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

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.

Temporal changes in chromosome abnormalities in human spontaneous abortions: Results of 40 years of analysis.

Studies during the past 50 years demonstrate the importance of chromosome abnormalities to the occurrence of early pregnancy loss in humans. Intriguingly, there appears to be considerable variation in the rates of chromosome abnormality, with more recent studies typically reporting higher levels than those reported in early studies of spontaneous abortions. We were interested in examining the basis for these differences and accordingly, we reviewed studies of spontaneous abortions conducted in our laboratories over a 40-year-time span. Our analyses confirm a higher rate of abnormality in more recent series of spontaneous abortions, but indicate that the effect is largely, if not entirely, attributable to changes over time in the maternal age structures of the study populations. © 2016 Wiley Periodicals, Inc.