California biodiversity

The persistence of biodiversity in southern California under future land-use scenarios


Collaborative research with Dr Helen Regan, UC-Riverside, Principal Investigator

Sponsored by the National Science Foundation, the Department of Energy National Institute for Climate Change Research (NICCR), and the California Landscape Conservation Cooperative (LCC)

We investigated the combined impacts of habitat loss and fragmentation, altered fire regime and invasive species on functional groups of plants found in Mediterranean-type and some other fire-prone ecosystems. In particular we addressed the questions: a) How does projected habitat loss and fragmentation due to urbanization, in conjunction with indirect or synergistic effects (altered fire regimes, competition from invasive species), affect the risk of decline or extinction for plant populations in southern California? b) Which plant species traits are the best predictors of extinction or decline due to habitat loss, altered fire regimes and competition with invasive species?

We linked four different modeling approaches to address this: 1) a spatially explicit simulation model of urban growth to project land use and land cover change over the next 50-100 years; 2) potential habitat models for focal species using existing location records and interpolated using statistical and machine learning methods; 3) a landscape model of habitat dynamics including disturbance (such as fire) and succession that incorporates dynamic land-use change from the urban growth model; and 4) stochastic population models for a selected set of focal species to estimate risk of population decline or extinction under the urban growth scenarios coupled with habitat dynamics from the landscape model.

With NICCR supplemental support we also examined the impact of climate change and interactions with land use change and disturbance regimes. With California LCC support we were able to apply this modeling framework to biodiversity and land manager's information needs and their management actions.

Highlights of Major Findings

  • Urban growth modeling results for the study area are sensitive to the source and scale of input data. Urban growth is projected to occur at the margins of existing urban areas and to a lesser extent in new satellite settlements in exurban areas. Therefore the species predicted to be most affected by urban growth are those whose habitat is concentrated at the current urban margins.
  • Current configurations of individual conservation areas will not support suitable habitat for species of conservation concern under urbanization and climate change scenarios, as projected by species distribution models. However, networks of conservation areas may collectively support suitable habitat under global change scenarios, and so coordination among reserves is necessary for their effective management.
  • Long-lived obligate seeding plants are more vulnerable to frequent fire than they are to distribution shifts due to climate change or habitat loss from urban growth as long as fire return intervals are short.
  • The rank order of threats to obligate seeding plants at longer fire return intervals is dependent upon spatial context.
  • Resprouting species are more vulnerable to habitat loss or habitat shifts due to climate change than they are to altered fire regime. Current known dispersal rates are insufficient to track shifting suitable habitat.
  • The annual herb we studied is most vulnerable to invasive species’ encroachment. The rank order of impacts of other threats depends on the global climate model and species distribution model used.
  • Species distribution models produce the greatest uncertainty, or variability, the results of linked SDM, GCM, population and fire models. This is followed by GCMs, land-use change and population model type. Uncertainty in parameter estimates for the population model had little impact on results relative to model choice for SDMs, GCMs and population models.
  • When measurement error is subsumed into the variability of population model parameter estimates (as is the common practice) matrix models are less reliable than scalar models in predicting population declines.

