DOI: 10.5061/dryad.6t1g1jx2b
title: Mixed population trends inside a California protected area: Evidence from long-term community science monitoring

description: Protected areas are one of the most widespread and accepted conservation
 interventions, yet their  population trends are rarely compared
 to regional trends to gain insight into their effectiveness. Here, we
 leverage two long-term community science datasets to demonstrate mixed
 effects of protected areas on long-term bird population trends. We
 analyzed 31 years of bird transect data recorded by community volunteers
 across all major habitats of Stanford University’s Jasper Ridge Biological
 Preserve to determine the population trends for a sample of 66 species. We
 found that nearly a third of species experienced long-term declines, and
 on average, all species declined by 12%. Further, we averaged species
 trends by conservation status and key life history attributes to identify
 correlates and possible drivers of these trends. Observed increases in
 some cavity-nesters and declines of scrub-associated species suggest that
 long-term fire suppression may be a key driver, reshaping bird communities
 through changes in forest and chaparral structure and composition.
 Additionally, we compared our results to those of the North American
 Breeding Bird Survey’s Central California Coast region (n = 55 species) to
 place Jasper Ridge in a broader context. Most species experienced similar
 directional population trends inside vs. outside of the preserve, and only
 eight species (14.5%) did better inside this small, protected area.
 Therefore, we must identify relevant management strategies for declining
 populations and explicitly consider how existing protected areas target
 and manage each species. Further, this analysis underscores the importance
 of local and national community science for revealing nuanced long-term
 bird population trends.
description: From 1989 to 2020, volunteer
 observers conducted monthly surveys of six sectors within Stanford
 University's Jasper Ridge Biological Preserve (JRBP). Each survey
 consisted of a trail-based transect in which a group of observers walked
 the trail in the morning and counted all birds detected over roughly 3
 hours. Observers recorded the number of each species seen or heard along
 the route, regardless of the distance to the bird. Over 31 years of
 surveys, 192 observers conducted 2,055 transects and recorded a total of
 473,401 observations of 184 species (91% of JRBP’s documented avian
 richness). We used these data to estimate long-term avian population
 trends at JRBP. Prior to analy- sis, we performed extensive data cleaning,
 including the standardization of species names and observer identity.
 Unlikely species without notes or supporting information were removed from
 the analysis. All transects with fewer than seven species (n = 30) were
 considered incidental and removed. These transects were often performed
 during suboptimal conditions (e.g. wind or rain) and/or were of abnormally
 short duration. Finally, we limited our analysis to the 100 most
 consistently detected species (those detected in the greatest number of
 transects).
description: # **Data and model code from: Mixed population trends inside a California
 protected area: evidence from long-term community science monitoring**  
   Here, we provide the R
 code used to model the abundance for each species in the Jasper Ridge
 Biological Preserve. We have also provided a spreadsheet with each
 species' life history traits, taxonomy, annual trends in the
 preserve, and annual trends in the surrounding region (BCR 32) from the
 North American Breeding Bird Survey. Finally, we have attached an R code
 that analyzes the trends for various life history traits and taxonomic
 families, compares trends within the protected area and in the surrounding
 region, and produces figures 2, 4, and 5 in the main manuscript and all
 supplementary material figures.   **Description of the data and file
 structure** \** ** The JRBP_Transect_Data_Species.R file provides the code
 required to create a generalized linear mixed model for each species in
 R-INLA and extract the percent change in abundance over the study period.
 Each model also includes the priors and distribution chosen for each
 species. Priors were selected individually for each species and adjusted
 so that the year and day-of-year random walks displayed an ecologically
 realistic amount of non-linearity. For example, in models for Neotropical
 migratory birds, the day-of-year random walks were expected to show a
 distinct peak in abundance during the April-July breeding season. The file
 also includes all code used to confirm or deny the validity of each model.
 While the raw Jasper Ridge bird transect dataset required to run this code
 is not publicly available, access can be granted to interested parties at
 .   The
 Species_Organization.csv document contains a list of all species observed
 (without incidental observations), associated life history and taxonomic
 traits, conservation priority, level of endemism, Jasper Ridge trends in
 abundance with associated model details, and surrounding regional trends
 from the North American Breeding Bird Survey's BCR 32 California
 Central Coast region. Each row is a different species, while the
 explanation for each column is outlined below. X: row names, from the
 species that was documented in the most surveys to the least.
