Deborah Dawson's BIRDMARKER Homepage

If you would like to contribute to the BIRDMARKER databases please contact Deborah Dawson on:

email : D.A.Dawson@Sheffield.ac.uk

Latest Developments

We have developed two sets of avian microsatellite markers with the highest recorded cross-species utility in passerines and of utility in other bird orders, please see:

TG markers
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
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.
  

Examples of studies successfully using the TG and CAM multi-species markers
Taxa
Family No. of species assessed in study
Species
Type of study
Reference
Various birds Multiple 12 Multiple passerine and non-passerine species Marker assessment Dawson et al. 2010, 2013
Various birds
Multiple 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
(multiplex set)
Ball et al. 2010, DAD unpublished data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, Burke et al. unpublished data
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 Hatchwell et al. unpublished data
Passerine Motacillidae 1 Bertolet’s pipit
Population structure
Spurgin et al. submitted
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, submitted
Passerine Paridae 12 Paridae species
Comparing genetic variability between species
Ball et al. unpublished data
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. unpublished data
Passerine Acrocephalidae 2 x 3 Multiple warblers
Hybrid identification:
marsh-sedge,
reed-marsh,
melodious-icterine
Lifjeld et al. 2010,
Otterbeck et al. 2013,
Engler et al. submitted
Passerine Sturnidae 1 Starling
Population structure
Walkup et al. in prep
Passerine Corvidae 1 Magpie
Parentage, behavioural study
Martin-Gálvez et al. 2010, Molina-Morales et al. 2012, submitted
Passerine Acanthisittidae 1 Rifleman
Mating strategies
Preston et al. 2013, in press
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, in press
Parrot, Psittaciformes Psittaculidae 1 Peach-faced lovebird
Parentage
Birkhead 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. in prep

 

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).

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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 an on-going study 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 passerine database see 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.

Please Note:
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.

Acknowledgement request

When using this data please include the following acknowledgements.

"This work was assisted by Deborah Dawson's 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.

Citation

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

These results are part of an on-going study into bird microsatellite loci cross-utility, the results will be published in the near future.

References

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.