Species Distribution Models

Invasive plants and their ecological strategies: prediction and explanation of woody plant invasion in New England

by Chris Martine

Co-authored with Patrick M. Herron, Andrew M. Latimer, and Stacey A. Leicht-Young. Published in Diversity and Distributions, 2007. 13: 633-644.

Modelling geographic patterns of population density of the white-tailed deer in central Mexico by implementing ecological niche theory

by Carlos Yañez Arenas

Yañez-Arenas, C., E. Martínez-Meyer, S. Mandujano & O. Rojas-Soto. 2012. Modelling Geographic Patterns of Population Density of the White-tailed Deer in Central Mexico by Implementing Ecological Niche Theory. Oikos, En prensa.

Conservation and management of species require basic knowledge on their geographic distribution and abundance. Here,... more Conservation and management of species require basic knowledge on their geographic distribution and abundance. Here, we propose a novel approach, based on the theory of the ecological niche, to model the spatial patterns of the white-tailed deer Odocoileus virginianus population density in two regions of central Mexico (Balsas Basin and Tehuacán- Cuicatlán Valley). We used an ecological niche model to generate binary geographic distribution maps of the white-tailed deer in each region based on occurrence data and a set of environmental variables. Then, the centroid of the distributions was calculated in ecological space (niche centroid) and the multidimensional Euclidian ecological distance of each pixel to the niche centroid was estimated. Finally, for each region the distance to the centroid (DC) was regressed against 14 independent occurrence points in each site containing white-tailed deer density information to determine the function describing the DC-density relationship, which was used to generate maps describing the distribution of white-tailed deer density. Our results indicated an inverse DC-density relationship in both regions (Balsas Basin: r2 = 0.90 and Tehuacán-Cuicatlán: r2 = 0.76) that was validated via bootstrapping resulting in a predicting capacity of near 62% for Balsas Basin and 65% for Tehuacán-Cuicatlán Valley. Our results suggest that the distance to the niche centroid method is a robust, science-based correlative approach that resulted useful to predict the population density of the white-tailed deer in a spatially explicit fashion. The proposed approach is suitable for predicting the distribution of density for white-tailed deer for which occurrence data with accompanying density information exists, but relative abundance can also be estimated when no abundance data are available.

When do conservation planning methods deliver? Quantifying the consequences of uncertainty

by Ascelin Gordon

Published in 'Ecological Informatics' 2009

The rapid global loss of biodiversity has led to a proliferation of systematic conservation planning methods. In spite... more The rapid global loss of biodiversity has led to a proliferation of systematic conservation planning methods. In spite of their utility and mathematical sophistication, these methods only provide approximate solutions to real-world problems where there is uncertainty and temporal change. The consequences of errors in these solutions are seldom characterized or addressed. We propose a conceptual structure for exploring the consequences of input uncertainty and oversimplified approximations to real-world processes for any conservation planning tool or strategy. We then present a computational framework based on this structure to quantitatively model species representation and persistence outcomes across a range of uncertainties. These include factors such as land costs, landscape structure, species composition and distribution, and temporal changes in habitat. We demonstrate the utility of the framework using several reserve selection methods including simple rules of thumb and more sophisticated tools such as Marxan and Zonation. We present new results showing how outcomes can be strongly affected by variation in problem characteristics that are seldom compared across multiple studies. These characteristics include number of species prioritized, distribution of species richness and rarity, and uncertainties in the amount and quality of habitat patches. We also demonstrate how the framework allows comparisons between conservation planning strategies and their response to error under a range of conditions. Using the approach presented here will improve conservation outcomes and resource allocation by making it easier to predict and quantify the consequences of many different uncertainties and assumptions simultaneously. Our results show that without more rigorously generalizable results, it is very difficult to predict the amount of error in any conservation plan. These results imply the need for standard practice to include evaluating the effects of multiple real-world complications on the behavior of any conservation planning method.

