DOI: 10.5061/dryad.xd2547dgb
title: Long-term trends in the phylogenetic and functional diversity of Anatidae in South China coastal wetlands

description: Species loss has attracted much attention among scientists for more than
 half a century. However, we have little information on the trends in
 phylogenetic and functional changes behind the species loss although this
 information is always asynchronous and important for conservation and
 management. We measured community trends in Anatidae (ducks and geese) for
 the last 50 years to quantify trends in phylogenetic and functional
 diversity patterns coinciding with taxonomic historical dynamics. We used
 one-way ANOVAs to test if there was a significant historical trend in
 communities of Anatidae. We characterized taxonomic, phylogenetic and
 functional diversity of communities. For taxonomic diversity, we used
 species richness (SR). For phylogenetic diversity, we calculated the
 standardized effect size of mean pairwise distances (ses.MPD) and the
 standard effect size of mean nearest taxon distances (ses.MNTD) in
 communities. For functional diversity, we calculated functional richness
 (FRic), functional evenness (FEve), functional divergence (FDiv) and the
 community-level weighted means (CWM) of trait values for diet, foraging
 stratum and body mass, separately. From the 1950’s to 2010’s, species
 richness declined without significant trends. The ses.MNTD of Anatidae
 communities showed no clear trends. However, ses.MPD of Anatidae
 communities declined dramatically during this period. For functional
 diversity, functional evenness of diet, foraging stratum, body mass and
 functional dispersion of diet, foraging stratum did not increase or
 decline significantly. However, functional evenness of all traits,
 functional richness and functional dispersion of body mass showed declined
 trends. The basic phylogenetic diversity and species body mass of Anatidae
 communities declined significantly because of a declining trend in the
 relative independent branch of geese. This makes it more challenging for
 implement community recovery in the future. More attention in conservation
 biology should consider taxonomic diversity and asynchrony in phylogenetic
 and functional diversity.
description: Anatidae species assemblages were obtained from monographs,
 literature, databases and expert surveys. Dataset of the 1950’s was
 extracted from <i>Bird Distribution Catalogue in China I.
 Non-Passeriformes</i> (Zheng 1955), with the dataset of the 1960’s
 extracted from Guan et al. (1963), datasets of the 1970’s was extracted
 from <i>Bird Distribution List of China</i> (Zheng 1975),
 datasets of the 1980’s was extracted from Deng et al. (1989), datasets
 from the 2000’s was extracted from China Bird Report (http://www.birdreport.cn/) and datasets from the 2010’s was extracted from our expert surveys. We downloaded 2,000 phylogenetic trees of the complete Anatidae species pool in our study from BirdTree (http://birdtree.org), the recently published phylogeny of the world's bird species, using the source of the “Ericson All Species” (Rubolini et al. 2015). We then calculated a maximum clade credibility tree with a 50% posterior probability limit by using the “TreeAnnotator” in the BEAST 2 software package (Bouckaert et al. 2014). Subsequent analyses of phylogenetic diversity were based on this annotated tree. We quantified three functional traits for birds that are commonly used to define functional diversity within the bird communities, categorical variables diet, foraging stratum and continuous variable body mass, which has shown to be functionally important (Wilman et al. 2014). We extracted those metrics from the Elton Traits database 1.0 (Wilman et al. 2014). Diet was classified into four categories, and each category was ranked based on percentage used for each species: (1) invertebrates, (2) vertebrates and fish and carrion, (3) plant and seeds and (4) omnivore.
description: Datasets from books (1950s and 1970s) included species but not
 abundance.