 Species_Code: four letter species codes prepared by the Institute for Bird
 Populations .
 Species_Common_Name: standardized by the American Birding Association;
 Check-List of North American Birds (Online). J. Ornithol. Scientific_Name:
 standardized by the American Birding Association Transects_Sighted: number
 of surveys the species was detected in, aka how common the species was in
 Jasper Ridge. Individuals_Sighted: number of individuals of the species
 detected across all surveys in Jasper Ridge. Taxonomic_Order: from most
 basal to least, retrieved from Wilman, Hamish, Jonathan Belmaker, Jennifer
 Simpson, Carolina de la Rosa, Marcelo M. Rivadeneira, and Walter Jetz.
 2014. EltonTraits 1.0: Species-Level Foraging Attributes of the World’s
 Birds and Mammals. Ecology 95: 2027–2027. Species_Level_Identification: 1
 if identified to species level, 0 if not identified to species level.
 PassNonPass: member of Passeriformes or not (Nonpasseriformes), NA if only
 identified as a bird. FamilyLatin: Family the species belongs to, NA if
 only identified as a bird. California.Near.Endemic.c: binary, over 80% of
 the species' range is in California. West.Coast.Endemic.c: binary,
 over 80% of the species' range is along the West Coast.
 No.Eastern.North.America.c: binary, this species is not a common resident
 or migrant east of the Mississippi River. Diet.Inv: percent of the species
 diet that is invertebrate prey (Wilman et al. 2014). ForStrat.ground:
 percent of time this species spends foraging on the ground (Wilman et al.
 2014). ForStrat.understory: percent of time this species spends foraging
 in the understory (Wilman et al. 2014). ForStrat.midhigh: percent of time
 this species spends foraging in the mid/high canopy (Wilman et al. 2014).
 ForStrat.canopy: percent of time this species spends foraging in the
 canopy (Wilman et al. 2014). ForStrat.ground.weighted: equals
 ForStrat.ground*4 + ForStrat.understory*3 + ForStrat.midhigh*2 +
 ForStrat.canopy*1. BodyMass.Value: body mass from (Wilman et al. 2014).
 Body_mass_log: logarithmic body mass (Wilman et al. 2014). Habitat.c:
 categorical preferred habitat from Powell, Hugh, Victoria Campbell,
 Gustave Axelson, Pat Leonard, and Miyoko Chu, eds. 2022. All About Birds.
 Ithaca, NY, USA: Cornell Laboratory of Ornithology; we only searched for
 values for species where we attempted models, NA if we did not search for
 a value. Food.c: categorical diet from (Powell et al. 2022); we only
 searched for values for species where we attempted models, NA if we did
 not search for a value. Nesting.c: categorical nesting location from
 (Powell et al. 2022); we only searched for values for species where we
 attempted models, NA if we did not search for a value. Behavior.c:
 categorical foraging behavior from (Powell et al. 2022); we only searched
 for values for species where we attempted models, NA if we did not search
 for a value. SF_Migratory.c: categorical migratory status in the San
 Francisco Bay Area around the study site from (Powell et al. 2022); we
 only searched for values for species where we attempted models, NA if we
 did not search for a value. HWI: hand wing index, 100*Dk/Lw, where Dk is
 Kipp's distance (the distance between the tip of the first secondary
 feather and the tip of the longest primary feather) and Lw is wing length;
 the hand wing index (an estimate of wingtip pointedness) is widely adopted
 as a proxy for flight efficiency and dispersal in birds.
 CA_Special_Concern: binary from Shuford, W.D. & Gardali, T. 2008.
 California Bird Species of Special Concern: A Ranked Assessment of
 Species, Subspecies, and Distinct Populations of Birds of Immediate
 Conservation Concern in California. Studies of Western Birds, Western
 Field Ornithologists, Camarillo, CA, USA and California Department of Fish
 and Game, Sacramento, CA, USA, 1. CA_PIF_Focal_Species: binary, 1 if noted
 in CalPIF (California Partners in Flight) (2002). Version 2.0. The Oak
 Woodland Bird Conservation Plan: A Strategy for Protecting and Managing
 Oak Woodland Habitats and Associated Birds in California (S. Zack, lead
 author). Point Reyes Bird Observatory, Stinson Beach, CA, USA.