Raising the bar for systematic conservation planning

by Ascelin Gordon

published in Trends in Ecology and Evolution

Systematic conservation planning (SCP) represents a significant step toward cost-effective, transparent allocation of... more Systematic conservation planning (SCP) represents a significant step toward cost-effective, transparent allocation of resources for biodiversity conservation. However, research demonstrates important consequences of uncertainties in SCP and of basing methods on simplified circumstances involving few real-world complexities. Current research often relies on single case studies with unknown forms and amounts of uncertainty as well as low statistical power for generalizing results. Consequently, conservation managers have little evidence for the true performance of conservation planning methods in their own complex, uncertain applications. To build effective and reliable methods in SCP, there is a need for more challenging and integrated testing of their robustness to uncertainty and complexity, and much greater emphasis on generalization to real-world situations.

Integrating conservation planning and landuse planning in urban landscapes

by Ascelin Gordon

Published in Landscape and Urban Planning, co-authored with Simondson, D, White M, Moilanen A, Bekessy SA.

The rapid growth of cities around the world is now seen as a major contributor to global biodiversity loss and many... more The rapid growth of cities around the world is now seen as a major contributor to global biodiversity loss and many governments include biodiversity conservation as an explicit policy goal. To help prevent further loss of biodiversity, there is an urgent need for more strategic approaches to conservation planning in urban environments based on a scientific understanding of landscape patterns, species requirements and development pressures. In this study, we demonstrate the use of new conservation planning tools to better integrate information on threatened species into landuse planning. We present a case study in the Greater Melbourne area that utilises the Zonation conservation planning tool with data for 30 threatened fauna species. We perform a multi-species spatial prioritisation that incorporates species-specific connectivity requirements and demonstrate the use of this information in a number of landuse planning contexts. First, we quantitatively assess the differences between Melbourne's current conservation areas with the locations prioritised by Zonation and determine priority areas for their extension. We then show how the prioritisation can be used in decisions regarding Melbourne's Urban Growth Boundary and in rezoning land for development. Finally, we demonstrate how the prioritisation can be used to identify areas of conservation significance within individual developments that account for the wider landscape context. These results demonstrate how conservation planning tools can be better integrated into the different stages of landuse planning for future urban growth.

Terra and Aqua satellites track tiger mosquito invasion: modeling the potential distribution of Aedes albopictus in north-eastern Italy

by Markus Neteler

Neteler, M., Roiz, D., Rocchini, D., Castellani, C. and Rizzoli, A. (2011). Terra and Aqua satellites track tiger mosquito invasion: modeling the potential distribution of Aedes albopictus in north-eastern Italy. International Journal of Health Geographics, 10:49

Background

The continuing spread of the Asian tiger mosquito Aedes albopictus in Europe is of increasing... more Background

The continuing spread of the Asian tiger mosquito Aedes albopictus in Europe is of increasing public health concern due to the potential risk of new outbreaks of exotic vector-borne diseases that this species can transmit as competent vector. We predicted the most favorable areas for a short term invasion of Ae. albopictus in north-eastern Italy using reconstructed daily satellite data time series (MODIS Land Surface Temperature maps, LST). We reconstructed more than 11,000 daily MODIS LST maps for the period 2001-09 (i.e. performed spatial and temporal gap-filling) in an Open Source GIS framework. We aggregated these LST maps over time and identified the potential distribution areas of Ae. albopictus by adapting published temperature threshold values using three variables as predictors (0°C for mean January temperatures, 11°C for annual mean temperatures and 1350 growing degree days filtered for areas with autumnal mean temperatures > 11°C). The resulting maps were integrated into the final potential distribution map and this was compared with the known current distribution of Ae. albopictus in north-eastern Italy.
Results

LST maps show the microclimatic characteristics peculiar to complex terrains, which would not be visible in maps commonly derived from interpolated meteorological station data. The patterns of the three indicator variables partially differ from each other, while winter temperature is the determining limiting factor for the distribution of Ae. albopictus. All three variables show a similar spatial pattern with some local differences, in particular in the northern part of the study area (upper Adige valley).
Conclusions

