DOI: 10.5061/dryad.m0cfxpp2s
title: Data from: Disturbed Amazonian forests support diminished breeding bird communities

description: Twenty percent of the Brazilian Amazon has now been deforested, and
 deforestation rates are increasing. This compels us to evaluate the
 conservation potential of human-modified landscapes, yet the ecological
 value of regenerating and fragmented Amazonian forests remains poorly
 understood. To date, most faunal studies in disturbed forests have
 examined metrics derived from presence or abundance. Although valuable,
 these data cannot tell us how old-growth species are using disturbed
 forests. In this study, we complement presence data with breeding
 observations to assess more comprehensively the habitat quality of
 disturbed forests in central Amazonia. We synthesized breeding evidence
 from standardized passive mist-netting, mixed-species flock-following, and
 opportunistic nest-searching across a full annual cycle in 30-35-year-old
 secondary forest, 10-ha fragments, and undisturbed forest. We then used
 multi-state occupancy models to estimate the number of undetected breeding
 species in each forest type, which illustrated that fewer species bred in
 secondary forest (-43%) and 10-ha fragments (-17%) than in undisturbed
 forest. Both of these losses are larger than the associated decrease in
 species richness alone (-17% and -10%, respectively). Notably, we
 confirmed breeding by only three terrestrial and near-ground insectivores
 in fragments and secondary forest combined (of the 9 species found in
 undisturbed forest). Disturbed forests also supported fewer breeding
 individuals (-35-50%) and, in secondary forest, fewer successful breeding
 attempts (-24%). Encouragingly, however, some forest-dependent birds are
 breeding and producing fledglings in disturbed forests, including
 representatives from almost every guild. This was especially apparent for
 mixed-species flocks and army-ant followers, two guilds that have
 historically been considered vulnerable to anthropogenic disturbance.
 Therefore, despite a loss of breeding habitat in disturbed forests, these
 data suggest that landscapes composed of regenerating forest and small
 fragments have conservation potential for forest bird populations.
description: The archived dataset is the full encounter history for the main
 analysis in this paper (a single-season multi-state occupancy model). This
 encounter history includes 15 months (encounter periods) of data for 166
 species, with each species*month denoted by one of three states: not
 detected (0), detected (1), and showcasing evidence of breeding when
 detected (2). (For the latter state, we considered a suite of physical and
 behavioral cues as evidence of breeding [Table 1].) Detection and
 breeding data were combined from standardized passive mist-netting and
 observational data collected while following mixed-species flocks. For
 more details on these two methods, please see the appropriate sections
 from the Methods: "Bird capture data" and "Flock-following
 observational data," respectively. Only the highest value
 was retained for each month. For example, if a given species was captured
 (detected = 1) in September 2015 and, while flock-following, was also seen
 feeding a recently fledged young (breeding = 2), then only a "2"
 would be displayed for that month. For every species,
 there are six rows of encounter history data, one for each of the six
 research plots (or "Replicates"). These six replicates fit
 into three discrete forest types (or "Treatments"): secondary
 forest, 10-ha fragments, and primary forest. (For more details on these
 forest types, please see the "Forest types" section in the
 Methods.) Therefore, because each species contains six rows of data, there
 are a total of 996 rows (6 replicates*166 species = 996
 replicates*species). Species taxonomy follows the South
 American Classification Committee
 (https://www.museum.lsu.edu/~Remsen/SACCBaseline10.htm), circa September
 2019. Finally, the notation for the 15 months is given by the last two
 digits of the year, followed by the first three letters of that month. So,
 for instance, September 2015 is indicated by "15-Sep".