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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.