Reconstructed daily land surface temperature data from satellites can be used to predict areas of short term invasion of the tiger mosquito with sufficient accuracy (200 m pixel resolution size). Furthermore, they may be applied to other species of arthropod of medical interest for which temperature is a relevant limiting factor. The results indicate that, during the next few years, the tiger mosquito will probably spread toward northern latitudes and higher altitudes in north-eastern Italy, which will considerably expand the range of the current distribution of this species.
Keywords:
Tiger mosquito; Aedes albopictus; Italy; predictive map; spatial distribution; spatial model; satellite; MODIS Land Surface Temperature; spatial entomological risk assessment

Modeling the Potential Distribution of Pine Forests Susceptible to Sirex Noctilio Infestations in Mpumalanga, South Africa

by Riyad Ismail

Riyad Ismail, Onisimo Mutanga,Lalit Kumar

Reducing the impact of the siricid wasp, Sirex noctilio is crucial for the future productivity and sustainability of... more Reducing the impact of the siricid wasp, Sirex noctilio is crucial for the future productivity and sustainability of commercial pine resources in South Africa. In this study we present a machine learning model that serves as a spatial guide and allows forest managers to focus their existing detection and monitoring efforts on key areas and proactively adopt the most appropriate course of intervention. We implemented the random forest model within a spatial framework to determine which pine forests in Mpumalanga are highly susceptible to S. noctilio infestations. Results indicate that a majority (63%) of pine forest plantations located in Mpumalanga have a high susceptibility (>70%) to S. noctilio infestation. A KHAT value of 0.84 and F measures above 0.87 indicate that the random forest model is a robust classifier that produces accurate results. Additionally, the use of the backward variable selection method enabled us to simplify the random forest modeling process and identify the minimum number of explanatory variables that offer the best discriminatory power and help in the empirical interpretation of the final random forest model. Overall, the results show that pine forests that experience stress caused by evapotranspiration and evaporation followed by rainfalls, especially during the summer months are more susceptible to S. noctilio infestations.

Los peces de la provincia de Salamanca. Atlas de distribución.

by César J. Pollo

Co-authored with J.C. Velasco, S.J. Peris & N. González Sánchez
Ediciones Universidad de Salamanca. 172 pp.

Living on predictability: modeling the density distribution of efficient foraging seabirds

by Isadora Christel Jimenez

Cama, A., Abellana, R., Christel, I., Ferrer, X., & Vieites, D. R. (2011). Living on predictability: modeling the density distribution of efficient foraging seabirds. Ecography. doi:10.1111/j.1600-0587.2011.06756.x

In areas with regular fishing coastal fleets seabirds may benefit from the predictability of discards from fishing... more In areas with regular fishing coastal fleets seabirds may benefit from the predictability of discards from fishing vessels, but it is not clear to what extent birds rely on this predictable resource and whether foraging is synchronized with the diel availability of discards. In this paper we investigate if a typical scavenger species, the yellow-legged gull (Larus michahellis), takes advantage of the temporal and spatial predictability of fish discards in the western Mediterranean Sea. The activity and distribution of the trawling fleet in this area is regulated and very predictable in time and space. We gathered aerial survey data across a relatively large area close to the coast to study the spatial distribution and density of L. michahellis, and modelled the density distribution of the species in relation to several oceanographic, ecological and temporal variables, using two different modelling approaches: MARS (Multivariate Adaptative Regression Splines) and GLM (Generalized Linear Models). Our models suggest that the spatial density of trawlers at sea and the time of the day are the best explanatory variables of gull distribution, and that gulls concentrate in areas with vessels mainly during fish discarding time, supporting the hypothesis that gulls time foraging to take advantage of fishery waste predictability. Additional surveys from the main gull roosting sites inshore support this hypothesis, as gulls start leaving to the sea just before fishing is completed and vessels begin discarding fish scraps when back to the harbour. This study represents one of the few examples of applying MARS to density distribution modelling, although its application to marine ecosystems should be conducted with caution because of large areas with real absence data. GLMs have shown to be more adaptable to such kind of data. Our data confirm the importance of fishery waste for L. michahellis, not only as a food resource but also as a major driver of their activity and distribution patterns. The ability of seabirds to predict accurately when a food resource will be available implies that modelling their distribution at sea needs to include such variables, both in spatial and temporal dimensions.

