Publications

2013
Kiniry JR, Anderson LC, Johnson M-VV, Behrman KD, Brakie M, Burner D, Cordsiemon RL, a. Fay P, Fritschi FB, Houx JH, et al. Perennial Biomass Grasses and the Mason–Dixon Line: Comparative Productivity across Latitudes in the Southern Great Plains. BioEnergy Research [Internet]. 2013;6 :276–291. Publisher's Version art3a10.10072fs12155-012-9254-7.pdf
Behrman KD, Kiniry JR, Winchell M, Juenger TE, Keitt TH. Spatial forecasting of switchgrass productivity under current and future climate change scenarios. Ecological Applications [Internet]. 2013;23 :73–85. Publisher's Version 12-04362e1.pdf
Lasky JR, Sun I-F, Su S-H, Chen Z-S, Keitt TH. Trait-mediated effects of environmental filtering on tree community dynamics Canham C. Journal of Ecology [Internet]. 2013;101 :722–733. Publisher's VersionAbstract

* Individual performance is a function of an individual's traits and its environment. This function, known as an environmental filter, varies in space and affects community composition. However, filters are poorly characterized because dispersal patterns can obscure environmental effects, and few studies utilize longitudinal data linking individual performance to environment. * We model the effects of environmental filters on demographic rates of nearly all tree species (99) in a 25-ha subtropical rain forest plot. We develop a hierarchical Bayesian model of environmental filtering, drawing inspiration from classic studies of intraspecific natural selection. We characterize the specific environmental gradients and trait axes most important in filtering of demographic rates across species. * We found that stronger filtering along a given trait axis corresponded to less spatial variation in the value of favoured traits. * Environmental gradients associated with filtering were different for growth versus survivorship. * Species maximum height was under the strongest filtering for growth, with shorter species favoured on convex ridges. Shorter stature species may be favoured on ridges because trees on ridges experience higher wind damage and lower soil moisture. * Wood density filtering had the strongest effects on survival. Steep slopes and high available P in the soil favoured species with low-density wood. Such sites may be favourable for fast-growing species that exploit resource-rich environments. * Synthesis: We characterized trait-mediated environmental filters that may underlie spatial niche differentiation and life-history trade-offs, which can promote species coexistence. Filtering along trait axes with the strongest effects on local community composition, that is, traits with the strongest filtering, may necessarily have a weaker potential to promote species coexistence across the plot. The weak spatial variation in filters with strong effects on demography may result from long-term processes affecting the species pool that favour habitat generalist strategies.

lasky_et_al-2013-journal_of_ecology.pdf
2012
Pinto N, Keitt TH, Wainright M. LORACS: JAVA software for modeling landscape connectivity and matrix permeability. Ecography [Internet]. 2012;35 :388–392. Publisher's Version
Keitt TH. Meshpoly. [Internet]. 2012. Publisher's Version
Lasky JR, Des Marais DL, McKay JK, Richards JH, Juenger TE, Keitt TH. Characterizing genomic variation of Arabidopsis thaliana : the roles of geography and climate. Molecular Ecology [Internet]. 2012;21 :5512–5529. Publisher's VersionAbstract

Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well-studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214 051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large-scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among nonsynonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation.

lasky_etal2012.pdf
Lasky JR, Keitt TH. The Effect of Spatial Structure of Pasture Tree Cover on Avian Frugivores in Eastern Amazonia. Biotropica [Internet]. 2012;44 :489–497. Publisher's Version lasky_et_al-2012-biotropica.pdf
Kreakie BJ, Fan Y, Keitt TH. Enhanced Migratory Waterfowl Distribution Modeling by Inclusion of Depth to Water Table Data Steinke D. PLoS ONE [Internet]. 2012;7 :e30142. Publisher's VersionAbstract

