DOI: 10.5061/dryad.9kd51c5gw
title: Avian Response to Hurricane Maria in Coffee Plantations

description: Insights on impacts and resiliency of avian species with respect to
 hurricanes in the Caribbean have largely focused on responses measured in
 protected habitats.  We assessed avian responses in non-protected
 habitat, specifically shade-restored coffee plantations, because their
 structural complexity retains many attributes of secondary forests, and
 may contribute to landscape scale species resiliency.  We tallied
 species richness and estimated occupancy probability of 12 resident avian
 species, after adjusting for imperfect detection, to assess the impact of
 hurricane Maria (20 September 2017) in shade-restored coffee
 plantations.  For five of those species, we also estimated local
 colonization and extinction probabilities to assess their prospect of
 rebounding (resiliency) in the context of two stages of shade
 restoration.  We used survey data collected March-June 2015-2017
 (pre-hurricane) and 2018 (post-hurricane) in 58 coffee farms and satellite
 imagery to assess vegetation structure.  Restored farms were
 grouped into two categories based on time-since-restoration:
 newly-restored and fully-restored. We predicted that mean percent forest
 cover in fully-restored farms (~30-40%) would revert to levels in
 newly-restored farms (&lt;15%), with concomitant changes in occupancy
 by avian species.  As predicted, mean percent forest cover (16.17
 ± 4.27%) in fully-restored farms post-hurricane reverted to pre-hurricane
 levels in newly-restored farms (15.00 ± 5.61%).  The loss
 represented 30-38% relative to the pre-hurricane cover levels. 
 Detections of focal species dropped an average of 41% post-hurricane, with
 associated reductions in occupancy for 9/11 species.  Occupancy
 of the Puerto Rican Bullfinch and Puerto Rican Spindalis reverted to
 levels detected in newly-restored plantations prior to the hurricane as
 predicted.  Prospects of rebounding were more likely for species
 with invariant or increases in colonization probability (e.g.,
 Yellow-faced Grassquit, Northern Mockingbird, Puerto Rican
 Spindalis).  Rebounding for frugivores like the Puerto Rican
 Bullfinch would be protracted given that colonization rates dropped from
 0.56 ± 0.12 (pre-hurricane) to 0.04 ± 0.2 (post-hurricane), regardless of
 restoration stage.  Our work showed that the avian community
 associated with restored coffee farms exhibited a high degree of
 ecological resistance as the similarity in species composition before and
 after the hurricane was 81%, and all 12 focal species continued to occupy
 farms under both restoration stages.  The prospect of the focal
 species to rebound (resiliency) was species-specific, and in some cases,
 mediated by their affinity to a particular farm restoration
 stage.  The strength of hurricanes is projected to intensify with
 global warming.  Pockets of undamaged or partially damaged
 shade-grown or fully-restored coffee plantations may contribute to species
 resiliency by increasing landscape level habitat redundancy, and
 facilitate habitat shifts to secure food resources or harbor source
 populations to colonize recovering, hurricane-damaged habitat tracts.
description: Data were collected by means
 of surveys at each farm (58 total)  three consecutive years (2015-17)
 prior to the hurricane and one year after the hurricane (2018).  Of the 58
 farms, 22 were newly-restored (0-4 years since shade layer restoration)
 and 36 were fully-restored (≥6 years since shade layer restoration)
 farms.  We conducted three (3) surveys at each farm between March and June
 each year.  We used fixed-radius point counts in which two observers
 recorded all bird species detected visually or by sound, within 50 meters
 of the center of the station for 10 minutes.  All surveys were conducted
 between 0600 and 1000 hrs under favorable weather conditions.  We
 converted survey data into a binary encounter history (1=species detected,
 0=species not detected).  We used these data to tally the number of unique
 species before and after the hurricane, and calculated the Jaccard
 Similarity Index as the number of species detected in both periods/the
 number of species in either period* 100.  We also calculated the
 cumulative number of detections per focal species (12 of them) for the
 years with equal number of surveys per year (i.e., constant effort; 174
 surveys/year). Lastly, we conducted two types of occupancy analyses.  The
 first type was a single-season, single-species modeling approach to
 contrast occupancy estimates between 2017 (pre-hurricane) and 2018
 (post-hurricane).  The second type of analysis was a single species-multi
 season occupancy model. 
description: There were three sampling occasions (surveys) per year (season)
 which are denoted as "v1, v2, v3", which is followed by the year
 the surveys was conducted.  Missing values are indicated by "-"
 or ".", depending on the program used to open files.   Lastly NR
 - newly restored, and FR = fully restored.  "Open" means percent
 area with no forest cover, and "forest" means percent area with
 forest cover.  Focal species codes are: ANEU= Antillean Euphonia, SNPI=
 Scaly-naped pigeon, PUEB= Puerto Rican Bullfinch, YFGQ=Yellow-faced
 grassquit, PRFL= Puerto Rican Flycatcher, PRTA= Puerto Rican Tanager,
 LAPE= Lesser Antillean Pewee, PRVI= Puerto Rican Vireo, NOMO= Northern
 Mockingbird, LOKI= Loggerhead Kingbird, PRSP= Puerto Rican Spindalis, and
 GRAK= Gray Kingbird.