Modeling the Biogeography of Fossil Baboons

by Caroline Bettridge

We use a model of modern baboon socio-ecology to explore the behavioral ecology and biogeography of the extinct... more We use a model of modern baboon socio-ecology to explore the behavioral ecology and biogeography of the extinct Plio-Pleistocene baboons (genera Parapapio, Gorgopithecus, Dinopithecus, and Papio). The model is based on the way climate affects the baboons’ time budgets, and focuses on intersite variability in behavior rather than on species-typical patterns of behavior, as most previous approaches have done. We use climate estimates for individual fossil sites based on matching modern habitats using faunal profiles and estimates of individual species’ body masses given in the literature. The model allows us to examine the minimum and maximum sizes of groups that individual species would have been able to support at particular localities, and hence the biogeography of a species on a continental scale. In doing so, the model allows us to examine which variables are most responsible for limiting a species’ ecological and biogeographic flexibility, and through this to explore a species’ capacity for coping with climate change. Feeding time is identified as the main constraint. In general, large-bodied species would have had more difficulty surviving in as wide a range of habitats as smaller-bodied species, and this may explain the limited geographical distribution of large-bodied baboons such as Gorgopithecus and Dinopithecus.

Past tree range dynamics in the Iberian Peninsula inferred through phylogeography and palaeodistribution modelling: A review

by Francisco Rodriguez-Sanchez

Rodríguez-Sánchez F, Hampe A, Jordano P & Arroyo J
Review of Palaeobotany and Palynology, 162: 507-521. 2010.

The forests in the Iberian Peninsula have been strongly influenced by past climatic changes, but reconstructing their... more The forests in the Iberian Peninsula have been strongly influenced by past climatic changes, but reconstructing their historical distributions and dynamics is very difficult due to the complex climatic characteristics and relief of the region. Research disciplines such as phylogeography and species distribution modelling can describe the past range dynamics of individual tree species in relatively great detail and help elucidate how these species have reacted to climatic changes. Here we review phylogeographical and modelling studies from species representative of the major Iberian forest types and attempt to extract general trends from the diversity of individual species histories in the Peninsula. To date most studies focus on geographical range dynamics during the Pleistocene, but an increasing body of evidence shows that some species have also retained the genetic imprints of much more ancient processes. Many widespread Iberian species show a deep and often remarkably clear-cut divide between populations from the Mediterranean and from the Atlantic regions of the Iberian Peninsula, suggesting that both areas have independently sustained viable populations over extended periods. In fact, phylogeographical studies commonly find that species had several glacial refugia across the Iberian Peninsula. On the other hand, distribution models help identifying further suitable areas that could have sustained so far undetected refugia. Such studies are of interest for species conservation, because refugium populations are high-priority targets due to their longterm persistence and unique evolutionary trajectory. Overall, we conclude that palaeoecology, phylogeography and species distribution modelling have a great potential to inform each other because of their complementary perspectives and results. A true integration of these approaches is therefore fundamental for
further progress in our understanding of past Iberian environments and the organisms they harboured.

Cenozoic climate changes and the demise of Tethyan laurel forests: lessons for the future from an integrative reconstruction of the past

by Francisco Rodriguez-Sanchez

In: Climate Change, Ecology and Systematics, pp. 280-303. Cambridge University Press, 2011.

Climate on earth has always been changing. Despite decades of investigation, our limited knowledge of the ecological... more Climate on earth has always been changing. Despite decades of investigation, our limited knowledge of the ecological and evolutionary effects of climate changes often translates into uncertain predictions about the impact of future climates on biodiversity. Integrative biogeographical approaches using palaeobotanical, phylogenetic and niche-based species distribution models, when permitted by data availability, may provide valuable insights to address these key questions. Here we combine palaeobotanical and phylogeographical information with hindcast modelling of species distribution changes to reconstruct the past range dynamics and differentiation in the bay laurel (Laurus spp., Lauraceae), an emblematic relict tree from the subtropical laurel forests that thrived in Tethyan realms during most of the Tertiary period. We provide plausible examples of climate-driven migration, extinction and persistence of populations and taxa, and discuss the factors that influence niche conservatism or adaptation to changing environments. Finally, we discuss the likely impacts of the predicted climate change on laurophyllous taxa in the Mediterranean and
Macaronesia.

