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Large-scale dark diversity estimates: new perspectives with combined methods.

ABSTRACT: Large-scale biodiversity studies can be more informative if observed diversity in a study site is accompanied by dark diversity, the set of absent although ecologically suitable species. Dark diversity methodology is still being developed and a comparison of different approaches is needed. We used plant data at two different scales (European and seven large regions) and compared dark diversity estimates from two mathematical methods: species co-occurrence (SCO) and species distribution modeling (SDM). We used plant distribution data from the Atlas Florae Europaeae (50 × 50 km grid cells) and seven different European regions (10 × 10 km grid cells). Dark diversity was estimated by SCO and SDM for both datasets. We examined the relationship between the dark diversity sizes (type II regression) and the overlap in species composition (overlap coefficient). We tested the overlap probability according to the hypergeometric distribution. We combined the estimates of the two methods to determine consensus dark diversity and composite dark diversity. We tested whether dark diversity and completeness of site diversity (log ratio of observed and dark diversity) are related to various natural and anthropogenic factors differently than simple observed diversity. Both methods provided similar dark diversity sizes and distribution patterns; dark diversity is greater in southern Europe. The regression line, however, deviated from a 1:1 relationship. The species composition overlap of two methods was about 75%, which is much greater than expected by chance. Both consensus and composite dark diversity estimates showed similar distribution patterns. Both dark diversity and completeness measures exhibit relationships to natural and anthropogenic factors different than those exhibited by observed richness. In summary, dark diversity revealed new biodiversity patterns which were not evident when only observed diversity was examined. A new perspective in dark diversity studies can incorporate a combination of methods.

SUBMITTER: Ronk A

PROVIDER: S-EPMC5016647 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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Large-scale dark diversity estimates: new perspectives with combined methods.

Ronk Argo A de Bello Francesco F Fibich Pavel P Pärtel Meelis M

Ecology and evolution 20160804 17

Large-scale biodiversity studies can be more informative if observed diversity in a study site is accompanied by dark diversity, the set of absent although ecologically suitable species. Dark diversity methodology is still being developed and a comparison of different approaches is needed. We used plant data at two different scales (European and seven large regions) and compared dark diversity estimates from two mathematical methods: species co-occurrence (SCO) and species distribution modeling ...[more]

PMID: 27648241

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Project description:Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat-specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so-called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co-occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co-occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods need attention, especially when dark diversity is estimated at the plot level.

Dataset Information

Large-scale dark diversity estimates: new perspectives with combined methods.

Publications

Large-scale dark diversity estimates: new perspectives with combined methods.

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