RT Journal Article
SR Electronic
T1 Population size history from short genomic scaffolds: how short is too short?
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 382036
DO 10.1101/382036
A1 Graham Gower
A1 Jono Tuke
A1 AB Rohrlach
A1 Julien Soubrier
A1 Bastien Llamas
A1 Nigel Bean
A1 Alan Cooper
YR 2018
UL http://biorxiv.org/content/early/2018/08/03/382036.abstract
AB The Pairwise Sequentially Markov Coalescent (PSMC), and its extension PSMC′, model past population sizes from a single diploid genome. Both models have been widely applied, even to organisms with scaffold-level genome reference assemblies of limited contiguity. However it is unclear how PSMC and PSMC′ perform on short scaffolds. We evaluated psmc and msmc, implementations of the PSMC and PSMC′ models respectively, on simulated genomes with low contiguity, and compared results to those from fully contiguous data. Simulations with scaffolds from 100 Mb to 10 kb revealed that psmc maintains high accuracy down to lengths of 100 kb, while msmc is accurate down to 1 Mb. The discrepancy is not due to differing models, but stems from an implementation detail of msmc—homozygous tracts at the ends of scaffolds are discarded, making msmc unreliable for low contiguity genomes. We recommend excluding data that are aligned to shorter scaffolds when undertaking demographic inference.