title: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).
abstract: The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content.
authors.affiliation: Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.|Área de Biología Animal, Dpto. de Zoología y Antropología Física, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Muñoz
authors.affiliation: Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.|Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors.forename: Dora
authors.initials: D
authors.lastname: Henriques
authors.affiliation: Área de Biología Animal, Dpto. de Zoología y Antropología Física, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Jara
authors.affiliation: Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA.
authors.forename: J Spencer
authors.initials: JS
authors.lastname: Johnston
authors.affiliation: Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.
authors.forename: Julio
authors.initials: J
authors.lastname: Chávez-Galarza
authors.affiliation: Área de Biología Animal, Dpto. de Zoología y Antropología Física, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain.
authors.forename: Pilar
authors.identifier: http://orcid.org/0000-0002-0058-1402
authors.initials: P
authors.lastname: De La Rúa
authors.affiliation: Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.
authors.forename: M Alice
authors.initials: MA
authors.lastname: Pinto
mesh_terms: D000818:Animals; D001516:Bees / Q000235:genetics*; D056727:Endangered Species; D005060:Europe; D005838:Genotype; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide
keywords: 
  Apis mellifera mellifera
  ; SNPs; dark European honeybee; honeybee conservation; introgression; microsatellites