Publications and Findings

  • Bonebrake, T. C., A. D. Syphard, J. Franklin, K. E. Anderson, T. Mizerek, H. R. Akçakaya, C. Winchell, and H. M. Regan, 2014, Fire management, managed relocation and land conservation options for long-lived obligate seeding plants under global change, Conservation Biology  28(4):1057-106 . DOI: 10.1111/cobi.1225 
Most species face multiple anthropogenic disruptions. Few studies have quantified the cumulative influence of multiple threats on species of conservation concern, and far fewer have quantified the potential relative value of multiple conservation interventions in light of these threats. We linked spatial distribution and population viability models to explore conservation interventions under projected climate change, urbanization, and changes in fire regime on a long-lived obligate seeding plant species sensitive to high fire frequencies, a dominant plant functional type in many fire-prone ecosystems, including the biodiversity hotspots of Mediterranean-type ecosystems. First, we investigated the relative risk of population decline for plant populations in landscapes with and without land protection under an existing habitat conservation plan. Second, we modeled the effectiveness of relocating both seedlings and seeds from a large patch with predicted declines in habitat area (habitat by definition is suitable) to two unoccupied recipient patches with increasing habitat area under two projected climate change scenarios.  Finally, we modeled eight fire return intervals approximating the outcomes of different management strategies that effectively control fire frequency.  Invariably, long-lived obligate seeding populations remained viable only when fire return intervals were maintained at or above a minimum level. Land conservation and seedling relocation efforts lessened the impact of climate change and land-use change on obligate seeding populations to differing degrees depending on the climate change scenario, but neither of these efforts was as generally effective as frequent translocation of seeds. While none of the modeled strategies fully compensated for the effects of land-use and climate change, an integrative approach managing multiple threats may diminish population declines for species in complex landscapes. Conservation plans designed to mitigate the impacts of a single threat are likely to fail if additional threats are ignored.    
  • Beltrán, B., Franklin, J., Syphard, A. D., Regan, H. M., Flint, L. E. and Flint, A. L., 2014, Effects of climate change and urban development on the distribution and conservation of plant functional types in a Mediterranean-type ecosystem, International Journal of Geographic Information Science  28(8):1561-1589. 
Aim To evaluate the effect of climate change and urban development on vegetation distribution in a Mediterranean Type Ecosystem.  To identify the primary source of uncertainty in habitat suitability predictions and to evaluate how well conservation areas protect future habitat under these different predictions. Location California Floristic Province, Southwest ecoregion. Methods We used consensus-based habitat suitability maps from three species distribution models to predict current and future suitable habitat for 19 plant species representing different plant functional types (PFT) defined by fire-response (obligate seeders, resprouting shrubs), and life forms (herbs, subshurbs).  We also examined the response of species grouped by range sizes (large, small).  We used two climate models, two emission scenarios, two thresholds, and high-resolution (90m resolution) environmental data.  We evaluated the effectiveness of an existing conservation network to protect suitable habitat for rare species in light of climate and land use change. Results While results vary depending on the climate model, emission scenario, and threshold combination, we predicted that suitable habitat could disappear from the ecoregion for up to four species, and decrease for up to 15.  Centroids of species’ suitable habitat could shift up to 440 km.  Large net gains in climatically suitable habitat were predicted for a few species.  We predicted herbs to have a small response to climate change, while obligate seeders could be the most affected as PFT.  We predicted the other two PFTs to gain area.  Several rare species could lose suitable habitat inside designated conservation areas while gaining area outside. Main conclusions Climate change is predicted to be more important than urban development as a driver of suitable habitat loss for vegetation in this region in the coming century.  Our results indicate that regional analyses of this type are useful and necessary to understand the dynamics of drivers of change at the regional scale    
  • Franklin, J., Regan, H. M., Syphard, A. D., 2014, Linking spatially explicit species distribution and population models to plan for the persistence of species under global change, Environmental Conservation 41(2):97-109. (Special Thematic Section: Spatial Simulation Models in Planning for Resilience) doi:10.1017/S0376892913000453
Conservation managers and policy makers require models that can rank the impacts of multiple, interacting threats on biodiversity so that actions can be prioritized. We apply an integrated modeling framework that links species distribution models, spatially explicit population models and global change scenarios, to predict the effects of threats and management to the viability of plant populations for five species in southern California’s Mediterranean-type ecosystem.  The framework integrates forecasts of land use change from an urban growth model with projections of future climatically suitable habitat from species distribution models, which are linked to a stochastic population model. The population model includes species life history and demographic parameters and incorporates the effects of disturbance regimes and management actions on population viability.  This framework has allowed us to: 1) rank threats by their relative and cumulative impacts on population viability, e.g., land use change, climate change, altered disturbance regimes, or invasive species, and 2) rank management responses in terms of their effectiveness, e.g., land protection, assisted dispersal, fire management and invasive species control.  Too-frequent fire was often the top threat for the plant species we studied, and thus, fire reduction was frequently ranked among the most important management options. Projected changes in the distribution of suitable habitat as a result of climate change were generally large, but varied across species and climate scenarios; urban development often served to exacerbate loss of suitable habitat.  This framework is most effective when management objectives are species-specific and when disturbance, such as fire, has a quantifiable impact on population dynamics    
  • Syphard, A. D., Regan, H. M., Franklin, J., Swab, R., 2013, Does functional type vulnerability to multiple threats depend on spatial context in Mediterranean-climate regions? Diversity & Distributions 19:1263-1274. DOI: 10.1111/ddi.12076
Aim: Conservation efforts in Mediterranean-climate regions are complicated by species’ variability in response to multiple threats. Functional type classifications incorporating life-history traits with disturbance response strategies provide a framework for predicting groups of species’ response to fire, but it is unclear whether these classifications will be useful when species are exposed to multiple threats, or differ in spatial context. We evaluate whether species of the same fire-response functional type exhibit similar responses to disturbance relative to, and in combination with, climate and land use change; and whether the dominant threat depends on spatial context. 
Location: Mediterranean southern California Methods: We developed species distribution models under current and future climate conditions for two fire-obligate seeding native shrub species that differ in geographical location and area of occupancy. Dynamic habitat maps representing alternative scenarios of climate change and urban growth were coupled with population models and simulated stochastic fire regimes. Results: The disturbance that defines their classification, fire, is projected to be the most serious threat to both species when fire frequency is high. At longer fire return intervals, however, the projected ranking of threats differed between the species, and spatial context played an important role in defining vulnerability. Main conclusions:  Considering ongoing increases in fire frequency in Mediterranean-climate regions worldwide, functional type classification based on disturbance response may continue to provide a useful framework for biodiversity conservation efforts, but spatial context should also be accounted for. It may be most useful to consider the distribution of vulnerable species with regards to urban development patterns, areas of “high-velocity” climate shifts, and places where altered fire regimes are likely to interact with other threats. 

