DOI: 10.5061/dryad.8w9ghx3x0
title: Multi-scale habitat selection and nest survival of whinchats and stonechats: Implications for grassland conservation management

description: Effective management for endangered grassland birds requires a sound
 understanding of habitat requirements and factors shaping reproductive
 success. We studied multi-level habitat selection of endangered whinchats
 (Saxicola rubetra) and locally increasing stonechats (Saxicola rubicola)
 in a nature reserve using Sentinel-2 images, LiDAR data, and habitat
 variables measured onsite. We monitored nest fates, and estimated how the
 causes of nest mortality varied with nest initiation date. Further, we
 analyzed how nest-site selection, precipitation, nest initiation date, and
 nest age influenced daily nest survival. At landscape- and site-level,
 both species primarily selected for territories in lightly farmed meadows.
 However, stonechats appeared to be less specialized and used most
 available habitat types. Within home-ranges, both species selected for
 nest-sites in fallow patches, but in contrast to stonechats, whinchats
 also selected for large viewsheds. In both species, the main causes of
 nest failure were predation by red foxes (Vulpes vulpes), weather-related,
 and nest desertion. In whinchats, the probability of nest desertion
 increased and predation risk decreased with nest initiation date, possibly
 due to better nest concealment in the later season. Daily nest survival
 decreased with nest age and precipitation in both species, and increased
 with nest initiation date in whinchats. None of the habitat variables
 examined were positively linked to daily nest survival, and viewshed was
 negatively related to whinchat daily nest survival. Our study suggests
 that extending core habitat may help to promote settlement and potentially
 reproductive success of whinchats. However, as habitat selection was not
 positively associated with daily nest survival, land management measures
 alone might not be sufficient to halt rapid population declines. To
 effectively conserve whinchats and other grassland bird populations, the
 causes of nest failures must be identified and addressed. Within the
 examined reserve and similar habitats, targeted flood and predator control
 may yield the biggest short-term conservation gains.
description: This dataset contains the data for our analysis of multi-scale
 habitat selection and nest survival in whinchats and stonechats. In this
 paper, we analyzed territory selection of whinchats and stonechats at
 landscape- and site-level using compositional analysis, and nest-site
 selection at home-range-level using conditional logistic regression. We
 monitored the nest fates and analyzed how the causes of nest mortality
 varied with nest initiation date using a multinomial model. Further, we
 used known fate models to estimate how environmental and temporal factors
 influenced daily nest survival.
description: # Multi-scale habitat selection and nest survival of whinchats and
 stonechats: implications for grassland conservation management This
 dataset contains the data used for our analysis of multi-scale habitat
 selection and nest survival in whinchats and stonechats. In this paper, we
 analyzed territory selection of whinchats and stonechats at landscape- and
 site-level, and nest-site selection at home-range-level. We monitored nest
 fates, and analyzed how the causes of nest mortality varied with nest
 initiation date. Further, we estimated how environmental and temporal
 factors influenced daily nest survival. The dataset is organized in five
 folders following the structure of the paper: Territory selection at
 reserve-level, territory selection at site-level, nest-site selection at
 home-range level, causes of nest mortality, and daily nest survival. Each
 folder contains multiple files with the data used for the respective
 analysis. ### The folder “habitat_selection_reserve_level” contains four
 files with the data used to analyze territory selection of whinchats and
 stonechats at reserve-level. Each table contains percentages of 11
 remotely sensed land use/cover classes (representing either use or
 availability of these classes). The column names are: o.bog: open bog, not
 overgrown by pines w.bog: wooded bog, overgrown by pines t.bog:
 transitional bog, in the transition stage from fen to raised bog built-up:
 e.g. roads, buildings, etc., light: lightly farmed meadows, i.e. mown only
 once a year not before 1 August or 1 September moderate: moderately farmed
 meadows, i.e. mown once or twice a year not before 1 June, 15 June or 1
 July fallow: fallow meadows, not mown for a year or longer forest:
 broadleaf and coniferous forests intensive: intensively farmed meadows,
 mown up to 6 times/year without any time restrictions reed: reed beds,
 dense stands of *Phragmites* sp. water: waterbodies such as rivers and
 lakes **avail_whin_reserve.csv** This file contains the percentages of 11
 remotely sensed land use/cover classes (as defined above) within the
 nature reserve, representing available areas. To run a compositional
 analysis via ‘compana’ from the *adehabitat* package, these percentages
 are repeated for the number of whinchat territories.
