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Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses

Fig 3

Next Generation sequencing results from mRNA of two New Zealand stick insects (A).

Length distributions of transcript assemblies produced from the cDNA sequence of two stick insects were similar. A log length frequency distribution plot used values rounded to 1 decimal place for the longest consensus sequence generated from each cluster. (B) Sequence divergence (measured by SNP density per nucleotide) observed when reads were mapped to ~2,600 loci (transcript assemblies). Loci without variation (SNP-free) were removed. The putative parental Clitarchus hookeri genome contains many loci with low allelic diversity. SNPs detected in less than 10% of the short reads were ignored but reads were included whether or not they passed the strand bias filter within VarScan. Only the longest assembled transcripts generated per cluster were included. (C) SNPs detectable on all transcript assemblies by BWA mapping to ~2,600 Acanthoxyla and Clitarchus transcript assemblies using VarScan with minimum variant frequency of 10% irrespective of strand filter results. The first violin of each color comprises all data, and the second excludes transcript assemblies with no sequence variation (SNP-free). Purple–Acanthoxyla reads mapped onto Acanthoxyla transcript assemblies; Pale green–Clitarchus reads mapped onto Acanthoxyla transcript assemblies; Pale purple–Acanthoxyla reads mapped onto Clitarchus transcript assemblies; Green–Clitarchus reads mapped onto Clitarchus transcript assemblies.

Fig 3