DOI: 10.5061/dryad.b47k938
title: Data from: Chloroplast phylogenomic data support Paleocene - Eocene amphi-Pacific early radiation for the Asian Palmate core Araliaceae

description: Traditional phylogenies based on analysis of multiple genes have failed to
 obtain a well-resolved evolutionary history for the backbone of the Asian
 Palmate group of Araliaceae, the largest clade of the family. In this
 study we applied the genome skimming approach of next-generation
 sequencing to address whether the lack of resolution at the base of the
 Asian Palmate tree is due to molecular sampling error or the footprint of
 an ancient radiation. Twenty-nine complete plastid genomes of Araliaceae
 (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, BioGeoBears)
 to provide the first phylogenomic reconstruction of the group (95% of
 genera included). As a result, the early divergences of the Asian Palmate
 group have been clarified but the backbone of its core is not totally
 resolved, with short internal branches pointing to an ancient radiation
 scenario. East Asia is inferred as the most likely ancestral area for the
 Asian Palmate group (early Upper Cretaceous and the Paleocene) from which
 an early colonization of the Neotropics is inferred during the late
 Paleocene – early Eocene. The radiation of the core took place during the
 Paleocene – early Eocene, most likely in the context of the Boreotropical
 hypothesis. Recurrent episodes of southward migration (to the tropics)
 coupled with northern latitude local extinctions (promoting lineages
 geographic isolation) and northward expansion (promoting lineages contact
 that erased the trace of preceding geographic isolation) are hypothesized
 to have linked to the alternation of the cold and warm periods of the
 Eocene.
description: Complete chloroplast
 genome alignment AraliaceaeNexus-interleaved format
 matrix including the complete chloroplast genome alignment of 29
 Araliaceae. 12 samples were downloaded from Genbank (names ending with GB
 in the alignment). Accession numbers are specified in the list of
 taxonomic names for these 12 samples. The remaining 17 samples were newly
 described in this study. Only one copy of the Inverted Repeated region is
 included, since there was no variation between the two copies of the IR
 regions. Partitions are specifiedAraliaceae_Plastome.nexAppendix S2 Complete plastid genome alignment AraliaceaeNexus-interleaved matrix including the complete chloroplast genome alignment of 29 Araliaceae analysed in this study. Genbank accession numbers are specified for the 12 samples that were downloaded from Genbank. The remaining 17 samples were newly sequenced in this study. Only one copy of the Inverted Repeated region is included, since there was no variation between the two copies of the IR regions. Partitions are specified.Appendix S2_Araliaceae_Plastome_Complete.nexAppendix S3 Intergenic Spacer Regions alignment AraliaceaeNexus-interleaved matrix including the alignment of the 111 intergenic spacers regions of the 29 Araliaceae analysed in this study. Genbank accession numbers are specified for the 12 samples that were downloaded from Genbank. The remaining 17 samples were newly sequenced in this study.Appendix S3_Araliaceae_Plastome_Intergenic Spacer Regions.nexAppendix S4 Introns alignment AraliaceaeNexus-interleaved matrix including the alignment of the 18 introns of the 29 Araliaceae analysed in this study. Genbank accession numbers are specified for the 12 samples that were downloaded from Genbank. The remaining 17 samples were newly sequenced in this study.Appendix S4_Araliaceae_Plastome_Introns.nexAppendix S5 Translated Protein Coding Regions alignment AraliaceaeNexus-interleaved matrix including the alignment of the 69 translated protein coding regions of the 29 Araliaceae analysed in this study. Genbank accession numbers are specified for the 12 samples that were downloaded from Genbank. The remaining 17 samples were newly sequenced in this study.Appendix S5_Araliaceae_Plastome_rRNAs and tRNAs.nexAppendix S6 tRNAs plus rRNAs alignment AraliaceaeNexus-interleaved matrix including the alignment of the 42 tRNAs and rRNAs of the 29 Araliaceae analysed in this study. Genbank accession numbers are specified for the 12 samples that were downloaded from Genbank. The remaining 17 samples were newly sequenced in this study. Partitions are specified.Appendix S6_Araliaceae_Plastome_Translated Protein Coding Regions.nex