Person: Ellison, Aaron
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Ellison
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Ellison, Aaron
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Publication Diverse Populations are Conflated with Heterogeneous Collectives(Philosophy Documentation Center, 2021) Shavit, Ayelet; Ellison, AaronThe concept of difference has a long and important research tradition. We identify and explicate a heretofore overlooked distinction in the meaning and measurement of two different meanings ‘difference’: ‘diversity’ and ‘heterogeneity’. We argue that ‘diversity’ can describe a population well enough but does not describe a collective well. In contrast, ‘heterogeneity’ describes a collective better than a population and therefore ought to describe a collective. We argue that ignoring these distinctions can lead to a surprising and disturbing conflict between diversity and heterogeneity. In particular, focusing on the ‘diversity’ of human communities can be self-defeating for those who truly care about the importance of diversity, inclusion, and belonging.Publication Should Species Distribution Models Account for Spatial Autocorrelation? A Test of Model Projections Across Eight Millennia of Climate Change(Wiley, 2013-03-12) Record, Sydne; Fitzpatrick, Matthew C.; Finley, Andrew O.; Veloz, Sam; Ellison, AaronAim: The distributions of many organisms are spatially autocorrelated, but it is unclear whether including spatial terms in species distribution models (SDMs) improves projections of species distributions under climate change. We provide one of the first comparative evaluations of the ability of a purely spatial SDM, a purely non-spatial SDM and a SDM that combines spatial and environmental information to project species distributions across eight millennia of climate change. Location: Eastern North America. Methods: To distinguish between the importance of climatic versus spatial explanatory variables we fit three Bayesian SDMs to modern occurrence data for Fagus and Tsuga, two tree genera whose distributions can be reliably inferred from fossil pollen: a spatially varying intercept model, a non-spatial model with climatic variables and a spatially varying intercept plus climate model. Using palaeoclimate data with a high temporal resolution, we hindcasted the SDMs in 1000-year time steps for 8000 years, and compared model projections with palynological data for the same periods. Results: For both genera, spatial SDMs provided better fits to the calibration data, more accurate predictions of a hold-out validation dataset of modern trees and higher variance in current predictions and hindcasted projections than non-spatial SDMs. Performance of non-spatial and spatial SDMs according to the area under the receiver operating curve varied by genus. For both genera, false negative rates between non-spatial and spatial models were similar, but spatial models had lower false positive rates than non-spatial models. Main conclusions: The inclusion of computationally demanding spatial random effects in SDMs may be warranted when ecological or evolutionary processes prevent taxa from shifting their distributions or when the cost of false positives is high.Publication When a foundation crumbles: forecasting forest dynamics following the decline of the foundation species Tsuga canadensis(Wiley-Blackwell, 2017) Case, Bradley S.; Buckley, Hannah L.; Barker-Plotkin, Audrey; Orwig, David; Ellison, AaronIn the forests of northeastern North America, invasive insects and pathogens are causing major declines in some tree species and a subsequent reorganization of associated forest communities. Using observations and experiments to investigate the consequences of such declines are hampered because trees are long-lived. Simulation models can provide a means to forecast possible futures based on different scenarios of tree species decline, death, and removal. Such modeling is particularly urgent for species such as eastern hemlock (Tsuga canadensis), a foundation species in many northeastern forest regions that is declining due to the hemlock woolly adelgid (Adelges tsugae). Here, we used an individual-based forest simulator, SORTIE-ND, to forecast changes in forest communities in Central Massachusetts over the next 200 yr under a range of scenarios: a no-adelgid, status quo scenario; partial resistance of hemlock to the adelgid; adelgid irruption and total hemlock decline over 25 yr, adelgid irruption and salvage logging of hemlock trees; and two scenarios of preemptive logging of hemlock and hemlock/white pine. We applied the model to six study plots comprising a range of initial species mixtures, abundances, and levels of hemlock dominance. Simulations indicated that eastern white pine, and to a lesser extent black birch and American beech, would gain most in relative abundance and basal area following hemlock decline. The relative dominance of these species depended on initial conditions and the amount of hemlock mortality, and their combined effect on neighborhood-scale community dynamics. Simulated outcomes were little different whether hemlock died out gradually due to the adelgid or disappeared rapidly following logging. However, if eastern hemlock were to become partially resistant to the adelgid, hemlock would be able to retain its dominance despite substantial losses of basal area. Our modeling highlights the complexities associated with secondary forest succession due to ongoing hemlock decline and loss. We emphasize the need both for a precautionary approach in deciding between management intervention or simply doing nothing in these declining hemlock forests, and for clear aims and understanding regarding desired community- and ecosystem-level outcomes.Publication Widespread sampling biases in herbaria revealed from large-scale digitization(Wiley-Blackwell, 2017) Daru, Barnabas; Park, Daniel; Willis, Richard; Barrington, David; Whitfield, Timothy; Seidler, Tristram; Sweeney, Patrick; Foster, David; Ellison, Aaron; Davis, CharlesSUMMARY 1. Non-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. 