title: On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations.
abstract: Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations.
  
  
  
  Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic-pituitary-thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors.
  
  
  
  We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.
authors: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.
authors: Aldemar
authors: A
authors: González-Rodríguez
authors: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.|Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, 1417, Buenos Aires, Argentina.
authors: Sebastián
authors: S
authors: Munilla
authors: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.
authors: Elena F
authors: EF
authors: Mouresan
authors: Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors: Jhon J
authors: JJ
authors: Cañas-Álvarez
authors: Departamento de Mejora Genética Animal, INIA, 28040, Madrid, Spain.
authors: Clara
authors: C
authors: Díaz
authors: Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors: Jesús
authors: J
authors: Piedrafita
authors: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.|Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain.
authors: Juan
authors: J
authors: Altarriba
authors: Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004, Palencia, Spain.
authors: Jesús Á
authors: JÁ
authors: Baro
authors: MERAGEM, Universidad de Córdoba, 14071, Córdoba, Spain.
authors: Antonio
authors: A
authors: Molina
authors: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain. lvarona@unizar.es.|Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain. lvarona@unizar.es.
authors: Luis
authors: 0000-0001-6256-5478
authors: L
authors: Varona
mesh_terms: D000818:Animals; D001947:Breeding / Q000379:methods*; D002417:Cattle / Q000235:genetics* / Q000502:physiology*; D005260:Female; D023281:Genomics; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008297:Male; D053858:Metabolic Networks and Pathways; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D013030:Spain