DOI: 10.5061/dryad.fxpnvx0qj
title: Data from: Ecological drivers of avian community assembly along a tropical elevation gradient

description: Community assembly theory hypothesizes that two main niche-based processes
 act to shape composition and organization of biological assemblages:
 abiotic filtering and biological interactions. Here, we conducted repeated
 surveys of bird abundance along an undisturbed elevational gradient in the
 tropical Andes to investigate (1) signals of deterministic processes
 driving community assembly and (2) potential mechanisms by which these
 forces operate (temperature, habitat complexity, fruit and insect
 availability), while correcting for imperfect detection and modeling
 species abundances with N-mixture models. We observed strong signals of
 abiotic filtering driving functionally and phylogenetically clustered
 assemblages towards higher elevations, and a weaker signal of limiting
 similarity resulting in few overdispersed assemblages at lower elevations.
 Whereas the decay in species richness with increasing elevation was
 explained by temperature, trait and phylogenetic dispersion were explained
 by both temperature and vegetation structure, implying that an interplay
 of abiotic and biotic mechanisms determines abundance-based community
 structure in our montane assemblages. Interestingly, trait and
 phylogenetic dispersion consistently decreased until ~3000 m but increased
 above this elevation, highlighting a potential role of competition in
 resource-scarce habitats. Combined, our findings suggest abiotic filters
 are still the main process shaping montane biotas across elevations,
 whereas resource availability might act locally upon assemblages further
 modifying them. Our study challenges recent studies in tropical mountains
 that suggest that biotic filters are a stronger force than abiotic filters
 in shaping tropical montane assemblages, and exemplifies how accounting
 for imperfect detection might overcome potential biases in detecting
 environmental filtering signals in community assembly studies.
description: Bird surveys were conducted between May and July 2014 and May and
 October 2015 and 2016  along an extensive gradient (1350 – 3650 m asl) in
 Cotapata National Park, a protected area in the Andes of western Bolivia
 (67°43′−68°03′ W/16°05′−16°20′ S, c. 80 km NE from La Paz city). For the
 purpose of analysis, we defined a ‘site’ as a band with 50-m elevational
 change along the gradient. We used a multi-season
 community N-mixture model implemented in a Bayesian framework to estimate
 abundance-based community diversity and structure while accounting
 explicitly for unobserved species and individuals. Detectability was modeled
 as logit-linear combination of site- or survey-specific covariates
 (i.e., date, start time,
 survey direction, and duration). Then,
 we calculated taxonomic, functional and
 phylogenetic diversity for each 50-m elevational band using the posterior
 samples of the <i>N</i>-matrix. For each posterior sample of
 the <i>N</i>-matrix (n=500), we calculated taxonomic diversity
 simply as species richness. Abundance-weighted functional and phylogenetic
 diversity were calculated with two dispersion metrics: mean pairwise
 dissimilarity (MPD) and mean nearest taxon distance (MNTD). Finally, we
 regressed taxonomic, functional and phylogeneetic diversity as a function
 of temperature, habitat complexity and the diversity of food resources
 (fruits and insects) across elevations.
description: <b>R files included
 as Supplementary materials </b> <b>AbundData.Rdata</b> Contains all data required to perform the MSAMs. List of 7 elements: <b>y</b> = array of observed counts of 300 species of birds surveyed in up to 20 visits to 45 50-m of elevation bands across an elevational gradient in the Bolivian Andes over 5 seasons <b>jday</b> = array of the normalized day of survey of each visit <b>tod</b> = array of the normalized time of the day each survey started, for each visit <b>effort </b>= array of the normalized time in minutes, spent at each site in each visit <b>direction </b>= array of the direction of survey during each visit. 0 = upslope, 1 = downslope <b>elev </b>= vector of the normalized elevation in m of each site <b>SiteCov</b> = dataframe with environmental variables for each of the 45 elevational bands temp = mean daily temperature in centigrade degrees (see text for details) fruits = fruit availability (see text for details) insects = arthropod diversity (see text for details) complexity = habitat complexity (see text for details) elevation = raw elevation, in meters above the sea level <b>MSAM.R</b> R Code to implement a multi-season N-mixture model implemented in JAGS within R environment. Code produces the N-matrix used in subsequent analyses, as described in text. <b>traits.csv</b> Database with nine functional traits used in the analyses, for 300 bird species. See main text and Supporting information for details. Code = species number Diet = Categorical, based on the main items included in bird diets. ForagStrata = Foraging strata, categorical. Based on the main vegetation strata used by birds for foraging. BodyMass.value = Log10 of body mass values, extracted from Wilman et al. 2014. billen = Average of Log10 of individual measurements of bill length (culmen). billhei = Average of Log10 of individual measurements of bill height. billwid = Average of Log10 of individual measurements of bill width (gape). wing = Average of Log10 of individual measurements of wing length. tail = Average of Log10 of individual measurements of tail length kipp = Average of Log10 of individual measurements of Kipp’s distance