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Norman, Anita J, 2011. De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos). Second cycle, A2E. Umeå: SLU, Dept. of Wildlife, Fish and Environmental Studies

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Abstract

Development of molecular markers that are well-suited for use in studies on wildlife dispersal can greatly enhance conservation efforts of species affected by climate change and human-induced landscape alterations. Single nucleotide polymorphisms (SNPs) are a promising marker for such studies; however, development of SNPs in non-model species with limited or no sequence data can be challenging. This study addresses these challenges in a unique way. Reduced representation libraries (RRL) of ten individual brown bears representing the geographic range in Sweden were high-throughput sequenced on one lane of the Illumina HiSeq2000, yielding reads 100 bases in length. These reads were filtered and processed following two methods: assembly using ABySS and alignment using Stacks. Putative SNPs were then called. The alignment-only method using Stacks was not only simpler and more efficient, it also utilized 4X more reads and yielded 30X more SNPs than the assembly method. The putative SNPs showed a clear haplotype pattern that distinguished the two known lineages of brown bear in Sweden. The outcome of this study is a good start for further work in the development of a SNP-based dispersal model with the brown bear as the model species.

Main title:De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos)
Authors:Norman, Anita J
Supervisor:Spong, Göran
Examiner:Thulin, Carl-Gustaf
Series:Examensarbete i biologi
Volume/Sequential designation:2011:6
Year of Publication:2011
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:SM003 Management of Fish and Wildlife Populations - Master's Programme 120 HEC
Department:(S) > Dept. of Wildlife, Fish and Environmental Studies
Keywords:SNPs, brown bear, Ursus arctos, reduced representation, high-throughput sequencing
URN:NBN:urn:nbn:se:slu:epsilon-s-447
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-447
Subjects:Animal ecology
Language:English
Deposited On:06 Jul 2011 12:43
Metadata Last Modified:20 Apr 2012 14:21

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