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.

Sternkopf et al. BMC Evolutionary Biology 2010 10:348   doi:10.1186/1471-2148-10-348

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