Effective population size: estimation methods and genome heterogeneity due to selection and recombination

• Autores: Irene Novo Jimenez
• Directores de la Tesis: Armando Caballero Rua (dir. tes.)
• Lectura: En la Universidade de Vigo ( España ) en 2024
• Idioma: inglés
• Tribunal Calificador de la Tesis: Emilio Rolán Álvarez (presid.), Jesús Fernández Martin (secret.), Silvia T. Rodríguez-Ramilo (voc.)
• Programa de doctorado: Programa de Doctorado en Metodología y Aplicaciones en Ciencias de la Vida por la Universidad de Vigo
• Menciones:
  • Internacional
• Calificación: Sobresaliente Cum Laude
• Materias:
  • Ciencias de la vida
    • Genética
      • Genética de poblaciones
  • Demografía
    • Características de la población
      • Características biológicas
• Enlaces
  • Tesis en acceso abierto en: Investigo
• Resumen

  • This doctoral thesis focuses on the concept of effective population size and the approaches available for its estimation, presenting two methods to estimate effective population size from linkage disequilibrium between genetic markers. The first one allows the accurate estimation of contemporary effective population size accounting for a diversity of mating systems. The second is intended for the estimation of the historical effective population size in the recent past, up to about 200 generations back. Along the first chapters, both methods are introduced, compared to other existing methods, and evaluated by means of simulations and empirical data. Thereafter, the thesis addresses the genomic heterogeneity generated by the combined effect of selection and recombination, both for the regional estimates of effective population size and for variants of the human genome that are associated with several traits (pleiotropic variants). The main conclusions of the thesis are: (1) the linkage disequilibrium methods presented improve the previous ones intended for the same purpose; (2) the method to estimate historical effective size is very robust and is mildly affected by genotyping errors, recombination rate heterogeneity and linked selection; (3) population structure analysis is advisable prior to effective population size estimation in order to reduce the artefacts generated by population structure; (4) the combined effects of selection and recombination generate heterogeneity in the effective population sizes along the genome; and (5) the most pleiotropic variants found in GWAS tend to be located in genomic regions in which background selection exerts a stronger impact and, therefore, are subjected to low regional effective population sizes.