On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations.

Autor: González-Rodríguez A; Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain., Munilla S; 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., Mouresan EF; Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain., Cañas-Álvarez JJ; Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain., Díaz C; Departamento de Mejora Genética Animal, INIA, 28040, Madrid, Spain., Piedrafita J; Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain., Altarriba J; Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.; Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain., Baro JÁ; Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004, Palencia, Spain., Molina A; MERAGEM, Universidad de Córdoba, 14071, Córdoba, Spain., Varona L; 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.
Jazyk: angličtina
Zdroj: Genetics, selection, evolution : GSE [Genet Sel Evol] 2016 Oct 28; Vol. 48 (1), pp. 81. Date of Electronic Publication: 2016 Oct 28.
DOI: 10.1186/s12711-016-0258-1
Abstrakt: Background: 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.
Results: 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.
Conclusions: 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.
Databáze: MEDLINE
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