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136798 - Contemporary demographic reconstruction methods are robust to genome assembly quality.pdf (5.32 MB)

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

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posted on 2023-05-20, 09:48 authored by Patton, AH, Margres, MJ, Stahlke, AR, Hendricks, S, Lewallen, K, Rodrigo Hamede RossRodrigo Hamede Ross, Ruiz-Aravena, M, Ryder, O, McCallum, HI, Menna JonesMenna Jones, Hohenlohe, PA, Storfer, A
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.

Funding

National Science Foundation

History

Publication title

Molecular Biology and Evolution

Volume

36

Issue

12

Pagination

2906-2921

ISSN

0737-4038

Department/School

School of Natural Sciences

Publisher

Oxford Univ Press

Place of publication

Great Clarendon St, Oxford, England, Ox2 6Dp

Rights statement

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

Repository Status

  • Open

Socio-economic Objectives

Control of pests, diseases and exotic species in terrestrial environments; Terrestrial biodiversity

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