DOI: 10.5061/dryad.95x69p8nn
title: Data from: Widespread bird species show idiosyncratic responses in residual body mass to selective logging and edge effects in the Colombian Western Andes

description: This dataset consists of banding data (N = 1589 captures, 129 bird
 species), including morphological and breeding biology measures, collected
 from understory birds in subtropical cloudforest at roughly 2000 m.a.s.l.
 in the municipality of El Cairo in Colombia's Western Andes (Serrania
 de los Paraguas range). Roughly 8,350 net hours were divided into two
 three-month field seasons (June-August 2017 and January-March 2018), both
 corresponding to local dry seasons. Birds were banded along 500-meter
 transects in forest interior across a gradient of forest fragment patch
 sizes (N = 8 fragments, area range = 10-173 ha) and a private ~750 ha
 reserve (Reserva Natural Cerro El Ingles) in the same landscape. Each
 non-hummingbird capture was fitted with an aluminum leg band with a unique
 combination, and we collected data on mass, tarsus length, wing chord,
 pectoral muscle score, cloacal protuberance and brood patch score, and age
 and sex (where possible due to plumage differences). We captured 101
 species (including 6 boreal migrants) in 844 captures (53%) during the
 January-March sampling period and 102 species in 745 captures during the
 June-August sampling period; each site was sampled during both sampling
 periods. The most captured bird families were Trochilidae (24 spp., 36% of
 total captures), Thraupidae (17 spp.), Tyrannidae (16 spp.), Furnariidae
 (14 spp.), and Turdidae (6 spp.). A subset of these data (uploaded as a
 separate file) were used to calculate body condition indices for 20
 species of commonly captured birds (N = 984 captures) that occured across
 much of the patch size gradient (at least 8 out of 14 transects), and were
 related to fragment area and measures of edge and selective logging
 effects (see Jones et al. 2022). In this file, we include all predictor
 variables necessary to run the generalized linear mixed models in Jones et
 al. (2022), including proportion forest cover within 1 km (a proxy for
 patch size), edge density, average distance to forest edge from the
 netting transect, average canopy cover and height along the transect,
 multivariate measures of understory plant density, large-diameter tree
 density, and vertical vegetation structure, elevation of each transect,
 and average yearly rainfall for each transect.
description: <strong>Study sites</strong> Study
 sites were located on the east slope of the Serrania de los Paraguas range
 in the Colombian Western Andes, specifically in the municipality of El
 Cairo (4°45′39″ N, 76°13′21″ W), Valle del Cauca department. The landscape
 consisted of a typical patchwork of forest fragments, cattle pasture, and
 shade coffee plantations, with ongoing forest clearing for the latter
 activities. Natural forest cover in this region is subtropical Andean
 forest, characterized by over 200 tree species, abundant epiphytes, and
 ~20-m canopies. Within this landscape, we identified all isolated forest
 fragments surrounded by cattle pasture and in the 1900-2300 m.a.s.l.
 elevational band using satellite images in Google Earth. We stratified
 this subset of fragments into large (≥ 100 ha), medium (30-50 ha), and
 small (≤ 20 ha) size categories, before selecting at least two of each to
 survey in detail (N = 8 fragments, range = 10-173 ha). Selected fragments
 were mid- to late-successional forest patches, which we defined as having
 &gt;10 m canopies, trees of &gt;10 cm diameter at breast height
 (DBH), a closed canopy, and a diversity of tree age classes. We only
 sampled two small-sized fragments because fragment size tended to increase
 with elevation in the focal landscape and because we wished to spend
 approximately equal sample effort at each site (limiting the number of
 surveys possible within the field season). We additionally sampled a
 private forest reserve within the same landscape (RNC Cerro El Inglés,
 ~750 ha) as a reference site. This site is connected to thousands of
 hectares of continuous forest along the spine of the Western Andes and in
 the Chocó lowlands to the west. Forest fragments were private lands
 (sampled with the help of a local NGO: Serraniagua) which varied in their
 land-use histories, particularly the intensity of selective logging, a
 common practice in the Colombian Andes (Aubad et al. 2008).  
 <strong>Quantification of Patch Size, Edge Effects, and
 Rainfall</strong> We used a buffer analysis to
 quantify landscape composition and configuration within a km of each
 sampling transect. This scale was selected because it affected the
 occupancy of tropical bird communities in lowland studies (Carrara et al.
 2015) and landscape composition at this scale was highly correlated with
 the composition at other buffer scales at our sites (e.g., 500 meters).
 All landscape analyses were conducted using ArcGIS (ArcMap 10.3.1; Esri,
 Redlands, CA), specifically the ‘isectpolyrst’ tool in the Geospatial
 Modelling Environment (version 0.7.4.0; Beyer 2015). Buffers were centered
 on the full length of the transect, resulting in a non-circular buffer
 shape. We used the proportion of forest cover within the buffer region as
 a proxy for the patch size of the fragment; we did not use patch size
 measurements directly because our continuous forest reference site had no
 patch size. We quantified fragment configuration (and edge effects) using
 the ‘edge density’ measure from Carrara et al. (2015), which is defined as
 the density of forest edge habitat within the 1 km buffer, measured in
 meters per hectare. We also calculated a straight-line distance to forest
 edge for each transect, which was the average of five measurements taken
 from the center point of each 100-meter transect segment to the nearest
 forest edge. We measured proportion of forest cover and edge density using
 a land-cover use map for our study area from the departmental conservation
 authority (Corporación Autónoma Regional del Valle del Cauca), which we
 converted to a 25-m cell-size raster. Yearly rainfall data for each
 transect from the WorldClim2 monthly data set (Fick and Hijmans 2017) were
 collected at ~1km2 resolution. Sampling transects were superimposed on the
 global raster of rainfall data. We summed the mean monthly historical
 rainfall data (1970-2000) for each transect to calculate a yearly average;
 where a transect overlapped multiple raster squares, monthly values for
 each were averaged.  <strong>Quantification of
 Local Vegetation Structure </strong> For each
 transect, we measured local vegetation structure and density to quantify
 the effects of human disturbance, particularly selective logging.
