DOI: 10.5061/dryad.zkh1893h8
title: Secondary Amazon rainforest partially recovers tree cavities suitable for nesting birds in 18–34 years

description: Passive restoration of secondary forests can partially offset loss of
 biodiversity following tropical deforestation. Tree cavities, an essential
 resource for cavity-nesting birds, are usually associated with old forest.
 We investigated the restoration time for tree cavities suitable for
 cavity-nesting birds in secondary forest at the Biological Dynamics of
 Forest Fragments Project (BDFFP) in central Amazonian Brazil. We
 hypothesized that cavity abundance would increase with forest age, but
 more rapidly in areas exposed to cutting only, compared to areas where
 forest was cut and burned. We also hypothesized that cavities would be
 lower, smaller, and less variable in secondary forest than in old-growth
 forest, which at the BDFFP is part of a vast lowland forest with no recent
 history of human disturbance. We used pole-mounted cameras and
 tree-climbing to survey cavities in 39 plots (each 200 × 40 m) across
 old-growth forests and 11–34 year-old secondary forests. We used
 generalized linear models to examine how cavity supply was related to
 forest age and land-use history (cut only vs cut-and-burn), and principal
 components analysis to compare cavity characteristics between old-growth
 and secondary forest. Cavity availability increased with secondary forest
 age, regardless of land-use history, but the oldest secondary forest
 (31–34 years) still had fewer cavities (mean ± SE = 9.8 ± 2.2 cavities/ha)
 than old-growth forest (20.5 ± 4.2 cavities/ha). Moreover, secondary
 forests lacked cavities that were high and deep, with large entrances –
 characteristics likely to be important for many species of cavity-nesting
 birds. Several decades may be necessary to restore cavity supply in
 secondary Amazonian forests, especially for the largest birds (e.g,
 forest-falcons and parrots &gt; 190 g). Retention of legacy trees as
 forest is cleared might help maintain a supply of cavities that could
 allow earlier recolonization by some species of cavity-nesting birds when
 cleared areas are abandoned.
description: We surveyed tree cavities in upland Terra Firme forest at the
 Biological Dynamics of Forest Fragments Project (BDFFP), north of Manaus
 in central Amazonas, Brazil (02<sup>°</sup>20'S,
 60<sup>°</sup>5'W).  At the time of
 our study, the area comprised a mosaic of old-growth forest, grasslands,
 and regenerating forest of different ages. Within this mosaic, we placed
 39 plots: 8 in old-growth forest and 31 in secondary forest aged 11–34
 years. Each plot measured 200 x 40 m (0.8 ha). For each stand age, we
 aimed to balance the number of plots in secondary forest that grew after
 cutting only vs. cutting and burning, but this was not always possible.
 Plots were centered along established linear transects or mist-net lines
 from other projects, with 200 m length and 20 m extension to each side. We
 spaced plots as well as was feasible given the existing trail network,
 which was limited, especially in secondary forest. From
 July to October 2013, two observers searched for cavities by examining
 each tree within each plot, with the aid of binoculars. To inspect the
 interior of cavities, we used a 2-cm diameter video camera, which was
 either mounted on a 15-m telescoping fibreglass pole, or carried up to the
 cavity using single-rope tree-climbing (Politi et al<em>.</em>
 2009, Di Sallo and Cockle 2022).<strong> </strong>Cavities
 were only included in our dataset if they had a sufficient diameter to
 permit the passage of a bird (&gt;2 cm), and an internal chamber
 capable of offering protection to eggs (i.e., with a floor, walls, and
 some overhead protection, at minimum; Politi et al. 2009). We excluded
 cavities that contained water. We measured the height of each cavity from
 the lower sill of the entrance to the ground, using the 15 m pole, marked
 every 10 cm. For cavities above 15 m we used the climbing rope to measure
 cavity height. Entrance dimensions and horizontal depth were measured to
 the nearest centimeter using a tape measure (if we climbed to the cavity)
 or a 35 cm ruler attached to the top of the 15 m pole. We used a tape
 measure to determine vertical depth of cavities to the nearest centimeter.
 In the few cases in which it was not possible to climb to the cavities
 (e.g., dead trees in decomposition), but where we could access the cavity
 with the pole-mounted camera, we estimated vertical depth using the camera
 image, after first practicing on cavities that were measured with a tape
 measure. Using either tree climbing or the pole, we were able to measure
 93% of cavities found in secondary forest and 92% of cavities found in
 primary forest.
description: # Secondary Amazon rainforest partially recovers tree cavities suitable
 for nesting birds in 18–34 years
 The dataset contains
 numbers of cavities and their measurements from 39 forest plots (each 200
 x 40 m in size) at the Biological Dynamics of Forest Fragments Project
 north of Manaus, Brazil, as well as code to produce the analyses in Dantas
 Oliveira et al. 2024. ## Description of the data and file structure
 Dataset 1: Secundaria.csv. Dataset of the Plot ID (IDTransecto), Reserve
 (Reserva), forest age (Idade), fire history (Fogo; 0 = unburned, 1 =
 burned), UTM coordinates, and number of cavities for each of the 31 0.8-ha
 plots in secondary forest. Dataset 2: Primario.csv. Dataset of the Plot ID
 (IDTransecto), Reserve (Reserva), forest age (Idade), UTM coordinates, and
 number of cavities for each of the 8 0.8-ha plots in old-growth forest.
 forest age (Idade) is 100 by default for all old-growth forest (where age
 is certainly &gt;100 years). Dataset 3: CRT.csv. Dataset of measurements
 of nearly all of the cavities listed in the datasets Secundaria.csv and
 Primario.csv. Column headings are as follows: Idade - age of the forest in
 years. "100" indicates old-growth forest (where age is certainly
 &gt;100 years). DAP - diameter of the tree at breast height. arvore_alt -
 height of the tree in meters. Class_degra - Tree decay class viva (alive)
 or morta (dead). altura_oco - Height of the cavity above ground (m).
 Diam_vert - Vertical diameter of the cavity entrance (cm). Diam_horiz -
 Horizontal diameter of the cavity entrance (cm). Prof_vert - Vertical
 depth of the cavity (cm). Prof_horiz - Horizontal depth of the cavity (cm)
 ## Code/Software The dataset includes R code to reproduce all models and
 figures reported in the paper. It was last run on R version 4.2.0
 (2022-04-22) for Mac.