Sydne Record

Advancing population ecology with integral projection models: a practical guide

Summary 1. Integral projection models (IPMs) use information on how an individual’s state influences its vital rates – survival, growth and reproduction – to make population projections. IPMs are constructed from regression models predicting vital rates from state variables (e.g. size or age) and covariates (e.g. environment). By combining regressions of vital rates, an IPM provides mechanistic insight into emergent ecological patterns such as population dynamics, species geographic distributions or life-history strategies. 2. Here, we review important resources for building IPMs and provide a comprehensive guide, with extensive R code, for their construction. IPMs can be applied to any stage-structured population; here, we illustrate IPMs for a series of plant life histories of increasing complexity and biological realism, highlighting the utility of various regression methods for capturing biological patterns. We also present case studies illustrating how IPMs can be used to predict species’ geographic distributions and life-history strategies. 3. IPMs can represent a wide range of life histories at any desired level of biological detail. Much of the strength of IPMs lies in the strength of regression models. Many subtleties arise when scaling from vital rate regressions to population-level patterns, so we provide a set of diagnostics and guidelines to ensure that models are biologically plausible. Moreover, IPMs can exploit a large existing suite of analytical tools developed for matrix projection models.

Pattern and process of biotic homogenization in the New Pangaea

Human activities have reorganized the earths biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from −0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization.

Rapid Inventory of the Ant Assemblage in a Temperate Hardwood Forest: Species Composition and Assessment of Sampling Methods

Abstract Ants are key indicators of ecological change, but few studies have investigated how ant assemblages respond to dramatic changes in vegetation structure in temperate forests. Pests and pathogens are causing widespread loss of dominant canopy tree species; ant species composition and abundance may be very sensitive to such losses. Before the experimental removal of red oak trees to simulate effects of sudden oak death and examine the long-term impact of oak loss at the Black Rock Forest (Cornwall, NY), we carried out a rapid assessment of the ant assemblage in a 10-ha experimental area. We also determined the efficacy in a northern temperate forest of five different collecting methods—pitfall traps, litter samples, tuna fish and cookie baits, and hand collection—routinely used to sample ants in tropical systems. A total of 33 species in 14 genera were collected and identified; the myrmecines, Aphaenogaster rudis and Myrmica punctiventris, and the formicine Formica neogagates were the most common and abundant species encountered. Ninety-four percent (31 of 33) of the species were collected by litter sampling and structured hand sampling together, and we conclude that, in combination, these two methods are sufficient to assess species richness and composition of ant assemblages in northern temperate forests. Using new, unbiased estimators, we project that 38–58 ant species are likely to occur at Black Rock Forest. Loss of oak from these forests may favor Camponotus species that nest in decomposing wood and open habitat specialists in the genus Lasius.

Projecting Global Mangrove Species and Community Distributions under Climate Change

Given the multitude of ecosystem services provided by mangroves, it is important to understand their potential responses to global climate change. Extensive reviews of the literature and manipulative experiments suggest that mangroves will be impacted by climate change, but few studies have tested these predictions over large scales using statistical models. We provide the first example of applying species and community distribution models (SDMs and CDMs, respectively) to coastal mangroves worldwide. Species distributions were modeled as ensemble forecasts using BIOMOD. Distributions of mangrove communities with high species richness were modeled in three ways: as the sum of the separate SDM outputs, as binary hotspots (with >3 species) using a generalized linear model, and continuously using a general boosted model. Individual SDMs were projected for 12 species with sufficient data and CDMs were projected for 30 species into 2080 using global climate model outputs and a range of sea-level rise projections. Species projected to shift their ranges polewards by at least 2 degrees of latitude consistently experience a decrease in the amount of suitable coastal area available to them. Central America and the Caribbean are forecast to lose more mangrove species than other parts of the world. We found that the extent and grain size, at which continuous CDM outputs are examined, independent of the grain size at which the models operate, can dramatically influence the number of pseudo-absences needed for optimal parameterization. The SDMs and CDMs presented here provide a first approximation of how mangroves will respond to climate change given simple correlative relationships between occurrence records and environmental data. Additional, precise georeferenced data on mangrove localities and concerted efforts to collect data on ecological processes across large-scale climatic gradients will enable future research to improve upon these correlative models.

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.

Changes in Forest Composition, Stem Density, and Biomass from the Settlement Era (1800s) to Present in the Upper Midwestern United States

EuroAmerican land use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Gridded (8×8km) estimates of pre-settlement (1800s) forests from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan) using 19th Century Public Land Survey (PLS) records provide relative composition, biomass, stem density, and basal area for 26 tree genera. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection. We compare pre-settlement to modern forests using Forest Inventory and Analysis (FIA) data, with respect to structural changes and the prevalence of lost forests, pre-settlement forests with no current analogue, and novel forests, modern forests with no past analogs. Differences between PLSS and FIA forests are spatially structured as a result of differences in the underlying ecology and land use impacts in the Upper Midwestern United States. Modern biomass is higher than pre-settlement biomass in the northwest (Minnesota and northeastern Wisconsin, including regions that were historically open savanna), and lower in the east (eastern Wisconsin and Michigan), due to shifts in species composition and, presumably, average stand age. Modern forests are more homogeneous, and ecotonal gradients are more diffuse today than in the past. Novel forest assemblages represent 29% of all FIA cells, while 25% of pre-settlement forests no longer exist in a modern context. Lost forests are centered around the forests of the Tension Zone, particularly in hemlock dominated forests of north-central Wisconsin, and in oak-elm-basswood forests along the forest-prairie boundary in south central Minnesota and eastern Wisconsin. Novel FIA forest assemblages are distributed evenly across the region, but novelty shows a strong relationship to spatial distance from remnant forests in the upper Midwest, with novelty predicted at between 20 to 60km from remnants, depending on historical forest type. The spatial relationships between remnant and novel forests, shifts in ecotone structure and the loss of historic forest types point to significant challenges to land managers if landscape restoration is a priority in the region. The spatial signals of novelty and ecological change also point to potential challenges in using modern spatial distributions of species and communities and their relationship to underlying geophysical and climatic attributes in understanding potential responses to changing climate. The signal of human settlement on modern forests is broad, spatially varying and acts to homogenize modern forests relative to their historic counterparts, with significant implications for future management.

