DOI: 10.6084/m9.figshare.25755504
title: <b>Bayesian Total-Evidence Dating Reshapes the Age and Historical Biogeography of Parnassiinae</b>

description: <b>ABSTRACT</b>Although incomplete, the fossil record offers direct evidence for the existence of a lineage, providing insights into its age and geographic location. Reconstructing time-calibrated phylogenies, including both extant and fossil taxa as lineages (total-evidence dating) under the fossilized birth-death process, can provide new information about the phylogenetic position of fossil specimens, the time at which they diverged from closely related species, and can impact inferences of clades’ historical biogeography. Here, we focus on the origin and radiation of Apollo butterflies (Papilionidae: Parnassiinae), whose origin has been estimated to be in the late Eocene of Central Asia. The two fossil taxa recovered in the subfamily Parnassiinae, dated to the late Oligocene (†<i>Thaites ruminiana</i>) and late Miocene (†<i>Doritites bosniaskii</i>) in the Western Palearctic, thus challenge the Central Asian origin. We performed a Bayesian total-evidence dating approach to explore the impact of dating analyses and past fossil distributions on the estimation of the evolutionary history of the group. We obtained a more credible dating and historical biogeography for the group, placing its origin at <i>ca.</i> 57 Ma in the late Paleocene in the Western Palearctic + Western Asia and Caucasus regions, followed by dispersals to Central Asia and the Himalayas. This study also highlights the importance of investigating fossil position in addition to clock partitioning and models for molecular dating. Furthermore, we confirm that a few fossils are sufficient to cast doubt on the origin and biogeographic history of a group, especially when  those fossils were dispersed outside of the current center of diversity.<b>SUPPLEMENTARY INFORMATION</b><b>Appendix S1. </b>Morphological characters. 180 characters: subsampling of the morphological dataset from Nazari et al. (2007)96 characters: subsampling matrix containing the characters of †<i>Doritites bosniaskii</i>81 characters: subsampling matrix containing the characters of †<i>Thaites ruminiana</i><b>Appendix S2. </b>Table of dating analysis results.<b>Appendix S3.</b> Fossil placement and node support analyses.One folder for each analysis: <b><i>[TEP_all_outgroups]</i></b><i> </i>total-evidence phylogeny (TEP) with 180 characters and all outgroups, <b><i>[TEP_Papilioninae</i></b><b><i>]</i></b> with 180 characters and as outgroups only (<i>Baronia</i> removed), <b><i>[TEP_Thaites]</i></b><i> </i>TEP with 81 characters (no missing data for †<i>Thaites ruminiana</i>) and all outgroups, <b><i>[TEP_Doritites]</i></b><b><i> </i></b>TEP with 96 characters (no missing data for †<i>Doritites bosniaskii</i>) and all outgroups, <b><i>[TED_all_outgroups]</i></b><i> </i>TED with 180 characters and all outgroups, <b><i>[TED_Papilioninae</i></b><b><i>]</i></b><i> </i>TED with 180 characters and Papilioninae as outgroups only (<i>Baronia</i> removed), <b><i>[TED_Thaites]</i></b><i> </i>TED with 81 characters (no missing data for †<i>Thaites ruminiana</i>) and all outgroups, and <b><i>[TED_Doritites]</i></b><i> </i>TED with 96 characters (no missing data for †<i>Doritites bosniaskii</i>) and all outgroupsIn each folder:<b><i> [Rogueplots.pdf] </i></b>Results from Rogueplot analyses for both fossils,<b><i> [.lstat]</i></b> Harmonic means, <b><i>[.nex]</i></b> input nexus file, <b><i>[.p]</i></b> model parameters for each run, <b><i>[.tre]</i></b> consensus tree file<b>Appendix S4.</b> Clock partitioning analyses.One folder for each analysis:<i> </i><b><i>[One_partition]</i></b><i> </i>a unique clock, <b><i>[Two_partitions]</i></b><i> </i>one clock for the molecular dataset and one clock for the morphological dataset, <b><i>[Three_partitions]</i></b> one clock for the mitochondrial genes, one clock for the nuclear gene, and one clock for the morphological dataset, <b><i>[Nine_partitions]</i></b><b> </b>one clock for each partition from PartitionFinder, and one clock for the morphological dataset, and<b><i> [Twelve_partitions]</i></b><i> </i>one clock for each partition from PartitionFinder and one clock for each partition of the morphological dataset. In each folder:<b><i> [tracer_clocks.pdf] </i></b>Marginal density for all clocks in the analysis,<b><i> [.lstat]</i></b> Harmonic means, <b><i>[.nex]</i></b> input nexus file, <b><i>[.p]</i></b> model parameters for each run, <b><i>[.tre]</i></b> consensus tree file<b>Appendix S5. </b>Clock model analyses.We chose to use three clock models (uncorrelated [<b><i>IGR]</i></b>, autocorrelated <b><i>[TK02]</i></b>, and strict model <b><i>[STRICT]</i></b>) for three partitions (one for the mitochondrial genes, one for the nuclear gene, and one for the morphological dataset <b><i>[mito_nucl_morpho]</i></b>), resulting in 12 analyses (corresponding to the 12 folders), considering that the strict clock model was tested only for the morphological dataset.In each folder:<b><i> </i></b><b><i>[.lstat]</i></b> Harmonic means, <b><i>[.nex]</i></b> input nexus file, <b><i>[.p]</i></b> model parameters for each run, <b><i>[.tre]</i></b> consensus tree file<b>Appendix S6. </b>Final total-evidence dating analysis.<b>Appendix S7. </b>Node dating analysis.<b>Appendix S8.</b> Historical biogeography analysis results.One folder for each analysis: <b>[M0]</b> a null model with no constraints or time slices, and <b>[M1]</b> a reference model using the area adjacency matrix and the time slices from Condamine et al. (2018). For each of these models, four analyses were performed resulting in a total of eight analyses: <b><i>[M0-1/M1-1]</i></b> with the dated phylogeny from Condamine et al. (2018) based on node dating (birth-death model using molecular and morphological datasets, see Condamine et al. 2018 for details), <b><i>[M0-2/M1-2]</i></b> with the dated phylogeny from TED without the fossils, <b><i>[M0-3/M1-3]</i></b> with the dated phylogeny from TED assuming that fossil ranges are true (no-fossil areas coded as “0”), <b><i>[M0-4/M1-4]</i></b> with the dated phylogeny from TED using the positive constraint strategy (no-fossil areas coded as “?” instead of true absence, which means that the range of the fossils can be extended by the model beyond the known area, see Coiro et al., 2023; and the rationale at http://phylo.wikidot.com/fossil-data-in-biogeographical-analysis-in-biogeobears).In each folder:<b><i> </i></b><b><i>[connectivity.txt]</i></b> areas adjacency, <b><i>[distributions.txt]</i></b> species distributions, <b><i>[times.txt]</i></b> time slices, <b><i>[.tre]</i></b> consensus tree file, <b><i>[.pdf]</i></b> Results from BioGeoBEARS, <b><i>[.Rdata]</i></b> inputs and outputs of BiogeoBEARS