DOI: 10.5061/dryad.4mw6m90hw
title: Saffron-cowled Blackbirds' reduced nest success in Argentina's agricultural land highlights the importance of non-agricultural habitat for its conservation

description: The Saffron-cowled Blackbird (Xanthopsar flavus) is a globally endangered
 icterid endemic to the southern South American grasslands. Temperate
 grasslands are among the most threatened ecosystems in South America due
 to their high rate of land use change. In northeastern Argentina, over the
 last century, the conversion of natural grasslands to livestock farming,
 croplands, and afforestation have resulted in significant losses of
 breeding habitat for the Saffron-cowled Blackbird. Consequently, it has
 suffered severe populational declines, and its remaining populations are
 fragmented. In order to understand the impact of agricultural systems on
 the Saffron-cowled Blackbird populations, we studied its breeding biology
 (clutch size, hatching success, nestling production, and fledgling
 success) and the main parameters that influence nest survival rate in five
 breeding habitat types. During the breeding seasons of 2015 to 2019 we
 located nests and monitored their fate. We found that the cumulative
 probability of nest survival over the entire nesting cycle (i.e., laying,
 incubation, and chick rearing) was 0.06, and was lower for nests situated
 in grazed land covers. Conversely, nest survival was greater in breeding
 sites without agricultural use, particularly in marshes. Predation was the
 main cause of nest failure (76%), followed by brood parasitism (10%) and
 trampling by cattle and agricultural machinery (6%). Brood parasitism
 rates were higher in grazed paddocks, contributing together with predation
 to the failure of nests in this habitat. Our findings indicate a negative
 impact of livestock ranching on Saffron-cowled Blackbird reproduction.
 Non-agriculture habitats, like wetlands and flooded areas, are important
 as refuges for nesting. Thus, the creation of breeding refuges
 (non-productive sites) within agricultural matrices, in association with
 biodiversity-friendly agricultural practices, is crucial to ensure the
 Saffron-cowled Blackbird's maintenance.
description: GENERAL INFORMATION  
 1. Dataset used for the article: Saffron-cowled
 Blackbirds' reduced nest success in Argentina's agricultural
 land highlights the importance of non-agricultural habitat for its
 conservation.   2. Study
 published in Ornithological Applications by Pucheta, M.F; Pereda, M.I, and
 Di Giacomo, A.S.    Corresponding author email:
 pucheta.mf@gmail.com    Correspondig author
 institution: Centro de Ecología Aplicada del Litoral, CONICET.
   3. Date of data collection:
 2015-2019   4. Geographic
 location of data collection: Argentina (Entre Ríos and Corrientes
 provinces).    For specific
 data collection methods please reefer to method section of the manscript
 in the DOI: 10.1093/ornithapp/duae006. Journal: The Condor: Ornithological
 Applications   5.
 Information about funding sources that supported the collection of the
 data: PICT2014–3397, PICT2014–2057, PIP2022-2024, Neotropical Bird Club,
 Neotropical Grassland Conservancy, The Rufford Fundation, Young
 Conservation Leadership Program from BirdLife International and Aves
 Argentinas.   SHARING/ACCESS
 INFORMATION   1.
 Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain   2. Links to
 publications that cite or use the data: Pucheta, Maria Florencia; Pereda,
 Maria Inés; Di Giacomo, Adrián Santiago (Forthcoming 2024). Saffron-cowled
 Blackbirds' reduced nest success in Argentina's  agricultural
 land highlights the importance of non-agricultural habitat for its
 conservation. Ornithological Applications.
   3. Links to other publicly accessible
 locations of the data: None  
 4. Links/relationships to ancillary data sets: None
   5. Was data derived from another
 source? No A. If yes, list source(s):
 NA   6. Recommended citation
 for this dataset:  Pucheta, Maria Florencia;
 Pereda, Maria Inés; Di Giacomo, Adrián Santiago (Forthcoming
 2024).  Data from: Saffron-cowled Blackbirds'
 reduced nest success in Argentina's agricultural land highlights the
 importance of non-agricultural habitat for its conservation.
 Dryad Digital Repository.
 &lt;https://doi.org/10.5061/dryad.4mw6m90hw&gt;
   DATA & FILE
 OVERVIEW   1. File List
 (nomenclature: abbreviated name of Xanthopsar flavus (xafl) + parameters
 presented in the datase)  
 A) xafl_Nest_Height.xlsx B)
 xafl_Brood_parasitism.xlsx C)
 xafl_Reproductive_Parameters.xlsx D)
 xafl_Nest_Failure_Causes.xlsx E)
 xafl_Nest_Survival_for_Mark.xlsx F)
 xafl_Nest_Attempts.xlsx G)
 xafl_Nest_survival_across_Breeding_Season.xlsx H)
 xafl_Nest_Survival_and_Brood_Parasitism_Graphs
   A) DATA-SPECIFIC INFORMATION FOR:
 xafl_Nest_Height.xlsx   1.
 Number of variables: 2   2.
 Number of cases/rows: 222  
 3. Variable List:  
     * breeding_habitat: the five breeding habitat studied
 (marsh, roadside, hedgerow, grazed_paddock, cropland)
       * nest_height: height in
 centimeters at which each of the nests was constructed.
