Academic Journal
Effect of collapsed duplications on diversity estimates: what to expect
| العنوان: | Effect of collapsed duplications on diversity estimates: what to expect |
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| المؤلفون: | Hartasánchez Frenk, Diego Andrés, 1982-, Brasó-Vives, Marina, 1990-, Heredia Genestar, José María, 1985-, Pybus Oliveras, Marc, 1985-, Navarro i Cuartiellas, Arcadi, 1969- |
| بيانات النشر: | Oxford University Press |
| سنة النشر: | 2018 |
| المجموعة: | UPF Digital Repository (Universitat Pompeu Fabra, Barcelona) |
| مصطلحات موضوعية: | Copy number variation, Neutrality statistics, Interlocus gene conversion |
| الوصف: | The study of segmental duplications (SDs) and copy-number variants (CNVs) is of great importance in the fields of genomics and evolution. However, SDs and CNVs are usually excluded from genome-wide scans for natural selection. Because of high identity between copies, SDs and CNVs that are not included in reference genomes are prone to be collapsed-that is, mistakenly aligned to the same region-when aligning sequence data from single individuals to the reference. Such collapsed duplications are additionally challenging because concerted evolution between duplications alters their site frequency spectrum and linkage disequilibrium patterns. To investigate the potential effect of collapsed duplications upon natural selection scans we obtained expectations for four summary statistics from simulations of duplications evolving under a range of interlocus gene conversion and crossover rates. We confirm that summary statistics traditionally used to detect the action of natural selection on DNA sequences cannot be applied to SDs and CNVs since in some cases values for known duplications mimic selective signatures. As a proof of concept of the pervasiveness of collapsed duplications, we analyzed data from the 1,000 Genomes Project. We find that, within regions identified as variable in copy number, diversity between individuals with the duplication is consistently higher than between individuals without the duplication. Furthermore, the frequency of single nucleotide variants (SNVs) deviating from Hardy-Weinberg Equilibrium is higher in individuals with the duplication, which strongly suggests that higher diversity is a consequence of collapsed duplications and incorrect evaluation of SNVs within these CNV regions. ; This work has been supported by Ministerio de Ciencia e Innovación, Spain (BFU2015-68649-P, MINECO/FEDER, UE), the Direcció General de Recerca, Generalitat de Catalunya (2014SGR1311 and 2014SGR866), the Spanish National Institute of Bioinformatics (PT13/0001/0026) of the Instituto de Salud Carlos III, grant ... |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| Relation: | Genome Biol Evol. 2018; 10(11):2899-2905; info:eu-repo/grantAgreement/ES/1PE/BFU2015-68649-P; http://hdl.handle.net/10230/42904; http://dx.doi.org/10.1093/gbe/evy223 |
| DOI: | 10.1093/gbe/evy223 |
| الاتاحة: | http://hdl.handle.net/10230/42904 https://doi.org/10.1093/gbe/evy223 |
| Rights: | © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. ; http://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.E60A8E74 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/gbe/evy223 |
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