Molecular Ecology Resources

© John Wiley & Sons Ltd

Cover image for Vol. 11 Issue s1

Special Issue: SNP Development in Non-Model Organisms

March 2011

Volume 11, Issue Supplement s1

Pages 1–298

  1. SNP Development in Non-Model Organisms

    1. Top of page
    2. SNP Development in Non-Model Organisms
    3. SNP DISCOVERY: CHAIN TERMINATION SEQUENCING
    4. SNP DISCOVERY: NEXT GENERATION SEQUENCING
    5. ANALYTICAL APPROACHES
    6. SNP GENOTYPING AND APPLICATIONS

    1. INTRODUCTION

      Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms (pages 1–8)

      J. E. SEEB, G. CARVALHO, L. HAUSER, K. NAISH, S. ROBERTS and L. W. SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02979.x

  2. SNP DISCOVERY: CHAIN TERMINATION SEQUENCING

    1. Top of page
    2. SNP Development in Non-Model Organisms
    3. SNP DISCOVERY: CHAIN TERMINATION SEQUENCING
    4. SNP DISCOVERY: NEXT GENERATION SEQUENCING
    5. ANALYTICAL APPROACHES
    6. SNP GENOTYPING AND APPLICATIONS
    1. A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida) (pages 9–19)

      MORTEN TANGE OLSEN, VERONICA HIRSH VOLNY, MARTINE BÉRUBÉ, RUNE DIETZ, CHRISTIAN LYDERSEN, KIT M. KOVACS, RICHARD S. DODD and PER J. PALSBøLL

      Article first published online: 10 JAN 2011 | DOI: 10.1111/j.1755-0998.2010.02941.x

    2. Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River (pages 20–30)

      NATHAN R. CAMPBELL and SHAWN R. NARUM

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2011.02977.x

    3. Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss (pages 31–49)

      ALICIA ABADÍA-CARDOSO, ANTHONY J. CLEMENTO and JOHN CARLOS GARZA

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02971.x

    4. Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha (pages 50–66)

      A. J. CLEMENTO, A. ABADÍA-CARDOSO, H. A. STARKS and J. C. GARZA

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02972.x

    5. Assembling a dual purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis (pages 67–70)

      METTE H. H. HANSEN, SEWALL YOUNG, HANNE B. H. JØRGENSEN, CARITA PASCAL, MARK HENRYON and JAMES SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02978.x

    6. Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod, Gadus morhua (pages 71–80)

      JAKOB HEMMER-HANSEN, EINAR EG NIELSEN, DORTE MELDRUP and CHRISTIAN MITTELHOLZER

      Article first published online: 10 JAN 2011 | DOI: 10.1111/j.1755-0998.2010.02940.x

  3. SNP DISCOVERY: NEXT GENERATION SEQUENCING

    1. Top of page
    2. SNP Development in Non-Model Organisms
    3. SNP DISCOVERY: CHAIN TERMINATION SEQUENCING
    4. SNP DISCOVERY: NEXT GENERATION SEQUENCING
    5. ANALYTICAL APPROACHES
    6. SNP GENOTYPING AND APPLICATIONS
    1. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing (pages 81–92)

      ARMANDO GERALDES, JOHNSON PANG, NINA THIESSEN, TIMOTHEE CEZARD, RICHARD MOORE, YONGJUN ZHAO, ANGELA TAM, SHUCAI WANG, MICHAEL FRIEDMANN, INANC BIROL, STEVEN J. M. JONES, QUENTIN C. B. CRONK and CARL J. DOUGLAS

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02960.x

    2. Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome (pages 93–108)

      M. V. EVERETT, E. D. GRAU and J. E. SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02969.x

    3. Unlocking the potential of genomic technologies for wildlife forensics (pages 109–116)

      ROB OGDEN

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02954.x

    4. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout (pages 117–122)

      PAUL A. HOHENLOHE, STEPHEN J. AMISH, JULIAN M. CATCHEN, FRED W. ALLENDORF and GORDON LUIKART

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02967.x

  4. ANALYTICAL APPROACHES

    1. Top of page
    2. SNP Development in Non-Model Organisms
    3. SNP DISCOVERY: CHAIN TERMINATION SEQUENCING
    4. SNP DISCOVERY: NEXT GENERATION SEQUENCING
    5. ANALYTICAL APPROACHES
    6. SNP GENOTYPING AND APPLICATIONS
    1. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges (pages 123–136)

