README



Data is supplied for the following paper: Walton, K., Scarsbrook, L., Mitchell, K., Verry, A., Marshall, B., Rawlence, N. & Spencer, H. (2022) Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone. Molecular Ecology Resources. Manuscript ID: MER-22-0140
Contact corresponding author: Kerry Walton, walton.kerry@gmail.com, Department of Zoology, University of Otago, Dunedin, New Zealand.
Date files finalised and uploaded: 7 July 2022



General notes: Metadata (voucher numbers and holding institution, date of sample collection, locality collected) can be found in Table 1 in the main text of the paper. Information on how samples were preserved, subsampled etc, and how sequence data and alignments was generated can be found in the methods section of the main text.
Data re-use: This data is freely available for research purposes in line with Molecular Ecology Resources journal policy.



File 1
File name: Final_alignment_Walton_et_al_2022.phy
File type: ".phy" alignment file
Description of contents: Alignment of 25 DNA sequences. These sequences are the near-complete (see Methods in the main text) mitochondrial genomes of the 24 Haliotis specimens that we newly sequenced, and the Haliotis iris sequence against which they were aligned. These sequences are all available for individual download on GenBank.



File 2
File name: Final_alignment2_Walton_et_al_2022.phy
File type: ".phy" alignment file
Description of contents: Alignment of 26 DNA sequences. These sequences are the trimmed alignment (trimmed from the above full alignment to leave roughly 10 kb of concatenated mitochondrial genes - see Methods in the main text to see which genes and why the alignment was trimmed so) of 25 Haliotis sequences and a fissurellid out-group sequence that were used for generation of Bayesian and Maximum Liklihood trees (see Methods in the main text). 



File 3
File name: Raw data for Walton et al 2022.zip
File type: contains compressed ("zipped") "fastq.gz" sequencing files 
Description of contents: Compressed raw sequencing (".fastq.gz") files for all 24 samples newly sequenced in Walton et al. (2022).
Within main zipped folder are two subfolders corresponding to: 1) the 12 samples that were dry-preserved shell (subfolder labelled: "Raw data for shell derived sequences") and 2) the 12 samples that were ethanol-preserved tissues (subfolder labelled: "Raw data for tissue derived sequences").
Samples are IDed by their museum voucher number (see Table 1 in the main text) - sample folders are clearly named by the voucher name.
Each shell derived sample folder has four subfolders, one for each of the four sequencing lanes, each of which, in turn, contains two files, corresponding to the paired-end sequencing.
For tissue derived sample folders, each folder contains the two files corresponding to the paired-end sequencing.



File 4
File name: Miseq dsDNA shotgun no capture prelim run.zip
File type: contains compressed ("zipped") "fastq.gz" sequencing files
Description of contents: Compressed raw sequencing (".fastq.gz") files for the nine samples that were included on a preliminary test sequencing run (not reported in detail in MS) to test viability of our project and if more conservative methods were needed, as proved to be the case.