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

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

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

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.

ISSN: 2730-7182