title: Measuring size and composition of species pools: a comparison of dark diversity estimates.
abstract: 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.
authors: Institute of BotanyThe Czech Academy of Sciences Dukelská 135 CZ-379 82 Třeboň Czech Republic; Department of Botany University of South Bohemia Na Zlaté stoce 1 CZ-370 05 České Budějovice Czech Republic.
authors: Francesco
authors: F
authors: de Bello
authors: Institute of BotanyThe Czech Academy of Sciences Dukelská 135 CZ-379 82 Třeboň Czech Republic; Department of Botany University of South Bohemia Na Zlaté stoce 1 CZ-370 05 České Budějovice Czech Republic.
authors: Pavel
authors: P
authors: Fibich
authors: Department of Botany and Zoology Masaryk University Kotlářská 2 CZ-611 37 Brno Czech Republic; Institute of Ecology and Evolutionary Biology National Taiwan University Roosevelt Rd. 110617 Taipei Taiwan.
authors: David
authors: D
authors: Zelený
authors: Institute of Botany The Czech Academy of Sciences Lidická 25/27 CZ-602 00 Brno Czech Republic; Department of Forest Ecology Faculty of Forestry and Wood Sciences Czech University of Life Sciences Prague Kamýcká 129 CZ-165 21 Prague 6 - Suchdol Czech Republic.
authors: Martin
authors: M
authors: Kopecký
authors: Institute of Botany The Czech Academy of Sciences Dukelská 135 CZ-379 82 Třeboň Czech Republic.
authors: Ondřej
authors: O
authors: Mudrák
authors: Department of Botany and Zoology Masaryk University Kotlářská 2 CZ-611 37 Brno Czech Republic.
authors: Milan
authors: M
authors: Chytrý
authors: Institute of Botany The Czech Academy of Sciences Zámek 1 CZ-252 43 Průhonice Czech Republic; Department of Ecology Faculty of Science Charles University in Prague Viničná 7 CZ-128 44 Prague Czech Republic; Department of Botany and Zoology Centre for Invasion Biology Stellenbosch University Matieland 7602 South Africa.
authors: Petr
authors: P
authors: Pyšek
authors: Institute of Botany The Czech Academy of Sciences Zámek 1 CZ-252 43 Průhonice Czech Republic; Faculty of Environmental Sciences Czech University of Life Sciences Prague Kamýcká 129 CZ-165 21 Prague 6 - Suchdol Czech Republic.
authors: Jan
authors: J
authors: Wild
authors: Department of Botany and Zoology Masaryk University Kotlářská 2 CZ-611 37 Brno Czech Republic.
authors: Dana
authors: D
authors: Michalcová
authors: Institute of Botany The Czech Academy of Sciences Zámek 1 CZ-252 43 Průhonice Czech Republic.
authors: Jiří
authors: J
authors: Sádlo
authors: Department of Ecosystem Biology Faculty of Science University of South Bohemia Branišovská 1970 CZ-370 05 České Budějovice Czech Republic.
authors: Petr
authors: P
authors: Šmilauer
authors: Department of Botany University of South Bohemia Na Zlaté stoce 1 CZ-370 05 České Budějovice Czech Republic; Biology Centre The Czech Academy of Sciences Branišovská 31370 05 České Budějovice Czech Republic.
authors: Jan
authors: J
authors: Lepš
authors: Institute of Ecology and Earth Sciences University of Tartu Lai 40 51005 Tartu Estonia.
authors: Meelis
authors: M
authors: Pärtel
keywords: Beals smoothing; Biomod; Ellenberg indicator values; biodiversity monitoring; dark diversity; method comparison; species distribution modeling