Separating the influences of environment and species interactions on patterns of distribution and abundance: competition between large herbivores

by Euan Ritchie

Modelos de distribución de especies: Una revisión sintética

by Angel M Felicisimo

En los últimos años se ha generalizado una nueva herramienta que permite analizar objetivamente los patrones... more En los últimos años se ha generalizado una nueva herramienta que permite analizar objetivamente los patrones espaciales de presencia de organismos: los modelos de distribución de especies. Estos modelos se basan en procedimientos estadísticos y cartográficos que partiendo de datos reales de presencia permiten inferir zonas potencialmente idóneas en función de sus características ambientales. Los datos de colecciones de historia natural pueden ser utilizados para este fin adquiriendo así una nueva utilidad. Los modelos han evolucionado desde su aplicación a especies aisladas hasta análisis de cientos o miles de taxones para combinarlos en el análisis de la biodiversidad y riqueza específica. En este trabajo se hace una revisión sobre la variedad de métodos utilizables, sus potencialidades e inconvenientes y los factores limitantes que influyen en la interpretación de lo que los modelos de distribución significan.

Past tree range dynamics in the Iberian Peninsula inferred through phylogeography and palaeodistribution modelling: A review.

by Pedro Jordano

Co-authored with Rodríguez-Sánchez, F., Hampe, A., and Arroyo, J.
Review of Palaeobotany and Palynology 162: 507-521. 2010. doi:10.1016/j.revpalbo.2010.03.008

The forests in the Iberian Peninsula have been strongly influenced by past climatic changes, but reconstructing their... more The forests in the Iberian Peninsula have been strongly influenced by past climatic changes, but reconstructing their historical distributions and dynamics is very difficult due to the complex climatic characteristics and relief of the region. Research disciplines such as phylogeography and species distribution modelling can describe the past range dynamics of individual tree species in relatively great detail and help elucidate how these species have reacted to climatic changes. Here we review phylogeographical and modelling studies from species representative of the major Iberian forest types and attempt to extract general trends from the diversity of individual species histories in the Peninsula. To date most studies focus on geographical range dynamics during the Pleistocene, but an increasing body of evidence shows that some species have also retained the genetic imprints of much more ancient processes. Many widespread Iberian species show a deep and often remarkably clear-cut divide between populations from the Mediterranean and from the Atlantic regions of the Iberian Peninsula, suggesting that both areas have independently sustained viable populations over extended periods. In fact, phylogeographical studies commonly find that species had several glacial refugia across the Iberian Peninsula. On the other hand, distribution models help identifying further suitable areas that could have sustained so far undetected refugia. Such studies are of interest for species conservation, because refugium populations are high-priority targets due to their long- term persistence and unique evolutionary trajectory. Overall, we conclude that palaeoecology, phylogeo- graphy and species distribution modelling have a great potential to inform each other because of their complementary perspectives and results. A true integration of these approaches is therefore fundamental for further progress in our understanding of past Iberian environments and the organisms they harboured.

Land use and climate influences on waterbirds in the Prairie Potholes

by Wayne Thogmartin

Forcey, G. M., W. E. Thogmartin, G. M. Linz, W. J. Bleier, and P. C. McKann.  2011.  Land use and climate influences on waterbirds in the Prairie Potholes.  Journal of Biogeography 38:1694–1707.

Aim We examined the influences of regional climate and land-use variables on mallard (Anas platyrhynchos), blue-winged... more Aim We examined the influences of regional climate and land-use variables on mallard (Anas platyrhynchos), blue-winged teal (Anas discors), ruddy duck (Oxyura jamaicensis) and pied-billed grebe (Podilymbus podiceps) abundances to inform conservation planning in the Prairie Pothole Region of the United States.

Location The US portion of Bird Conservation Region 11 (US-BCR11, the Prairie Potholes), which encompasses six states within the United States: Montana, North Dakota, South Dakota, Nebraska, Minnesota and Iowa.

