DOI: 10.5068/d1mt2p
title: Individual variation in tolerance of human activity by urban dark-eyed juncos (Junco hyemalis) 2021 Stansell et al data file

description: An important goal of urban ecology is determining what differentiates
 urban-tolerant populations of birds from their non-urban ancestors and
 urban-intolerant species. One key to urban success may be reacting
 appropriately to human activity, and the degree to which birds view humans
 as threats can be quantified by their escape behavior.
  Understanding individual-level plasticity, however, requires the
 tracking of known individuals. We compared flight-initiation distances
 (FID) and distances fled (DF) from approaches by a human between an urban
 and a non-urban population of individually-marked Dark-eyed Juncos (Junco
 hyemalis) in southern California. The urban population is more tolerant to
 people as evidenced by attenuated FIDs and DFs relative to non-urban
 birds.  Although individual urban birds either habituated or
 sensitized to repeated approaches, there was no significant pattern at the
 population level.  Overall, the behavioral patterns exhibited by
 this urban population of juncos is more supportive of in situ evolution
 than either being a biased sample from an ancestral non-urban population
 or intrinsic behavioral plasticity that produces a uniform adjustment to
 urban life.
description: All encounters were recorded by the
 same individual (HMS) following the protocol in commonly used to study FID
 (Cooper and Blumstein 2015). An encounter began when a bird was observed
 foraging or stationary, and not alarm calling or otherwise visibly
 agitated. Because juncos are territorial, most encounters with a given
 bird occurred near where it was initially captured and banded. Birds were
 always approached in a straight line at a practiced pace (approximating
 0.5m/sec) when on the ground and exposed from vegetation, with no
 obstacles or other juncos between the observer and the focal bird. This
 ensured consistent, readily-detectable approaches to each individual (Frid
 and Dill 2002, Tätte et al. 2018). A colored marker was dropped at the
 location where the experimental approach began (the starting distance,
 SD), a second at the observer location when the focal subject fled (the
 FID), and a third at the location from where the focal subject fled, later
 converting paces to meters (0.825m/step). The distance fled (DF) was
 recorded by visually estimating the horizontal and vertical distance
 travelled in meters, then converting to a Euclidian distance. In some
 cases, it was not possible to collect data on DF because the bird left the
 immediate area.  Such occurrences were arbitrarily recorded as a distance
 fled of 50m. We also recorded
 the time of day, presence/absence of conspecifics within a 5 m radius of
 the focal bird, distance to nearest cover (either bushes and trees, or
 structures such as walls and outdoor furniture), and pedestrian density.
  Distance to cover was measured in paces from the targeted bird’s location
 when the approach began. Pedestrian density (only at UCLA – there were
 almost never pedestrians at the James) was recorded categorically as low
 (defined as &lt;5 people per minute crossing a 10m sample transect in
 the immediate vicinity of the approach) or moderate to high (≥5
 people/min). At UCLA, we
 collected repeated measures for 22 series on both a short time scale (4
 attempted approaches to the same bird on the same day) and on a longer
 time scale (over a consecutive 4-day period).  Not every series had the
 complete sequence of 16 approaches (6 had one missing value in terms of a
 missed approach on one day, 4 had two missing values, and 1 had four
 missing values because of a missed day).  The median time between
 sequential approaches within a day across 198 approaches was 3 minutes,
 with 183 times being 30 minutes or less. Only 6 approaches were separated
 by more than an hour. Birds were approached during the 2017 breeding
 season while rearing chicks (February to July at UCLA; June to July at the
 James) in order to be consistent across sites relative to foraging needs
 (i.e., risk-taking can differ in individuals when breeding versus
 non-breeding: Mikula et al. 2018).  In total, we collected 404 approaches
 across 31 individuals at UCLA, and 104 approaches across 22 individuals at
 the James Reserve.  At both sites, the majority of data were collected
 between 08:00 and 13:00 h. Statistical tests on the
 multiple approaches towards marked birds in UCLA followed standardized
 analytical methodology (Pezner et al. 2017, Dehaudt et al. 2019, Andrade
 and Blumstein, 2020). All analyses used R 3.4.2 (R Core Team 2017), on
 code modeled after Pezner et al. (2017), which had an identical
 experimental design: 4 trials per day, repeated across 4 consecutive days.
