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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)

Citation

Keeley, Sterling C.; Cantley, Jason T.; Gallaher, Timothy J. (2022), 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), Dryad, Dataset, https://doi.org/10.5061/dryad.6wwpzgmtp

Abstract

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.

Methods

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 Hesperomannia 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).

Usage Notes

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.

Funding

National Science Foundation, Award: DEB-0075095

G. P. Wilder Endowment

G. P. Wilder Endowment