From genes to landscapes: the distribution of western conifers

2013 Summer.Includes bibliographical references.Managing and conserving forest ecosystems under a rapidly changing climate will require an understanding of the drivers of species distributions across a gradient of temporal and spatial scales. My dissertation research evaluated the relationship between distributional patterns of tree species and the processes driving these patterns from local to continental scales. I addressed three questions: 1) Which local abiotic and biotic processes are most important in determining the distribution of tree species along a hydrologic gradient in southeast Alaska? 2) How is genetic variation partitioned across the range of Pinus contorta, and is this variation explained by geographic or landscape variables? 3) How will Pinus contorta respond to predicted climate change? At the local scale, I assessed the role of abiotic and biotic constraints in limiting three tree species (Pinus contorta, Picea sitchensis, and Tsuga heterophylla) along a hydrologic gradient in southeast Alaska. I used a Bayesian hierarchical model to identify the strongest predictors of species' occurrence and biomass. Model predictions identified abiotic variables, including soil nitrogen, pH, and depth to water, as the primary factors limiting species' success in anaerobic wetland ecosystems. Competition was identified as the limiting factor in aerobic forest ecosystems. At the continental scale, I quantified the impact of historic evolutionary processes in shaping patterns of genetic diversity across the range of Pinus contorta, a widespread and morphologically variable species. I estimated gene flow and assessed the effect of the landscape on population structure. Gene flow is high across the range of the species, and patterns of variation are most strongly influenced by landscape barriers to gene flow and the environmental variation associated with its heterogeneous range. This suggests that, despite widespread gene flow, subspecies are adapted to local conditions. I then used correlative and mechanistic species distribution models to evaluate potential, future habitat suitability at the species and subspecies levels of Pinus contorta. Model results predict that P. contorta will maintain a large portion of its current habitat, but two of the more geographically constrained subspecies will lose a significant portion of suitable habitat. My work provides an understanding of the ecological and evolutionary processes shaping tree species distributions across a gradient of temporal and spatial scales, from historic to current timeframes and local to range-wide extents. Results from my research show that different processes determine patterns of distribution across this gradient of scales. Linking these patterns and processes will be essential for forest management and conservation in light of a rapidly changing climate

A foundation of ecology rediscovered: 100 years of succession on the William S. Cooper plots in Glacier Bay, Alaska

Understanding plant community succession is one of the original pursuits of ecology, forming some of the earliest theoretical frameworks in the field. Much of this was built on the long-term research of William S. Cooper, who established a permanent plot network in Glacier Bay, Alaska, in 1916. This study now represents the longest-running primary succession plot network in the world. Permanent plots are useful for their ability to follow mechanistic change through time without assumptions inherent in space-for-time (chronosequence) designs. After 100-yr, these plots show surprising variety in species composition, soil characteristics (carbon, nitrogen, depth), and percent cover, attributable to variation in initial vegetation establishment first noted by Cooper in the 1916–1923 time period, partially driven by dispersal limitations. There has been almost a complete community composition replacement over the century and general species richness increase, but the effective number of species has declined significantly due to dominance of Salix species which established 100-yr prior (the only remaining species from the original cohort). Where Salix dominates, there is no establishment of “later” successional species like Picea. Plots nearer the entrance to Glacier Bay, and thus closer to potential seed sources after the most recent glaciation, have had consistently higher species richness for 100 yr. Age of plots is the best predictor of soil N content and C:N ratio, though plots still dominated by Salix had lower overall N; soil accumulation was more associated with dominant species. This highlights the importance of contingency and dispersal in community development. The 100-yr record of these plots, including species composition, spatial relationships, cover, and observed interactions between species provides a powerful view of long-term primary succession.Ye

Cognitive estimation:Performance of patients with focal frontal and posterior lesions

The Cognitive Estimation Test (CET) is a widely used test to investigate estimation abilities requiring complex processes such as reasoning, the development and application of appropriate strategies, response plausibility checking as well as general knowledge and numeracy (e.g., Shallice and Evans, 1978; MacPherson et al., 2014). Thus far, it remains unknown whether the CET is both sensitive and specific to frontal lobe dysfunction. Neuroimaging techniques may not represent a useful methodology for answering this question since the complex processes involved are likely to be associated with a large network of brain regions, some of which are not functionally necessary to successfully carry out the CET. Instead, neuropsychological studies may represent a more promising investigation tool for identifying the brain areas necessary for CET performance. We recently developed two new versions of the CET (CET-A and CET-B; MacPherson et al., 2014). We investigated the overall performance and conducted an error analysis on CET-A in patients with focal, unilateral, frontal (n= 38) or posterior (n= 22) lesions and healthy controls (n=39). We found that frontal patients' performance was impaired compared to healthy controls on CET demonstrating that our CET-A is affected by frontal lobe damage. We also found that frontal patients generated significantly poorer estimates than posterior patients on CET-A. This could not be explained by impairments in fluid intelligence. The error analyses suggested that for CET-A, extreme and very extreme responses are impaired following frontal lobe damage. However, only very extreme responses are significantly more impaired following frontal lobe than posterior damage and so represent a measure restricted to frontal "executive" impairment, in addition to overall CET performance

Carbon Storage in Old-Growth Western Larch (Larix occidentalis) Forests of Western Montana

