Reconstructing the complex evolutionary history of the Papuasian Schefflera radiation through herbariomics

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