#README NOTES

This supplementary material pertains to the dataset analysed by Quek et al. (2020). Listed below are descriptions of files deposited in alphabetical order.

1. analyses.txt: commands used for analyses in the study.

2. Astral_exons_only.tre: Astral-derived phylogenetic tree with posterior probability values labelled on nodes.

3. baitfile_452.fa: baitfile to be used for identification and extraction loci in HybPiper; also includes sequences used for bait design.

4. baits_designed.fa: original set of baits designed (15,919 sequences).

5. baits_designed_filtered.fa: set of baits limited to that designed based on 452 loci found in baitfile_452.fa (13,479 sequences).

6. barcoding_baits_designed.fa: barcoding baits for both COI and histone H3; barcodes targeted are specified in fasta headers.

7. barcoding_baits_summary.csv: summary of barcoding check as mentioned in the manuscript.

8. concat_seq_exons_only.fa: concatenated sequence file for RAxML and ExaBayes analyses; contains exons-only dataset.

9. concat_seq_exons_supercontigs.fa: concatenated sequence file for RAxML and ExaBayes analyses; contains exons+supercontigs dataset.

10. ExaBayes_exons_only.tre: ExaBayes-derived phylogenetic tree with posterior probability values labelled on nodes for exons-only dataset.

11. ExaBayes_exons_supercontigs.tre: ExaBayes-derived phylogenetic tree with posterior probability values labelled on nodes for exons+supercontigs dataset.

12. exons_only_seq.tar.gz: sequences from all of the taxa sampled per loci recovered that include exons-only.

13. exons_supercontigs_seq.tar.gz: sequences from all of the taxa sampled per loci recovered that include exons+supercontigs.

14. RAxML_exons_only.tre: RAxML-derived phylogenetic tree with bootstrap values labelled on nodes for exons-only dataset.

15. RAxML_exons_supercontigs.tre: RAxML-derived phylogenetic tree with bootstrap values labelled on nodes for exons+supercontigs dataset.