 Vegetation measurements were taken from June-August 2017, though we
 observed little annual variation. We followed the sampling methodology of
 Stratford and Stouffer (2013), which we modified to be used along belt
 transects. The methodology was broadly comprised of two components: (1)
 the quantification of canopy height, percentage canopy cover, and foliage
 height diversity using point sampling situated every 10 meters along the
 transect and (2) the quantification of tree size category and understory
 vegetation density, respectively, using 3-meter-wide belt sampling.
 Because transects ran along trails, we measured vegetation at least three
 meters from the trail edge on a randomly selected side of the trail. For
 the point sampling, we measured variables at ten-meter intervals, for 50
 points per transect. As a measure of foliage height diversity, we noted
 the presence or absence of live vegetation in five height bands:
 &lt;0.5 m, &gt;0.5–3 m, &gt;3–10 m, &gt;10–20 m, and
 &gt;20 m. We used a laser rangefinder (Raider 550; Redfield,
 Beaverton, OR) to determine heights above 3 meters, sighting through a
 tube with crosshairs while straddling the point. For each point, we also
 recorded the highest canopy height, to the nearest meter. The proportion
 of canopy cover at each point was calculated to the nearest eighth of the
 field of view using a vertical densiometer (Densitometer; Geographic
 Resource Solutions, Arcata, CA). For each transect, we averaged values for
 both canopy height and canopy cover and calculated the proportion of
 points at which vegetation was present for each height category. To
 quantify foliage height diversity, we calculated the Shannon diversity
 index of the proportion of points with vegetation present in each of the
 five height bands for each transect. Foliage height diversity was highly
 correlated with canopy height at our sites (Pearson’s r = 0.90), so we
 retained foliage height diversity. For the belt
 sampling, we surveyed all trees (woody vegetation &gt; 2 m in height)
 on 1.5 meters to either side of the observer and measured their DBH. Trees
 were later categorized into six DBH size classes for analysis: 1-7 cm,
 8-15 cm, 16-23 cm, 24-30 cm, 31-50 cm, and &gt; 50 cm. We also
 recorded the largest tree DBH recorded on each transect. Because selective
 logging targets large, old-growth trees we consider this to be a proxy
 measure for current and historical logging pressure at each site. To
 capture differences in understory vegetation density, we also recorded the
 density of shrubs, ferns, lianas (vines), palms, and tree ferns along the
 same belt survey for each transect. To reduce redundancy and minimize
 correlation between variables, we used ordinated measures of the tree DBH
 and understory vegetation data for each transect from respective principal
 component analyses (PCAs), taken from Jones and Robinson (2020). In each
 case, we used the first principal component axis; greater values indicate
 higher densities of large-diameter trees and understory vegetation,
 respectively. We inverted the sign of the understory vegetation PC axis so
 that larger values would indicate higher densities for ease of
 interpretation of results.  <strong>Mist Netting
 and Morphological Measurements</strong> We
 surveyed understory bird communities along each transect using passive
 mist netting. Each site was sampled twice, from June-August 2017 and from
 January-March 2018; both correspond to a local dry season. In each case,
 we surveyed transects for two and a half consecutive field days, and
 staggered visits to small, medium, and large fragments to avoid any
 correlation between fragment size and day of year. We deployed twelve 12x3
 m mist nets (38 mm mesh; Avinet Research Supplies, Portland, ME) along
 each transect, placed in locations likely to capture understory birds
 (i.e., with dense understory vegetation and outside of direct sunlight).
 Nets were open from dawn to dusk (~0700-1700 hrs.) and were operated by
 two or more technicians. We closed nets during periods of heavy rainfall
 and high winds. All captures were brought to a central banding station
 where they were identified to species and fitted with an aluminum leg band
 with a unique number before being released. We did not band hummingbirds
 (Trochilidae), and instead cut the tip off a unique rectrix for each
 capture at a site. For each unique capture, we measured the length of the
 right tarsus and wing chord to the nearest millimeter; tarsus length was
 not recorded for hummingbirds. We also recorded body mass for each
 capture. For the first field season, mass was measured in a bag using a
 spring scale (± 0.5 g.; Pesola Precision Scales, Schindellegi,
 Switzerland). In the second field season, we used a more precise digital
 scale (± 0.01 g.; American Weigh Scales, Cummingham, GA), with the focal
 individual placed in a measuring cone. We also evaluated the breeding
 condition of all non-hummingbird captures by scoring the presence and
 extent of a cloacal protuberance (0-3 scale) and brood patch (0-4 scale)
 according to the criteria in Pyle (1997). Finally, we identified juvenile
 individuals, where possible, using a combination of plumage differences,
 molt limits, and enlarged or colorful rictal flanges. Plumage differences
 and molt limits are poorly described for our focal species,
 however.