DOI: 10.5061/dryad.zw3r2286h
title: Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study

description: Aim: The abundance-frequency relationship (AFR) is among the
 most-investigated pattern in biogeography, yet the relative contributions
 of niche-based processes related to ecological strategies, and of neutral
 processes related to spatial colonization-extinction dynamics, remains
 uncertain. Here, we tested the influences of ecological specialization and
 functional traits on local abundance and regional frequency, to determine
 the contribution of niche-based processes. Location: France and the UK.
 Taxon: Vascular plants. Methods: We used two arable weed surveys covering
 1544 fields in Western Europe (France, UK), along with functional traits
 related to resource acquisition, flowering phenology and dispersal. We
 quantified specialization both to arable habitat and to individual crop
 types, and performed phylogenetic path analyses to test competing models
 accounting for direct and indirect relationships between traits,
 specialization, abundance and frequency. We performed the analyses for all
 species in each country, as well as for a subset of the most abundant
 species. Results: Local abundance of weeds increased with their regional
 frequency, but the relationship became negative or null when considering
 only the most abundant weeds. Specialization to arable habitat and to
 individual crop type either had a similar or opposite effect on regional
 frequency and local abundance explaining these positive and negative
 relationships, respectively. Regional frequency was not directly explained
 by any trait but indirectly by resource requirement traits conferring
 specialization to the arable habitat. Conversely, high local abundance was
 directly related to low seed mass, high SLA, early and short flowering.
 Main Conclusions: Direct/indirect effects of functional traits on local
 abundance/regional frequency, respectively, supports a significant role of
 niche-based processes in AFR. Neutral spillover dynamics could further
 explain a direct linkage of abundance and frequency. Similar causal paths
 and consistent influences of traits on specialization and abundance in the
 two studied regions suggest genericity of these findings.
description: We analyzed two nationwide surveys of arable weed communities
 conducted in France: Biovigilance Flore, BVG hereafter (Fried et al.,
 2008), and in the UK: Farm scale evaluation, FSE hereafter (Heard et al.,
 2003). The regional frequency of a species was defined as the proportion
 of sampled fields where the species was present. Local mean abundance was
 calculated as the average density in sites where the species was
 present. We used a fidelity measure to represent
 ecological specialization to the arable habitat, based on the relative
 frequency of a species in a reference habitat compared to other habitats
 (Chytrý<i> et al.</i>, 2002). In France, we assessed weed
 frequency in 5,382 vegetation samples in arable fields (the complete BVG
 dataset), and in 96,438 samples covering diverse grassland habitats in the
 DIVGRASS database (Violle<i> et al.</i>, 2015). In the UK, we
 assessed weed frequency in 268 samples in arable fields (the complete FSE
 dataset), and in 15,756 samples from other habitats excluding arable and
 horticulture habitats (Carey<i> et al.</i>, 2008). We
 quantified the <i>phi</i> coefficient of
 association: <i>phi</i> = , with <i>N</i> the total number of samples used (101,820 for France, 16,024 for UK), <i>N<sub>p</sub></i>, the number of samples in arable habitats (5,382 for France and 268 for UK respectively), <i>n</i>, the number of occurrences of the species in the dataset, and <i>n<sub>p</sub></i> the number of occurrences of the species in arable habitats. The phylogeny was derived from a dated and comprehensive megaphylogeny of spermaphytes, by using the function S.PhyloMaker provided by Qian and Jin (2016) with scenario "S3."
description: The dataset provides three files: - a csv file
 with the regional frequency, local abundance and specialization to arable
 fields of 265 plant species - a csv file with the trait
 values for 150 plant species used in the phylogenic path analysis (122
 species for the BVG French dataset and 102 sepcies for the FSE UK
 dataset) - the phylogeny of the same 150
 species