Meares K, Dawson DA, Horsburgh GH, Perrin MR, Burke T, Taylor TD (2008) Characterisation
Erratum
Meares K, Dawson DA, Horsburgh GH, Perrin MR, Burke T, Taylor TD (2008) Characterisation of 14 blue crane Grus paradisea (Gruidae, AVES) microsatellite loci for use in detecting illegal trade. Conservation Genetics, in press.
This manuscript was published in Conservation Genetics in 2008 (online early) since publication we have observed errors in the second part of Table 1 and Table 2.
The first part of Table 1 involving the characterization of the loci in blue crane did not contain errors and remains unchanged.
The second part of Table 1 involving the cross-utility of the markers in other species, “Table 1 continued” which is highlighted in yellow, contains errors. In the published version of this part of the table the samples sets of both species were contaminated by individuals from other species. The grey-crowned cranes (Balearica regulorum) genotyped mistakenly included 3 blue crane individuals and the wattled cranes (Grus carunculatus) genotyped included one blue crane and one grey-crowned crane. The true number of alleles and heterozygosity observed for all of the 14 blue crane loci when genotyped in grey-crowned and wattled crane is therefore much lower in these two species than previously published. The species origins of the samples which were originally mis-identified were confirmed by comparison of allele sizes between species using several loci which displayed species-specific alleles (see Meares et al. 2008, submitted to Molecular Ecology Resources).
After correction, eleven of the blue crane loci were polymorphic in grey-crowned crane (not 14) and 11 were polymorphic in wattled crane (not 14). Due to the reduced number of grey-crowned crane and wattled crane individuals genotyped, tests for Hardy Weinberg equilibrium and estimated null allele frequencies were not performed.
These errors have been rectified in the Table below.
Table 2 contains two minor errors. The numbers of grey-crowned cranes tested was 7 (not 10) and the number of wattled cranes tested was 8 (not 10). These corrections have been highlighted in yellow in the Table below.
We sincerely apologise for these errors.
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Table 1 Characterisation of 14 blue crane (Grus paradisea) microsatellite loci in the blue crane, grey-crowned crane (Balearica regulorum) and wattled crane (Grus carunculatus).
Blue crane (Grus paradisea)Locus‡ / EMBL accession number and clone name / Primer sequence (5’ – 3’) with pigtail sequence underlined§ / PRIMER3 Tm (oC) / Ta (oC) / MgCl2 (mM) / Repeat motif in blue crane / n / A / Exp. allele size (bp) ¥ / Genotype of library source individual (J17718) / Observed allele sizes (bp) ‡ / HO / HE / Deviation from HWE
(P-value if >0.10) / Est. null allele freq.
Gpa01 / AM085152, BC17E04 / F: HEX - TTTGGTTGCCGTCAGAATTG R: GTTTCTT-CTGACCTGGGTGTGTTCTGC / 61.97
61.76 / 63 / 1.5 / (CA)8 / 19 / 4 / 297 (290) / 291, 297 / 291, 293, 297, 299 / 0.58 / 0.54 / NS / -0.04
