Development and characterization of 15 polymorphic microsatellite markers for North Pacific albatrosses using paired-end
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Development and characterization of 15 polymorphic microsatellite markers for North Pacific albatrosses using paired-end Illumina shotgun sequencing Luis D. Hernandez • Zachary T. Lounsberry Paul W. Collins • Robert W. Henry • Seth D. Newsome • Benjamin N. Sacks
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Received: 12 December 2013 / Accepted: 30 December 2013 Ó Springer Science+Business Media Dordrecht 2014
Abstract All three species of North Pacific albatross are vulnerable or near threatened (IUCN 2013) yet microsatellite markers to study their population characteristics are lacking. We employed 250-bp paired-end whole genome shotgun sequencing on an Illumina MiSeq platform to discover microsatellite markers. We selected 16 candidate loci for screening in 36 Black-footed (Phoebastria nigripes), 12 Laysan (P. immutabilis), and 3 Short-tailed (P. albatrus) albatrosses from which we characterized 15 markers.
Electronic supplementary material The online version of this article (doi:10.1007/s12686-013-0138-8) contains supplementary material, which is available to authorized users. L. D. Hernandez Z. T. Lounsberry B. N. Sacks Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, One Shields Avenue/Old Davis Rd., Davis, CA 95616, USA P. W. Collins Santa Barbara Museum of Natural History, 2559 Puesta Del Sol, Santa Barbara, CA 93105, USA R. W. Henry Long Marine Laboratory, Center for Ocean Health, Institute of Marine Sciences, University of California, Santa Cruz, 100 Shaffer Rd, Santa Cruz, CA 95060, USA S. D. Newsome Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA B. N. Sacks (&) Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA e-mail: [email protected]
Keywords Albatross Illumina Microsatellite PAL FINDER PCR primers Phoebastria
North Pacific albatrosses, including Black-footed (BFAL), Laysan (LAAL), and Short-tailed (STAL) albatrosses, were historically hunted for their feathers and eggs, precipitating dramatic population crashes in the early twentieth century. Although conservation efforts have helped to stabilize population numbers, these albatrosses continue to face threats from longline fisheries and rising sea levels (e.g., IUCN 2013). Only one study attempted to use microsatellite markers (derived from distantly related seabirds) to study a North Pacific albatross, and only five markers were polymorphic in that species. The microsatellites described here will provide tools needed to better understand the population structure of these threatened seabirds. We extracted genomic DNA from muscle tissue of 36 BFAL, 12 LAAL, and 3 STAL using the Qiagen DNeasy blood and tissue kit following the manufacturer’s protocol. We prepared sequencing libraries using the NEBNextÒ UltraTM DNA Library Prep Kit for IlluminaÒ (New England Biolabs) and NEBNextÒ Multiplex Oligos for Illumina (New England Biolabs) to individually barcode a BFAL, LA
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