The files in this document all relate to the publication "Next Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing." Authors: van der Merwe M, McPherson H, Siow J and Rossetto M. 3 file types: 1. GB flatfile: Eleven files each with a species specific chloroplast reference sequences (SSCrefs). These sequences were assembled from chloroplast contigs selected from the output from de novo assembles of whole genome Illumina paired-end read sequencing. The annotations in the gb flatfile indicates the start and end of each of the contigs used in each assembly. Brachychiton_acerifolius_SSCref.gb Cinnamomum_oliveri_SSCref.gb Claoxylon_australe_SSCref.gb Dendrocnide_excelsa_SSCref.gb Diploglottis_cunninghamii_SSCref.gb Doryphora_sassafras_SSCref.gb Elaeocarpus_reticulatus_SSCref.gb Pittosporum_multiflorum_SSCref.gb Stenocarpus_salignus_SSCref.gb Synoum_glandulosum_SSCref.gb Wilkiea_huegeliana_SSCref.gb 2. Alignment files in FASTA format: nine files contain two aligned sequences each and three files only contain one sequence. These sequences are the output files where whole genome paired end Illumina reads were mapped to the SSCREfs for each species and SNPs were detected using the settings given in the manuscript. SNP positions are indicated by ambiguity codes. For each species where Illumina libraries were avaialble from two regions the consensus files were aligned and areas of low coverage were removed. Brachychiton_acerifolius_NNSW_IL_alignment.fasta Cinnamomum_oliveri_NNSW_IL_alignment.fasta Claoxylon_australe_NNSW_IL_alignment.fasta Diploglottis_cunninghamii_NNSW_IL_alignment.fasta Doryphora_sassafras_NNSW_IL_alignment.fasta Elaeocarpus_reticulatus_NNSW_IL_alignment.fasta Pittosporum_multiflorum_NNSW_IL_alignment.fasta Stenocarpus_salignus_NNSW_IL_alignment.fasta Synoum_glandulosum_NNSW_IL_alignment.fasta Toona_Ciliata_NNSW_IL_alignment.fasta Wilkiea_hugeliana_NNSW_IL_alignment.fasta 3. FASTA files each containing paired and non-paired Illumina quality trimmed reads used in the mappings against the SSCrefs and SNP detection. Brachychiton_acerifolius_IL_non_paired.fa Brachychiton_acerifolius_IL_paired.fa Brachychiton_acerifolius_NNSW_non_paired.fa Brachychiton_acerifolius_NNSW_paired.fa Cinnamomum_oliveri_IL_non_paired.fa Cinnamomum_oliveri_IL_paired.fa Cinnamomum_oliveri_NNSW_non_paired.fa Cinnamomum_oliveri_NNSW_paired.fa Claoxylon_australe_IL_non_paired.fa Claoxylon_australe_IL_paired.fa Claoxylon_australe_NNSW_non_paired.fa Claoxylon_australe_NNSW_paired.fa Dendrocnide_excelsa_NNSW_non_paired.fa Dendrocnide_excelsa_NNSW_paired.fa Diploglottis_cunninghamii_IL_non_paired.fa Diploglottis_cunninghamii_IL_paired.fa Diploglottis_cunninghamii_NNSW_non_paired.fa Diploglottis_cunninghamii_NNSW_paired.fa Doryphora_sassafras_IL_non_paired.fa Doryphora_sassafras_IL_paired.fa Doryphora_sassafras_NNSW_non_paired.fa Doryphora_sassafras_NNSW_paired.fa Elaeocarpus_reticulatus__NNSW_non_paired.fa Elaeocarpus_reticulatus_NNSW_paired.fa Pittosporum_multiflorum_IL_non_paired.fa Pittosporum_multiflorum_IL_paired.fa Pittosporum_multiflorum_NNSW_non_paired.fa Pittosporum_multiflorum_NNSW_paired.fa Stenocarpus_salignus_IL_non_paired.fa Stenocarpus_salignus_IL_paired.fa Synoum_glandulosum_IL_non_paired.fa Synoum_glandulosum_IL_paired.fa Synoum_glandulosum_NNSW_non_paired.fa Synoum_glandulosum_NNSW_paired.fa Toona_ciliata_IL_non_paired.fa Toona_ciliata_IL_paired.fa Toona_ciliata_NNSW_non_paired.fa Toona_ciliata_NNSW_paired.fa Wilkiea_huegeliana_IL_paired.fa Wilkiea_huegeliana_NNSW_non_paired.fa Wilkiea_huegeliana_NNSW_paired.fa Wilkiea_hugeliana_IL_non_paired.fa