Skills and Knowledge for Data-Intensive Environmental Research.

The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap

Economic Impacts of Non-Native Forest Insects in the Continental United States

Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United States but estimates of broad-scale economic impacts associated with these species are largely unavailable. We developed a novel modeling approach that maximizes the use of available data, accounts for multiple sources of uncertainty, and provides cost estimates for three major feeding guilds of non-native forest insects. For each guild, we calculated the economic damages for five cost categories and we estimated the probability of future introductions of damaging pests. We found that costs are largely borne by homeowners and municipal governments. Wood- and phloem-boring insects are anticipated to cause the largest economic impacts by annually inducing nearly $1.7 billion in local government expenditures and approximately$830 million in lost residential property values. Given observations of new species, there is a 32% chance that another highly destructive borer species will invade the U.S. in the next 10 years. Our damage estimates provide a crucial but previously missing component of cost-benefit analyses to evaluate policies and management options intended to reduce species introductions. The modeling approach we developed is highly flexible and could be similarly employed to estimate damages in other countries or natural resource sectors

Economic Impacts of Non-Native Forest Insects in the Continental United States

Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United States but estimates of broad-scale economic impacts associated with these species are largely unavailable. We developed a novel modeling approach that maximizes the use of available data, accounts for multiple sources of uncertainty, and provides cost estimates for three major feeding guilds of non-native forest insects. For each guild, we calculated the economic damages for five cost categories and we estimated the probability of future introductions of damaging pests. We found that costs are largely borne by homeowners and municipal governments. Wood- and phloem-boring insects are anticipated to cause the largest economic impacts by annually inducing nearly $1.7 billion in local government expenditures and approximately$830 million in lost residential property values. Given observations of new species, there is a 32% chance that another highly destructive borer species will invade the U.S. in the next 10 years. Our damage estimates provide a crucial but previously missing component of cost-benefit analyses to evaluate policies and management options intended to reduce species introductions. The modeling approach we developed is highly flexible and could be similarly employed to estimate damages in other countries or natural resource sectors

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Dispersal and spatial distribution of the desert mistletoe, Phoradendron californicum, at multiple scales: Patterns, processes and mechanisms

Describing processes that lead to the distribution of parasites in space is important for understanding disease transmission and spread. Similarly, describing plant distribution patterns is important to understanding ecological processes. Indeed, distinguishing between dispersal and establishment limitation is central in plant ecology. Mistletoes allow doing both because they are plant parasites with clearly defined spatial distributions among hosts. Most mistletoes are dispersed by birds that consume mistletoe berries and defecate seeds onto host trees in a mutualistic relationship. I studied desert mistletoes, Phoradendron californicum (Viscaceae), which in the Sonoran desert, parasitize legume trees and are dispersed by Phainopepla nitens (phainopeplas). I examined patterns of spatial distribution and dispersal of P. californicum and the processes and mechanisms underlying these patterns at multiple scales. By counting mistletoes and deposited mistletoe-seeds, and watching phainopepla behavior, I found that mistletoes were aggregated within host trees, and that seed deposition was highest in tall and infected hosts. Likewise, phainopeplas perched preferentially in these trees, creating a positive feedback in which highly infected trees received many seeds and were likely to become reinfected. However, phainopeplas spent less time in trees than it takes for a seed to pass through their guts, which suggested interhost seed dispersal. I conducted a mistletoe removal experiment that confirmed a high degree of inter-host seed dispersal. These observations suggested that mistletoes would be aggregated at scales larger than individual trees. By mapping mistletoes and defecated seeds within a 4-hectare plot, I found that mistletoes were spatially correlated to at least 145 meters. Sampling at larger scales indicated that mistletoe prevalence was spatially correlated to approximately 1500 m and at scales larger than 4000 m. I also found that seed deposition increased with mistletoe prevalence in local neighborhoods. In conclusion, mistletoes are dispersal limited plants and are spatially correlated at several scales. Desert mistletoes are aggregated within hosts and their prevalence is spatially correlated at 4000 m. At the individual and local scales, their distribution is shaped by where birds defecate, which is influenced by host and neighborhood characteristics. At larger scales, their distribution may be primarily influenced by abiotic effects

Distribution and dispersal of desert mistletoe is scaledependent, hierarchically nested

Spatial patterns are important to many ecological processes, and scale is a critical component of both patterns and processes. I examined the pattern and scale of the spatial distribution of infection of host plants by the desert mistletoe, Phoradendron californicum, in a landscape that spans several square kilometers. I also studied the relationship between mistletoe infection and seed dispersal. I found elevated seed rain in areas with a high prevalence of mistletoes and I found that a greater proportion of trees receive seeds than are infected, suggesting that mistletoes will be aggregated in space. Using nested analysis of variance and variograms, I found that mistletoe infections were distributed in hierarchical patches. Mistletoes were aggregated within trees and mistletoe prevalence was correlated at scales of B/1500 m, and at scales /4000 m. Patterns at the largest scales were correlated with elevation: sites at higher elevations showed reduced mistletoe infection compared to those at lower elevations. I propose that at small scales, mistletoe distributions are primarily the result of aggregation of seed-dispersing birds, and that the elevational effect could reflect the recent colonization of higher elevations by the mistletoes&apos; mesquite hosts or the limits of the mistletoes&apos; physiological tolerance to freezing-induced cavitation

Appendix A. A table showing results of multiple regression models.

A table showing results of multiple regression models

Landscape assessment of tree communities in the northern karst region of Puerto Rico

The northern karst of Puerto Rico is a unique formation that contains one of the island’s largest remaining forested tracts. The region is under ever-increasing human pressure, but large portions of it are being considered for conservation. Forest classification of the region is at a coarse scale, such that it is considered one vegetation type. We asked whether there were distinct tree assemblages which would necessitate targeted conservation strategies to ensure their protection. We examined tree species and communities across the region at three different major topographic positions along mogotes, or haystack-shaped hills. We found distinct tree communities on hilltops and valleys, with significantly more non-native species in valleys and significantly more endemic species on hilltops and hillsides. At a landscape level, we identified at least four different communities within each topographic position. Two mogote top communities were separated geographically (west and south) within the region, while two others co-occurred in the east-central part of the region. Mogote side and valley communities were less distinct geographically. Temperature, elevation, and precipitation were important variables in separating some communities, suggesting that abiotic stress may play an important role in the distribution of some species. In contrast, the lack of geograp hic separations of other communities suggested that variables such as soil conditions, land use and biotic interactions such as dispersal limitation may also be important. Conservation planning strategies should target the south, west, and east-central areas that harbor distinct mogote top plant communities to ensure protection of the widest range of tree species and communities in the karst region