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Contemporary demographic reconstruction methods are robust to genome assembly quality: a case study in Tasmanian devils

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Patton, AH, Margres, MJ, Stahlke, AR, Hendricks, S, Lewallen, K, Hamede, R ORCID: 0000-0003-1526-225X, Ruiz-Aravena, MI ORCID: 0000-0001-8463-7858, Ryder, O, McCallum, HI, Jones, ME ORCID: 0000-0001-7558-9022, Hohenlohe, PA and Storfer, A 2019 , 'Contemporary demographic reconstruction methods are robust to genome assembly quality: a case study in Tasmanian devils' , Molecular Biology and Evolution, vol. 36, no. 12 , pp. 2906-2921 , doi: 10.1093/molbev/msz191.

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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.

Item Type: Article
Authors/Creators:Patton, AH and Margres, MJ and Stahlke, AR and Hendricks, S and Lewallen, K and Hamede, R and Ruiz-Aravena, MI and Ryder, O and McCallum, HI and Jones, ME and Hohenlohe, PA and Storfer, A
Keywords: whole-genome assembly, demographic history, simulation, SMC, SFS, Tasmanian devil, disease
Journal or Publication Title: Molecular Biology and Evolution
Publisher: Oxford Univ Press
ISSN: 0737-4038
DOI / ID Number: 10.1093/molbev/msz191
Copyright Information:

Copyright 2019 the authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

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