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Further reading

A short, annotated selection to go beyond this course. The reference lists at the end of each chapter give the primary sources of every method.

Textbooks

  • Turner, M. G., & Gardner, R. H. (2015). Landscape Ecology in Theory and Practice: Pattern and Process (2nd ed.). Springer. The standard graduate textbook: pattern, process, scale, neutral models, metrics, disturbance and management. Start here.
  • Gergel, S. E., & Turner, M. G. (Eds.) (2017). Learning Landscape Ecology: A Practical Guide to Concepts and Techniques (2nd ed.). Springer. Laboratory exercises on scale, metrics, neutral models and connectivity; a hands-on companion to the previous book.
  • Forman, R. T. T. (1995). Land Mosaics: The Ecology of Landscapes and Regions. Cambridge University Press. The patch–corridor–matrix model and the spatial processes of land transformation, with a planning perspective.
  • Fletcher, R., & Fortin, M.-J. (2018). Spatial Ecology and Conservation Modeling: Applications with R. Springer. Spatial statistics, scale, habitat selection, connectivity and populations, with worked examples.
  • Fortin, M.-J., & Dale, M. R. T. (2005). Spatial Analysis: A Guide for Ecologists. Cambridge University Press. The statistics of spatial pattern: autocorrelation, point patterns, surfaces and boundaries.
  • Crooks, K. R., & Sanjayan, M. (Eds.) (2006). Connectivity Conservation. Cambridge University Press. Concepts, methods and case studies of connectivity for conservation.

Key papers by topic

Foundations and scale

  • Turner, M. G. (1989). Landscape ecology: the effect of pattern on process. Annual Review of Ecology and Systematics, 20, 171–197. The paper that set the pattern–process agenda.
  • Wiens, J. A. (1989). Spatial scaling in ecology. Functional Ecology, 3(4), 385–397.
  • Levin, S. A. (1992). The problem of pattern and scale in ecology. Ecology, 73(6), 1943–1967.
  • Jackson, H. B., & Fahrig, L. (2012). What size is a biologically relevant landscape? Landscape Ecology, 27, 929–941.
  • Metzger, J. P. (2001). O que é ecologia de paisagens? Biota Neotropica, 1(1–2). A concise introduction in Portuguese to the two traditions of landscape ecology.

Habitat loss and fragmentation

  • Fahrig, L. (2003). Effects of habitat fragmentation on biodiversity. Annual Review of Ecology, Evolution, and Systematics, 34, 487–515. The distinction between habitat loss and fragmentation per se.
  • Fahrig, L. (2017). Ecological responses to habitat fragmentation per se. Annual Review of Ecology, Evolution, and Systematics, 48, 1–23; and Fletcher, R. J., Jr., et al. (2018). Is habitat fragmentation good for biodiversity? Biological Conservation, 226, 9–15. Read together: the two sides of the debate.
  • Haddad, N. M., et al. (2015). Habitat fragmentation and its lasting impact on Earth's ecosystems. Science Advances, 1(2), e1500052.
  • Ribeiro, M. C., Metzger, J. P., Martensen, A. C., Ponzoni, F. J., & Hirota, M. M. (2009). The Brazilian Atlantic Forest: how much is left, and how is the remaining forest distributed? Implications for conservation. Biological Conservation, 142(6), 1141–1153. A landmark application of patch, edge and connectivity analyses to a whole biome.

Conservation planning

  • Margules, C. R., & Pressey, R. L. (2000). Systematic conservation planning. Nature, 405, 243–253. The framework: explicit goals, gap analysis, complementary selection, implementation.
  • Moilanen, A., Wilson, K. A., & Possingham, H. P. (Eds.) (2009). Spatial Conservation Prioritization: Quantitative Methods and Computational Tools. Oxford University Press. The methods and software of spatial prioritization, Zonation and Marxan among them, by their authors.
  • Kukkala, A. S., & Moilanen, A. (2013). Core concepts of spatial prioritisation in systematic conservation planning. Biological Reviews, 88(2), 443–464. Complementarity, irreplaceability, efficiency and the other concepts, defined and related.
  • Moilanen, A., Lehtinen, P., Kohonen, I., Jalkanen, J., Virtanen, E. A., & Kujala, H. (2022). Novel methods for spatial prioritization with applications in conservation, land use planning and ecological impact avoidance. Methods in Ecology and Evolution, 13(5), 1062–1072. Zonation 5: the iterated ranking, its rules and uses.

