Stable, low-growing plant communities in the western Cascade Mountains : species processes and their implications for rights-of-way management

The processes that lead to stable, low-growing plant communities and the characteristics of the species that form them are of great interest to rights-of-way (ROW) managers and others wishing to better understand plant community resistance to tree invasion on managed landscapes. The use of stable, low-growing plant communities as a mechanism to control tree invasion on ROWs has been widely acknowledged, but little is known about what plant characteristics lead to stable communities or how different treatment methods affect low-growing communities in the Pacific Northwest. The goal of this study was to assess the resistance of stable, low-growing communities to tree invasion on ROW in the Pacific Northwest and to identify common characteristics among the species in these communities that contributed to the formation of stable communities. To address this goal, we investigated 1) the abilities of different species within the low-growing component of the ROW communities to resist invasion by trees and to fill newly created gaps caused by disturbance, 2) the growth patterns and potential for vegetative reproduction of trailing blackberry (Rubus ursinus Cham and Schlecht) and creeping snowberry (Symphoricarpos mollis Nutt.) to understand how different clonal propagation patterns affect spread into unoccupied space and infilling of currently colonized areas, and 3) the effectiveness of several common vegetation control methods for reducing the density of undesirable species and promoting the development of lowgrowing plant communities on ROW. These factors are important processes that determine the stability of a low-growing plant community. This project was conducted at three sites in the western foothills of the Cascade Mountains of Oregon and Washington. Species composition and abundance was measured in roughly 330 2x2 m plots at each site prior to the application of three different treatments aimed at removing tall-growing target species. The plots were measured again two years later to assess changes in species cover. The growth pattern and architecture of trailing blackberry and creeping snowberry was also investigated through the careful excavation of both individual plants and lxi m plots centered in dense thickets of each species. The various treatments used in this study resulted in an average increase in nontarget cover of 65% from 2000 to 2002 while reducing tall target cover by an average of 53%. No difference was found in the change in average nontarget cover or tall target cover among treatments. The effectiveness of the various treatments in reducing target cover varied significantly based on the type of target species being treated. There were no strong differences in resistance among the common lowgrowing species to invasion by tall target species. The range in increase in tall target cover in plots dominated by low-growing species was highly skewed, as tall target cover increased very little in many plots and by as much as 28% in a very few. In the first two years following disturbance, shrubs capable of rapid horizontal expansion through vegetative reproduction, such as trailing blackberry and bracken fern (Pteridium aquilinum), were most successful filling gaps. Their ability to expand rapidly led to their high abundance following disturbance. The successful colonization of gaps by trailing blackberry was a result of its growth pattern, which focused on rapid spread as this species produced new canes annually that grew up to 1.9 m during their first year. This may allow it to be a successful colonizer of gaps. It was also capable of forming dense thickets and averaged 113 stems/m2. The growth pattern of creeping snowberry, which focused more on infilling, may allow it to maintain areas of dense, persistent cover, as it averaged 237 stems/m2 in dense thickets. It was also capable of horizontal spread through the initiation of new ramets along creeping stems. These stems averaged 0.6 m during their first year of growth. Both strategies of growth and spread allowed these shrubs to form thickets of dense vegetation. The use of stable low-growing plant communities as a management tool to reduce tree seedling establishment and growth can have many benefits including reduced costs due to lower tree density and longer periods of time between treatments, increased wildlife habitat, and aesthetic appeal. However, for this management approach to be most successful, one must have an understanding of the plant community where it is being applied, the plant characteristics that will lead to the formation of stable, low-growing communities, and how the different available treatment options will affect the resulting plant community. This study addressed many of these topics to produce a more comprehensive understanding of how stable, low-growing plant communities can be used as a management tool for reducing tree invasion in the Pacific Northwest. The two-year duration of this study, while allowing for many new insights, limited the scope of some of our conclusions. Continued monitoring of these research sites, as has been done in several locations in the northeast United States, would greatly increase the strength of our conclusions

Growth, drought response, and climate‐associated genomic structure in whitebark pine in the Sierra Nevada of California

Abstract Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease‐free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate‐associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens

Assessing trends and vulnerabilities in the mutualism between whitebark pine (Pinus albicaulis) and Clark's nutcracker (Nucifraga columbiana) in national parks of the Sierra-Cascade region.

Dispersal of whitebark pine (Pinus albicaulis Engelm.), a keystone species of many high-elevation ecosystems in western North America, depends on Clark's nutcracker (Nucifraga columbiana Wilson), a seed-caching bird with an affinity for whitebark seeds. To the extent that this dependence is mutual, declines in whitebark seed production could cause declines in nutcracker abundance. Whitebark pine is in decline across much of its range due to interacting stressors, including the non-native pathogen white pine blister rust (Cronartium ribicola J. C. Fisch.). We used avian point-count data and tree surveys from four national park units to investigate whether trends in whitebark pine can explain trends in Clark's nutcracker. Spatial trends were modeled using recent data from two parks, while temporal trends were modeled using longer time-series of nutcracker and whitebark data from two additional parks. To assess the potential dependence of nutcrackers on whitebark, we linked a model of nutcracker density (accounting for detection probability) with a model of whitebark trends, using a Bayesian framework to translate uncertainty in whitebark metrics to uncertainty in nutcracker density. In Mount Rainier National Park, temporal models showed dramatic declines in nutcracker density concurrent with significant increases in whitebark crown mortality and trees infected with white pine blister rust. However, nutcrackers did not trend with whitebark metrics in North Cascades National Park Service Complex. In spatial models of data from Yosemite National Park and Sequoia-Kings Canyon National Park, nutcracker density varied not only with local cover of whitebark but also with elevation and, in Sequoia-Kings Canyon, with cover of another species of white pine. Our results add support for the hypothesis that the mutualism between whitebark pine and Clark's nutcracker is vulnerable to disruption by blister rust, and our approach integrates data across monitoring programs to explore trends in species interactions

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.11Nsciescopu

Expanded encyclopaedias of DNA elements in the human and mouse genomes

AbstractThe human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.11Nsciescopu