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Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils.
Patton, Austin H; Margres, Mark J; Stahlke, Amanda R; Hendricks, Sarah; Lewallen, Kevin; Hamede, Rodrigo K; Ruiz-Aravena, Manuel; Ryder, Oliver; McCallum, Hamish I; Jones, Menna E; Hohenlohe, Paul A; Storfer, Andrew.
Afiliación
  • Patton AH; School of Biological Sciences, Washington State University, Pullman, WA.
  • Margres MJ; School of Biological Sciences, Washington State University, Pullman, WA.
  • Stahlke AR; Department of Organismic and Evolutionary Biology, Harvard University, MA.
  • Hendricks S; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
  • Lewallen K; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
  • Hamede RK; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
  • Ruiz-Aravena M; School of Natural Sciences, University of Tasmania, Hobart, Australia.
  • Ryder O; School of the Environment, Griffith University, Nathan, Australia.
  • McCallum HI; Institute for Conservation Research, San Diego, CA.
  • Jones ME; School of the Environment, Griffith University, Nathan, Australia.
  • Hohenlohe PA; School of Natural Sciences, University of Tasmania, Hobart, Australia.
  • Storfer A; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
Mol Biol Evol ; 36(12): 2906-2921, 2019 12 01.
Article en En | MEDLINE | ID: mdl-31424552
ABSTRACT
Reconstructing species' demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ∼300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species' effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Demografía / Genoma / Genómica / Marsupiales Tipo de estudio: Evaluation_studies Límite: Animals Idioma: En Revista: Mol Biol Evol Asunto de la revista: BIOLOGIA MOLECULAR Año: 2019 Tipo del documento: Article

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Demografía / Genoma / Genómica / Marsupiales Tipo de estudio: Evaluation_studies Límite: Animals Idioma: En Revista: Mol Biol Evol Asunto de la revista: BIOLOGIA MOLECULAR Año: 2019 Tipo del documento: Article