In addition to being used as a tool for ecological understanding, management and conservation of migratory waterfowl rely heavily on distribution models; yet these models have poor accuracy when compared to models of other bird groups. The goal of this study is to offer methods to enhance our ability to accurately model the spatial distributions of six migratory waterfowl species. This goal is accomplished by creating models based on species-specific annual cycles and introducing a depth to water table (DWT) data set. The DWT data set, a wetland proxy, is a simulated long-term measure of the point either at or below the surface where climate and geological/topographic water fluxes balance. For species occurrences, the USGS' banding bird data for six relatively common species was used. Distribution models are constructed using Random Forest and MaxEnt. Random Forest classification of habitat and non-habitat provided a measure of DWT variable importance, which indicated that DWT is as important, and often more important, to model accuracy as temperature, precipitation, elevation, and an alternative wetland measure. MaxEnt models that included DWT in addition to traditional predictor variables had a considerable increase in classification accuracy. Also, MaxEnt models created with DWT often had higher accuracy when compared with models created with an alternative measure of wetland habitat. By comparing maps of predicted probability of occurrence and response curves, it is possible to explore how different species respond to water table depth and how a species responds in different seasons. The results of this analysis also illustrate that, as expected, all waterfowl species are tightly affiliated with shallow water table habitat. However, this study illustrates that the intensity of affiliation is not constant between seasons for a species, nor is it consistent between species.

journal.pone_.0030142.pdf
Kreakie BJ, Keitt TH. Integration of distance, direction and habitat into a predictive migratory movement model for blue-winged teal (Anas discors). Ecological Modelling [Internet]. 2012;224 :25–32. Publisher's VersionAbstract

Historically, the migration of birds has been poorly understood in comparison to other life stages during the annual cycle. The goal of our research is to present a novel approach to predict the migratory movement of birds. Using a blue-winged teal case study, our process incorporates not only constraints on habitat (temperature, precipitation, elevation, and depth to water table), but also approximates the likely bearing and distance traveled from a starting location. The method allows for movement predictions to be made from unsampled areas across large spatial scales. We used USGS’ Bird Banding Laboratory database as the source of banding and recovery locations. We used recovery locations from banding sites with multiple within-30-day recoveries were used to build core maximum entropy models. Because the core models encompass information regarding likely habitat, distance, and bearing, we used core models to project (or forecast) probability of movement from starting locations that lacked sufficient data for independent predictions. The final model for an unsampled area was based on an inverse-distance weighted averaged prediction from the three nearest core models. To illustrate this approach, three unsampled locations were selected to probabilistically predict where migratory blue-wing teals would stopover. These locations, despite having little or none data, are assumed to have populations. For the blue-winged teal case study, 104 suitable locations were identified to generate core models. These locations ranged from 20 to 228 within-30-day recoveries, and all core models had AUC scores greater than 0.80. We can infer based on model performance assessment, that our novel approach to predicting migratory movement is well-grounded and provides a reasonable approximation of migratory movement.

1-s2.0-s0304380011005047-main.pdf
Keitt TH. Productivity, nutrient imbalance and fragility in coupled producer–decomposer systems. Ecological Modelling [Internet]. 2012;245 :12–18. Publisher's VersionAbstract

Ecosystem development is mediated by coupled synthesis–decomposition cycles that capture, store and release energy necessary for maintenance and growth. I present a minimal ecosystem model with explicit energy and matter conservation. Energy is captured and stored via synthesis and release through decomposition. This energy is used for biomass production and maintenance. I examine materially closed systems where growth is limited by nutrient availability. I present two key findings. First, maximum biomass production does not occur under conditions of equal nutrient concentrations. Instead, production is maximized when the initial environmental concentration of the energy carrying substrate is increased. Second, the system is characterized by an abrupt collapse when the concentration of the energy carrying substrate is increased above a threshold. This model indicates that in the region of maximum biomass production, ecosystems are fragile rather than resilient.