2. We determined spatial, temporal, trait, phylogenetic, and collector biases in ~5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). 3. We identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during biological spring and summer; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, and along with their associated preferences and idiosyncrasies, shaped patterns of collection bias via ‘founder effects’. 4. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.Publication Commentary: All species are important, but some species are more important than others(Wiley-Blackwell, 2008) Ellison, Aaron; Degrassi, Allyson L.Foundation species control biodiversity and ecosystem processes, but are difficult to identify. In this issue of Journal of Vegetation Science, Elumeeva et al. show that Festuca varia and Nardus stricta act as foundation species in the Caucasus’ alpine. This paper augments the piecemeal literature on foundation species while highlighting the need for more comprehensive approaches to their identification and conservation.Publication Genotypic variability enhances the reproducibility of an ecological study(Springer Nature, 2018) Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron; Blouin, Manuel; Scheu, Stefan; Freschet, Grégoire T.; Rose, Laura; Barot, Sebastien; Cesarz, Simone; Eisenhauer, Nico; Girin, Thomas; Assandri, Davide; Bonkowski, Michael; Buchmann, Nina; Butenschoen, Olaf; Devidal, Sebastien; Gleixner, Gerd; Gessler, Arthur; Gigon, Agnès; Greiner, Anna; Grignani, Carlo; Hansart, Amandine; Kayler, Zachary; Lange, Markus; Lata, Jean-Christophe; Le Galliard, Jean-François; Lukac, Martin; Mannerheim, Neringa; Müller, Marina E. H.; Pando, Anne; Rotter, Paula; Scherer-Lorenzen, Michael; Seyhun, Rahme; Urban-Mead, Katherine; Weigelt, Alexandra; Zavattaro, Laura; Roy, JacquesMany scientific disciplines are currently experiencing a “reproducibility crisis” because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduces reproducibility by amplifying impacts of lab-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the “reproducibility crisis”, deliberately including genetic variation may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.Publication Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem(Wiley-Blackwell, 2017) Northrop, Amanda C.; Brooks, Rachel K.; Ellison, Aaron; Gotelli, Nicholas J.; Ballif, Bryan A.Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea. Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.Publication If these data could talk(Springer Nature, 2017) Pasquier, Thomas; Lau, Matthew; Trisovic, Ana; Boose, Emery; Couturier, Ben; Crosas, Merce; Ellison, Aaron; Gibson, Valerie; Jones, Chris R.; Seltzer, MargoIn the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software have enabled the rapid implementation of novel methods to manage and analyze the growing flood of data. However, it has become apparent that many scientfic fields exhibit distressingly low rates of repeatability and reproducibility. Although there are many dimensions to this issue, we believe that there is a lack of formalism used when describing end-to-end published results, from the data source to the analysis to the final published results. Even when authors do their best to make their research and data accessible, this lack of formalism reduces the clarity and effciency of reporting, which contributes to issues of reproducibility. Data provenance aids both repeatability and reproducibility through systematic and formal records of the relationships among data sources, processes, datasets, publications and researchers.Publication Critical temperature and precipitation thresholds for the onset of xylogenesis of Juniperus przewalskii in a semi-arid area of the north-eastern Tibetan Plateau(Oxford University Press (OUP), 2017-12-29) Ren, Ping; Rossi, Sergio; Camarero, J; Ellison, Aaron; Liang, Eryuan; Penuelas, JosepBackground and Aims The onset of xylogenesis plays an important role in tree growth and carbon sequestration, and it is thus a key variable to model the responses of forest ecosystems to climate change. Temperature regulates the resumption of cambial activity, but little is known about the effect of water availability on the onset of xylogenesis in cold but semi-arid regions. Methods We monitored the onset of xylogenesis during 2009–2014 by weekly microcoring Juniperus przewalskii trees at upper and lower treelines on the northeastern Tibetan Plateau. We used a logistic regression to calculate the probability of xylogenic activity at a given temperature and a two-dimensional reverse Gaussian model to fit the differences between the observed and estimated days of xylogenesis onset at given temperatures and precipitation within a certain time window. Key Results The thermal thresholds at the beginning of the growing season were highly variable, suggesting that temperature was not the only factor initiating xylem growth under cold and dry climatic conditions. The onset of xylogenesis was predicted well for climatic thresholds characterized by a cumulative precipitation of 17.0 ± 5.6 mm and an average minimum temperature of 1.5 ± 1.4 °C for a period of 12 days. Conclusions Xylogenesis in semi-arid regions with dry winters and springs can start when both critical temperature and precipitation thresholds reached. Such findings contribute to our knowledge of the environmental drivers of growth resumption that previously had been investigated mostly in cold regions without water shortages during early growing seasons. Models of the onset of xylogenesis should include water availability to improve predictions of xylem phenology in dry areas. A mismatch of the thresholds of temperature and moisture for the onset of xylogenesis may increase forest vulnerability in semi-arid areas under forecasted warmer and drier conditions.Publication Projecting Global Mangrove Species and Community Distributions under Climate Change(Ecological Society of America, 2013) Record, Sydne; Charney, N. D.; Zakaria, R. M.; Ellison, AaronGiven 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.