DOI: 10.5061/dryad.85q50
title: Data from: Timing marine-freshwater transitions in the diatom order Thalassiosirales

description: With species found throughout both marine and fresh waters, the diatom
 order Thalassiosirales is one of the most phylogenetically and
 ecologically diverse lineages of planktonic diatoms. A clear understanding
 of the timescale of Thalassiosirales evolution would provide novel
 insights into the rates and patterns of species diversification associated
 with major habitat shifts, as well as provide valuable context for
 understanding the age and evolutionary history of the model species,
 Cyclotella nana (= Thalassiosira pseudonana). The freshwater fossil record
 for Thalassiosirales is extensive, well characterized, and generally
 supportive of a Miocene origin for the major freshwater lineages. The
 marine record is, by comparison, more sparse and in many cases,
 unverified. The discovery of freshwater thalassiosiroids in Eocene
 sediments pushed the freshwater fossil record considerably further back in
 time, highlighting an apparent gap of some 30 million years. An
 alternative interpretation is that the Miocene and Eocene reports
 represent competing hypotheses. In the absence of additional independent
 and decisive fossil data, I explored the relative plausibility of these
 two scenarios with Bayesian relaxed molecular clock methods under a range
 of fossil calibration schemes. Although I found no support for the Eocene
 fossil dates, the two major freshwater colonization events probably
 occurred much earlier than previously thought—as early as the Paleocene
 for Cyclotella, followed by an Eocene origin for the cyclostephanoid
 lineage. Much of the extant freshwater diversity in both lineages traces
 back to the Miocene, however, giving the impression of a single Miocene
 origin. Efforts to infer the timescale of Thalassiosirales evolution more
 accurately would benefit from a systematic reevaluation of the marine
 fossil record and formal integration of fossil species into existing
 phylogenetic hypotheses.
description: AlignmentConcatenated alignment of SSU, partial LSU, psbC, and rbcL genes. Ambiguously aligned sites have been removed. This alignment was used for the MCMCtree analyses.split_by_part.phyCladogram (analysis #3)Cladogram used for MCMCtree analysis #3 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.estimate_wolfe_siver.treCladogram (analysis #1)Cladogram used for MCMCtree analysis #1 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.thal67_all_calibrations.treCladogram (analysis #2)Cladogram used for MCMCtree analysis #2 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.wolfe_siver_test_tree.treCladogram (analysis #4)Cladogram used for MCMCtree analysis #4 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.wolfe_siver_upper_lower_test.treCladogram (analysis #5)Cladogram used for MCMCtree analysis #5 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.upper110_lower75.treCladogram (analysis #6)Cladogram used for MCMCtree analysis #6 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.analysis06.treCladogram (analysis #7)Cladogram used for MCMCtree analysis #7 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.wolfe_siver_est_others.treSupplementary Figure 1Specified prior probability distributions for fossil calibrations used in this study (Table 1). Vertical red lines mark minimum ages, based on fossil evidence outlined in the Materials and Methods section.Fig_S1_specified_priors.pdfSupplementary Figure 2Effective prior distributions (red) and posterior distributions (blue and green) for two separate MCMC runs for six nodes of interest to this study (Fig. 1). The rows correspond to the seven different fossil calibration schemes detailed in Table 1. The y-axis scales are identical within, but not across, columns.Fig_S2_prior_posterior_plots_combined.pdf