Development, characterisation and cross-species amplification of 16 novel microsatellite markers for the endangered Blac
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Development, characterisation and cross-species amplification of 16 novel microsatellite markers for the endangered Blackthroated Finch (Poephila cincta) in Australia Lei Tang • Carolyn Smith-Keune • Michael G. Gardner Britta Denise Hardesty
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Received: 30 July 2013 / Accepted: 13 August 2013 / Published online: 19 August 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract The Black-throated Finch (Southern) (Poephila cincta cincta) is threatened by the substantial landscape changes in northern Australia. We developed 16 polymorphic microsatellite markers using 454-shotgun wholegenome sequencing technology. We identified an average of 4.7 alleles per locus based on 63 wild caught individuals from Townsville, Queensland. Thirteen and 9 markers were also successfully cross-amplified in two confamilial species, the Double-barred Finch (Taeniopygia bichenovii) and the chestnut-breasted Mannikin (Lonchura castaneothorax) with 11 and 5 were polymorphic, respectively. These markers will help understand the population genetic structure of the endangered Black-throated Finch and determine genetic consequences of landscape changes for the species. Keywords Black-throated Finch Poephila cincta Microsatellite Conservation genetics Next generation sequencing
Approximately one-third of granivorous birds in northern Australia are in decline due to the substantial landscape changes in the region (Franklin et al. 2005). The Blackthroated Finch (Poephila cincta cincta) is one such declining species and it is listed as ‘‘Endangered’’ under the Environmental Protection and Biodiversity Conservation Act 1999 (Commonwealth). We described the development of 16 polymorphic nuclear microsatellite markers for P. c. cincta using 454-shotgun whole-genome sequencing technology. These markers are useful to quantify population connectivity of P. c. cincta and to investigate the genetic consequences of landscape changes. We also described preliminary tests of cross-species amplification of these markers on two confamilial species, the Double-barred Finch (Taeniopygia bichenovii) and the chestnut-breasted Mannikin (Lonchura castaneothorax). We extracted and purified genomic DNA (5 lg) from one blood sample of P. c. cincta stored on Classic FTAÒ cards (Whatman, USA) using ISOLATE Genomic DNA
L. Tang School of Earth and Environmental Sciences, James Cook University, Townsville, QLD 4811, Australia
M. G. Gardner School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
L. Tang CSIRO Ecosystem Sciences, Private Bag PO Aitkenvale, Townsville, QLD 4811, Australia
M. G. Gardner Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, SA 5000, Australia
L. Tang C. Smith-Keune School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
M. G. Gardner Evolutionary Biology Unit, South Australian Museum, Adelaide, SA 5000, Australia
Present Address: L. Tang (&) Australian Tropical Science and Innovation Precinct,
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