Assessing the sensitivity of divergence time estimates to locus sampling,calibration points,and model priors in a RAD-seq phylogeny of Carex section Schoenoxiphium

Restriction site-associated DNA sequencing (RAD-seq) and related methods have become relatively common approaches to resolve species-level phylogeny. It is not clear, however, whether RAD-seq data matrices are well suited to relaxed clock inference of divergence times, given the size of the matrices and the abundance of missing data. We investigated the sensitivity of Bayesian relaxed clock estimates of divergence times to alternative analytical decisions on an empirical RAD-seq phylogenetic matrix. We explored the relative contribution of secondary calibration strategies, amount of missing data, and the data partition analyzed to overall variance in divergence times inferred using BEAST MCMC analyses of Carex section Schoenoxiphium (Cyperaceae)—a recent radiation for which we have nearly complete species sampling of RAD-seq data. The crown node for Schoenoxiphium was estimated to be 15.22 (9.56–21.18) Ma using a single calibration point and low missing data, 11.93 (8.07–16.03) Ma using multiple calibration points and low missing data, and 8.34 (5.41–11.22) using multiple calibrations but high missing data. We found that using matrices with more than half of the individuals with missing data inferred younger mean ages for all nodes. Moreover, we have found that our molecular clock estimates are sensitive to the positions of the calibration(s) in our phylogenetic tree (using matrices with low missing data), especially when only a single calibration was applied to estimate divergence times. These results argue for sensitivity analyses and caution in interpreting divergence time estimates from RAD-seq data.     

Involvement of the Reparative DNA Polymerase Pol X of African Swine Fever Virus in the Maintenance of Viral Genome Stability In Vivo

The function of the African swine fever virus (ASFV) reparative DNA polymerase, Pol X, was investigated in the context of virus infection. Pol X is a late structural protein that localizes at cytoplasmic viral factories during DNA replication. Using an ASFV deletion mutant lacking the Pol X gene, we have shown that Pol X is not required for virus growth in Vero cells or swine macrophages under one-step growth conditions. However, at a low multiplicity of infection, when multiple rounds of replication occur, the growth of the mutant virus is impaired in swine macrophages but not in Vero cells, suggesting that Pol X is needed to repair the accumulated DNA damage. The replication of the mutant virus in Vero cells presents sensitivity to oxidative damage, and mutational analysis of viral DNA shows that deletion of Pol X results in an increase in the mutation frequency in macrophages. Therefore, our data reveal a biological role for ASFV Pol X in the context of the infected cell in the preservation of viral genetic information.     

Linkages between unpaved forest roads and streambed sediment: why context matters in directing road restoration

Unpaved forest roads remain a pervasive disturbance on public lands and mitigating sediment from road networks remains a priority for management agencies. Restoring roaded landscapes is becoming increasingly important for many native coldwater fishes that disproportionately rely on public lands for persistence. However, effectively targeting restoration opportunities requires a comprehensive understanding of the effects of roads across different ecosystems. Here, we combine a review and a field study to evaluate the status of knowledge supporting the conceptual framework linking unpaved forest roads with streambed sediment. Through our review, we specifically focused on those studies linking measures of the density of forest roads or sediment delivery with empirical streambed sediment measures. Our field study provides an example of a targeted effort of linking spatially explicit estimates of sediment production with measures of streambed sediment. Surprisingly, our review uncovered few studies (n = 8) that empirically tested the conceptual framework linking unpaved forest roads and streambed sediment, and the results varied considerably. Field results generally supported the conceptual model that unpaved forest roads can control streambed sediment quality, but demonstrated high‐spatial variability in the effects of forest roads on streambed sediment and the need to address hotspots of sediment sources. The importance of context in the effects of forest roads is apparent in both our review and field data, suggesting the need for in situ studies to avoid misdirected restoration actions.