 We used linear (FID) and logistic (DF, with distances ≤2 m as near and
 &gt;2 m as far) mixed-effects models for individual responses to
 repeated approaches on the UCLA campus. Effects within UCLA and across the
 James population values were compared by regression analysis, paired
 t-tests and two-sample, unpaired t-tests, as appropriate.
 We fitted models using the R package "lme4" v1.1-14
 (Bates et al. 2015) (supporting package "car" v2.1-6: Fox and
 Weisberg 2011). A null model used individual bird as a random intercept,
 then iteratively incorporated fixed effects (contextual variables), with
 stepwise selection to find the combination of fixed effects with the
 lowest AIC value. Each predictor variable was added to the model and then
 selectively removed depending on their effect on AIC relative to the null
 model. In cases where a fixed effect resulted in only a non-significant
 decrease in AIC, likelihood ratio tests used "lmerTest" v2.0-33
 (Kuznetsova et al. 2016) to measure significance. Fixed effects without
 significant model improvement were discarded. After
 selecting a model via this process, a likelihood ratio test evaluated
 whether either the inclusion of trial iteration as a fixed effect or as a
 random slope significantly improved the explanatory power over the model
 containing contextual predictor variables and the random intercept. Best
 mixed-models were compared against their fixed effects-only counterparts
 via likelihood ratio test using "RLRsim" v3.1-3 (Scheipl et al.
 2008), supporting packages "MASS" v7.3-47 and "arm"
 v1.9-3 (Gelman and Su 2016) to determine whether individual differences
 among birds explained a significant portion of behavioral variation. Where
 individual was a significant random effect in models, adjusted
 repeatability was calculated using code provided by Jean-Nicolas Audet,
 modified from "rptR" v0.9.21 (Stoffel et al. 2017). Analyses
 were based on 334 individual approaches.
description: This dataset was used in the following paper: Individual
 variation in tolerance of human activity by urban dark-eyed juncos
 (<i>Junco hyemalis</i>). (2021) Hayley M. Stansell, Daniel T.
 Blumstein, Pamela J. Yeh and Peter Nonacs. Submitted to <i>The
 Wilson Journal of Ornithology</i>. The data (in
 Excel) are arranged on 3 datasheets (note that not all the data was taken
 for each approach of a bird).  The first sheet is for all the data
 collected on the UCLA campus.  The columns are as follows:
 Date: Day of encounter with bird. Time: Time
 of encounter Location: Site on
 campus; for map:
 http://map.ucla.edu/downloads/pdf/UCLA_Campus_Colored_Map.pdf
 Bird ID: By band combination on leg Bird ID:
 By number (1-31) Series #:
 Completed series = 4 encounters/day over 4 consecutive days.  Not all
 series were completed. A few birds experienced more than one
 series. Sex: Male or
 female. Conspecifics: If
 other juncos were within 5 m at the time of approach. Day of the
 sequence: 1-4. Encounter within
 a day: 1-4. Cover: Distance
 bird was to cover (in meters) when an approach was started.
 Overall
 encounters: All the approaches a given bird experienced. The number varied
 across birds. Pedestrian
 density when approached: Low or Moderate (= less than or greater than
 5/min). Starting
 distance: Paces away from bird when an approach was begun. Starting
 distance: Converted to meters (1 step = 0.825 m). Travel distance:
 Steps taken towards bird until bird moved. Flight initiation
 distance (FID): Steps from end of travel distance to where bird was when
 it fled. FID: Converted to
 meters. Response type:
 Moved by hopping or flying away. Distance moved
 horizontally: Estimated in meters. Distance moved
 vertically: Estimated in meters. Total distance
 moved: Square root of (h<sup>2</sup> +
 v<sup>2</sup>); some birds flew away out site – this was given
 a value of 50 m. The second sheet contains abstracted
 values for where a series (16 approaches across 4 days) was completed or
 almost completed for UCLA birds. The third sheet are the data collected at
 the James Reserve in the UC Natural Reserve System (for more info:
 https://james.ucnrs.org/). The individual columns are as described above. 
 At the James, conspecifics were almost never present when a bird was
 approached, so those data were not recorded.  No bird at the James ever
 experienced an entirely completed series of 4 approaches/day for 4
 consecutive days.