Enhanced cross-species utility of conserved microsatellite markers in shorebirds

Küpper, Clemens; Burke, Terry; Székely, Tamás; Dawson, Deborah A

doi:10.1186/1471-2164-9-502

BMC Genomics

Table 3 Observed allele sizes, heterozygosities and estimated frequency of null alleles of conserved microsatellite loci

From: Enhanced cross-species utility of conserved microsatellite markers in shorebirds

Locus	Charadri: Kentish plover							Lari: whiskered auklet							Scolopaci: ruff
	N	k	Allele size (bp)	H _o	H _e	Est. null alleles*	p_HW¹	N	k	Allele size (bp)	H _o	H _e	Est. null alleles*	p_HW¹	N	k	Allele size (bp)	H _o	H _e	Est. null alleles*	p _HW ¹
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
H_o, observed heterozygosity
H_e, 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.

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