Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian Devils. Sarcophilus harrisii isolate:DoveGen-2018

Reconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods using either the sequential Markovian coalescent (SMC) or the site-frequency spectrum (SFS) have been developed to reconstruct population size histories from genomic sequence data. However, despite their widespread use, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we assess the performance of two recently developed methods, SMC++, Stairway Plot and two more commonly used methods (PSMC and MSMC) on two genome assemblies of the Tasmanian Devil that differ in assembly quality. We scaffold-length distribution, although results differ among methods leveraging either the SMC or SFS. Methods dependent on the SMC appear to detect accurately population declines associated with relatively ancient geological, climatic and anthropogenic events, whereas methods dependent on the SFS detect demonstrate each method is robust to genome quality, producing similar estimates of Ne regardless of more recent population declines. Taken together, our results suggest: 1) that whole genome methods for reconstructing species’ effective population size histories can be applied to non-model organisms without highly curated reference genomes; 2) methods are capable of accurately detecting independently documented effects of historical geological events; and, 3) a combination of methods should be used, with methods reliant on the SFS detecting recent demographic events and those reliant on the SMC more accurately detecting older events.