The Next Generation of Scientists: Examining the Experiences of Graduate Students in Network-Level Social-Ecological Science

By integrating the research and resources of hundreds of scientists from dozens of institutions, network-level science is fast becoming one scientific model of choice to address complex problems. In the pursuit to confront pressing environmental issues such as climate change, many scientists, practitioners, policy makers, and institutions are promoting network-level research that integrates the social and ecological sciences. To understand how this scientific trend is unfolding among rising scientists, we examined how graduate students experienced one such emergent social-ecological research initiative, Integrated Science for Society and Environment, within the large-scale, geographically distributed Long Term Ecological Research (LTER) Network. Through workshops, surveys, and interviews, we found that graduate students faced challenges in how they conceptualized and practiced social-ecological research within the LTER Network. We have presented these conceptual challenges at three scales: the individual/project, the LTER site, and the LTER Network. The level of student engagement with and knowledge of the LTER Network was varied, and students faced different institutional, cultural, and logistic barriers to practicing social-ecological research. These types of challenges are unlikely to be unique to LTER graduate students; thus, our findings are relevant to other scientific networks implementing new social-ecological research initiatives.

Novel and Lost Forests in the Upper Midwestern United States, from New Estimates of Settlement-Era Composition, Stem Density, and Biomass

Background EuroAmerican land-use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Here we present new gridded (8x8km) reconstructions of pre-settlement (1800s) forest composition and structure from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan), using 19th Century Public Land Survey System (PLSS), with estimates of relative composition, above-ground biomass, stem density, and basal area for 28 tree types. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection. Changes in Forest Structure We compare pre-settlement to modern forests using US Forest Service Forest Inventory and Analysis (FIA) data to show the prevalence of lost forests (pre-settlement forests with no current analog), and novel forests (modern forests with no past analogs). Differences between pre-settlement and modern forests are spatially structured owing to differences in land-use impacts and accompanying ecological responses. Modern forests are more homogeneous, and ecotonal gradients are more diffuse today than in the past. Novel forest assemblages represent 28% of all FIA cells, and 28% of pre-settlement forests no longer exist in a modern context. Lost forests include tamarack forests in northeastern Minnesota, hemlock and cedar dominated forests in north-central Wisconsin and along the Upper Peninsula of Michigan, and elm, oak, basswood and ironwood forests along the forest-prairie boundary in south central Minnesota and eastern Wisconsin. Novel FIA forest assemblages are distributed evenly across the region, but novelty shows a strong relationship to spatial distance from remnant forests in the upper Midwest, with novelty predicted at between 20 to 60km from remnants, depending on historical forest type. The spatial relationships between remnant and novel forests, shifts in ecotone structure and the loss of historic forest types point to significant challenges for land managers if landscape restoration is a priority. The spatial signals of novelty and ecological change also point to potential challenges in using modern spatial distributions of species and communities and their relationship to underlying geophysical and climatic attributes in understanding potential responses to changing climate. The signal of human settlement on modern forests is broad, spatially varying and acts to homogenize modern forests relative to their historic counterparts, with significant implications for future management.

Graduate students navigating social-ecological research: insights from the Long-Term Ecological Research Network

Interdisciplinary, collaborative research capable of capturing the feedbacks between biophysical and social systems can improve the capacity for sustainable environmental decision making. Networks of researchers provide unique opportunities to foster social-ecological inquiry. Although insights into interdisciplinary research have been discussed elsewhere, they rarely address the role of networks and often come from the perspectives of more senior scientists. We have provided graduate student perspectives on interdisciplinary degree paths from within the Long-Term Ecological Research (LTER) Network. Focusing on data from a survey of graduate students in the LTER Network and four self-identified successful graduate student research experiences, we examined the importance of funding, pedagogy, research design and development, communication, networking, and culture and attitude to students pursuing social-ecological research. Through sharing insights from successful graduate student approaches to social-ecological research within the LTER Network, we hope to facilitate dialogue between students, faculty, and networks to improve training for interdisciplinary scientists.

Seedling survival responses to conspecific density, soil nutrients, and irradiance vary with age in a tropical forest.

Understanding processes that promote species coexistence is integral to diversity maintenance. In hyperdiverse tropical forests, local conspecific density (LCD) and light are influential to woody seedling recruitment and soil nutrients are often limiting, yet the simultaneous effects of these factors on seedling survival across time remain unknown. We fit species- and age-specific models to census and resource data of seedlings of 68 woody species from a Costa Rican wet tropical forest. In decreasing order of prevalence, seedling survivorship was related to LCD, soil base cations, irradiance, nitrogen, and phosphorus. Species-specific responses to factors did not covary, providing evidence that species life history strategies have not converged to one continuum of high-surviving stress tolerant to low-surviving stress intolerant species. Survival responses to all factors varied over the average seedlings lifetime, indicating seedling requirements change with age and conclusions drawn about processes important to species coexistence depend on temporal resolution.