 ; RHJV (Riparian Habitat
 Joint Venture) (2004). The riparian bird conservation plan: A strategy for
 reversing the decline of riparian associated birds in California, version
 2.0. California Partners in Flight.
 ; or CalPIF
 (California Partners in Flight) (2004). Version 2.0. The Coastal Scrub and
 Chaparral Bird Conservation Plan: A Strategy for Protecting and Managing
 Coastal Scrub and Chaparral Habitats and Associated Birds in California
 (J. Lovio, lead author). PRBO Conservation Science, Stinson Beach, CA,
 USA. . " PIF: binary, 1
 if noted in Will, T., Stanton, J.C., Rosenberg, K.V., Panjabi, A.O.,
 Camfield, A., Shaw, A., Thogmartin, W.E., Blancher, P.J., Will, T. &
 Stanton, J.C. 2019. Handbook to the Partners in Flight Population
 Estimates Database Version 3.0. Partners in Flight Technical Series, no.
 7. U_value: specified for each species' R-INLA model, determines
 prior, NA indicates that the model failed validation or was not attempted
 if X &gt; 100. Distribution: Selected distribution for each species'
 R-INLA model, chosen to limit over- or under-dispersion, NA indicates that
 the model failed validation or was not attempted if X &gt; 100.
 Dispersion: a measure of the amount of variability in the data set based
 on the model; under dispersed models have a value less than 1 while over
 dispersed models are greater than 1, NA indicates that the model failed
 validation or was not attempted if X &gt; 100. WAIC: a generalized version
 of the Akaike Information Criterion (AIC), NA indicates that the model
 failed validation or was not attempted if X &gt; 100. DIC: Deviance
 Information Criterion is a hierarchical modelling generalization of the
 AIC, NA indicates that the model failed validation or was not attempted if
 X &gt; 100. Credible_Trend: binary, 1 if credible, 0 if not, NA indicates
 that the model failed validation or was not attempted if X &gt; 100.
 Population_Trend_Magnitude: percent population change over the 31 year
 study, NA indicates that the model failed validation or was not attempted
 if X &gt; 100. PTM_LowerCI: lower credible interval of population trend
 magnitude, NA indicates that the model failed validation or was not
 attempted if X &gt; 100. PTM_UpperCI: upper credible interval of
 population trend magnitude, NA indicates that the model failed validation
 or was not attempted if X &gt; 100. PTM_Credible_Interval: credible
 interval of population trend magnitude, NA indicates that the model failed
 validation or was not attempted if X &gt; 100. PTM_Standard_Error:
 PTM_Credible_Interval divided by 1.96, NA indicates that the model failed
 validation or was not attempted if X &gt; 100. PTM_Variance: square of
 PTM_Standard_Error, NA indicates that the model failed validation or was
 not attempted if X &gt; 100. PTM_Average_Annual_Trend: equals (1 +
 Population_Trend_Magnitude)^(1/31 years) - 1, NA indicates that the model
 failed validation or was not attempted if X &gt; 100. AAT_LowerCI: equals
 (1 + PTM_LowerCI)^(1/31 years) - 1, NA indicates that the model failed
 validation or was not attempted if X &gt; 100. AAT_UpperCI: equals (1 +
 PTM_UpperCI)^(1/31 years) - 1, NA indicates that the model failed
 validation or was not attempted if X &gt; 100. AAT_Credible_Interval: the
 average distance from the average annual trend to AAT_LowerCI and
 AAT_UpperCI, NA indicates that the model failed validation or was not
 attempted if X &gt; 100. AAT_Standard_Error: equals
 AAT_Credible_Interval/1.96, NA indicates that the model failed validation
 or was not attempted if X &gt; 100. AAT_Variance: square of
 AAT_Standard_Error, NA indicates that the model failed validation or was
 not attempted if X &gt; 100. S32_C: credibility of North American Breeding
 Bird Survey (BBS) trend from the BCR_32 California Coast region, 1 blue on
 webpage, 2 indicates yellow, and 3 indicates red, NA indicates that the
 Jasper Ridge model failed validation, was not attempted if X &gt; 100, or
 was not available. BBS_ERROR: 1 if there was an error in loading, 0 if
 none, excluded from analysis, NA indicates that the Jasper Ridge model
 failed validation, was not attempted if X &gt; 100, or was not available.
