Data and analysis of Diorhabda population structure using RADseq and a de novo reference genome.
Manuscript in prep!
Goals are to
- Quantify prevalence and levels of hybridization among the four introduced species and source populations.
- Examine the consequences of population bottlenecks and admixture on genome-wide diversity across broad, landscape-wide expansion fronts and the hybrid zone.
Most work was performed on the IBEST cluster, usually crick or watson.
- Assembled de novo Diorhabda carinulata reference genome, combining shotgun scaffolds assembled in Spades with in-silico 'linked' 10X reads.
- raw reads for shotgun
- raw reads for 10X
- spades assembly
- LINK/Arcs pipeline
- BUSCO and QUAST assessment
- Generated SNPs across lots of individuals and populations (raw2vcftask.sh)
- raw reads
- clone_filtered
- process_radtags
- aligned to reference
- gstacks
- populations
- Model-based ancestry assignment in Structure
- downloaded vcf to local computer
- converted vcf to structure format with PGDspider
- uploaded this back to cluster
- ran K= 1-10 for 10 reps each
- Re-ran this for carinulata and elongata to examine population substructure
- Examined population genetics in the context of hybridization
- Popgen stats
- Isolation by distance
- RangeExpansion analysis on carinulata
- upload scripts for genome assembly
- upload raw data for genome assembly
- upload raw data for population genetics
- associate each of the steps above with scripts and directories