DOI: 10.5061/dryad.s1rn8pk5s
title: Data from: Long-term change in the avifauna of undisturbed Amazonian rainforest: Ground-foraging birds disappear and the baseline shifts

description: How are rainforest birds faring in the Anthropocene? We use bird captures
 spanning &gt;35 years from 55 sites within a vast area of intact
 Amazonian rainforest to reveal reduced abundance of terrestrial and
 near-ground insectivores in the absence of deforestation, edge effects, or
 other direct anthropogenic landscape change. Because undisturbed
 forest includes far fewer terrestrial and near-ground insectivores than it
 did historically, today’s fragments and second growth are more
 impoverished than shown by comparisons with modern ‘control’ sites. Any
 goals for bird community recovery in Amazonian second growth should
 recognize that a modern bird community will inevitably differ from a
 baseline from &gt;35 years ago. Abundance patterns driven by landscape
 change may be the most conspicuous manifestation of human activity, but
 biodiversity declines in undisturbed forest represent hidden losses,
 possibly driven by climate change, that may be pervasive in intact
 Amazonian forests and other systems considered to be
 undisturbed. 
description: These count data were collected using a standard operating
 procedure of avian mist-netting across time (1980-1984 and 2007-2016) and
 space (70 unique mist net lanes) at the Biological Dynamics of Forest
 Fragments Project, ~80 km north of Manaus, Brazil (2º20’S, 60ºW). For
 specifics about field protocols, data quality control, subsetting, and
 categorization, we refer the reader to the pertinent sections of the
 Methods: Site selection, Bird sampling, and Bird data.
description: For starters, we would direct anyone interested in these data to
 begin by examining Figure 1 in the main text. This provides
 an illustrative schematic of our sampling design, as well as the three
 combinations of time period+forest type that we compared: historical
 primary, modern primary, and modern disturbed. These three
 samples directly align with the three principal datasets that we uploaded
 separately to Dryad (e.g., Historical_primary_forest_captures_BDFFP.csv).
 For each of the three forest samples (differentiated in
 the 'Time_period' column), we provide the number of captures
 ('Count') for all 'Species' at a given
 'Site', along with the 'Effort' (in net-hours) that
 accrued at each site. Even though some datasets completely lack captures
 for a given species (Count = 0), each file nonetheless contains a row for
 every combination of site and species (n=79 species). However, because the
 datasets differ in the number of sites sampled, they also differ
 in length: Historical primary forest - 34 sites*79
 species = 2686 rows Modern primary forest - 21 sites*79
 species = 1659 rows Modern disturbed forest - 15
 sites*79 species = 1185 rows These count data were then
 used to make relative abundance comparisons between samples in order to
 detect long-term changes within primary forest (Figure 2A) as well as the
 shifting baseline (Figure 2B). We also used a categorical column for
 'Guild' to more generally describe long-term changes within
 primary forest (Figure 3A) and following deforestation and
 fragmentation (Figure 3B). Additionally,
 "NMDS_community_ordination_BDFFP.csv" integrates captures and
 effort to generate capture rates (captures/1000 mist-net hours) for all 79
 species (now 79 columns) at each of our 70 sites (rows): 15 sites in
 modern disturbed, 34 in historical primary, and 21 in modern primary
 forest. We used these data to generate the NMDS ordination evident in
 Figure 4. For more information, please see the Methods
 section of the main text and Table S1 for a list of all 79 species, with
 summed captures across sites for each of the three datasets. Finally, we
 provide the coordinates for each of the 70 sites in UTMs (Zone 21S):
 "BDFFP_site_coordinates_21S.csv".