Over the last 30 years, the structural development of western old-growth ecosystems has been of great interest in ecological research. As the loss of historical forested acreage in western Montana became more widely recognized, the preservation of frequent-fire old-growth stands became a focus of forest management. And, although old-growth studies are commonly found in the literature, few studies focus on long-term carbon (C) storage associated with interior old-growth. This limited understanding of the C storage capacity and patterns in old-growth forests of western Montana leaves little ability to evaluate the role of old-growth forests in ecosystem level C storage capacity. Further, there is a disconnect between old-growth definitions and old-growth management. Forest Service definitions for interior old-growth ecosystems inadequately describe the structure, composition, and function of these ecosystems, and definitions applied from the Pacific Northwest do not capture the unique qualities of old-growth of the Northern Rockies. In this thesis, I first present a review of existing literature on definitions and characteristics of old-growth ecosystems of the Pacific Northwest and contrast these with old-growth forests of the Northern Rockies. In the second chapter, I present studies undertaken to generate empiric data on C storage in old-growth forests of this region. Specifically, studies were conducted to compare ecosystem C of old-growth western larch (Larix occidentalis) stands to that of paired 30-40 year old second growth stands in western Montana. Old-growth forests were found to store nearly three times more C than second growth forests, with most of the difference coming from C stored in the overstory. Finally, the third chapter describes a web-based plant guide that simplifies the challenge of plant identification by eliminating the use of technical vocabulary, focusing instead on visually recognizable plant characters and providing students with a more user-friendly means of identifying specimens and obtaining species-specific information

Callitropsis nootkatensis southeast Alaska decline raw plot data (2011-2016)

Callitropsis nootkatensis canopy mortality and regeneration field-collected data from plots across southeast Alaska, USA

Callitropsis nootkatensis southeast Alaska decline summary plot data (2011-2016)

Callitropsis nootkatensis canopy mortality and regeneration field-collected data from plots across southeast Alaska, USA, summarized to the plot level. Additionally, this file includes extracted plot-level climate data (ClimateWNA)

Data from: From canopy to seed: loss of snow drives directional changes in forest composition

Climate change is altering the conditions for tree recruitment, growth, and survival, and impacting forest community composition. Across southeast Alaska, USA, and British Columbia, Canada, Callitropsis nootkatensis (Alaska yellow-cedar) is experiencing extensive climate change-induced canopy mortality due to fine root death during soil freezing events following warmer winters and the loss of insulating snowpack. Here, we examine the effects of ongoing, climate-driven canopy mortality on regeneration and identify potential shifts in stand trajectories due to loss of a single canopy species. We sampled canopy and regenerating communities across the extent of C. nootkatensis decline in southeast Alaska to identify the drivers of C. nootkatensis canopy mortality and regeneration as well as post-decline regenerating community composition. Across the plot network, C. nootkatensis exhibited significantly higher mortality than co-occurring conifers across all size classes and locations. Regenerating community composition was highly variable but closely related to the severity of C. nootkatensis mortality. Callitropsis nootkatensis canopy mortality on the plot network was correlated with winter temperatures and precipitation as well as soil drainage, with C. nootkatensis regeneration abundances and regenerating community composition best explained by available seed source. In areas of high C. nootkatensis mortality, C. nootkatensis regeneration was low and was replaced by Tsuga. Our study suggests that climate-induced forest mortality is driving alternate successional pathways in forests where C. nootkatensis was once a major component. These pathways are likely to lead to long-term shifts in forest community composition and stand dynamics. Our analysis fills a critical knowledge gap on forest ecosystem response and rearrangement following the climate-driven decline of a single species, providing new insight into stand dynamics in a changing climate. As tree species across the globe are increasingly stressed by climate change-induced alteration of suitable habitat, identifying the autecological factors contributing to successful regeneration, or lack thereof, will provide key insight into forest resilience and persistence on the landscape

Alternative interpretation and scale-based context for No evidence of recent (1995-2013) decrease in yellow-cedar in Alaska (Barrett and Pattison 2017)

In their analysis of resampled and remeasured plot data from the U.S. Forest Service Forest Inventory and Analysis (FIA) program, Barrett and Pattison (2017) suggest that there is neither evidence of a recent regional decrease in yellow-cedar (Callitropsis nootkatensis) live tree basal area nor a decrease in the speciesâ extent in southeast Alaska. Here, we identify substantial, broad-scale agreement between their estimated extent of concentrated yellow-cedar mortality and that which results from a complementary, existing body of research into yellow-cedar decline spanning 35 years. We also, however, discuss concerns that the FIA remeasurement data used did not match the spatial distribution of the decline (e.g., excluding areas of known active decline in Wilderness areas) and that the temporal coverage of FIA data (1990s to 2000s) was inappropriately compared to a cumulative decline map that spans several decades, meshing recent mortality with mortality that occurred up to a century ago. We provide an alternative explanation of Barrett and Pattison's results in the context of ongoing yellow-cedar distribution and decline research in southeast Alaska and support our interpretation by focusing on the temporal and spatial aspects of decline.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental variation, phylogeographic history, and population demographic processes all contribute to spatially structured genetic variation, however few current models attempt to separate these confounding effects. To illustrate the benefits of using a spatially-explicit model for identifying potentially adaptive loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi-scale spatial variation present in a data set, were incorporated into a landscape genetic approach relating AFLP frequencies with 23 environmental variables. Four major findings emerged. 1) Fifteen loci were significantly correlated with at least one predictor variable (R (adj) (2) > 0.5). 2) Models including PCNM variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major environmental factors driving potentially adaptive genetic variation in G. nivalis. Techniques presented in this paper offer an efficient method for identifying potentially adaptive genetic variation and associated environmental forces of selection, providing an important step forward for the conservation of non-model species under global change