DOI: 10.5061/dryad.z612jm6mh
title: Bird capture and vegetation structure data from 12 forest sites in Allpahuayo-Mishana National Reserve, Peru

description: As tropical forests are frequently impacted by human disturbance, forests
 in various stages of disturbance recovery are increasingly important for
 maintaining biodiversity. However, the mechanisms through which
 disturbance affects wildlife remain poorly understood. Here, we used mist
 net capture data to compare bird communities in three tropical forest
 habitats representing various disturbance intensities: undisturbed primary
 forest, selectively logged forest (low disturbance), and secondary forest
 regenerating on abandoned agricultural fields (high disturbance). We found
 that after a 19-year recovery period, low disturbance sites contained
 similar bird communities to undisturbed sites. Regenerating agricultural
 fields, however, had lower species richness and distinct bird communities,
 with fewer insectivores and more nectarivores than other sites. Structural
 equation models revealed that the impacts of disturbance intensity on bird
 communities were partially explained by changes in vegetation structure:
 ant-following insectivore abundance declined with disturbance intensity as
 ground cover vegetation increased, and nectarivore abundance increased
 with disturbance intensity as tree density decreased. Our results suggest
 that selectively logged forests can regain pre-disturbance bird diversity
 and vegetation structure within two decades, provided that they are
 protected from further disturbance and located near source species pools.
 Increasing tree density and decreasing ground-level vegetation in
 secondary forests may improve these areas as habitat for forest-interior
 birds.
description: <strong>Bird Sampling</strong>
       Fieldwork for this study took place at Allpahuayo-Mishana
 National Reserve (RNAM) in Loreto, Peru, from March 11 to May 24, 2023.
 This timeframe corresponds with the local rainy season, which is the
 breeding period for most tropical birds in the area. At each site, we
 established a network of 10 mist nets (2.6 x 12 m, 36 mm mesh size) to
 sample the understory bird community. Nets were generally set up in an L
 formation, with two straight lines of five nets established at a 90°
 angle, though the exact formation depended on the presence and avoidance
 of natural obstacles such as slopes, streams, and large trees at each
 site. The size of each net array was approximately 70 x 70 m. Mist nets
 were opened at dawn and operated for approximately 8 hours each day,
 except during periods of inclement weather such as rain or strong wind,
 and were checked for birds every 15-20 minutes. No speakers or callback
 devices were used to attract birds to nets. All captured birds were
 identified to species using the field guide Birds of Peru [39], and then
 released at the location of their capture. To distinguish new captures
 from recaptures, we snipped approximately 1 cm from the farthest right
 tail feather of each newly captured bird. We did not band birds because
 the vast majority of the region’s birds are nonmigratory, and all sampling
 at a given site occurred within 2-3 consecutive days. We operated nets for
 2-3 consecutive days at each site until completing 160 net hours (where 1
 net hour is the equivalent of 1 mist net being open for 1 hour). Sites of
 different forest types were sampled on a rotating basis, in an effort to
 reduce temporal pseudoreplication by minimizing successive sampling of
 sites with the same disturbance history. However, back-to-back sampling of
 sites with the same disturbance history did occasionally occur due to
 logistic constraints. To verify that sampling date was independent of
 disturbance history in our dataset, we used an ANOVA to test for a
 significant relationship (p &lt; 0.1) between the sampling date and
 disturbance history. All mist netting and fieldwork activities were
 approved by the Servicio Nacional de Áreas Naturales Protegidas por el
 Estado (SERNANP) of Peru, and carried out under SERNANP Permit #
 003-2023-SERNANP-JEF. <strong>Vegetation
 Sampling</strong>       We characterized the
 vegetation structure of each site by quantifying the following seven
 vegetation variables: tree density, average tree diameter, liana density,
 average liana diameter, canopy cover, understory vegetation density, and
 ground cover vegetation density. To this end, we performed vegetation
 surveys in three 10 x 10 m plots at each site. Each plot contained five
 discreet sampling points: one in each of the four corners, and one in the
 middle of the plot. We established the first plot one m to the right (from
 the perspective of a researcher facing down the net formation) of the
 beginning of the first net lane, the second plot one m to the left of the
 beginning of the sixth net lane, and the third plot one m to the right of
 the end of the tenth net lane. Within each 10 x 10 m plot, we counted and
 measured dbh (cm) of each tree &gt; 10 cm, and each liana &gt; 2.5
 cm. At each of the five sampling points within a plot, we estimated the
 percent cover of understory vegetation (within 0.5 and 3 m height), ground
 cover vegetation (&gt; 0.5 m), and bare ground, within a 1 x 1 m
 frame. At the center sampling point of each plot, we estimated percent
 canopy cover using a spherical densiometer (Forestry Suppliers, convex
 model A). Measurements of each variable were averaged within a site to
 estimate site-scale vegetation structure.
description: # RNAM\_2023
 [https://doi.org/10.5061/dryad.z612jm6mh](https://doi.org/10.5061/dryad.z612jm6mh) The dataset includes bird capture data (via mist nets) and vegetation structure data for 12 forest sites in Allpahuayo-Mishana National Reserve, in Peruvian Amazonia.  ## Description of the data and file structure The Excel datasheet contains XXXX tabs. The first two tabs contain the raw data. In the "Birds" tab, the bird capture data consists of 5 columns: Site (site name, 12 total), Treatment (3 different treatments correspond to 3 different disturbance histories: undisturbed forest [no timber harvesting], low disturbance [selective logging occurred ~20 years ago], and high disturbance [former crop fields]), Date (date of capture, year 2023), Species (English common name), Recap (y for yes if the bird was a recapture, n for no if the bird was a new capture).  In the "Veg" tab, there are 7 variables in addition to the Site and Treatment columns that were quantified at various sampling locations at each site: Canopy (percent tree canopy cover), Understory (percent cover of trees under 3 meters tall), Ground Cover (percent cover of herbaceous ground vegetation), Trees (number of trees in a 10 x 10m plot), Tree Diameter (average tree diameter in cm), Lianas (number of lianas in a 10x10m plot), Liana Diameter (average liana diameter in cm).  The spacc tab contains bird capture data formatted to calculate species accumulation curves using the iNext package in R (see code below). The permanova tab contains data formatted to perform a PERMANOVA relating disturbance history to bird community composition, and the SEM tab contains data formatted to create a structural equation model representing the impacts of disturbance history on bird foraging guild abundance (ant followers, insectivores, and nectarivores) mediated through vegetation structure.