"Genetics of the Scandinavian brown bear (Ursus arctos): implication for biology and conservation"

• Main Author: Bellemain, Eva
• Other Authors: Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS), Université Joseph-Fourier - Grenoble I, Dr Pierre Taberlet - Pr Jon Swenson (cotutelle)([e-mail] - [e-mail]), Scandinavian Brown Bear Research Project, Norvège
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: HAL CCSD 2004
• Subjects: genetics; population size estimates; mate choice; non invasive methods; mating system; genotyping errors; parentage analysis; Ursus arctos; génétique; conservation; estimation de tailles de populations; infanticide; choix du partenaire; méthodes non invasive; système d'appariement; erreurs de genotypage; analyse de parenté; [SDV.EE]Life Sciences [q-bio]/Ecology; environment
• Online Access: https://theses.hal.science/tel-00122944; https://theses.hal.science/tel-00122944/document; https://theses.hal.science/tel-00122944/file/These_Eva_Bellemain.pdf

This thesis deals with the application of molecular tools, combined with field data, in wildlife management, in conservation and in understanding species' biology and behavior. We used the brown bear (Ursus arctos) as a model species and the Scandinavian bear population as a case study. The first part of this thesis is a methodological part, in which we developed or reviewed technical aspects in molecular biology and parentage analysis; the second part is devoted to the application of molecular genetics to estimate population sizes and to understand mating systems. Noninvasive methods are gaining widespread use in genetic studies as they do not require the handling or disturbance of the study animal. However, DNA recovered from noninvasive samples, such as hairs or feces, is usually degraded and/or in small quantities, leading to genotyping errors and resulting in the identification of incorrect genotypes. This is a major concern, especially for small or endangered populations, as it can lead to biases in population size estimates. With the aim of increasing the quality and quantity of the desired DNA template, and to avoid the need for numerous replicates, we devised a two-step polymerase chain reaction (PCR) method. This “multiplex pre-amplification method” was tested on different species and compared with a conventional PCR approach. It significantly improved microsatellite amplification and decreased error rates for fecal DNA in limiting conditions. To more specifically amplify DNA from noninvasive samples of brown bears, we also redesigned microsatellite primers and one sex-specific primer and combined a semi-nested PCR with the multiplex pre-amplification method. These new approaches could be transposed to other species where conventional PCR methods experience low success due to limiting DNA concentration and/or quality. Genotyping errors remain a taboo subject in population genetics studies, in spite of their occurrence in most datasets and the negative consequences they may cause in the interpretation ...