If you would like to contribute to the BIRDMARKER databases please contact Dr Deborah Dawson:
email : D.A.Dawson@Sheffield.ac.uk
We have successfully developed two sets of avian microsatellite markers with the highest recorded cross-species utility in songbirds (ca 5000 species) and that are of utility in many other groups of birds. The availability of these markers will save resources (time and money) by alleviating the need to develop species-specific markers. These markers will also enable new comparisons to be made between different bird species using the same marker set and so avoiding ascertainment bias.
The method we used to develop these markers has been applied to multiple other animal taxa - from seahorses, ants and beans to bats and squirrels.
Details of the markers are available in the following publications:
TG markers (n=34)
Dawson et al. (2010) New methods to identify conserved microsatellite loci and develop primer sets of high utility – as demonstrated for birds. Molecular Ecology Resources, 10, 475–494.
CAM markers (n=24)
Dawson et al. (2013) High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics, 14, 176.
Suitability to different bird species:
Songbirds (passerines): Both sets are of utility in songbirds and can be tested in a week.
Non-passerine birds: For non-passerine we recommend testing all the 34 TG markers and the six "Set 1" CAM markers (CAM-06, CAM-13, CAM-17, CAM-18, CAM-20 and CAM-24). These are both a 100% match to chicken (as well as zebra finch). These six CAM loci are expected to display slightly higher variability in non-passerines than the TG loci.
The TG and CAM bird markers have been successfully used in the following species:
|Taxa||Family||No. of species assessed in study||Species||Type of study||Reference|
|Various birds||12 families||12||Multiple passerine and non-passerine species||Marker assessment||Dawson et al. 2010, 2013|
|Various birds||12+ families||23||Multiple passerine and non-passerine species||Assessing egg swabbing as a source of parental DNA||Martin-Gálvez et al. 2011|
|Passerine||Estrildidae||1||Zebra finch||Linkage mapping, parentage
|Ball et al. 2010, DAD unpublished data|
|Passerine||Estrildidae||2||Long-tailed finch subspecies||Population structure and gene flow||Rollins et al. 2012|
|Passerine||Estrildidae||1||Gouldian finch||Plumage genetics||Kim et al. 2015|
|Passerine||Fringillidae||4||Bullfinch, Chaffinch, Crossbill, Greenfinch||Comparing genetic variability between species||Durrant et al. 2010|
|Passerine||Passeridae||1||House sparrow||Population structure||Vangestel et al. 2011, 2012, Dawson et al. 2012|
|Passerine||Passeridae||1||Sociable weaver||Relatedness||van Dijk et al. 2014|
|Passerine||Motacillidae||1||Bertolet’s pipit||Population structure||Spurgin et al. 2014|
|Passerine||Prunellidae||1||Dunnock||Genetic variability UK versus New Zealand||Santos et al. 2013|
|Passerine||Paridae||1||Blue tit||Heterozygosity-fitness, parentage, extra-pair paternity||Olano-Marin et al. 2010,
Smith et al. 2012, Reynolds et al. 2017
|Passerine||Remizidae||12||Penduline tits||Extra-pair paternity||Ball et al. 2017|
|Passerine||Aegithalidae||2||Aegithalos tits||Extra-pair paternity||Li et al. 2012|
|Passerine||Muscicapidae||1||Blackbird||Comparing urban and rural populations||Simeoni et al. 2009, Evans et al. 2009|
|Passerine||Muscicapidae||1||Stonechat||Population structure and song||Mortega et al. in prep|
|Passerine||Acrocephalidae||2 x 3||Multiple warblers||Hybrid identification:
|Lifjeld et al. 2010,
Otterbeck et al. 2013,
Engler et al. 2016
|Passerine||Sturnidae||1||Starling||Population structure||Walkup J. (2013) PhD Thesis|
|Passerine||Corvidae||1||Magpie||Parentage, behavioural study||Martin-Gálvez et al. 2010, Molina-Morales et al. 2012, 2013|
|Passerine||Acanthisittidae||1||Rifleman||Mating strategies||Preston et al. 2013a, 2013b|
|Passerine||Campephagidae||1||Réunion Cuckooshrike||Conservation||Salmona et al. 2010|
|Shorebird, Charadriiformes||Charadriidae||1||Plover||Heterozygosity-fitness and triploid identity||Küpper et al. 2010, 2012|
|Shorebird, Charadriiformes||Scolopacidae||1||Ruff||Linkage mapping, plumage genetics||Farrell et al. 2012, 2013, Küpper et al. 2016|
|Parrot, Psittaciformes||Psittaculidae||1||Peach-faced lovebird||Parentage||Birkhead, Burke et al. in prep|
|Seabird, Procellariiformes||Hydrobatidae||1||Leach’s storm petrel||Population structure||Bicknell et al. 2011, 2012|
|Owl, Strigiformes||Tytonidae||1||Barn owl||Population bottlenecks||Klein et al. 2009, Matics et al. 2017|
Bird microsatellite loci : sources, references, stocks in Sheffield, cross-species utility databases and predicted genome maps
