DOI: 10.5061/dryad.w9ghx3fmc
title: Occupancy of two Colombian endemic birds (Habia gutturalis) and White-Mantled Barbet (Capito hypoleucus) in fragmented forests of the Central Andes in Colombia

description: The Sooty Ant-Tanager (Habia gutturalis) and White-mantled Barbet (Capito
 hypoleucus) are endangered and endemic birds of Colombia. Both species
 have small geographic ranges and presumably low population sizes possibly
 due to habitat destruction and fragmentation. In order to estimate the
 effects of landscape features on the occupancy of both species, we sampled
 a variety of landscape configurations within the buffer zones of two
 hydroelectric impoundments in the Central Andes of Colombia and applied
 occupancy models to estimate the proportion of area occupied as a function
 of these covariates. We surveyed 35 point-counts in each hydroelectric
 impoundment, between June and July of 2014 and 2015. We used single-season
 models to estimate occupancy while recognizing imperfect detection. Mean
 occupancy estimates in the study area were similar for both species (0.61
 SD=0.33 for the Sooty Ant-Tanager and 0.63 SD=0.25 for the White-mantled).
 Nonetheless, occupancy probability within the study area was very
 different between them. The best model for the Sooty Ant-Tanager indicated
 a decrease in occupancy with elevation, whereas the top model for the
 White-mantled Barbet indicated an increase in occupancy with distance from
 streams. Detection probabilities were similar for both species
 (&gt;0.4) and declined significantly during the second year. Our
 results provide quantitative guidelines that can be used to evaluate and
 monitor the state of these populations on the short and long term.
description: <strong>Study Area</strong> The
 study was conducted in fragmented secondary forests within the buffer
 zones of two hydroelectric power plants located in the department of
 Antioquia in the Central Andes of Colombia: one in the municipality of San
 Carlos (Punchiná), and the other in the municipalities of San Rafael,
 Alejandría, Santo Domingo and San Roque (San Lorenzo). These protected
 areas encompass ~80 km2 (ISAGEN 2008) of transitional forest from
 premontane to tropical wet forests (Holdridge 1947), a key elevation band
 (580-1420 m) characterized by high levels of fragmentation (Cardona et al.
 2011). <strong>Sampling</strong>
 Our sampling units were point counts defined as circles of 125 m
 radius, within which birds were registered during 30 minutes. We defined
 the maximum radius, as the longest distance at which there was a record of
 any of the two species. Point counts were distributed along transects of
 ~1 km each. Transects were located near trails and separated by more than
 2 km from each other. Each transect consisted of five point-counts spaced
 at 250 m intervals along a route. A total of 70-point counts (14
 transects) were located within the study area, subject to security and
 transportation restrictions, with the intention to include a broad range
 of landscape configurations. The landscape features were based on a
 remotely-sensed Landsat 2013 image. We surveyed 35 sites in the buffer
 zone of each hydroelectric impoundment between June and July of 2014 and
 2015. One of the occupancy modeling assumptions is that detection
 histories are independent across sites (Mackenzie et al. 2002). In order
 to quantitatively assess this assumption, we performed spatial
 correlograms on the residuals of a logistic regression between detections
 and occupancy covariates. We conducted all surveys from
 sunrise (06:00) until 10:00, waiting silently for three minutes before the
 beginning of observations. For each target species, we registered all
 individuals seen or heard during a 30-min period, and we recorded each
 survey with an omnidirectional microphone Sennheiser ME62. Two observers
 (AMR in 2014 and JSB in 2015) conducted the surveys for two consecutive
 days. During a survey, we scored the distance to each detection with prior
 training using a range finder (Nikon 8397 ACULON). We also quantified the
 number of individuals of each species and if the detection was visual or
 auditory. The two species are medium sized birds (~20 cm) that are at
 least seasonally vocal with distinct and easily recognizable songs and
 calls (Willis 1972, Hilty & Brown 2001, Laverde et al. 2005). In
 total we conducted 70-point counts with two repetitions during the course
 of one year.
 <strong>References</strong>
 Cardona, N., H. S. David, H. Gómez & P. Roldán. 2011.
