Reply to Elmendorf and Ettinger: Photoperiod playsa dominantand irreplaceable role in triggering secondary growth resumption

In their Letter, Elmendorf and Ettinger (1) question the dominant role of photoperiod in driving secondary growth resumption (hereafter referred to as xylem formation onset) of the Northern Hemisphere conifers, recently reported by Huang et al. (2). Their opinions are grounded on the following three aspects, including 1) the seasonality of the photoperiod, 2) the dependence of the predictor variables (e.g., photoperiod, forcing, and chilling) on the response variable (the date of onset of xylem formation, day of the year [DOY]), and 3) the limited value of the obtained models for interannual forecasting. We think they bring up an interesting issue that deserves further discussion and clarification. Photoperiod is acknowledged to regulate spring bud swelling while wood formation starts (3, 4). Although photoperiod seasonality occurs at each site, its influence is marginal in our study given that the analysis involved comparisons among sites across the Northern Hemisphere. Our conclusion that photoperiod plays a dominant role was built upon the combination of several coherent pieces of evidence, rather than “the crux of Huang et al….” as they pointed out. First, we clearly stated that model 2, which modeled DOY as a function of the mean annual temperature of the site (MAT), forcing, chilling, and soil moisture, was considered the best model in terms of parsimony according to minimum Akaike information criterion and Bayesian information criterion, rather than R2 as referred to in their Letter. Second, photoperiod interacted with MAT and can explain 61.7% of the variance of MAT alone (2). Therefore, we concluded that secondary growth resumption was driven primarily by MAT and photoperiod or by their interaction, which is challenging to be disentangled without experimental data, we agree. In terms of biological functioning, they play an ..

Sensitivity analysis, molecular systematics and natural history evolution of Scathophagidae (Diptera: Cyclorrhapha: Calyptratae)

The 60 000 described species of Cyclorrhapha are characterized by an unusual diversity in larval life-history traits, which range from saprophagy over phytophagy to parasitism and predation. However, the direction of evolutionary change between the different modes remains unclear. Here, we use the Scathophagidae (Diptera) for reconstructing the direction of change in this relatively small family ( 250 spp.) whose larval habits mirror the diversity in natural history found in Cyclorrhapha. We subjected a molecular data set for 63 species (22 genera) and DNA sequences from seven genes (12S, 16S, Cytb, COI, 28S, Ef1-alfa, Pol II) to an extensive sensitivity analysis and compare the performance of three different alignment strategies (manual, Clustal, POY). We find that the default Clustal alignment performs worst as judged by character incongruence, topological congruence and branch support. For this alignment, scoring indels as a fifth character state worsens character incongruence and topological congruence. However, manual alignment and direct optimization perform similarly well and yield near-identical trees, although branch support is lower for the direct-optimization trees. All three alignment techniques favor the upweighting of transversion. We furthermore confirm the independence of the concepts ‘‘node support’’ and ‘‘node stability’’ by documenting several cases of poorly supported nodes being very stable and cases of well supported nodes being unstable. We confirm the monophyly of the Scathophagidae, its two constituent subfamilies, and most genera. We demonstrate that phytophagy in the form of leaf mining is the ancestral larval feeding habit for Scathophagidae. From phytophagy, two shifts to saprophagy and one shift to predation has occurred while a second origin of predation is from a saprophagous ancestor