Format

Send to

Choose Destination
Mol Biol Evol. 2019 Dec 1;36(12):2906-2921. doi: 10.1093/molbev/msz191.

Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils.

Author information

1
School of Biological Sciences, Washington State University, Pullman, WA.
2
Department of Organismic and Evolutionary Biology, Harvard University, MA.
3
Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
4
School of Natural Sciences, University of Tasmania, Hobart, Australia.
5
School of the Environment, Griffith University, Nathan, Australia.
6
Institute for Conservation Research, San Diego, CA.

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.

KEYWORDS:

SFS; SMC; Tasmanian devil; demographic history; simulation; whole-genome assembly

PMID:
31424552
PMCID:
PMC6878949
DOI:
10.1093/molbev/msz191
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center