Gpa11† / AM282892, BC43B09 / F: HEX - CCCTCCTGGAATACATGACAAA R: AAGTCATTCTCAACAAGAAAGGAAAA / 61.09
60.82 / 60 / 3.0 / (TTTC)34 / 20 / 21 / 300 / 216, 236 / 186–346 / 0.75 / 0.96 / ** (0.01) / 0.11
Gpa12 / AM282893, BC43C11& AM282894 / F: FAM - GATCAATGCGAAGGATAGGGAGGT R: TCATCAATCTATTATTTGCCTCAGC / 61.70
60.78 / 60 / 3.0 / (GATA)11 / 20 / 7 / 232, 236 / 232, 236 / 212, 216, 220, 224, 228, 232, 236 / 0.75 / 0.83 / NS / 0.04
Gpa14 / AM282896, BC43F06 / F: FAM - TTTCGTACTCTGGTCATTGGATTT R: GTTTCTT-AATAGGACAGCAGTGCTAAGAAGAAA / 61.07
61.07 / 57 / 2.0 / (TTTC)12 / 20 / 12 / 283 (276) / 286, 294 / 278–324 / 0.85 / 0.90 / NS / 0.02
Gpa24 / AM282908, BC45A12 / F: HEX -GAGGGAATCTAGCACGCTCCAA R: GTTTCTT-TCAAAGCATCGTGTCCATGAAGT / 64.96
64.06 / 57 / 2.0 / (GTTA)6 / 20 / 5 / 250 (243) / 243, 251 / 239, 243, 247, 251, 255 / 0.50 / 0.62 / NS (0.06) / 0.12
Gpa32 / AM282918, BC45H08 / F: HEX -CCCAGCACACCGTGCATAAG R: GTTTCTT-GCAGTCGGTCACATCCTTGG / 64.85
64.02 / 57 / 2.0 / (GT)11 / 20 / 7 / 190 (183) / 183, 189 / 177, 183, 185, 187, 189, 191, 193 / 0.75 / 0.85 / NS (0.07) / 0.05
Gpa33 / AM282919, BC45H10 / F: FAM - GGCTTAGAAATGGGATACAGTTG R: CCGTCCAAGCAAGAAGAAA / 60.63
60.05 / 60 / 2.0 / (TTTC)14 (TCTCTTTC)16 / 19 / 24 / 316 / 243, 243 / 205–417 / 0.90 / 0.97 / NS / 0.03
Gpa34 / AM282920, BC47A04 / F: HEX -GCACACAGTGAGGAGACCAGTGA R: CCTTGATGTGGGAAGACAACTGC / 65.10
65.22 / 60 / 3.0 / (TTTCTC)22 / 17 / 18 / 265 / NA / 249–413 / 0.88 / 0.95 / NS / 0.02
Gpa35 / AM282921, BC47A05 / F: FAM - TCATCAGCTTCCAACAGGTCTCC R: GTTTCTT-TCAGGCACAATGTATAAGTGTTTGTGG / 65.01
65.09 / 57 / 2.0 / (GT)13 (TA)4 / 18 / 7 / 176 (169) / 176, 178 / 172, 174, 176, 178, 180, 182, 184 / 0.89 / 0.81 / NS / -0.07
Gpa36 / AM282922, BC47A12 / F: HEX -TTCATAGACATATGCTTACCTGTTCT R: ATCCATCCATCTATCTATCTATCTATCTATC / 57.65
57.57 / 60 / 2.0 / (GATA)10 (GATG)2 / 19 / 5 / 228 / 228, 228 / 220, 224, 228, 232, 236 / 0.53 / 0.67 / NS / 0.10
Gpa37 / AM282923, BC47D01 / F: HEX -TGAACGTGTCTGATTTAAGGAA R: AAAGTAGTCACTAGCCTGGGTTT / 57.43
57.64 / 60 / 2.0 / (TC)2 CTC (TTTC)43 (TTC)2 / 19 / 27 / 231 / 194, 194 / 174–390 / 0.95 / 0.98 / NS / 0.00
Gpa38 / AM282924, BC47H05 / F: HEX -GGGCAGAAGCAAGTCTTTCA R: GAAGATGTTTGCTGGTTGCAC / 60.52
60.69 / 60 / 3.0 / (CTAT)13 / 20 / 6 / 193 / 188, 192 / 180, 184, 188, 192, 196, 200 / 0.90 / 0.81 / NS / -0.06
Gpa39 / AM282925, BC47H08 / F: HEX -TGCACAGGTTTGGCCAAGAAG R: GTTTCTT-TTCCAAAGTGAAATTAAAGGTGTGTGG / 65.66
65.13 / 57 / 2.0 / (GA)2 (GATA)13 / 20 / 7 / 125 (118) / 122, 126 / 114, 118, 122, 126, 130, 134, 138 / 0.85 / 0.81 / NS / -0.04
Gpa41 / AM282932, BC49F10 / F: FAM - AATTCAGTCTAATGTAAATGTCCAAG R: CCATCATTAATGGAAAGAAAGAG / 57.12
56.99 / 54 / 2.0 / (TTTCTTCC)6 (TC)5 (TTTCTCTC)3 (TTTCTCTC)3 (TTTC)2 / 20 / 4 / 242 / 245, 245 / 237, 245, 253, 261 / 0.60 / 0.60 / NS / 0.00
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Table 1 continued
Grey-crowned crane (Balearica regulorum) / Wattled crane (Grus carunculatus)Locus‡ / TD temp. (oC) / n / A / Allele sizes (bp) ‡ / HO / HE / Deviation from HWE / Est. null allele freq. / n / A / Allele sizes (bp) ‡ / HO / HE / Deviation from HWE / Est. null allele freq.