1. Table of Passerine microsatellite loci with references (550 as of November 2004).
2. Reference list for ALL passerine primers currenty available (620 as of November 2004)
3. Seychelles warbler (Ase) loci including unpublished primer sequences
Many of these loci were monomorphic in Seychelles warbler (due to the low genetic variability of this species). The primer sequences for the monomorphic were not permitted to be included in the Richardson et al. 2000 Molecular Ecology paper (standard procedure for monomorphic loci as dictated by the journal, Molecular Ecology).
4. Microsatellites for the zebra finch (Appendix)
5. Microsatellites for the buzzard, Buteo buteo (Johnson et al. 2004, Appendix)
6. Reference list for passerine microsatellite loci in stock at the NBAF-S.
7. Passerine BIRDMARKER Database (a passerine primer cross-utility database)
8. Falconiforme BIRDMARKER Database (an Eagle and Falcon primer cross-utility database)
9. Great reed warbler pedigree linkage map (Hansson et al. 2005, Figure 1)
10. Passerine predicted microsatellite map (Dawson et al. 2006, Figure 1)
11. Comparison of linkage groups in the great reed warbler (left) and predicted passerine chromosomes (right) (Dawson et al. 2006, Figure 2)
12. Predicted chromosome locations of passerine microsatellites (Dawson et al. 2006, Appendix 1).
13. Passerine-chicken sequence alignments (Dawson et al. 2006, Appendix 2).
14. Blank passerine primer test sheet
Blank passerine form to fill in by people wishing to contribute data for any new passerine species tested. Alternatively please add a row to the existing exel databases and highlight your results in red font.
Sources of this data
These databases are the result of Dr Deborah Dawson's work to identify a set of microsatellite markers suitable for genotyping in most species belonging to each family of birds. This data is also being used for a study into avian microsatellite evolution, the factors responsible for cross-species utility and comparative studies of loci across different species.
Additional cross-species utility data from other bird genotyping projects has been kindly contributed from researchers working in Prof Burke's laboratory, here in the Department of Animal and Plant Sciences at Sheffield University and whilst the group was at Leicester. Published data where appropriate has also been added (for source references see the downloadable - Passerine primer references file).
The "Passerine BIRDMARKER Database" includes data from the testing of 99 passerine primers in 43 passerine bird species.
The "Falconiforme BIRDMARKER Database" includes data from the testing of 58 eagle and falcon primers in 15 raptors and 2 other bird species.
We have provided this data as a courtesy in the hope that this will help you in your research. Although we have taken great care to record this data accurately, we do not accept any responsibility for the accuracy or for any costs or damages that you might suffer as a consequence of mistakes in this data.
When using this data please include the following acknowledgements.
"This work was assisted by the BIRDMARKER webpage maintained at the NERC Biomolecular Analysis Facility - Sheffield, UK."
Please also acknowledge the individuals who performed the primer testing for each individual species used and any associated published references (see Table).
Dawson DA (2005) BIRDMARKER database. Department of Animal and Plant Sciences, University of Sheffield, UK. http://www.shef.ac.uk/nbaf-s/databases-BIRDMARKER.html
Dawson DA, Horsburgh GJ, Küpper C, Stewart IRK, Ball AD, Durrant KL, Hansson B, Bacon I, Bird S, Klein Á, Lee J-W, Martín-Gálvez D, Simeoni M, Smith G, Spurgin LG, Burke T (2010) New methods to identify conserved microsatellite loci and develop primer sets of high utility – as demonstrated for birds. Molecular Ecology Resources, 10, 475–494.
Dawson DA, Burke T, Hansson B, Pandhal J, Hale MC, Hinten GN, Slate J (2006) A predicted microsatellite map of the passerine genome based on chicken-passerine sequence similarity. Molecular Ecology, 15, 1299-1320.
Dawson DA, Åkesson M, Burke T, Pemberton JM, Slate J, Hansson B (2007) Gene order and recombination in homologous regions of the chicken and a passerine bird. Molecular Biology and Evolution, 24, 1537-1552.