      S. J. HELYAR, J. HEMMER-HANSEN, D. BEKKEVOLD, M. I. TAYLOR, R. OGDEN, M. T. LIMBORG, A. CARIANI, G. E. MAES, E. DIOPERE, G. R. CARVALHO and E. E. NIELSEN

      Article first published online: 10 JAN 2011 | DOI: 10.1111/j.1755-0998.2010.02943.x

    2. Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River Basin (pages 137–149)

      J. E. HESS, A. P. MATALA and S. R. NARUM

      Article first published online: 10 JAN 2011 | DOI: 10.1111/j.1755-0998.2010.02958.x

    3. An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population (pages 150–161)

      LORENZ HAUSER, MELISSA BAIRD, RAY HILBORN, LISA W. SEEB and JAMES E. SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02961.x

    4. Inbreeding effective population size and parentage analysis without parents (pages 162–171)

      ROBIN S. WAPLES and RYAN K. WAPLES

      Article first published online: 10 JAN 2011 | DOI: 10.1111/j.1755-0998.2010.02942.x

    5. Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources (pages 172–183)

      MARINE S. O. BRIEUC and KERRY A. NAISH

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02948.x

    6. Comparison of FST outlier tests for SNP loci under selection (pages 184–194)

      SHAWN R. NARUM and JON E. HESS

      Article first published online: 6 FEB 2011 | DOI: 10.1111/j.1755-0998.2011.02987.x

  5. SNP GENOTYPING AND APPLICATIONS

    1. Top of page
    2. SNP Development in Non-Model Organisms
    3. SNP DISCOVERY: CHAIN TERMINATION SEQUENCING
    4. SNP DISCOVERY: NEXT GENERATION SEQUENCING
    5. ANALYTICAL APPROACHES
    6. SNP GENOTYPING AND APPLICATIONS
    1. Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon (pages 195–217)

      L. W. SEEB, W. D. TEMPLIN, S. SATO, S. ABE, K. WARHEIT, J. Y. PARK and J. E. SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02966.x

    2. Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua (pages 218–225)

      IAN R. BRADBURY, SOPHIE HUBERT, BRENT HIGGINS, SHAREN BOWMAN, IAN G. PATERSON, PAUL V. R. SNELGROVE, COREY J. MORRIS, ROBERT S. GREGORY, DAVID C. HARDIE, TUDOR BORZA and PAUL BENTZEN

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02949.x

    3. Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies (pages 226–246)

      WILLIAM D. TEMPLIN, JAMES E. SEEB, JAMES R. JASPER, ANDREW W. BARCLAY and LISA W. SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02968.x

    4. Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip (pages 247–253)

      STEN KARLSSON, THOMAS MOEN, SIGBJØRN LIEN, KEVIN A. GLOVER and KJETIL HINDAR

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02959.x

    5. Outlier SNPs show more genetic structure between two Bay of Fundy metapopulations of Atlantic salmon than do neutral SNPs (pages 254–267)

      HEATHER FREAMO, PATRICK O’REILLY, PAUL R. BERG, SIGBJØRN LIEN and ELIZABETH G. BOULDING

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02952.x

    6. Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales (pages 268–277)

      MATT J. SMITH, CARITA E. PASCAL, ZAC GRAUVOGEL, CHRISTOPHER HABICHT, JAMES E. SEEB and LISA W. SEEB

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02965.x

    7. Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA (pages 278–298)

      SARAH L. MESNICK, BARBARA L. TAYLOR, FREDERICK I. ARCHER, KAREN K. MARTIEN, SERGIO ESCORZA TREVIÑO, BRITTANY L. HANCOCK-HANSER, SANDRA CAROLINA MORENO MEDINA, VICTORIA L. PEASE, KELLY M. ROBERTSON, JANICE M. STRALEY, ROBIN W. BAIRD, JOHN CALAMBOKIDIS, GREGORY S. SCHORR, PAUL WADE, VLADIMIR BURKANOV, CHRIS R. LUNSFORD, LUKE RENDELL and PHILLIP A. MORIN

      Article first published online: 17 FEB 2011 | DOI: 10.1111/j.1755-0998.2010.02973.x

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