Table 3

Observed allele sizes, heterozygosities and estimated frequency of null alleles of conserved microsatellite loci

Locus

Charadri: Kentish plover

Lari: whiskered auklet

Scolopaci: ruff


N

k

Allele size (bp)

Ho

He

Est. null alleles*

pHW1

N

k

Allele size (bp)

Ho

He

Est. null alleles*

pHW1

N

k

Allele size (bp)

Ho

He

Est. null alleles*

pHW1


a) standard primer

BmaTATC371

16

6

144, 148, 150, 152, 154, 156

0.75

0.62

-0.12

0.45

16

12

158, 161, 169, 171, 173, 174, 176, 177, 178, 180, 181, 190

0.88

0.88

-0.01

0.53

16

1

140

0

0

0

na

Mopl 18

16

1

139

0

0

0

na

16

2

128, 136

0.06

0.06

-0.01

na

16

1

137

0

0

0

na

Mopl 21

15

2

315, 321

0.47

0.48

-0.02

1

16

2

315, 322

0.13

0.12

-0.02

1

16

3

308, 314, 320

0.69

0.54

-0.14

0.31

Mopl 6

16

4

290, 292, 294, 296

0.81

0.70

-0.09

0.94

15

1

278

0

0

0

na

16

5

299, 301, 303, 305, 307

0.44

0.38

-0.11

1

Cmms 26

16

1

320

0

0

0

na

14

5

304, 306, 308, 310, 312

0.79

0.75

-0.05

0.92

8

2

316, 324

0.38

0.33

0

1

Cmms 9

16

2

239, 241

0.13

0.12

-0.02

1

15

8

250, 252, 254, 256, 258, 260, 262, 268

0.87

0.75

-0.11

0.94

14

1

246

0

0

0

na

LarsZAP26/K32

16

2

100, 102

0.38

0.39

0

1

12

10

101, 106, 108, 117, 119, 123, 125, 129, 130, 133

0.58

0.90

0.20

0.01

15

1

106

0

0

0

na

b) consensus primer

54F2

14

2

215, 217

0.14

0.42

0.48

0.03

16

1

220

0

0

0

na

16

1

212

0

0

0

na

Apy07

16

1

146

0

0

0

na

16

8

170, 182, 186, 190, 194, 198, 202, 206

0.75

0.78

0.01

0.80

16

1

145

0

0

0

na

BmaAGGT503

16

1

249

0

0

0

na

16

4

251, 252, 253, 254

0.69

0.72

0.02

0.23

16

1

257

0

0

0

na

BmaTATC453

16

2

235, 239

0.06

0.06

-0.01

na

16

1

239

0

0

0

na

16

2

239, 241

0.13

0.12

-0.02

1

BmaTGAA523

16

1

71

0

0

0

na

16

2

69, 77

0.06

0.06

-0.01

na

16

1

71

0

0

0

na

Calex-01

13

11

201, 205, 209, 211, 213, 215, 217, 219, 221, 223,227

1

0.91

-0.07

0.32

16

3

199, 201, 203

0.19

0.54

0.52

<0.001

16

2

207, 209

0.06

0.06

-0.01

na

Calex-05

14

6

173, 179, 180, 181, 183, 184

0.64

0.71

0.03

0.60

16

2

173, 175

0.38

0.32

-0.10

1

16

1

173

0

0

0

na

Mopl 15

16

6

170, 172, 174, 176, 180, 182

0.75

0.71

0.03

0.48

15

2

174, 182

0.07

0.07

-0.01

na

15

1

172

0

0

0

na

Mopl 22

13

2

394, 404

0.31

0.27

-0.08

1

16

1

402

0

0

0

na

16

1

401

0

0

0

na

Mopl 26

16

9

188, 190, 194, 196, 198, 200, 208, 210, 212

0.69

0.82

0.08

0.05

16

6

189, 190, 191, 192, 193, 194

0.75

0.73

-0.04

0.80

16

1

184

0

0

0

na

Cmms3

14

1

95

0

0

0

na

16

6

102, 106, 108, 110, 112, 114

0.81

0.78

-0.03

0.02

16

1

95

0

0

0

na

SNIPE B2

16

2

170, 172

0.19

0.35

0.29

0.11

16

1

164

0

0

0

na

16

8

168, 172, 176, 180, 184, 192, 196, 200

0.75

0.80

0.03

0.32

Pgt 83

14

1

132

0

0

0

na

16

1

142

0

0

0

na

16

2

149, 151

0.06

0.06

-0.01

na

Rbg 18

16

7

259, 263, 265, 267, 269, 275, 277

0.75

0.77

0.01

0.76

8

4

260, 264, 266, 272

0.38

0.66

0

0.08

16

3

257, 259, 261

0.13

0.12

-0.02

1

Rbg 27

16

1

184

0

0

0

na

16

2

180, 182

0.06

0.06

-0.01

na

15

1

184

0

0

0

na

Rbg 29

15

1

127

0

0

0

na

16

12

116, 118, 120, 124, 126, 128, 130, 132, 136, 138, 144, 146

0.69

0.90

0.13

<0.01

14

1

127

0

0

0

na


N, number of individuals amplified in polymorphism test

k, number of alleles found in test sample

Ho, observed heterozygosity

He, expected heterozygosity

* estimated null allele frequency using CERVUS v. 2.0

1probability that locus is in Hardy-Weinberg equilibrium estimated by GENEPOP v 3.3

All primers were tested in 16 unrelated individuals from single populations of each of Kentish plover Charadrius alexandrinus, whiskered auklet Aethia pygmaea and ruff Philomachus pugnax. Populations with significant deviation from Hardy-Weinberg equilibrium are indicated in bold.

K├╝pper et al. BMC Genomics 2008 9:502   doi:10.1186/1471-2164-9-502

Open Data