A new individual-based spatial approach for identifying genetic discontinuities in natural populations

S. Manel, F. Berthoud, E. Bellemain, M. Gaudeul, G. Luikart, J. E. Swenson, L. P. Waits, Pierre Taberlet, Wolfgang Ahlmer, Paolo Ajmone Marsan, Nadir Alvarez, Enzo Bona, Maurizio Bovio, Elbieta Cieslak, Gheorghe Coldea, Licia Colli, Vasile Cristea, Jean Pierre Dalmas, Thorsten Englisch, Luc GarraudMyriam Gaudeul, Ludovic Gielly, Felix Gugerli, Walter Gutermann, Rolf Holderegger, Nejc Jogan, Alexander A. Kagalo, Grayna Korbecka, Philippe Küpfer, Benoît Lequette, Dominik Roman Letz, Stéphanie Manel, Guilhem Mansion, Karol Marhold, Fabrizio Martini, Zbigniew Mirek, Riccardo Negrini, Harald Niklfeld, Fernando Niño, Massimiliano Patrini, Ovidiu Paun, Marco Pellecchia, Giovanni Perico, Halina Piekos-Mirkowa, Peter Poschlod, Filippo Prosser, Mihai Puscas, Micha Ronikier, Patrizia Rossi, Martin Scheuerer, Gerald Schneeweiss, Peter Schönswetter, Luise Schratt-Ehrendorfer, Fanny Schüpfer, Alberto Selvaggi, Katherina Steinmann, Conny Thiel, Andreas Tribsch, Marcela Van Loo, Manuela Winkler, Thomas Wohlgemuth, Tone Wraber, Niklaus Zimmermann, Gabriel Alziar, Carlo Argenti, Tinka Bacic, Jean Eric Berthouse, Alessio Bertolli, Enrico Bressan, Franc̃ois Breton, Massimo Buccheri, Sonia D'Andrea, Sergio Danieli, Rosanna De Mattei, Thierry Delahaye, Roberto Della Vedova, Cédric Dentant, Alessandra Di Turi, Wolfgang Diewald, Rolland Douzet, Constantin Dragulescu, Philippe Druart, Siegrun Ertl, Delphine Fallour-Rubio, Gino Fantini, Paolo Fantini, Germano Federici, Franco Fenaroli, Viera Feráková, Roberto Ferranti, Francesco Festi, Bozo Frajman, Jean Claude Gachet, Bruno Gallino, Federica Gironi, Gheorghe Groza, Andreas Hilpold, Catherine Jollibert, Denis Jordan, Thomas Kiebacher, Michael Kleih, Michel Lambertin, Cesare Lasen, Petra Mair, Luca Mangili, Diego Marangoni, Carlo Marconi, Marisa Marconi, Hugues Merle, Marco Merschel, Henri Michaud, Luca Miserere, Gian Paolo Mondino, Patrik Mráz, Benoît Offerhaus, Adrian Oprea, Marziano Pascale, Roberto Pascal, Giorgio Perazza, Marián Perny, Jean Louis Polidori, Guy Rebattu, Jean Pierre Roux, Ioan Sârbu, Silvio Scortegagna, Paola Sergo, Natalia Skibitska, Adriano Soldano, Jean Marie Solichon, Simona Strgulc Krajsek, Nadiya Sytschak, Zbigniew Szelag, Filippo Tagliaferri, Peter Turis, Tudor Mihai Ursu, Jérémie Van Es, Jean Charles Villaret, Lukasz Wilk, Sarah Boudon, Sabine Brodbeck, Véronique Finiels, Jean Michel Genis, Hanna Kuciel, Philippe Lagier-Bruno, Chritian Miquel, Virgile Noble, Tjasa Pogacnik Lipovec, Delphine Rioux, Dirk Schmatz, Ivan Valko, Stéphanie Zundel, Christian Boucher, Jean Marie Cevasco, Guillaume Chaude, Dominique Chavy, Bruno Cuervan, Gil Deluermoz, Daniel Demontoux, Laurence Foucault, Jean Félix Gandioli, Ernest Grenier, Emmanuel Icardo, Zoltan Jablonovski, Vincent Kulesza, Mihai Miclãus, Monique Perfus, Daniel Reboul, Alain Rocchia, Robert Salanon

Research output: Contribution to journalArticlepeer-review

Abstract

The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of populations made by adopting an individual-centred approach. Our method is based on assignment tests applied in a moving window over an extensively sampled study area. For each individual, a spatially explicit probability surface is constructed, showing the estimated probability of finding its multilocus genotype across the landscape, and identifying putative migrants. Population boundaries are localized by estimating the mean slope of these probability surfaces over all individuals to identify areas with genetic discontinuities. The significance of the genetic discontinuities is assessed by permutation tests. This new approach has the potential to reveal cryptic population structure and to improve our ability to understand gene flow dynamics across landscapes. We illustrate our approach by simulations and by analysing two empirical datasets: microsatellite data of Ursus arctos in Scandinavia, and amplified fragment length polymorphism (AFLP) data of Rhododendron ferrugineum in the Alps.

Original languageEnglish
Pages (from-to)2031-2043
Number of pages13
JournalMolecular Ecology
Volume16
Issue number10
DOIs
StatePublished - May 1 2007

Keywords

  • Assignment test
  • Genetic discontinuity
  • Moving windows
  • Multilocus genotype
  • Spatial genetics

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