  • Conlisk, E., Syphard, A. D., Franklin, J., Flint, L., Flint, A., and Regan, H. M. 2013. Management implications of uncertainty in assessing impacts of multiple landscape-scale threats to species persistence using a linked modeling approach. Global Change Biology  3(3):858-869.  DOI: 10.1111/gcb.12090
Concern over rapid global changes and the potential for interactions among multiple threats is prompting scientists to combine multiple modeling approaches to understand impacts on biodiversity. A relatively recent development is the combination of species distribution models, land use change predictions, and dynamic population models to predict the relative and combined impacts of climate change, land use change, and altered disturbance regimes on species’ extinction risk. Each modeling component introduces its own source of uncertainty through different parameters and assumptions, which, when combined, can result in compounded uncertainty that can have major implications for management. Although some uncertainty analyses have been conducted separately on various model components – such as climate predictions, species distribution models, land use change predictions, and population models – a unified sensitivity analysis comparing various sources of uncertainty in combined modeling approaches is needed to identify the most influential and problematic assumptions. We estimated the sensitivities of long-run population predictions to different ecological assumptions and parameter settings for a rare and endangered annual plant species (Acanthomintha ilicifolia, or San Diego thornmint). Uncertainty about habitat suitability predictions, due to the choice of species distribution model, contributed most to variation in predictions about long-run populations.
  • Conlisk, E., Lawson, D., Syphard, A. D., Franklin, J., Flint, A., Flint, L., Regan, H. M. 2012. The roles of dispersal, fecundity, and predation in the population viability of an oak species (Quercus engelmannii) under global change. PLoS One 7(5): e36391. doi:10.1371/journal.pone.0036391
A species’ response to climate change depends on the interaction of biotic and abiotic factors that define future habitat suitability and species’ ability to migrate or adapt. The interactive effects of processes such as fire, dispersal, and predation have not been thoroughly addressed in the climate change literature. Our objective was to examine how life history traits, short-term global change perturbations, and long-term climate change interact to affect the likely persistence of an oak species - Quercus engelmannii (Engelmann oak). Specifically, we combined dynamic species distribution models, which predict suitable habitat, with stochastic, stage-based metapopulation models, which project population trajectories, to evaluate the effects of three global change factors – climate change, land use change, and altered fire frequency – emphasizing the roles of dispersal and seed predation. Our model predicted dramatic reduction in Q. engelmannii abundance, especially under drier climates and increased fire frequency. When masting lowers seed predation rates, decreased masting frequency leads to large abundance decreases. Current rates of dispersal are not likely to prevent these effects, although increased dispersal could mitigate population declines. The results suggest that habitat suitability predictions by themselves may under-estimate the impact of climate change for other species and locations.
  • Regan, H. M., Syphard, A. D., Franklin, J., Swab, R. Markovchick-Nicholls, L., Flint, A. L., Flint, L. E. and Zedler, P. H. 2012. Evaluation of assisted colonization strategies under climate change for a rare, fire-dependent plant. Global Change Biology 18:936-947. doi: 10.1111/j.1365-2486.2011.02586.x
As a clear consensus is emerging that suitable habitat for many species will dramatically reduce and/or shift with climate change, attention is turning to adaptation strategies to address these impacts. Assisted colonization is one such strategy that has been predominantly discussed in terms of the costs of introducing potential competitors into new communities and the benefits of reducing extinction risk. However, the success or failure of assisted colonization will depend on a range of population-level factors on which the climate change literature has been relatively silent—the quality of the recipient habitat, the number and life stages of translocated individuals, the establishment of translocated individuals in their new habitat and whether the recipient habitat is subject to ongoing threats all will play an important role in population persistence. We link a population model with dynamic bioclimate envelopes to investigate expected changes in populations with climate change, the impact of altered fire regimes on population persistence, and how much assisted colonization is necessary to minimize risk of decline in populations of Tecate cypress, a rare endemic tree in the California Floristic Province, a biodiversity hotspot. We show that when there are large source populations that are expected to decline dramatically due to habitat contractions, multiple nearby sites predicted to contain suitable habitat, minimal natural dispersal, high rates of establishment of translocated populations, and the absence of more serious ongoing threats, assisted colonization may be a risk-minimizing adaptation strategy. However, when serious ongoing threats exist, assisted colonization is ineffective
  • Syphard, A. D., K. C. Clarke, J. Franklin, H. M. Regan and M. McGinnis, 2011. Forecasts of habitat loss and fragmentation due to urban growth are sensitive to input data quality and scale. Journal of Environmental Management 92: 1882-1893. doi:10.1016/j.jenvman.2011.03.014
The conversion of natural habitat to urban settlements is a primary driver of biodiversity loss, and species’ persistence is threatened by the extent, location, and spatial pattern of development. Urban growth models are widely used to anticipate future development and to inform conservation manage- ment, but the source of spatial input to these models may contribute to uncertainty in their predictions. We compared two sources of historic urban maps, used as input for model calibration, to determine how differences in definition and scale of urban extent affect the resulting spatial predictions from a widely used urban growth model for San Diego County, CA under three conservation scenarios. The results showed that rate, extent, and spatial pattern of predicted urban development, and associated habitat loss, may vary substantially depending on the source of input data, regardless of how much land is excluded from development. Although the datasets we compared both represented urban land, different types of land use/land cover included in the definition of urban land and different minimum mapping units contributed to the discrepancies. Varying temporal resolution of the input datasets also contributed to differences in projected rates of development. Differential predicted impacts to vegetation types illustrate how the choice of spatial input data may lead to different conclusions relative to conservation. Although the study cannot reveal whether one dataset is better than another, modelers should carefully consider that geographical reality can be represented differently, and should carefully choose the defi- nition and scale of their data to fit their research objectives
  • Lawson, D. M., Regan, H. M., Zedler, P. H. and Franklin, J., 2010, Cumulative effects of land use, altered fire regime and climate change on persistence of Ceanothus verrucosus, a rare, fire-dependent plant species, Global Change Biology 16(9):2518-2529.

