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Table 2 Primer sequences and names used for screening and scoring of AFLP fragments

From: Introgressive hybridization and the evolutionary history of the herring gull complex revealed by mitochondrial and nuclear DNA

EcoR - primer sequences
for pre-amplification: 5'-GACTGCGTACCAATTC-C-3'
for sequencing 5'-GACTGCGTACCAATTC-Cxx-3'
ending: primer name:
CAA EcoC1
CAC EcoC2
CAT EcoC3
CCA EcoC4
CCC EcoC5
CCT EcoC6
CGC EcoC7
CGT EcoC8
CTA EcoC9
CTT EcoC10
Mse - primer sequences
for pre-amplification: 5'-GATGAGTCCTGAGTAA-C-3
for sequencing 5'-GATGAGTCCTGAGTAA-Cxx-3
ending: primer name:
CAC Mse1
CAG Mse2
CAT Mse3
CCA Mse4
CCT Mse5
CGA Mse6
CGT Mse7
CTA Mse8
CTG Mse9
CTT Mse10
Selected 17 primer-pairs
Primer combinations used number of detected variable loci
EcoC1 Mse8 13
EcoC1 Mse10 18
EcoC2 Mse4 6
EcoC2 Mse5 5
EcoC2 Mse6 20
EcoC2 Mse7 5
EcoC2 Mse8 12
EcoC3 Mse1 17
EcoC3 Mse2 13
EcoC3 Mse4 9
EcoC3 Mse5 10
EcoC3 Mse10 22
EcoC4 Mse1 17
EcoC4 Mse7 27
EcoC5 Mse1 14
EcoC5 Mse3 11
EcoC7 Mse1 11
  1. This table lists the used EcoR1 and Mse1 core-primer and their triplet endings for the pre- amplification and sequencing step. For the pre-amplification only one primer pair was chosen (EcoR1+C/Mse1+C). The full primer sequences are indicated. In order to find the best sequence primer pairs (showing the highest level of variable loci) for final analyses we screened all possible 100 combinations of triplet-endings. We selected those 19 combinations that showed more than five variable loci when screening a set of six cachinnans and six michahellis (the two most distinct taxa in the mtDNA shown in reference [8]. Of these, 2 combinations were subsequently removed because they were not sufficiently variable among our full set of gulls. The remaining final set of 17 primer pairs are given in this table, together with their number of variable loci resulting in the whole dataset.