Gpa01 / 66-60 / 7 / 1 / 293 / 0.00 / 0.00 / - / - / 8 / 1 / 291 / 0.00 / 0.00 / - / -
Gpa11 / 63-57 / 7 / 7 / 234, 248, 258, 262, 270, 274, 310 / 1.00 / 0.90 / NA / NA / 8 / 9 / 224, 230, 245, 248, 254, 258, 266, 282, 294 / 0.88 / 0.93 / NA / NA
Gpa12 / 63-57 / 7 / 3 / 196, 200, 204 / 0.43 / 0.63 / NA / NA / 8 / 3 / 192, 196, 200 / 0.75 / 0.63 / NA / NA
Gpa14 / 60-54 / 6 / 6 / 246, 250, 254, 262, 266, 270 / 0.67 / 0.88 / NA / NA / 8 / 5 / 270, 294, 298, 308, 358 / 0.38 / 0.81 / NA / NA
Gpa24 / 60-54 / 1 / 2 / 243, 247 / 1.00 / 1.00 / NA / NA / 8 / 1 / 243 / 0.00 / 0.00 / - / -
Gpa32 / 60-54 / 2 / 1 / 177 / 0.00 / 0.00 / - / - / 8 / 2 / 179, 181 / 0.50 / 0.50 / NA / NA
Gpa33 / 63-57 / 7 / 3 / 206, 214, 218 / 0.29 / 0.56 / NA / NA / 5 / 8 / 218, 254, 314, 318, 326, 334, 336, 344 / 1.00 / 0.96 / NA / NA
Gpa34 / 63-57 / 7 / 7 / 132, 138, 144, 152, 164, 176, 220 / 0.86 / 0.85 / NA / NA / 7 / 7 / 280, 286, 292, 298, 304, 320, 322 / 0.86 / 0.87 / NA / NA
Gpa35 / 60-54 / 7 / 2 / 159, 161 / 0.14 / 0.36 / NA / NA / 8 / 1 / 169 / 0.00 / 0.00 / - / -
Gpa36 / 63-57 / 7 / 3 / 228, 232, 236 / 0.57 / 0.56 / NA / NA / 8 / 4 / 220, 224, 228, 232 / 1.00 / 0.70 / NA / NS
Gpa37 / 63-57 / 2 / 2 / 197, 205 / 0.50 / 0.50 / NA / NA / 8 / 8 / 121, 123, 129, 131, 133, 137, 141, 147 / 0.88 / 0.88 / NA / NA
Gpa38 / 63-57 / 2 / 1 / 189 / 0.00 / 0.00 / - / - / 7 / 4 / 181, 185, 193, 197 / 1.00 / 0.67 / NA / NA
Gpa39 / 60-54 / 7 / 9 / 176, 198, 202, 206, 216, 222, 224, 234, 250 / 0.57 / 0.90 / NA / NA / 8 / 2 / 102, 106 / 0.13 / 0.13 / NA / NA
Gpa41 / 57-51 / 7 / 7 / 187, 191, 207, 211, 215, 219, 227 / 1.00 / 0.88 / NA / NA / 8 / 4 / 233, 249, 257, 265 / 0.38 / 0.35 / NA / NA
Tm, Melting temperature assigned by PRIMER v3 software (Rozen et al. 2000);
Ta, annealing temperature;
n, number of crane individuals that successfully amplified and were genotyped of the 20 blue crane, 10 wattled crane and 10 grey-crowned crane individuals tested, respectively;
A, number of alleles;
¥, expected allele size based on the sequenced clone including the 7-bp length of the pigtail when used. The expected allele size excluding the length of the pigtail is shown in parentheses;
HO, observed heterozygosity calculated using CERVUS v2.0 (Marshall et al. 1988);
HE, expected heterozygosity calculated using CERVUS v2.0 (Marshall et al. 1988);
Deviation from HWE, deviations from Hardy-Weinberg equilibrium (HWE) calculated using GENEPOP 3.4 (Raymond, 1995);
Est. null allele freq., estimated null allele frequency calculated using CERVUS v2.0 (Marshall et al. 1988);
†, locus has high predicted null allele frequency of equal or above 0.1;
§, for some loci a “pigtail” sequence GTTTCTT added, to reduce noise from variable adenylation during the PCR (Brownstein et al. 1996);
‡, the seven bases of the pigtail are included in the observed allele size;
NS, non-significant; NA, not available; *significant at the 5% level, **significant at the 1% level;