 Flora de embalses, centrales hidroeléctricas de ISAGEN en el oriente
 antioqueño San Carlos, Jaguas y Calderas. Guía ilustrada. ISAGEN -
 Universidad de Antioquia, Herbario Universidad de Antioquia, Medellín,
 Colombia. Hilty, S.L., & W.L. Brown. 2001. Guía
 de las aves de Colombia. American Bird Conservancy, Imprelibros S. A.,
 Cali, Colombia. Isagen S.A. 2008. Centrales de
 generación Isagen.
 Https://www.isagen.com.co/comunicados/centrales_generacion.pdf. 
 Laverde, O., C. Munera, & L. M. Renjifo. 2005.
 Preferencia de hábitat por Capito hypoleucus, ave colombiana endémica y
 amenazada. Ornitología Colombiana 3:62–73. Willis, E.
 O. 1972. Taxonomy, ecology, and behavior of the Sooty Ant-Tanager (Habia
 gutturalis) and other anttanagers (aves). American Museum Novitates no.
 2480.
description: Dataset contains the following files (detailed information about
 each in the README section:
 <strong>Detection_histories.csv</strong>: Detection
 histories for <em>Capito hypoleucus</em> and <em>Habia
 gutturalis</em>. Numbers refer to number of individuals detected.
 Notice that we use only presence/absence in our manuscript.
 <strong>Detection_covariates.csv</strong>: Detection
 covariates for both species. 
 <strong>Occupancy_covariates.csv</strong>: Site
 covariates for both species. 
 <strong>Point_counts.csv</strong>: Geographic
 coordinates (WGS84) for each site. 
 <strong>CH_single_season.R</strong>: R script to run
 occupancy analyses for Capito hypoleucus.
 <strong>HG_single_season.R</strong>: R script to run
 occupancy analyses for Habia gutturalis.
description: # Occupancy of two Colombian endemic birds (Habia gutturalis) and
 White-Mantled Barbet (Capito hypoleucus) in fragmented forests of the
 Central Andes in Colombia
 [https://doi.org/10.5061/dryad.w9ghx3fmc](https://doi.org/10.5061/dryad.w9ghx3fmc) ## Description of the data and file structure Dataset contains the following files necessary to run the two R scripts (also included) to run occupancy models for two species *Habia gutturalis* and *Capito hypoleucos*: **Detection_histories.csv**: Detection histories for *Capito hypoleucus* and *Habia gutturalis*. Five columns: Species name, and four columns that refer to the number of individuals detected each repetition (2014-1, 2014-2, 2015-1, 2015-2). Notice that we use only presence/absence in our manuscript. **Detection_covariates.csv**: Detection covariates for both species. Columns refer to: *   covariate*: name of the covariate. Three covariates were used in analyses. We included original time format in the table: time of the survey (time of visit in format hours:minutes AM/PM), Aseno(sqrt(time of the survey): transformation of time variable due to circular nature of time, daily average temperature during the survey (°C), precipitation of the previous day of the visit (mm).    Point count: unique name id for each point count.    Survey2014_1, Survey2014_2, Survey2015_1, Survey2015_2: Values for each variable at each visit.  **Occupancy covariates.csv**: Site covariates for both species. Columns refer to:    Point count: unique name id for each point count.    Elevation (m): Elevation of point count in meters.    Forest (%): the percentage of the area of fragmented forest (Forest) in a 125m radius.    Mosaic (%): the percentage of the area of crop mosaic cover (Mosaic) in a 125m radius.    Euclidean distance to streams (m): the shortest straight distance to streams in meters.    Euclidean distance to impoundments (m): the shortest straight distance to impoundments in meters.    Nests depredated_2014: nest predation intensity (Predation-number of nests depredated) in 2014.    Nests depredated_2015: nest predation intensity (Predation-number of nests depredated) in 2015. **Point_counts.csv**: Geographic coordinates (WGS84) for each site.  ## Code/Software CH_single_season.R: R script to run occupancy analyses for *Capito hypoleucus*. All the inputs for the R scripts are provided (same name).  HG_single_season.R: R script to run occupancy analyses for *Habia gutturalis*. All the inputs for the R scripts are provided (same name).