DOI: 10.5061/dryad.9kd51c5d5
title: Dark diversity reveals importance of biotic resources and competition for plant diversity across habitats

description: Species richness is the most commonly used metric to quantify
 biodiversity. However, examining dark diversity, the group of missing
 species which can potentially inhabit a site, can provide a more thorough
 understanding of the processes influencing observed biodiversity and help
 evaluate the restoration potential of local habitats. So far, dark
 diversity has mainly been studied for specific habitats or largescale
 landscapes while less attention has been given to variation across broad
 environmental gradients or as a result of local conditions and biotic
 interactions. In this study, we investigate the importance of local
 environmental conditions in determining dark diversity and observed
 richness in plant communities across broad environmental gradients. Using
 the ecospace concept, we investigate how these biodiversity measures
 relate to abiotic gradients (defined as position), availability of biotic
 resources (defined as expansion), spatiotemporal extent of habitats
 (defined as continuity), as well as species interactions through
 competition. Position variables were important for both observed and dark
 diversity, some with quadratic relationships, e.g., plant richness showing
 a unimodal response to soil fertility corresponding to the intermediate
 productivity hypothesis. Interspecific competition represented by
 community mean Grime C had a negative effect on plant species richness.
 Besides position-related variables, organic carbon was the most important
 variable for dark diversity, indicating that in late succession habitats
 such as forests and shrubs, dark diversity is generally low. The
 importance of highly competitive species indicates that intermediate
 disturbance, such as grazing, may facilitate higher species richness and
 lower dark diversity.
description: The dataset consists of three subsets: 1) a
 dataset with plant (excl. bryophytes) observations from a large number of
 5 m radius circular vegetation plots from terrestrial habitats (including
 many different habitats, also bogs, fens and other wet habitats, but not
 purely freshwater (lakes and streams) and not marine) in Denmark. These
 data were both collected as part of the Danish Monitoring of NATURA2000
 sites (NOVANA) and as part of the Danish biodiversity research project
 called Biowide. The data consists of species lists from the aforementioned
 vegetation plots. This lists can be thought of as complete, i.e. species
 not in a given plot were most likely absent. The dataset was cleaned by
 lumping together subspecies and varieties and the species level, removing
 all non-plants, removing all hybrids and removing observations at a lower
 than species level (genus, familiy etc.). There are two related works
 given. One that documents the Biowide data and another one describing
 every detail of the whole NOVANA national monitoring programme, but this
 is only available in Danish. The file is called tmp-bionova.tsv.
 2) Environmental factors used for statistical analysis. These
 were recorded as part of the Biowide project. This dataset also holds the
 calculated response variables for statistical analysis. The file is called
 responsevar-and-env-bw115.csv. 3) A dataset with all
 vegetation data from each Biowide site. Each site consisted of four 5 m
 radius vegetation plots (data for each plot available in (1)). These data
 were cleaned in the same manner as (1). The file is called
 biowide-site-matrix-115.csv.
description: If using this dataset please contact us, we used a lot of time to
 do the processing. Also please contact the project leader of the Biowide
 project, see
 https://bios.au.dk/om-instituttet/organisation/biodiversitet/projekter/data/ .