Dataset and scripts companions of the publication "Molecular identification and diversity assessment of Tyrrhenian Romulea species (Iridaceae)" in PlosOne

Multi-locus genetic data obtained using the hybseq method with the Angiosperms353 kit;  nuclear (vcf file) and plastid data (fasta) analysed with 5 scripts deposited here. All the details are described in a paper in press in PlosOne and in a preprint deposited on ecoevorxiv and availalbe at https://doi.org/10.32942/X2N95H.

This research was funded by the Port-Cros National Park (convention 2022-593).

(1) data_files 

Metadata: metaTyrr_ordered.txt, metaTyrr_ordered_k15.txt, S1_file.csv 

Reference for nuclear variant calling : ,Cons_superconti_331.fas

Reference for plastid variant calling : FloFrBag2_plastome.fasta (R. florentii plastome)

Nuclear data : Tyrr-331-snpbi-maf001.vcf, Tyrr_genoC_AutoAllo4X_ref331.Rdata

Plastid data : Tyrr_PTD_min3_kpi_clean_kpi.fasta

The S1_file.csv allow to link all data and results with the ENA archive accessions.

(2) Scripts

1_HindHE_&_Continous_Genotype_Calling.R

2_Heatmap_completness.R

3_Clustering_&_heatmap_genotypes.R

4_DAPC.R

5_plastid_ML5tree_iqtree.bash

(3) Graphical results

Plastid_phylogeny.pdf

HindHE_distribution.tif

Genotypes_similarities_heatmap.tiff

DAPC.tiff