Calibration of hybrid species distribution models: The value of general-purpose vs. targeted monitoring data

De Cáceres M., Brotons L. (2012) Calibration of hybrid species distribution models: The value of general-purpose vs. targeted monitoring data. Diversity and Distributions. 18: 977-989.
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Doi: 10.1111/j.1472-4642.2012.00899.x

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Aim Temporally replicated observations are essential for the calibration and validation of species distribution models (SDMs) aiming at making temporal extrapolations. We study here the usefulness of a general-purpose monitoring programme for the calibration of hybrid SDMs. As a benchmark case, we take the calibration with data from a monitoring programme that specifically surveys those areas where environmental changes expected to be relevant occur. Location Catalonia, north-east of Spain. Methods We modelled the distribution changes of twelve open-habitat bird species in landscapes whose dynamics are driven by fire and forest regeneration. We developed hybrid SDMs combining correlative habitat suitability with mechanistic occupancy models. We used observations from two monitoring programmes to provide maximum-likelihood estimates for spread parameters: a common breeding bird survey (CBS) and a programme specifically designed to monitor bird communities within areas affected by wildfires (DINDIS). Results Both calibration with CBS and DINDIS data yielded sound spread parameter estimates and range dynamics that suggested dispersal limitations. However, compared to calibration with DINDIS data, calibration with CBS data leads to biased estimates of spread distance for seven species and to a higher degree of uncertainty in predicted range dynamics for six species. Main conclusions We have shown that available monitoring data can be used in the calibration of the mechanistic component of hybrid SDMs. However, if the dynamics of the target species occur within areas not well covered, general-purpose monitoring data can lead to biased and inaccurate parameter estimates. To determine the potential usefulness of a given monitoring data set for the calibration of the mechanistic component of a hybrid SDM, we recommend quantifying the number of surveyed sites that are predicted to undergo habitat suitability changes. © 2012 Blackwell Publishing Ltd.

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Using species combinations in indicator value analyses

De Cáceres M., Legendre P., Wiser S.K., Brotons L. (2012) Using species combinations in indicator value analyses. Methods in Ecology and Evolution. 3: 973-982.
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Doi: 10.1111/j.2041-210X.2012.00246.x

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1. Indicator species are often determined using an analysis of the relationship between the species occurrence or abundance values from a set of sites and the classification of the same sites into site groups (habitat types, community types, disturbance states, etc.). It may happen, however, that a particular site group has no indicator species even if its sites have a community composition that is clearly distinct from the sites of other site groups. This motivates an exploration of the indicator value of not only individual species but also species combinations. 2. Here, we present a novel statistical approach to determine indicators of site groups using species data. Unlike traditional indicator value analysis, we allow indicators to be species combinations in addition to single species. We require that all the species forming the combination must occur in the site to use the combination as an indicator. We present a simple algorithm that identifies the set of indicators (each one being either a single species or a species combination) that show high positive predictive value for the target site group. Moreover, we demonstrate the use of the percentage of sites of the site group where at least one of its valid indicators occurs to determine whether the group can be reliably predicted throughout its range. 3. Using a simulation study, we show that if two species are not strongly correlated and their frequency in the data set is larger than the frequency of sites belonging to the site group, the joint occurrence of the two species has higher positive predictive value for the site group than the two species taken independently. 4. We illustrate the proposed method by determining which combinations of vascular plants can be used as indicators for 29 shrubland and forest vegetation types of New Zealand. 5. The proposed methodology extends traditional indicator value analyses and will be useful to develop multispecies ecological or environmental indicators. Further, it will allow newly surveyed sites to be reliably assigned to previously defined vegetation types. © 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society.

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