 **used_whin_reserve.csv** This file contains the percentages of 11 land
 use/cover classes (as described above) in each of 66 whinchat territories.
   **avail_stone_reserve.csv** This file contains the percentages of 11
 remotely sensed land use/cover classes (as defined above) within the
 nature reserve, representing available areas. To run a compositional
 analysis via ‘compana’ from the *adehabitat* package, these percentages
 are repeated for the number of stonechat territories.
 **used_stone_reserve.csv** This file contains the percentages of 11 land
 use/cover classes (as described above) used in each of 238 stonechat
 territories. ### The folder “habitat_selection_site_level” contains eight
 files with the data used to analyze territory selection of whinchats and
 stonechats at site-level. Each table contains percentages of up to seven
 land use/cover classes assessed onsite and from aerial pictures. The
 percentages represent either use or availability. The column names are:
 light: lightly farmed meadows, mown once a year not before 1 August or 1
 September, unfertilized moderate: mown either once or twice a year not
 before 15 June or 1 July, infrequently fertilized with horse
 dung             intensive: mown 4-6 times a year, frequently fertilized
 with liquid manure             pasture: cattle pastures reed: dense stands
 of *Phragmites* sp. shrub: lower shrubs e.g. *Pinus mugo* or *Salix* sp. 
 forest: broadleaf and coniferous forests, groups of large trees Note that
 marginally used and unused classes were removed from the respective sample
 to get an unbiased ranking of selected land use/cover classes. The
 percentages are repeated for the number of whinchat territories.
 **avail_whin_A.csv** Percentages of 7 land use/cover types within site A
 (defined as available). **used_whin_A.csv** Percentages of 7 land
 use/cover classes used in each of 48 whinchat territories at site A.
 **avail_stone_A.csv** Percentages of 7 land use/cover types within site A
 (defined as available). **used_stone_A.csv** Percentages of 7 land
 use/cover classes used in each of 17 stonechat territories at site A.
 **avail_whin_B.csv** Percentages of 5 land use/cover types within site B
 (defined as available). **used_whin_B.csv** Percentages of 5 land
 use/cover classes used in each of 43 whinchat territories at site B.
 **avail_stone_B.csv** Percentages of 7 land use/cover types within site B
 (defined as available). **used_stone_B.csv** Percentages of 7 land
 use/cover classes used in each of 48 stonechat territories at site B. ###
 The folder “habitat_selection_nest_site” contains four files used to
 analyze nest-site selection of whinchats and stonechats at
 home-range-level. The files contain measurements of habitat variables at
 nest-sites (presence) and each ten control points distributed randomly in
 240 m radius home-range (absence) for whinchats at site A. The column
 names are: viewshed: the area visible from a nest location (in m², see the
 paper for a detailed description of the settings)   viewshed.z: scaled
 viewshed (as described in the paper) dist_int: distance to intensively
 farmed meadows (in meter). dist_int.z:  scaled dist_int (as described in
 the paper) fallow: 0/1 denotes whether a nest was found inside or outside
 a fallow (unmown area) no: unique nest ID PA: Presence/Absence (1 means
 nest, 0 means random point) Note that in the columns dist_int and
 dist_int_z are only present in the files concerning site A, and the column
 fallow is only present in the files concerning site B. In addition, the
 folder contains a file with the orientation of whinchat nests and
 stonechat nests. **data_A_whin.csv** This file contains measurements of
 habitat variables at nest-sites (presence) and each ten control points
 distributed randomly in 240 m radius home-range (absence) for whinchats at
 site A. **data_B_whin.csv** This file contains measurements of habitat
 variables at nest-sites (presence) and each ten control points distributed
 randomly in 240 m radius home-range (absence) for whinchats at site B.
