Using large-scale tropical dry forest restoration to test successional theory.

Microclimatic conditions change dramatically as forests age and impose strong filters on community assembly during succession. Light availability is the most limiting environmental factor in tropical wet forest succession; by contrast, water availability is predicted to strongly influence tropical dry forest (TDF) successional dynamics. While mechanisms underlying TDF successional trajectories are not well understood, observational studies have demonstrated that TDF communities transition from being dominated by species with conservative traits to species with acquisitive traits, the opposite of tropical wet forest. Determining how functional traits predict TDF tree species' responses to changing environmental conditions could elucidate mechanisms underlying tree performance during TDF succession. We implemented a 6-ha restoration experiment on a degraded Vertisol in Costa Rica to determine (1) how TDF tree species with different resource-use strategies performed along a successional gradient and (2) how ecophysiological functional traits correlated with tree performance in simulated successional stages. We used two management treatments to simulate distinct successional stages including: clearing all remnant vegetation (early-succession), or interplanting seedlings with no clearing (mid-succession). We crossed these two management treatments (cleared/interplanted) with two species mixes with different resource-use strategies (acquisitive/conservative) to examine their interaction. Overall seedling survival after 2 yr was low, 15.1-26.4% in the four resource-use-strategy × management-treatment combinations, and did not differ between the management treatments or resource-use-strategy groups. However, seedling growth rates were dramatically higher for all species in the cleared treatment (year 1, 69.1% higher; year 2, 143.3% higher) and defined resource-use strategies had some capacity to explain seedling performance. Overall, ecophysiological traits were better predictors of species' growth and survival than resource-use strategies defined by leaf and stem traits such as specific leaf area. Moreover, ecophysiological traits related to water use had a stronger influence on seedling performance in the cleared, early-successional treatment, indicating that the influence of microclimatic conditions on tree survival and growth shifts predictably during TDF succession. Our findings suggest that ecophysiological traits should be explicitly considered to understand shifts in TDF functional composition during succession and that using these traits to design species mixes could greatly improve TDF restoration outcomes.

EditR: A Method to Quantify Base Editing from Sanger Sequencing.

CRISPR-Cas9-Cytidine deaminase fusion enzymes-termed "base editors"-allow targeted editing of genomic deoxycytidine to deoxythymidine (C:G→T:A) without the need for double-stranded break induction. Base editors represent a paradigm shift in gene editing technology due to their unprecedented efficiency to mediate targeted, single-base conversion. However, current analysis of base editing outcomes rely on methods that are either imprecise or expensive and time-consuming. To overcome these limitations, we developed a simple, cost-effective, and accurate program to measure base editing efficiency from fluorescence-based Sanger sequencing, termed "EditR." We provide EditR as a free online tool or downloadable desktop application requiring a single Sanger sequencing file and guide RNA sequence. EditR is more accurate than enzymatic assays, and provides added insight to the position, type, and efficiency of base editing. Furthermore, EditR is likely amenable to quantify base editing from the recently developed adenosine deaminase base editors that act on either DNA (adenosine deaminase base editors [ABEs]) or RNA (REPAIRs) (catalyzes A:T→G:C). Collectively, we demonstrate that EditR is a robust, inexpensive tool that will facilitate the broad application of base editing technology, thereby fostering further innovation in this burgeoning field.