 BBS_Notes: notes on trend, often errors, NA indicates that the Jasper
 Ridge model failed validation, was not attempted if X &gt; 100, or was not
 available. S32_CredTrend: binary, 1 if credible, 0 if not, NA indicates
 that the Jasper Ridge model failed validation, was not attempted if X &gt;
 100, or was not available. S32_Trend: BBS average annual trend in the
 BCR_32 region between 1989 and 2019, NA indicates that the Jasper Ridge
 model failed validation, was not attempted if X &gt; 100, or was not
 available. S32_LowerCI: lower credible interval of the BBS average annual
 trend in the BCR_32 region between 1989 and 2019, NA indicates that the
 Jasper Ridge model failed validation, was not attempted if X &gt; 100, or
 was not available. S32_UpperCI: upper credible interval of the BBS average
 annual trend in the BCR_32 region between 1989 and 2019, NA indicates that
 the Jasper Ridge model failed validation, was not attempted if X &gt; 100,
 or was not available. S32_Credible_Interval: average distance from the
 S32_Trend to S32_LowerCI or S32_UpperCI, NA indicates that the Jasper
 Ridge model failed validation, was not attempted if X &gt; 100, or was not
 available. S32_Standard_Error: S32_Credible_Interval/1.96, NA indicates
 that the Jasper Ridge model failed validation, was not attempted if X &gt;
 100, or was not available. S32_Variance: square of S32_Credible_Interval,
 NA indicates that the Jasper Ridge model failed validation, was not
 attempted if X &gt; 100, or was not available.   The
 BBS_and_JRBP_Comparison.R file contains all code used to analyze the
 trends for various life history traits and taxonomic families, compare
 trends within the protected area and in the surrounding region, and
 produce figures 2, 4, and 5 in the main manuscript and all supplementary
 material figures. Please put all files into a folder named
 "Data_JRBP_Bird_Transect" on your desktop for the file paths in
 the R code to work correctly.   Finally, the meta_analysis_results.csv
 document contains the results of many random effects models (REM)
 conducted in BBS_and_JRBP_Comparison.R. Each row is a different grouping
 of species, while the explanation for each column is outlined below.
 Group: For each REM, we restricted the species to those that shared this
 attribute (life history trait, endemism, taxonomy, conservation status,
 etc.). YesFigure: binary, notates if the group's averaged trend was
 included in Figure 4. FigureOrder: indicates the order of many REM results
 in Figure 4; NA indicates that the REM’s results were not included in the
 figure. JRBPonly: binary, TRUE if the species’ population trends fed into
 the REM are solely from Jasper Ridge; FALSE if the trends are the
 difference between the Jasper Ridge and BBS BCR_32 region. n: how many
 species trends were fed into REM; also the number of species that share
 that attribute and have valid models for Jasper Ridge or both Jasper Ridge
 and the BBS BCR_32 region. beta: provides the group's average annual
 trend from the REM. se: standard error from the REM. zval: z-value from
 the REM. pval: p-value from the REM ci.lb: lower bound of the 95%
 confidence interval from the REM. ci.ub: upper bound of the 95% confidence
 interval from the REM. tau2: the τ2 from the REM, the extent of variation
 among the effects observed in different population trends (between-trend
 variance), estimated using the restricted maximum-likelihood estimator.
 se.tau2: standard error of τ2 from the REM. I2: I2 statistic from the REM
 (total heterogeneity / total variability); see Higgins, J. P. T., &
 Thompson, S. G. (2002). Quantifying heterogeneity in a meta-analysis.
 Statistics in Medicine, 21(11), 1539–1558.
 for more detail. H2: H2 statistic
 from the REM (total variability / sampling variability). QE: results of
 the *Q*-test for heterogeneity, a test to quantify the level of
 heterogeneity among the trends fed into the REM. QEp: p-value from the
 *Q*-test for heterogeneity; significance notes that the trends fed into
 the REM are heterogeneous. mag: the group's average percent increase
 or decrease between 1989 and 2020.   **Sharing/Access information** \** **
 Access to the raw Jasper Ridge bird transect dataset is not publicly
 available, but it can be granted to interested parties:
 Analyzed results from the
 North American Breeding Bird Survey Dataset can be found here: