The Papuasia floristic region, comprising New Guinea and its surrounding islands, represents an ideal natural experiment in biogeography due to its high plant endemism, complex geological past, and location between the Southeast Asian archipelago and the Australian continent. However, the evolutionary history of Papuasian plants remains poorly understood because herbarium specimens from the region are scarce and scattered (limiting the usefulness of morphological analyses) and often several decades old (resulting in fragmented DNA that is unsuitable for traditional Sanger sequencing approaches). Our study capitalises on these historical herbarium specimens and novel high-throughput sequencing technology (Hyb-Seq, a combined target capture and genome skimming approach) to produce the first ever time-calibrated phylogeny for a mostly Papuasian plant lineage. 1_trim: Reads trimmed with Trimmomatic 2_1kp: Sequences from OneKP 2_caps: Nuclear sequences captured with HybPiper 2_genbank: Sequences downloaded from GenBank 2_ITS: ITS sequences captured with HybPiper 3_sequences: Sequences distributed according to gene region 4a_raw_alignments: Sequences aligned with UPP 4b_trimmed_alignments: Alignments trimmed with optrimAl 5_gene_trees: Gene trees inferred with IQ-Tree 6a_shrunk_taxa: Taxa removed from gene trees by TreeShrink 6b_shrunk_trees: Gene trees after taxa removed by TreeShrink 7a_raw_reduced_alignments: Alignments after taxa removed by TreeShrink re-aligned with UPP 7b_trimmed_reduced_alignments: Re-aligned alignments trimmed with optrimAl 8a_raw_reduced_trees: Gene trees inferred by IQ-Tree from re-aligned alignments 8b_shrunk_reduced trees: Gene trees inferred by IQ-Tree from re-aligned alignments after taxa removed by TreeShrink 9_species_trees: Species trees inferred with ASTRAL dating_area_code: Coded geographical regions used for BEAST divergence time estimation and ancestral area reconstruction Schefflera_dating: Sequences aligned with UPP and trimmed with optrimAl, used for BEAST divergence time estimation and ancestral area reconstruction

LP had funding from the Garfield Weston Foundation (Global Tree Seed Bank Project) and EU-SYNTHESYS (NL-TAF-6894). RC had funding from EU-SYNTHESYS (GB-TAF-6305). This article is based on a final paper by ZQS for his MSc in Plant and Fungal Taxonomy, Diversity and Conservation at Queen Mary, University of London and at RBG Kew, funded by a scholarship from the National Parks Board, Singapore.