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Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.
Darolti, Iulia; Almeida, Pedro; Wright, Alison E; Mank, Judith E.
Afiliación
  • Darolti I; Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
  • Almeida P; Department of Genetics, Evolution and Environment, University College London, London, UK.
  • Wright AE; Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.
  • Mank JE; Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
J Evol Biol ; 35(12): 1646-1658, 2022 12.
Article en En | MEDLINE | ID: mdl-35506576
Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Ciprinodontiformes / Poecilia Tipo de estudio: Guideline / Prognostic_studies Límite: Animals Idioma: En Revista: J Evol Biol Asunto de la revista: BIOLOGIA Año: 2022 Tipo del documento: Article País de afiliación: Canadá

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Ciprinodontiformes / Poecilia Tipo de estudio: Guideline / Prognostic_studies Límite: Animals Idioma: En Revista: J Evol Biol Asunto de la revista: BIOLOGIA Año: 2022 Tipo del documento: Article País de afiliación: Canadá