DOI: 10.5061/dryad.sf7m0cg30
title: Data from: Multi-taxon inventory reveals highly consistent biodiversity responses to ecospace variation

description: Amidst the global biodiversity crisis, identifying general principles for
 variation in biodiversity remains a key challenge. Scientific consensus is
 limited to a few macroecological rules, such as species richness
 increasing with area, which provide limited guidance for conservation. In
 fact, few agreed ecological principles apply at the scale of sites or
 reserve management, partly because most community-level studies are
 restricted to single habitat types and species groups. We used the
 recently proposed ecospace framework and a comprehensive data set for
 aggregating environmental variation to predict multi-taxon diversity. We
 studied richness of plants, fungi, and arthropods in 130 sites
 representing the major terrestrial habitat types in Denmark. We found the
 abiotic environment (ecospace position) to be pivotal for the richness of
 primary producers (vascular plants, mosses, and lichens) and, more
 surprisingly, little support for ecospace continuity as a driver. A peak
 in richness at intermediate productivity adds new empirical evidence to a
 long-standing debate over biodiversity responses to productivity. Finally,
 we discovered a dominant and positive response of fungi and insect
 richness to organic matter accumulation and diversification (ecospace
 expansion). Two simple models of producer and consumer richness accounted
 for 77 % of the variation in multi-taxon species richness suggesting a
 significant potential for generalization beyond individual species
 responses. Our study widens the traditional conservation focus on
 vegetation and vertebrate populations unravelling the importance of
 diversification of carbon resources for diverse heterotrophs, such as
 fungi and insects.
description: The Biowide project including major aspects of collection of soil
 and Malaise trapping has been described elsewhere (Brunbjerg et al 2019),
 with specific publication and analysis of the fungal data in Frøslev et al
 (2019) and the eukaryote data in Fløjgaard et al (2019). For the arthropod
 data, a malaise trap ws placed in the centre of each of the 130 sampling
 sites and left open for 1 week. Two such trapping events were performed
 with some weeks apart in the same year. The arthropod DNA dataset was
 produced by extracting DNA from the ethanol from the bulk insect Malaise
 traps and metabarcoding with the arthropod specific COI primers ZBJ-ArtF1c
 and ZBJ-ArtR2c. 45 ml ethanol and 1.5 ml of 3M sodium acetate were added
 to a 50 ml centrifuge tube, and left in a freezer for DNA precipitation
 overnight, then centrifuged for 40 minutes. The dried pellet was extracted
 with the Qiagen DNeasy blood and tissue kit (Qiagen, Germany) with minor
 modifications. The extracted DNA was normalized, amplified, sequenced and
 analyzed according to the overall procedures described in Brunbjerg, et al
 (2019). As for the eukaryote and fungal datasets OTU tables were
 constructed following the overall pipeline suggested in Frøslev, et al.
 (2017), to derive OTUs that approximates species level delimitation.This
 consisted of an initial processing with DADA2 to identify exact amplicon
 sequence variants including removal of chimeras and post-clustering
 curation using LULU. Taxonomic assignment was done with a custom script
 (as in Fløjgaard, et al 2019). OTUs not assigned to Arthropoda were
 discarded before further analyses. Brunbjerg, A. K.,
 Bruun, H. H., Brøndum, L., Classen, A. T., Dalby, L., Fog, K., ...
 & Høye, T. T. (2019). A systematic survey of regional multi-taxon
 biodiversity: evaluating strategies and coverage. BMC ecology, 19(1),
 43. Fløjgaard C, Frøslev TG, Brunbjerg AK, Bruun HH,
 Moeslund J, Hansen AJ, & Ejrnæs R. 2019. Predicting provenance of
 forensic soil samples: Linking soil to ecological habitats by
 metabarcoding and supervised classification. PloS one, 14(7),
 e0202844. Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R,
 Hansen AJ, Læssøe T, Heilmann-Clausen J. 2019. Man against machine: Do
 fungal fruitbodies and eDNA give similar biodiversity assessments across
 broad environmental gradients? Biological Conservation 233,
 201-212. Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R,
 Brunbjerg AK, Pietroni C, Hansen AJ. 2017. Algorithm for post-clustering
 curation of DNA amplicon data yields reliable biodiversity estimates.
 Nature Communications 8:1188. doi:10.1038/s41467-017-01312-x.<br>
  
description: We studied species richness of different organism groups in 130
 sites representing the major terrestrial habitat types in Denmark. Some of
 these groups were represented by DNA metabarcoding data. This dataset
 represents the DNA data for arthropods trapped in Malaise traps. Datasets
 for eukaryotes and fungi from soil eDNA were previously published and used
 in conjunction with the present data. Overall we found the abiotic
 environment (ecospace position) to be pivotal for the richness of primary
 producers (vascular plants, mosses, and lichens) and, more surprisingly,
 little support for ecospace continuity as a driver.
 Here we provide the "raw" Illumina files. They need to
 be demultiplexed using the information of primers and tags. All this
 information including all further downstream analyses are given in the
 github repository connected with the manuscript (https://github.com/tobiasgf/biowide_synthesis).