 **data_A_stone.csv** This file contains measurements of habitat variables
 at nest-sites (presence) and each ten control points distributed randomly
 in 240 m radius home-range (absence) for stonechats at site A.
 **data_B_stone.csv** This file contains measurements of habitat variables
 at nest-sites (presence) and each ten control points distributed randomly
 in 240 m radius home-range (absence) for stonechats at site B.
 **orientation.csv** This file contains the orientation of 81 whinchat
 nests and 40 stonechat nests with a recognizable lateral entrance. The
 column names are: no: unique nest ID degree: orientation of the lateral
 nest opening in degree Species: species, whinchat or stonechat ### The
 folder “mortality” contains one file with the data used to analyze how the
 causes of mortality for whinchat nests varied with nest initiation date.
 **nest_fates.csv** This file contains the fate (success, or failure due to
 predation, desertion, weather) of 114 whinchat nests and the day of the
 year (yday) of nest initiation. The column names are: fate: the fate of
 the nest (success, or failure due to predation, desertion, weather) yday:
 day of the year when the nest was initiated ### The folder “survival”
 contains six files with the data used to analyze daily nest survival of
 whinchats and stonechats with the overall models and with the
 site-specific models. The .RDS-file can be read in R and contains a list
 of 11 and 12 elements for the overall and the site-specific models,
 respectively. The element names are: y: survival matrix with individual
 nests in rows and days in columns (1 = nest is alive, 0 = nest is dead)
 NNests: number of nests last: last observation (alive or dead) first:
 first observation (alive or dead) cover: viewshed (in m², a covariate of
 the nest) distance: distance (in meter) to the nearest intensively farmed
 meadow. As intensively farmed meadows were only present at site A, this
 column is only present in the site-specific datasets for site A. fallow:
 indicating whether a nest was inside or outside a fallow. As fallows were
 created only at site B, this column is only present in the site-specific
 datasets for site B. init: nest initiation day (day of the year when the
 nest was initiated, a covariate of the nest) age: nest age (in days, a
 covariate of the date) maxage: maximum of age rain: a matrix containing
 the amount of rain (in mm) for each day (in columns) of each nest (in
 rows). parentID: a vector with mother ID (as integer) Nparents: number of
 unique mother IDs Numeric covariates were scaled and centered.
 **datax_whin** This file contains all data used for the overall model of
 daily nest survival in whinchats. The .RDS-file can be read in R and
 contains a list of 11 elements (element names are described above).
 **datax_stone** This file contains all data used for the overall model of
 daily nest survival in stonechats. The .RDS-file can be read in R and
 contains a list of 11 elements (element names are described above).
 **datax_whin_A** This file contains all data used for the site-specific
 model of daily nest survival in whinchats at site A. The .RDS-file can be
 read in R and contains a list with 12 elements (element names are
 described above). **datax_stone_A** This file contains all data used for
 the site-specific model of daily nest survival in stonechats at site A.
 The .RDS-file can be read in R and contains a list with 12 elements
 (element names are described above). **datax_whin_B** This file contains
 all data used for the site-specific model of daily nest survival in
 whinchats at site B. The .RDS-file can be read in R and contains a list
 with 12 elements (element names are described above). **datax_stone­_B**
 This file contains all data used for the site-specific model of daily nest
 survival in stonechats at site B. The .RDS-file can be read in R and
 contains a list with 12 elements (element names are described above). ##
 **Sharing/access information** Satellite images were downloaded from the
 Copernicus Open Access Hub
 ([https://scihub.copernicus.eu/](https://scihub.copernicus.eu/)), flood
 data and the digital surface model from Landesamt für Digitalisierung,
 Breitband und Vermessung
 ([https://www.ldbv.bayern.de/](https://www.ldbv.bayern.de/)), and weather
 data from meteorological stations run by Deutscher Wetterdienst
 ([https://www.wetter-by.de/](https://www.wetter-by.de/)). ##
 **Code/software** Spatial analyses were conducted in QGIS, and all models
 were run in R and Stan. Code is available upon request. RDS files can be
 read in R using the readRDS().