1-s2.0-s0304380012002414-main.pdf
2011
Lasky JR, Jetz W, Keitt TH. Conservation biogeography of the US-Mexico border: a transcontinental risk assessment of barriers to animal dispersal. Diversity and Distributions [Internet]. 2011;17 :673–687. Publisher's Version usmex2011.pdf
Avnery S, Dull RA, Keitt TH. Human versus climatic influences on late-Holocene fire regimes in southwestern Nicaragua. The Holocene [Internet]. 2011;21 :699–706. Publisher's Version the_holocene-2011-avnery-0959683610391314.pdf
Noble AE, Temme NM, Fagan WF, Keitt TH. A sampling theory for asymmetric communities. Journal of Theoretical Biology [Internet]. 2011;273 :1–14. Publisher's VersionAbstract

We introduce the first analytical model of asymmetric community dynamics to yield Hubbell's neutral theory in the limit of functional equivalence among all species. Our focus centers on an asymmetric extension of Hubbell's local community dynamics, while an analogous extension of Hubbell's metacommunity dynamics is deferred to an appendix. We find that mass-effects may facilitate coexistence in asymmetric local communities and generate unimodal species abundance distributions indistinguishable from those of symmetric communities. Multiple modes, however, only arise from asymmetric processes and provide a strong indication of non-neutral dynamics. Although the stationary distributions of fully asymmetric communities must be calculated numerically, we derive the first analytical sampling distributions for nearly neutral local communities and metacommunities where symmetry is broken by a single species distinct from all others in ecological fitness and dispersal ability. Novel asymptotic expansions of hypergeometric functions are provided to make evaluations of each distribution tractable for large communities. Employing these results in a Bayesian analysis may provide a novel statistical test to assess the consistency of species abundance data with the neutral hypothesis.

