DOI: 10.5061/dryad.6wwpzgmtp
title: The 'Evil Tribe' spreads across the land: A dated molecular phylogeny provides insight into dispersal, expansion, and biogeographic relationships within one of the largest tribes of the sunflower family (Vernonieae: Compositae)

description: Premise: With over 1500 species, the globally distributed Vernonieae is
 one of the most successful members of the Compositae. However,
 due to its morphological complexity and limited geographic
 representation in previous studies, subtribal and
 biogeographic relationships are unclear. Here new DNA sequence
 data spanning the geographical range of the tribe provides a
 taxonomically robust time-calibrated phylogeny, an estimation of
 migration pathways and timing of important biogeographical events
 and allows inference of environmental factors that have
 contributed to the success of the Vernonieae worldwide.
 Methods: Phylogenetic relationships were estimated for 368 taxa
 representing all Vernonieae subtribes. Molecular clock and
 ancestral range estimation analyses provide a framework for
 inference of the tribe's biogeographic history.
 Results: Relationships among the subtribes were established. We
 confirmed that the Moquinieae are nested in Vernonieae,
 determined the correct placement of several problematic taxa, and
 conducted the first model-based assessment of the biogeographical
 history of the tribe. The . Vernonieae were estimated to
 have evolved ~50 Ma ago. Africa was the first center of
 diversity, from which a single dispersal event established the
 monophyletic New World lineage. Long-distance dispersal from
 Africa and Brazil established the tribe on five continents and Oceania.
 Conclusions: Moquinieae are nested in Vernonieae. The New World
 lineage is monophyletic, but Old World taxa are not. New
 subtribal taxonomies are needed. Long-distance dispersal from
 Africa beginning 45 Ma was key to establishing the tribe’s near-global
 distribution. Migration corridors created by volcanic mountain
 chains and iron-rich soils in Africa and the Americas promoted
 radiation and range expansion.
description: A total of 438 taxa were sampled, including 368
 Vernonieae representing all 24 subtribes and 70 outgroup taxa. Total
 genomic DNA was obtained from herbarium vouchers or silica dried fresh
 leaf material. Following the work of Keeley et al. (2007), the full nuclear
 ITS region, chloroplast gene ndhF, and the non-coding spacer region trnL-F
 were sequenced and used for the analyses. Additional sequences were
 downloaded from Genbank, including sequences
 from the rpl32-trnL intergenic spacer. Sequences were compared against
 generated reference sequences to check for miscalled or ambiguous bases.
 Alignments were performed using MAFFT version 7.310 (Katoh et al., 2002).
 To test for topological congruence, chloroplast and nuclear regions were
 analyzed separately and phylogenies compared using “tanglegrams” produced
 in Dendroscope (Scornavacca et al., 2011; Huson and Scornavacca, 2012) as
 well as by the partition homogeneity test (ILD) as implemented in PAUP*
 ver. 4.0b10 (Swofford, 2002).  jModelTest (Guindon and
 Gascuel, 2003; Posada, 2008) was used to determine the best-fit models of
 molecular evolution (GTR+I+G) using the Akaike Information Criterion (AIC)
 for individual gene regions as well as the concatenated dataset. Maximum
 likelihood phylogeny inference was done in RAxML v8.2.12 (Stamatakis,
 2014) on the RAxML-HPC2 Workflow on XSEDE on the CIPRES science gateway
 (Miller et al., 2010). The tree with the highest log-likelihood from 1000
 alternative runs on distinct starting trees was selected, and clade support
 was calculated from 1000 nonparametric bootstrap replicates.
 Joint Bayesian Inference (BI) on phylogeny and clade divergence
 times was implemented in BEAST 2.6.1 (Bouckaert et al., 2014) on the
 CIPRES Science Gateway (Miller et al., 2010). The GTR+I+G evolution model
 was used for the ITS, and combined
 chloroplast partitions based on AIC results from jModelTest (Guindon and
 Gascuel, 2003; Posada, 2008). We used eight clade
 priors to estimate divergence times, including one
 secondary calibration, six fossils, and island ages for the crown
 radiation of the Hawaiian Endemic <i>Hesperomannia </i>A.
 Gray. We followed Mandel et al. (2019) in setting a maximum age of 91.5 Ma
 for the stem ancestor of Asteraceae based on previous work (Huang et al.,
 2016; Panero and Crozier, 2016).  We conducted inference on the
 biogeographic history of the Vernonieae using the maximum likelihood
 implementation of the program BioGeoBEARS 1.1.2 (BioGeography with
 Bayesian (and likelihood) Evolutionary Analysis in R (Matzke, 2013a;b,
 2014; Dupin et al., 2016) Ancestral ranges and biogeographical events were
 inferred using the Bayesian calibrated tree trimmed to include only
 members of the Vernonieae tribe. The geographical areas of extant taxa
 were recorded from various sources. Nine areas were used covering the
 range of Vernonieae distribution: Asia, Africa, Australia, Hawaii, Andes,
 Brazilian Shield, North America, Mesoamerica, and the Caribbean. The
 phylogeny was partitioned into five time-slices (0-10 Ma, 10-20 Ma, 20-30
 Ma, 30-40 Ma, 40-50 Ma) to include the period from the estimated date of
 origin of the tribe to the present. Distances among geographic areas were
 calculated as the relative minimum edge-to-edge distance among them using
 Paleomap reconstructions (Scotese 2014 a,b).
description: Chloroplast_Calibrated.xml: BEAST XML file including
 chloroplast DNA regions and time calibration priors.
 ITS_Calibrated.xml: BEAST XML file including Nuclear ITS and time
 calibration priors. Concatenated_Calibrated.xml: BEAST
 XML file including all DNA regions and time calibration priors.
 All_concatenated2.fas - Concatenated alignment of all DNA
 regions  (ITS=1-802, ndhF=803-1479, rpl32-trnL=1480-2419,
 trnL=2420-3308) ITS_only_BEAST_output.log:  log output
 of BEAST time-calibrated phylogenetic analysis including nuclear sequences
 only. Chloroplast_only_BEAST_output.log:  log output of
 BEAST time-calibrated phylogenetic analysis including chloroplast
 sequences only. Concatenated_all_Beast_Output.log: log
 output of BEAST time-calibrated phylogenetic analysis including
 both nuclear and chloroplast sequences.
 vern_Distributions_ready3.txt: Geographic distribution of taxa
 used in the Biogeographical analysis.
 VERNONIEAE_BIOGEOGRAPHY_R_Code.txt: R code used to run the
 Biogeographical analysis using BioGeoBEARS v. 1.1.2.
 Concatenated_all_BEAST_output.trees: Set of trees from the BEAST
 2 run using Concatenated_Calibrated.xml
 Chloroplast_only_BEAST_output.trees: Set of trees from the BEAST
 2 run using Chloroplast_Calibrated.xml
 Final_Calibrated_Conca_tree_Sum_clade.tre: The highest sum of
 clade credibilities tree from the BEAST 2 run
 using Concatenated_Calibrated.xml.
 ITS_only_BEAST_output.trees: Set of trees from the BEAST 2 run
 using ITS_Calibrated.xml.
 RAXML_OUTPUT_Bipartitions.tre: Maximum Likelihood tree.