DOI: 10.5061/dryad.7231d
title: Data from: Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

description: Incorporation of fossils into biogeographic studies can have a profound
 effect on the conclusions that result, particularly when fossil ranges are
 nonoverlapping with extant ranges. This is the case in archaeid spiders,
 where there are known fossils from the Northern Hemisphere, yet all living
 members are restricted to the Southern Hemisphere. To better understand
 the biogeographic patterns of archaeid spiders and their palpimanoid
 relatives, we estimate a dated phylogeny using a relaxed clock on a
 combined molecular and morphological data set. Dating information is
 compared with treating the archaeid fossil taxa as both node calibrations
 and as noncontemporaneous terminal tips, both with and without additional
 calibration points. Estimation of ancestral biogeographic ranges is then
 performed, using likelihood and Bayesian methods to take into account
 uncertainty in phylogeny and in dating. We find that treating the fossils
 as terminal tips within a Bayesian framework, as opposed to dating the
 phylogeny based only on molecular data with the dates coming from node
 calibrations, removes the subjectivity involved in assigning priors, which
 has not been possible with previous methods. Our analyses suggest that the
 diversification of the northern and southern archaeid lineages was
 congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This
 analysis provides a rare example, and perhaps the most strongly supported,
 where a dated phylogeny confirms a biogeographical hypothesis based on
 vicariance due to the breakup of the ancient continental plates.
description: Supp. Fig. 7 analysis
 iiAnalysis (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.Supp. Fig. 8 analysis
 vAnalysis (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.analysis_i_CORRECTED_link_tip_datesBEAST file for analysis (i)analysis_ii_BEAST file for analysis (ii)analysis_iii_BEAST file for analysis (iii)analysis_iv_BEAST file for analysis (iv)analysis_v_CORRECTED_link_tip_datesBEAST file for analysis (v)LAGRANGE 7 areaFile for LAGRANGE 7 area range reconstructionLAGRANGE 2 areaFile for LAGRANGE 2 area range reconstructionLAGRANGE_treePruned tree used for input in LAGRANGE 7 and 2 area range reconstructionPalpimanoidea Morphology + DNA_BayesNexus file containing molecular and morphological characters used for MrBayes total evidence phylogenetic analysis, from Wood et al. 2012