1010.2829.pdf
2010
Lasky JR, Keitt TH. Abundance of Panamanian dry-forest birds along gradients of forest cover at multiple scales. Journal of Tropical Ecology [Internet]. 2010;26 :67. Publisher's VersionAbstract
Community structure and species' abundances may be strongly correlated to patterns of forest cover, although such patterns are poorly known for tropical dry-forest birds, especially for those in Panamanian dry forests. Birds were distance-sampled during point counts in five dry-forest fragments in Panama. Distance from point count to forest, edge and forest coverage at three spatial scales (500, 1000 and 2000-m radius) were compared as covariate predictors of the abundance of avian species and guilds. Each covariate was selected in at least two models of species or guild abundance. Abundance patterns were consistent with previously reported habitat associations for only two of seven open-habitat or forest-preferring species that. showed forest cover-abundance relationships. Null models best described the abundance of all forest species and the subset of uncommon forest species. Thus many of these species appear insensitive to the forest-cover gradients studied. Total abundance of open-habitat-preferring species increased in dry forests with increasing forest coverage within 500 m, suggesting that the relationship between their abundance and vegetation structure are spatial-scale and habitat. dependent. Nectarivores had lower abundance as forest cover within 1000 m increased, supporting previous claims that this group is tolerant of forest edges.
Keitt TH, Bivand R, Pebesma E, Rowlingson B. rgdal: bindings for the Geospatial Data Abstraction Library. [Internet]. 2010. Publisher's Version
Economo EP, Keitt TH. Network isolation and local diversity in neutral metacommunities. Oikos [Internet]. 2010;119 :1355–1363. Publisher's Version j.1600-0707.2010.18272.x.pdf
2009
Keitt TH. Habitat conversion, extinction thresholds, and pollination services in agroecosystems. Ecological Applications [Internet]. 2009;19 :1561–1573. Publisher's VersionAbstract
Parallel declines of wild pollinators and pollinator-dependent plants have raised alarms over the loss of pollination services in agroecosystems. A spatially explicit approach is needed to develop specific recommendations regarding the design of agricultural landscapes to sustain wild pollinator communities and the services they provide. I modeled pollination services in agroecosystems using a pair of models: a stochastic individual-based simulation model of wild pollinators, pollinator-dependent plants, and crop pollination; and a set of coupled difference equations designed to capture the nonspatial component of the simulation model. Five spatially explicit models of habitat conversion to crops were simulated, and results for pollination services were compared. Mean-field behavior of the simulation model was in good agreement with analysis of the difference equations. A major feature of the models was the presence of a cusp leading to loss of stability and extinction of pollinators and pollinator-dependent plants beyond a critical amount of habitat loss. The addition of pollen obtained from crop visitation caused a breakdown of the cusp preventing extinction of pollinators, but not of wild pollinator-dependent plants. Spatially restricted foraging and dispersal also altered model outcomes relative to mean-field predictions, in some cases causing extinction under parameter settings that would otherwise lead to persistence. Different patterns of habitat conversion to crops resulted in different levels of pollination services. Most interesting was the finding that optimal pollination services occurred when the size of remnant habitat patches was equal to half the mean foraging and dispersal distance of pollinators and the spacing between remnant patches was equal to the mean foraging and dispersal distance. Conservation of wild pollinators and pollinator-dependent plants in agroecosystems requires careful attention to thresholds in habitat conversion and spatial pattern and scale of remnant habitats. Maximization of pollination services was generally incompatible with conservation of wild pollinator-dependent plants. My prediction is that pollination services will be maximized by providing islands of nesting habitat where interisland distance matches mean foraging distances of wild pollinators.
keitt-2009-ecological_applications.pdf
Brooks CP, Holmes C, Kramer K, Barnett B, Keitt TH. The Role of Demography and Markets in Determining Deforestation Rates Near Ranomafana National Park, Madagascar Chave J. PLoS ONE [Internet]. 2009;4 :e5783. Publisher's VersionAbstract
The highland forests of Madagascar are home to some of the world's most unique and diverse flora and fauna and to some of its poorest people. This juxtaposition of poverty and biodiversity is continually reinforced by rapid population growth, which results in increasing pressure on the remaining forest habitat in the highland region, and the biodiversity therein. Here we derive a mathematical expression for the subsistence of households to assess the role of markets and household demography on deforestation near Ranomafana National Park. In villages closest to urban rice markets, households were likely to clear less land than our model predicted, presumably because they were purchasing food at market. This effect was offset by the large number of migrant households who cleared significantly more land between 1989-2003 than did residents throughout the region. Deforestation by migrant households typically occurred after a mean time lag of 9 years. Analyses suggest that while local conservation efforts in Madagascar have been successful at reducing the footprint of individual households, large-scale conservation must rely on policies that can reduce the establishment of new households in remaining forested areas.
Pinto N, Lasky J, Bueno R, Keitt TH, Galetti M. South American Primates Garber PA, Estrada A, Bicca-Marques JC, Heymann EW, Strier KB. South American Primates [Internet]. 2009 :413–431. Publisher's Version
Pinto N, Keitt TH. Beyond the least-cost path: evaluating corridor redundancy using a graph-theoretic approach. Landscape Ecology [Internet]. 2009;24 :253–266. Publisher's VersionAbstract

The impact of the landscape matrix on patterns of animal movement and population dynamics has been widely recognized by ecologists. However, few tools are available to model the matrix's influence on the length, relative quality, and redundancy of dispersal routes connecting habitat patches. Many GIS software packages can use land use/land cover maps to identify the route of least resistance between two points-the least-cost path. The limitation of this type of analysis is that only a single path is identified, even though alternative paths with comparable costs might exist. In this paper, we implemented two graph theory methods that extend the least-cost path approach: the Conditional Minimum Transit Cost (CMTC) tool and the Multiple Shortest Paths (MSPs) tool. Both methods enable the visualization of multiple dispersal routes that, together, are assumed to form a corridor. We show that corridors containing alternative dispersal routes emerge when favorable habitat is randomly distributed in space. As clusters of favorable habitat start forming, corridors become less redundant and dispersal bottlenecks become visible. Our approach is illustrated using data from a real landscape in the Brazilian Atlantic forest. We explored the effect of small, localized disturbance on dispersal routes linking conservation units. Simulated habitat destruction caused the appearance of alternative dispersal routes, or caused existing corridors to become narrower. These changes were observed even in the absence of significant differences in the length or cost of least-cost paths. Last, we discuss applications to animal movement studies and conservation initiatives.

pinto-keitt-blcp.pdf

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