BIRDMARKER

Latest developments

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, 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Passerine	Estrildidae	1	Zebra finch	Linkage mapping, parentage (multiplex set)	Ball et al. 2010, DAD unpublished data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	4	Gouldian finch	Plumage genetics	Kim et al. 2015
Passerine	Fringillidae	1	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: marsh-sedge, reed-marsh, melodious-icterine	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 currently 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 NEOF
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 Excel 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 School of Biosciences 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.

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

When using this data please include the citation:

"Dawson DA (2005) BIRDMARKER database. School of Biosciences, University of Sheffield, UK."

Please also acknowledge the individuals who performed the primer testing for each individual species used, and any associated published references (see above table).

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.