DOI: 10.5061/dryad.0gb5mkm45
title: Data from: Beaver activity and red squirrel presence predict bird assemblages in boreal Canada

description: Wetlands and predation in boreal ecosystems play essential roles
 throughout the breeding season for bird assemblages. We found a positive
 association of beaver activity and a negative influence of American red
 squirrels (Tamiasciurus hudsonicus) on bird assemblages. We used a
 multispecies hierarchical model to investigate whether bird communities
 differ between two major wetland habitats in boreal Canada: beaver ponds
 and peatland ponds. In addition to including variables such as forest
 cover and latitude, we adopted a structural equation model approach to
 estimate the occupancy of American red squirrels and its potential
 influence on bird communities. Using automated recording stations deployed
 at 50 ponds, we detected 96 bird species in 2018 and 2019. Bird species
 were grouped into four taxonomic guilds according to their habitat
 successional requirements: early successional species, late successional
 species, generalists, and wetland species. Beaver ponds harbored higher
 species richness, a pattern driven primarily by early successional
 species. The occupancy of almost a quarter of the species was lower in the
 presence of red squirrels. Late successional species responded positively
 to the cover of forest surrounding the pond. Our results highlight the
 value of considering acoustic data of red squirrels to quantify habitat
 quality in boreal forests. We conclude that beaver activity shapes bird
 assemblages through modification of their habitat, and that some bird
 guilds are associated negatively with the presence of American red
 squirrels.
description: <strong>Acoustic sampling and
 covariates.</strong> We used a SM4 Song meter
 (Wildlife Acoustics Incorporation, Concord, Massachusetts, USA) at each
 pond to record bird and squirrel vocalizations. During a given sampling
 period, ARUs were set with both microphones facing upward for four
 consecutive days to record a 5-min sample at 00600 h. Each file was
 encoded at a sampling rate of 44.1 kHz and a 16-bit resolution. Each pond
 was sampled for four consecutive days during two periods in both years,
 yielding an average of 80 minutes per pond. All recording data were
 analyzed by an ornithologist with extensive field experience in the study
 region to identify species based on their vocalizations or other aural
 cue. Species were categorized into four guilds based on their requirements
 for various successional stages of black spruce: (1) early successional
 species, associated with open areas of low-vegetation such as young
 forests or regenerating shrublands; (2) late-successional species
 preferring older forest stands; (3) generalists, consisting of species
 that use a wide range of successional stages; and (4) wetland and aquatic
 species. In addition to birds, we identified the vocalizations of the
 American red squirrel from recordings for use in occupancy analysis. We
 included four candidate variables as potential predictors of boreal bird
 occupancy: pond type, red squirrel latent occupancy, proportion of all
 forest types over 2 m (deciduous, mixed, and coniferous forest) within
 circular buffers of 1000 m centered on acoustic recorder locations, and we
 included latitude to reflect habitat changes in the study area. We
 considered two parameters that potentially influenced detection
 probability during acoustic surveys: the quality of the recording and the
 number of days after snowmelt. <strong>Data
 processing and analysis.</strong> We investigated
 occupancy patterns of the American red squirrel, and the entire bird
 community detected at least once in our recordings. We prepared detection
 histories for each species at each pond, where we indicated detection (1)
 or non-detection (0) in each recording of the two periods of four
 consecutive days in each year. Each pond in each year was considered as an
 independent site and we included a fixed year effect as well as a site
 random effect to account for potential differences in occupancy between
 years. Thus, detection histories for a given species were arranged in a
 matrix of 100 rows (50 sites x 2 years) and 8 columns (4 recordings x 2
 periods). We estimated bird community structure with a multispecies
 site-occupancy model. We adapted a structural equation strategy to our
 multispecies occupancy model. Specifically, one component of our model
 estimated the occupancy of American red squirrels as a function of
 different explanatory variables, and then used the latent squirrel
 occupancy as an explanatory variable in the multispecies occupancy model
 for the bird communities. We used the multispecies model to derive the
 species richness from the posterior distribution of the true occurrence of
 each species at each site, expressed as the mean of the posterior
 distribution. We investigated the relationship between species richness
 against the explanatory variables pond type, forest cover, latitude, and
 the posterior mean of the squirrel occupancy state in a linear
 mixed-effect model.
description: The description of each column header for each spreadsheet is
 provided in an associated ReadMe file. The steps to follow for each
 analysis are provided in Supplementary material the R code files. The
 final dataset included detection/non-detection data for 96 species from 50
 ponds from May to August 2018 and 2019
 ("Bird_multisp_v2.Rdata"). This dataset is shared in one file in
 the form of a 3-dimensional array table, which contained rows for pond
 units (n=100), columns for visits (n=8), and rectangular matrices for
 species (n=96). Please contact the author for any additional inquiries of
 how data was collected and analyze.