Recommended order to test markers to find those useful for genetic studies in passerines |
Marker name |
Reference |
Notes |
(a) Passerines† |
1 |
TG markers (n=33) |
Dawson et al. 2010DAWSON DA et al. 2010. New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility as demonstrated for birds. Mol Ecol Resour 10: 475-494.
|
Engineered EST markers: both primers are a 100% match to chicken and zebra finch, possessed no degenerate bases, with a repeat in zebra finch. Test all markers except TG01-092 and TG09-014 * |
2 |
All 24 CAM markers |
Dawson et al. 2013DAWSON DA et al. 2013. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 14: 176.
|
Engineered markers: both primers were a 100% match to chicken and zebra finch, possessed 0-3 degenerate bases per set and included a repeat in both chicken and zebra finch * |
3 |
LOX1, Phtr2, ZL04, Pca7, HrU2, FhU2, Phtr4, Pca9, Pca4 |
Primmer et al. 2005PRIMMER CR, PAINTER JN, KOSKINEN MT, PALO JU and MERILÄ J. 2005. Factors affecting avian cross-species microsatellite amplification. J Avian Biol 36: 348-360.
|
9 loci isolated from various passerines and tested in many species* |
4 |
Tgu6 (=Pte24) |
Slate et al. 2007SLATE J, HALE MC and BIRKHEAD TR. 2007. Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: A new resource for evolutionary genetic studies of passerines. BMC Genomics 8: 52. (see Klein et al. 2009KLEIN A, HORSBURGH GJ, KÜPPER C, MAJOR A, LEE PL, HOFFMANN G, MÁTICS R and DAWSON DA. 2009. Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES). Mol Ecol Resour 9: 1512-1519., Martín-Gálvez et al. 2009, Simeoni et al. 2009SIMEONI M, DAWSON DA, GENTLE L, COIFFAIT L, WOLFF K, EVANS KL, GASTON K and HATCHWELL BJ. 2009. Characterization of 38 microsatellite loci in the blackbird Turdus merula (Turdidae, AVES). Mol Ecol Resour 9: 1520-1526., Martín-Gálvez et al. 2014) |
Zebra finch EST locus known to be of utility in distantly related species including multiple passerines, an owl and a roller. |
5 |
GG-C25, Tgu-EST09, 10, 13, 16, 32, 46, 48, 62, 69, 75, 81, 85 |
Karaiskou et al. 2008KARAISKOU N, BUGGIOTTI L, LEDER E and PRIMMER CR. 2008. High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. J Hered 99: 688-693.
|
Zebra finch EST loci, Amplified in at least 7 of 8 species tested (7 passerines and an owl) and polymorphic in at least 5 of 8 species. |
6 |
Ppi2, Pdoµ5, Mjg1, Mcy4 (Mcyµ4), Pcaµ3 (Pca3), Pcaµ9 (Pca9), Pat14 (PAT MP 2-14), Pat43 (PAT MP 2-43), Ls1, Ls2, Phtr3. Gf4, Gf6, Zl04, LOX1. |
Galbusera et al. 2000GALBUSERA P, VAN DONGEN S and MATTHYSEN E. 2000. Cross-species amplification of microsatellite primers in passerine birds. Conserv Genet 1: 163-168., (see also Martín-Gálvez et al. 2009 (Pdoµ5, Mcyµ4); Simeoni et al. 2007SIMEONI M, DAWSON DA, ROSS DJ, CHALINE N, BURKE T and HATCHWELL BJ. 2007. Characterisation of 20 microsatelite loci in the long-tailed tit Aegithalos caudatus (Aegithalidae, AVES). Mol Ecol Notes 7: 1319-1322. (Ppi2, Pca3, LOX1, plus Ase18, Man13-Gga), Simeoni et al. 2009, (PAT MP 2-14 and PAT MP 2-43 ) |
Loci isolated from various passerines and display cross-species utility in multiple species. |
Recommended order to test markers to find those useful for genetic studies in non-passerines |
Marker name |
Reference |
Notes |
(b) Non-passerines† |
1 |
CAM-06, CAM-13, CAM-17, CAM-18, CAM-20 and CAM-24 (CAM set 1, n=6 markers) |
Dawson et al. 2013DAWSON DA et al. 2013. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 14: 176.
|
Engineered markers: both primers are a 100% match to chicken and zebra finch, possessed no degenerate bases and included a repeat in both chicken and zebra finch. |
2 |
TG markers (n=33) |
Dawson et al. 2010DAWSON DA et al. 2010. New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility as demonstrated for birds. Mol Ecol Resour 10: 475-494.
|
Engineered EST markers: both primers are a 100% match to chicken and zebra finch, possessed no degenerate bases, with a repeat in zebra finch. Test all except TG01-092 and TG09-014* |
3 |
Bb111-TG, HvoB1-TGG and TG04-061 |
Klein et al. 2009KLEIN A, HORSBURGH GJ, KÜPPER C, MAJOR A, LEE PL, HOFFMANN G, MÁTICS R and DAWSON DA. 2009. Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES). Mol Ecol Resour 9: 1512-1519., Martín-Gálvez et al. 2014 |
Utility in distantly related species including owls, eagle and roller. Homology to passerines and Galliformes. |
4 |
Tgu6 (=Pte24) |
Slate et al. 2007SLATE J, HALE MC and BIRKHEAD TR. 2007. Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: A new resource for evolutionary genetic studies of passerines. BMC Genomics 8: 52. (see Klein et al. 2009KLEIN A, HORSBURGH GJ, KÜPPER C, MAJOR A, LEE PL, HOFFMANN G, MÁTICS R and DAWSON DA. 2009. Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES). Mol Ecol Resour 9: 1512-1519., Martín-Gálvez et al. 2009, Simeoni et al. 2009SIMEONI M, DAWSON DA, GENTLE L, COIFFAIT L, WOLFF K, EVANS KL, GASTON K and HATCHWELL BJ. 2009. Characterization of 38 microsatellite loci in the blackbird Turdus merula (Turdidae, AVES). Mol Ecol Resour 9: 1520-1526., Martín-Gálvez et al. 2014) |
Zebra finch EST locus known to be of utility in many distantly related species (including owl, multiple passerines and roller). |
5 |
Rest of the CAM markers (n=18) |
Dawson et al. 2013DAWSON DA et al. 2013. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 14: 176.
|
Engineered markers: both primers were a 100% match to chicken and zebra finch, possessed 1-3 degenerate bases per primer set and included a repeat in both chicken and zebra finch* |
6 |
BmaTATC317, Mopl 6, 15, 21, 26, LarsZAP26/K32, BmTATC403, Calex-01, Calex-05, SNIPE B2, Rbg 18 |
Küpper et al. 2008KÜPPER C, BURKE T, SZÉKELY T and DAWSON DA. 2008. Enhanced cross-species utility of conserved microsatellite markers in shorebirds. BMC Genomics 9: 1-20.
|
Markers for shorebirds: markers that successfully amplified and showed polymorphism in at least 2 of the 3 species tested (amplification success >50%). |