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Table 3 Assays selected for genotyping population samples using newly-developed nuclear loci, following SSCP pre-screening. Taxon and genotyping assay abbreviations follow Table 1 and Table 2, respectively. The genetic basis of polymorphism at each locus was determined via sequencing. The Sm8 locus was initially assayed using SSCP [31], but here we deemed RFLP more appropriate. The latter dataset was used for Bayesian clustering, calculating allelic richness, and estimating phenetic relationships among populations.

From: Development and application of three-tiered nuclear genetic markers for basal Hexapods using single-stranded conformation polymorphism coupled with targeted DNA sequencing

Taxon/locus Fragment
length (bp)a
Substitutions Indelsb Total no. of
mutations
Genotyping assay No. of alleles
resolved
No. of animals
screened
GenBank accession
no.
Pseud.         
Sm2 161–189 17 4 21 SSCP (HhaI) 13 378 DQ322462-DQ322474
Sm8 232–234 21 4 25 SSCP/RFLP (HinfI, NlaIV) 12/4 102/377 DQ322492-DQ322503
SmEF-1α 228–232 20 5 25 SSCP 21 373 DQ322508-DQ322528
Sm6 61–76   6   Indel 5 380 DQ322485-DQ322491
Sm4 231–325   10–12   Indel 4 379 DQ322475-DQ322484
Sm150 129–131   2   Indel 2 380 DQ322504-DQ322507
Acanth.         
Uc180 92–96 10 2 12 SSCP 9 201 DQ322552-DQ322560
Uc3 146–150 24 2 25 SSCP 17 203 DQ322529-DQ322545
UcEF-1α 264–266 26 1 27 SSCP (HincII) 21 203 DQ322566-DQ322586
Uc44 117–133   5   Indel 6 203 DQ322546-DQ322551
UcANT 173–174     RFLP (AluI, DraI) 3 203 DQ322561-DQ322565
UcWnt 139     RFLP (FokI, NlaIII) 3 203 DQ322587-DQ322590
  1. aAllele size range minus primers and ambiguous sequence.
  2. bContiguous aligment gaps were treated as a single indel, Sm4 alleles cannot be unambiguously aligned. For loci assayed using the indel genotyping procedure, the number of indels observed in a subset of representative allele sequences in given.