pumilioAnalysis

Publication and preprint associated

Evolution and Diversification of the Aposematic Poison Frog, Oophaga pumilio, in Bocas del Toro Diana Aguilar-Gómez, Layla Freeborn, Lin Yuan, Lydia L. Smith, Alex Guzman, Andrew H. Vaughn, Emma Steigerwald, Adam Stuckert, Yusan Yang, Tyler Linderoth, Matthew MacManes, Corinne Richards-Zawacki, Rasmus Nielsen bioRxiv 2024.08.02.606438; doi: https://doi.org/10.1101/2024.08.02.606438

Analysis of Bocas del Toro exome sequecing Oophaga pumilio samples

1 Process reads:

• Trimmomatic:
  • Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
  • Remove leading low quality or N bases (below quality 3) (LEADING:3)
  • Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
  • Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
  • Drop reads below the 75 bases long (MINLEN:75)
• Prinseq:
  • Remove low complexity reads
  • Remove overrepresented reads
• Fastqc
  • Asses quality of reads

2 Mapping:

• Bwa mem
• Samtools:
  • Samfile flags to exclude:
    • read unmapped (0x4), mate unmapped (0x8), not primary alignment (0x100), read fails platform/vendor quality checks (0x200), read is PCR or optical duplicate (0x400) = 1804

3 Filtering:

• Angsd:

  • Minimum individuals with 1x: 250, Maximum depth per individual: 50x
  • minMapQ: 25, minQ: 25
  • SNP_pval: 1e-6 (this was removed when we wanted to process all sites including non-variant)
  • skipTriallelic, Remove_bads, uniqueOnly, onlyProper pairs

• snpCleaner

  • Excess of heterozygous pval: 1e-6
  • Base quality bias pval: 1e-100
  • Strand bias pval: 1e-4
  • End distance bias pval: 1e-4
  • Map quality bias pval: 1e-4

4 Population structure:

• PCAngsd

5 Color genomics

• gemma
• selscan
• PBS and FST scans

6 Selection test

• HKA test
• Tajima`s D
• Pi

7 Demographic History

• dadi
• Treemix
• Admixed Bayes
• 4-pop test