Species distributions

  • Franklin, J. (2010). Mapping Species Distributions: Spatial Inference and Prediction. Cambridge University Press. A textbook of the whole workflow, from data to evaluation, by an ecologist and geographer.
  • Peterson, A. T., Soberón, J., Pearson, R. G., Anderson, R. P., Martínez-Meyer, E., Nakamura, M., & Araújo, M. B. (2011). Ecological Niches and Geographic Distributions. Princeton University Press. The niche-centred view: the BAM diagram, the accessible area, environmental and geographic space.
  • Guisan, A., Thuiller, W., & Zimmermann, N. E. (2017). Habitat Suitability and Distribution Models: With Applications in R. Cambridge University Press. Concepts and practice, with worked examples of every step.
  • Elith, J., & Leathwick, J. R. (2009). Species distribution models: ecological explanation and prediction across space and time. Annual Review of Ecology, Evolution, and Systematics, 40, 677–697. The review to start with.
  • Elith, J., Phillips, S. J., Hastie, T., Dudík, M., Chee, Y. E., & Yates, C. J. (2011). A statistical explanation of MaxEnt for ecologists. Diversity and Distributions, 17(1), 43–57. What Maxent estimates and how its settings act, without the black box.
  • Roberts, D. R., et al. (2017). Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure. Ecography, 40(8), 913–929. Why random cross-validation is optimistic, and what to do instead.
  • Valavi, R., Guillera-Arroita, G., Lahoz-Monfort, J. J., & Elith, J. (2022). Predictive performance of presence-only species distribution models: a benchmark study with reproducible code. Ecological Monographs, 92(1), e01486. Which algorithms and settings work, compared on species from six regions of the world.
  • Zurell, D., et al. (2020). A standard protocol for reporting species distribution models. Ecography, 43(9), 1261–1277. The ODMAP protocol: what a paper must say about data, model, assessment and prediction.

Landscape metrics

  • McGarigal, K. (2015). FRAGSTATS Help. University of Massachusetts, Amherst. The definitions and interpretation of every classic metric; the reference manual behind most metric names.
  • Li, H., & Wu, J. (2004). Use and misuse of landscape indices. Landscape Ecology, 19, 389–399.
  • Cushman, S. A., McGarigal, K., & Neel, M. C. (2008). Parsimony in landscape metrics: strength, universality, and consistency. Ecological Indicators, 8(5), 691–703.
  • Hesselbarth, M. H. K., Sciaini, M., With, K. A., Wiegand, K., & Nowosad, J. (2019). landscapemetrics: an open-source R tool to calculate landscape metrics. Ecography, 42, 1648–1657.

Morphology

  • Soille, P., & Vogt, P. (2009). Morphological segmentation of binary patterns. Pattern Recognition Letters, 30(4), 456–459.
  • Vogt, P., & Riitters, K. (2017). GuidosToolbox: universal digital image object analysis. European Journal of Remote Sensing, 50(1), 352–361. The toolbox whose pattern, fragmentation and restoration methods Landschaft reproduces.

Connectivity

  • Taylor, P. D., Fahrig, L., Henein, K., & Merriam, G. (1993). Connectivity is a vital element of landscape structure. Oikos, 68(3), 571–573.
  • Saura, S., & Pascual-Hortal, L. (2007). A new habitat availability index to integrate connectivity in landscape conservation planning. Landscape and Urban Planning, 83(2–3), 91–103.
  • Saura, S., & Rubio, L. (2010). A common currency for the different ways in which patches and links can contribute to habitat availability and connectivity in the landscape. Ecography, 33(3), 523–537.
  • McRae, B. H., Dickson, B. G., Keitt, T. H., & Shah, V. B. (2008). Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology, 89(10), 2712–2724.
  • Zeller, K. A., McGarigal, K., & Whiteley, A. R. (2012). Estimating landscape resistance to movement: a review. Landscape Ecology, 27, 777–797.
  • Correa Ayram, C. A., Mendoza, M. E., Etter, A., & Salicrup, D. R. P. (2016). Habitat connectivity in biodiversity conservation: a review of recent studies and applications. Progress in Physical Geography, 40(1), 7–37.

Restoration and change

  • Tambosi, L. R., Martensen, A. C., Ribeiro, M. C., & Metzger, J. P. (2014). A framework to optimize biodiversity restoration efforts based on habitat amount and landscape connectivity. Restoration Ecology, 22(2), 169–177.
  • Strassburg, B. B. N., et al. (2020). Global priority areas for ecosystem restoration. Nature, 586, 724–729.
  • Olofsson, P., et al. (2014). Good practices for estimating area and assessing accuracy of land change. Remote Sensing of Environment, 148, 42–57.

Software whose methods Landschaft reproduces

Software Methods Reference
GuidosToolbox MSPA, SPA, accounting, fragmentation, landscape mosaic, distance, restoration, change Vogt & Riitters (2017)
FRAGSTATS, landscapemetrics landscape metrics McGarigal et al. (2012); Hesselbarth et al. (2019)
Conefor, Makurhini habitat networks, ProtConn Saura & Torné (2009); Godínez-Gómez & Correa Ayram (2020)
Circuitscape, Omniscape circuit connectivity Anantharaman et al. (2020); Landau et al. (2021)
CoordinateCleaner, spThin, usdm, blockCV, ENMeval, ecospat, predicts cleaning, thinning, predictors, folds and evaluation of species distribution models Zizka et al. (2019); Aiello-Lammens et al. (2015); Valavi et al. (2019); Muscarella et al. (2014)

The benchmarks page describes how each reproduction is tested.

  • Godínez-Gómez, O., & Correa Ayram, C. A. (2020). Makurhini: Analyzing landscape connectivity (R package). Zenodo.