Methods We used data from the North American Breeding Bird Survey (NABBS), the National Land Cover Data Set, and the National Climatic Data Center to model the effects of environmental variables on waterbird abundance. We evaluated land-use covariates at three logarithmically related spatial scales (1000, 10,000 and 100,000 ha), and constructed hierarchical spatial count models a priori using information from published habitat associations. Model fitting was performed using a hierarchical modelling approach within a Bayesian framework.

Results Models with the same variables expressed at different scales were often in the best model subset, indicating that the influence of spatial scale was small. Both land-use and climate variables contributed strongly to predicting waterbird
abundance in US-BCR11. The strongest positive influences on waterbird abundance were the percentage of wetland area across all three spatial scales, herbaceous vegetation and precipitation variables. Other variables that we included in our models did not appear to influence waterbirds in this study.

Main conclusions Understanding the relationships of waterbird abundance to climate and land use may allow us to make predictions of future distribution and abundance as environmental factors change. Additionally, results from this study can suggest locations where conservation and management efforts should befocused.

Reconstructing the demise of Tethyan plants: climate‐driven range dynamics of Laurus since the Pliocene

by Francisco Rodriguez-Sanchez

Aim

Climate changes are thought to be responsible for the retreat and eventual extinction of subtropical... more Aim

Climate changes are thought to be responsible for the retreat and eventual extinction of subtropical lauroid species that covered much of Europe and North Africa during the Palaeogene and early Neogene; little is known, however, of the
spatial and temporal patterns of this demise. Herein we calibrate ecological niche models to assess the climatic requirements of
Laurus L. (Lauraceae), an emblematic relic from the Tethyan subtropical flora, subsequently using these models to infer
how the range dynamics of Laurus were affected by Plio-Pleistocene climate changes. We also provide predictions of likely range changes resulting from future climatic scenarios.


Location

The Mediterranean Basin and Macaronesian islands (Canaries, Madeira, Azores).


Methods

We used a maximum-entropy algorithm (Maxent) to model the
relationship between climate and Laurus distribution over time. The models were fitted both to the present and to the middle Pliocene, based on fossil records. We employed climatic reconstructions for the mid-Pliocene (3 Ma), the Last Glacial
Maximum (21 ka) and a CO2-doubling future scenario to project putative species distribution in each period. We validated the model projections with Laurus fossil and present occurrences.


Results

Laurus preferentially occupied warm and moist areas with low seasonality, showing a marked stasis of its climatic niche. Models fitted to Pliocene conditions successfully predicted the current species distribution. Large suitable areas existed
during the Pliocene, which were strongly reduced during the Pleistocene, but humid refugia within the Mediterranean Basin and Macaronesian islands enabled long-term persistence. Future climate conditions are likely to re-open areas suitable for
colonization north of the current range.


Main conclusions

The climatic requirements of Laurus remained virtually unchanged over the last 3 Myr. This marked niche conservatism imposed largely deterministic range dynamics driven by climate conditions. This species’s relatively high drought tolerance might account for the survival of Laurus in continental Europe throughout the Quaternary whilst other Lauraceae became extinct. Climatic scenarios for the end of this century would favour an expansion of the species’s range towards northern latitudes, while severely limiting southern populations due to
increased water stress.

Lista preliminar de los mamíferos (Mammalia: Theria)

by Elkin A. Noguera-Urbano

Héctor E. Ramírez-Chaves y Elkin A. Noguera-Urbano. 2010. Biota Colombiana 11 (1 y 2). 177-140.

To consolidate the available information on terrestrial and marine mammals of the department of Nariño, voucher... more To consolidate the available information on terrestrial and marine mammals of the department of Nariño, voucher specimens from national collections as well as records from international museum databases and the scientific literature were investigated. A checklist of 182 mammalian species is presented. Out of those, 24 species are considered as threatened under some category in Colombia. Our work reveals the need of new efforts to fill out the mammalian information gaps for this portion of the country.

The effects of governmental protected areas and social initiatives for land protection on the conservation of Mexican amphibians

by Nicolas Urbina-Cardona

Applying niche-based models to predict endangered-hylid potential distributions: are neotropical protected areas effective enough?

by Nicolas Urbina-Cardona