TD temp., maximum and minimum temperatures used in touchdown PCR. Touchdown PCR program used: 94°C for 3 min; 5 cycles of 94°C for 30 s, highest Ta, decreasing with 1°C increments per cycle, 72°C for 30 s; followed by 25 cycles of 94°C for 30 s, lowest Ta for 30 s, 72°C for 30 s, completing the profile with an extension at 72°C for 4 min;
‡Locus Gpa26 (clone BC45E05, AM282912) was monomorphic in 76 blue crane individuals but was not tested in wattled crane and grey-crowned crane. Primer sequences for this locus are F: AACTAGGTTAACAGATGCATTAACAGG, R: GGAAGTGGCGGGTATAGGAA.
Sources of individuals genotyped:
Blue crane individuals originated from a wild population inhabiting the Karoo region, South Africa;
Wattled crane individuals originated from KwaZulu-Natal South Africa;
Grey-crowned crane individuals originated from KwaZulu-Natal, Eastern Cape and Mpumalanga provinces, South Africa (population structure currently uncertain).
Table 2 Cross-species utility of 14 blue crane Grus paradisea microsatellite loci.
Species / Binomial name / Order / n / Genetic distance to blue crane‡ / Gpa01 / Gpa11 / Gpa12 / Gpa14 / Gpa24 / Gpa32 / Gpa33 / Gpa34 / Gpa35 / Gpa36 / Gpa37 / Gpa38 / Gpa39 / Gpa41Grey-crowned crane* / Balearica regulorum / Gruiformes / 7 / 0.7 / + / + / + / + / + / + / + / + / + / + / + / + / + / +
Wattled crane* / Grus carunculatus / Gruiformes / 8 / 0.7 / + / + / + / + / + / + / + / + / + / + / + / + / + / +
Houbara bustard† / Chlamydotis undulata / Gruiformes / 1 / 16.9 / + / + / – / – / – / – / – / – / – / – / – / – / – / –
Grey-headed albatross† / Diomedea chrysostma / Procellariiformes / 1 / 20.1 / – / + / – / – / – / – / – / – / + / – / + / + / + / –
Seychelles warbler† / Acrocephalus sechellensis / Passeriformes / 1 / 21.6 / – / – / – / – / – / – / – / – / – / – / – / – / – / –
Cape parrot† / Poicephalus robustus / Psittaciformes / 2 / 23.1 / + / + / – / – / + / + / – / – / – / – / – / – / – / –
Red jungle-fowl† / Gallus gallus / Galliformes / 1 / 28.0 / – / – / – / – / – / – / – / – / – / – / – / – / – / –
Saltwater crocodile† / Crocodylus porosus / Crocodilia / 1 / NA / – / – / – / – / – / – / – / – / – / – / – / – / – / –
Human† / Homo sapiens / Primates / 2 / NA / – / – / – / – / – / – / – / – / – / – / – / – / – / –
n, number of individuals tested for amplification;
+, amplification observed on 2% agarose gel;
–, no amplification observed on 2% agarose gel, or non-specific amplification or amplification of a product over 200 bp larger or smaller than the size observed in blue crane;
*amplified using touchdown PCR (temperature range provided in Table 1) and genotyped using an ABI 3730 DNA Analyzer;
†, amplified using same PCR conditions as blue crane and visualised on a 2% agarose gel;
‡, delta T50H DNA–DNA hybridisation distances based on Sibley et al. (1990);
NA, not available.
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