We linked a spatially explicit stochastic population model to dynamic bioclimate envelopes to investigate the effects of climate change, habitat loss and fragmentation and altered fire regime on population abundances of a long-lived obligate seeding shrub, Ceanothus verrucosus, a rare endemic species of southern California. We tested a range of fire return intervals under the present and two future climate scenarios. We also assessed the impact of potential anthropogenic land-use change by excluding land identified as developable by local governments. We found that the 35–50 year fire return interval resulted in the highest population abundances. Expected minimum population abundance (EMA) declined declined dramatically for shorter fire intervals. Simulated future development resulted in a 33% decline in EMA, but relatively stable population trajectories over the time frame modeled. Relative changes in EMA for alternative fire intervals were similar for all climate and habitat loss scenarios, except under the more severe climate scenario which resulted in a change in the relative ranking of the fire scenarios. Our results show climate change to be the most serious threat facing obligate seeding shrubs embedded in urban landscapes, resulting in population decline and increased local extirpation, and that likely interactions with other threats increase risks to these species.

  • Franklin, J., 2010, Moving beyond static species distribution models in support of conservation biogeography, Diversity & Distributions 16(3): 321-330. Invited paper Special Issue on Issues, Concepts, Challenges in Conservation Biogeography. DOI: 10.1111/j.1472-4642.2010.00641.x
Linking species–environment relationships, landscape dynamics and population dynamics in a multi-modelling framework allows the combined impacts of climate change (affecting species distribution and vital rates) and land cover dynamics (land use change, altered disturbance regimes) on species to be predicted. This approach is only feasible if the life history parameters and habitat requirements of the species are well understood. Main conclusions Forecasts of the impacts of global change on species may be improved by considering multiple causes. A range of methods are available to address the interactions of changing habitat suitability, habitat dynamics and population response that vary in their complexity, realism and data requirements.