Development of polymorphic microsatellite loci markers for the Asp viper (Vipera aspis) using high-throughput sequencing and their use for other European vipers

in Amphibia-Reptilia
Restricted Access
Get Access to Full Text
Rent on DeepDyve

Have an Access Token?

Enter your access token to activate and access content online.

Please login and go to your personal user account to enter your access token.


Have Institutional Access?

Access content through your institution. Any other coaching guidance?


The Asp viper (Vipera aspis) is a highly endangered species in the Swiss Plateau and in the Jura Mountains of Switzerland. In the past, numerous populations disappeared due to human activities, but currently the trend is reversed and several locations seem favourable for this species. However, it is not known if the remaining populations are still genetically variable and viable. In this study, 12 new microsatellite loci markers were developed for Vipera aspis using Next Generation Sequencing (NGS) techniques (454 sequencing). All markers proved to be polymorphic with 2-9 alleles. When cross-tested with two Eurasian widespread viper species, 8 of the newly developed loci provided reliable amplification for V. berus and 3 loci for V. ammodytes.

Development of polymorphic microsatellite loci markers for the Asp viper (Vipera aspis) using high-throughput sequencing and their use for other European vipers

in Amphibia-Reptilia


  • AbdelkrimJ.RobertsonB.C.StantonJ.A.L.GemmellN.J. (2009): Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 46: 185-192.

  • BuehlerD.GrafR.HoldereggerR.GugerliF. (2011a): Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpina (Brassicaceae). Am. J. Bot. 98(5): e103-e105.

  • CarlssonM.IsakssonM.HoggrenM.TegelstromH. (2003): Characterization of polymorphic microsatellite markers in the adder, Vipera berus. Mol. Ecol. Notes 3: 73-75.

  • KoningA.P.J.DazaJ.M.SmithE.N.PollockD.D. (2010): Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol. Ecol. Resour. 10: 341-347.

  • CegelskiC.C.WaitsL.P.AndersonN.J. (2003): Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment-based approaches. Mol. Ecol. 12: 2907-2918.

  • ChappleD.G.ThompsonM.B. (2009): Isolation and characterization of microsatellite loci from the invasive delicate skink (Lampropholis delicata), with cross-amplification in other Australian Eugongylus group species. Conserv. Genet. Resour. 1: 55-58.

  • FairclothB.C. (2008): MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol. Ecol. Resour. 8: 92-94.

  • FrereC.H.PrentisP.J.EzazT.GeorgesA. (2012): Isolation and characterisation of novel microsatellite and mitochondrial DNA markers for the Eastern Water Dragon (Physignathus lesueurii). Conserv. Genet. Resour. 4: 113-116.

  • GoudetJ. (1995): FSTAT (Version 1.2): A computer program to calculate F-statistics. J. Hered. 86: 485-486.

  • Gutierrez-RodriguezC.LaskerH.R. (2004): Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas. Mol. Ecol. 13: 2211-2221.

  • HendrixR.HauswaldtJ.S.VeithM.SteinfartzS. (2010): Strong correlation between cross-amplification success and genetic distance across all members of ‘True Salamanders’ (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci. Mol. Ecol. Resour. 10: 1038-1047.

  • HoferU.MonneyJ.-C.DušejG. (2001): Die Reptilien der Schweiz. Verbreitung Lebensräume Schutz. Birkhäuser VerlagBasel. 202 S.

  • JäggiC.BaurB. (1999): Overgrowing forest as a possible cause for the local extinction of Vipera aspis in the northern Swiss Jura mountains. Amphibia-Reptilia 20: 25-34.

  • JogerU.StümpelN. (2005): Handbuch der Reptilien und Amphibien Europas. Band.3/IIB Schlangen (Serpentes) III Viperidae. AULA-Verlag GmbH Weibelsheim.

  • JohnsonJ.A.ToepferJ.E.DunnP.O. (2003): Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens. Mol. Ecol. 12: 3335-3347.

  • KaufmannM. (1893): Les Vipères de France: morsures – traitement. Asselin et HouzeauParis.

  • MetzgerC.FerchaudA.L.GeiserC.UrsenbacherS. (2011): New polymorphic microsatellite markers of the endangered meadow viper (Vipera ursinii) identified by 454 high-throughput sequencing: when innovation meets conservation. Conserv. Genet. Resour. 3: 589-592.

  • MonneyJ.-C.MeyerA. (2005): Rote Liste der gefährdeten Reptilien der Schweiz. Hrsg. Bundesamt für Umwelt Wald und Landschaft Bern und Koordinationsstelle für Amphibien- und Reptilienschutz in der Schweiz Bern. BUWAL-Reihe: Vollzug Umwelt. 50 S.

  • MüllerP.DušejG. (2000): Reptilieninventar beider Basel. Schlussbericht für die Abteilung Natur- und Landschaftsschutz Amt für Raumplanung Kanton Basel Landschaft und für die Fachstelle für Natur- und Landschaftsschutz Stadtgärtnerei Kanton Basel-Stadt. 93 S.

  • OuborgN.J.PiquotY.Van GroenendaelJ.M. (1999): Population genetics, molecular markers and the study of dispersal in plants. J. Ecol. 87: 551-568.

  • PeakallR.SmouseP.E. (2006): GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295.

  • PearseD.E.CrandallK.A. (2004): Beyond F(ST): Analysis of population genetic data for conservation. Conserv. Genet. 5: 585-602.

  • PrimmerC.R.PainterJ.N.KoskinenM.T.PaloJ.U.MeriläJ. (2005): Factors affecting avian cross-species microsatellite amplification. J. Avian. Biol. 36: 348-360.

  • SantanaQ.C.CoetzeeM.P.A.SteenkampE.T.MlonyeniO.X.HammondG.N.A.WingfieldM.J.WingfieldB.D. (2009): Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 46: 217-223.

  • SelkoeK.A.ToonenR.J. (2006): Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9: 615-629.

  • UrsenbacherS.MonneyJ.-C.FumagalliL. (2009): Limited genetic diversity and high differentiation among the remnant adder (Vipera berus) populations in the Swiss and French Jura Mountains. Conserv. Genet. 10: 303-315.

Index Card

Content Metrics

Content Metrics

All Time Past Year Past 30 Days
Abstract Views 47 47 5
Full Text Views 133 133 1
PDF Downloads 20 20 1
EPUB Downloads 0 0 0