analysis (ii)
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Title analysis_iii_
Description BEAST file for analysis (iii)
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Title analysis_iv_
Description BEAST file for analysis (iv)
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Title analysis_v_CORRECTED_link_tip_dates
Description BEAST file for analysis (v)
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Title LAGRANGE 7 area
Description File for LAGRANGE 7 area range reconstruction
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Title LAGRANGE 2 area
Description File for LAGRANGE 2 area range reconstruction
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Title LAGRANGE_tree
Description Pruned tree used for input in LAGRANGE 7 and 2 area range reconstruction
Download LAGRANGE_tree.tre (1.418 Kb)
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Title Palpimanoidea Morphology + DNA_Bayes
Description Nexus file containing molecular and morphological characters used for MrBayes total evidence phylogenetic analysis, from Wood et al. 2012
Download Palpimanoidea Morphology + DNA_Bayes.txt (200.0 Kb)
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When using this data, please cite the original publication:

Wood HM, Matzke NJ, Gillespie RG, Griswold CE (2012) Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Systematic Biology 62(2): 264-284. http://dx.doi.org/10.1093/sysbio/sys092

Additionally, please cite the Dryad data package:

Wood HM, Matzke NJ, Gillespie RG, Griswold CE (2012) Data from: Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7231d.2
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