Table 4

Details of the 12 species tested and a summary of utility of the Conserved Avian Microsatellite (CAM) markers*
Species Status Sample type and storage Gen dist to ZF (ΔTmH) Gen dist to CH (ΔTmH) Order & Family ([[25]] / NCBI Taxonomy Database) PCR profile Pop Loci amp. (%) Loci poly. (%) Geno-typer Samples taken and DNA extracted by Sample supplier(s)
NEOGNATHAE
Passerines
Zebra finch Captive T/E & 0 28 Passeriformes 56 1 100 92 ADB Jayne Pellatt, Tim Birkhead
Taeniopygia guttata B/E Passeridae/Estrildidae Jon Chittock
Berthelot’s pipit Wild B/E 8.3 28 Passeriformes 56 4 96 70 LGS LGS David Richardson,
Anthus berthelotii Passeridae Juan Carlos Illera
House sparrow Wild B/E 8.5 28 Passeriformes 56 1 96 78 ADB Nancy Ockendon TB
Passer domesticus Passeridae
Chaffinch Wild B/E 10.0 28 Passeriformes TD1 1 96 83 JP Ben Sheldon Ben Sheldon
Fringilla coelebs Fringillidae
Eurasian bullfinch Wild B/E 10.0 28 Passeriformes TD1 1 96 65 JP Kate Durrant, Tim Birkhead
Pyrrhula pyrrhula Fringillidae Stuart Sharp, Simone Immler
Great tit Wild B/E 11.1 28 Passeriformes TD1 1 96 56 JP Louise Gentle, TB
Parus major Paridae Harrie Bickle
European blackbird Wild B/E 11.7 28 Passeriformes TD1 1 83 60 JP Michelle Simeoni Ben Hatchwell
Turdus merula Muscicapidae/Turdidae
Rifleman Wild B/E 19.7 28 Passeriformes 56 1 96 61 SAJP SAJP Ben Hatchwell
Acanthisitta chloris Acanthisittidae
Non-passerines
Leach’s storm-petrel Wild B/E 21.6 28 Ciconiiformes 56 4 96 56 AWJB AWJB AWJB
Oceanodroma leucorhoa Procellariidae
Barn owl Wild B/E 22.5 28 Strigiformes TD1 1 92 32 JP Akos Klein Akos Klein
Tyto alba Tytonidae
European roller Wild B/E 25.0 28 Coraciiformes B, 1 96 39 DM-G, DM-G Deseada Parejo,
Coracias garrulus Coraciidae TD2 MM-M Jesus Avilés
PALAEOGNATHAE
Chicken (domestic) Captive B/E 28.0 0 Galliformes TD1 1 100 38 JP Hans Cheng Hans Cheng
Gallus gallus domesticus Phasianidae

*Four individuals were tested per species with 24 Conserved Avian Microsatellite (CAM) primer sets. All PCR failures were rechecked for amplification by a different researcher (GJH) using the touchdown PCR program (TD1);

PCR profiles:

A: QIAGEN Multiplex PCR Master Mix; 95°C for 15 minutes, followed by 35 cycles of 94°C for 30 seconds, 56°C for 90 seconds, 72°C for 1 minute, and finally 60°C for 30 minutes.

B: (used only for the unrelated rollers), Bioline DNA Taq polymerase, 94°C 3 min, then 35 cycles of 94°C for 30 s, 56°C for 30 s, 72°C for 30 s, and finally 72°C for 10 min.

TD1: QIAGEN Multiplex PCR Master Mix; touchdown PCR program, 95°C for 15 min followed by 16 cycles of 94°C for 30 s, 65°C for 90 s decreasing by 1°C per cycle, 72°C for 60 s for 10 cycles, followed by 94°C for 30 s, 55°C for 90 s, 72°C for 60 for 25 cycles, with a final step of 72°C for 10 min.

TD2: (used only for the related European rollers) Bioline DNA Taq polymerase, touchdown PCR profile, 94°C for 3 min, then 10 cycles of 94°C for 30 s, 65°C for 30 s (and decreasing by 1°C for 15 cycles), 72°C for 1 min, followed by 28 cycles of 94°C for 30 s, 50°C for 30 s and 72°C for 30 s, followed by one cycle of 5 min at 72°C.

T, tissue; B, blood; E, ethanol; Pop., number of populations represented in the four individuals tested; amp., amplifying; poly., polymorphic; Loci poly. (%) indicates the proportion of loci polymorphic of those amplifying.

Genetic distance to ZF, genetic distance from species tested to zebra finch based on [33] and the classification of [25]; Genetic distance to CH, genetic distance from species tested to chicken [33].

Dawson et al.

Dawson et al. BMC Genomics 2013 14:176   doi:10.1186/1471-2164-14-176

Open Data