      4. Missing data codes:
 None   B) DATA-SPECIFIC
 INFORMATION FOR: xafl_Brood_parasitism.xlsx
   1. Number of variables: 3
   2. Number of cases/rows:
 223   3. Variable
 List:       * nest_ID:the
 identity of each nest.      
 * BreedingHabitat: the five breeding habitat analyzed (marsh, roadside,
 hedgerow, grazed_paddock, cropland)  
     * BroodParasitism: binary variable: presence (1) or absence
 (0) of brood parasitism in each nest.  
    4. Missing data codes: None
   C) DATA-SPECIFIC INFORMATION FOR:
 xafl_Reproductive_Parameters.xlsx  
 1. Number of variables: 9  
 2. Number of cases/rows: 107
   3. Variable List:
       * Hatching_success:Hatching
 success per nest (number of eggs hatched over the total number of eggs
 laid).       *
 Breeding_habitat_HS: reproductive habitats types for nests with
 information on hatching success(marsh, roadside, hedgerow, grazed_paddock,
 cropland).       * Year_HS:
 the corresponding year (2015-2019) of the breeding season for which
 hatching success was calculated.  
     * Clutch_size:clutch size (number of eggs) per
 nest.       *
 Breeding_habitat_CS: reproductive habitats types for nests with
 information on clutch size.  
     * Year_CS: the corresponding year (2015-2019) of the
 breeding season for which clutch size was calculated.
       * Fledgling_success: fledging
 success for each nest (chicks that successfully flew from the nest over
 total chicks present in the nest).  
     * Breeding_habitat_FS: reproductive habitats types for
 nests with information on fledgling success.
       * Year_FS: the corresponding year
 (2015-2019) of the breeding season for which fledgling
 success.   4. Missing data
 codes: rows with "n/a" for nests with some parameter data not
 available.   D)
 DATA-SPECIFIC INFORMATION FOR: xafl_Nest_Failure_Causes.xlsx
   1. Number of variables: 2
   2. Number of cases/rows:
 168   3. Variable
 List:       *
 BreedingHabitat: the five breeding habitat analyzed (marsh, roadside,
 hedgerow, grazed_paddock, cropland).  
     * FailureCause: the causes that led to failure in each nest
 (depredated, parasitated, trampling, abandonment, storms).
   4. Missing data codes:
 None   E) DATA-SPECIFIC
 INFORMATION FOR: xafl_Nest_Survival_for_Mark.xlsx
   1. Number of variables: 17
   2. Number of cases/rows:
 223   3. Variable
 List:       * NestID: nest
 identity number       *
 FirstFound: Julian day of the encounter date.
       * LastCheck: Julian day of the
 last date of the nest with contents.  
     * Fate: Final status of the nest: successful (0) or failed
 (11).       * NestAge: Days
 elapsed since the laying of the first egg on day 0.
       * year2015: Dummy variable for the
 year 2015 (nest of 2015 season are 1, nest from another seadon are
 0).       * year2016: Dummy
 variable for the year 2016 (nest of 2016 season are 1, nest from another
 seadon are 0).       *
 year2017: Dummy variable for the year 2017 (nest of 2017 season are 1,
 nest from another seadon are 0).  
     * year2018: Dummy variable for the year 2018 (nest of 2018
 season are 1, nest from another seadon are 0).
       * Roadside:Dummy variable for the
 roadside habitat.       *
 Hedgerow: Dummy variable for the hedgerow habitat.
       * GrazedPaddock: Dummy variable
 for the grazed paddock habitat.  
     * Cropland: Dummy variable for the cropland
 habitat.       *
 BroodParasitism: Binary variable for brood parasitism
 presence.       *
 NestHeight: cuantitative variable measured as nest height in
 cm.       * ColonySize: The
 number of total nest in the colony.  
 4. Missing data codes: None. 
      This dataset (E) is for Daily
 survival rate estimations in the software Mark, tool "Nest
 survival"   F)
 DATA-SPECIFIC INFORMATION FOR: xafl_Nest_Attempts.xlsx
   1. Number of variables: 4
   2. Number of cases/rows: 8
   3. Variable List:
       * TimeOfBreeding: The progression
 of the breeding season expressed in fortnights.
       * TimeOfBreeding_name: The name
 assigned to each fortnight on the x-axis of the graph.
       * n: The number of nest attempts
 per fortnigh.          *
 PercentageNestAttemps: The percentage of nest attempts per fortnight
 relative to the total nest attempts.  
 4. Missing data codes: None. 
   This dataset (F) was used to plot nest
 attempts against the progression of the breeding season.
     G)
 DATA-SPECIFIC INFORMATION FOR:
 xafl_Nest_survival_across_Breeding_Season.xlsx
   1. Number of variables:
 417   2. Number of
 cases/rows: 124   3.
 Variable List:      *
 Breeding_time: Progression of the breeding season in days.
      * Daily_survival_rate: Daily
 survival rate calculated with MARK for each day within the breeding
 season.        * LCI:Lower
 confidence interval of the daily survival rate.
      * UCI:Upper confidence interval of
 the daily survival rate.  
 4. Missing data codes: None
   The present dataset (G) was used to
 plot the daily survival rate against the quadratic trend of the breeding
 time.   H) DATA-SPECIFIC
 INFORMATION FOR:
 xafl_Nest_Survival_and_Brood_Parasitism_Graphs.xlsx
   1. Number of variables: 7
   2. Number of cases/rows: 5
   3. Variable List:
      * Environment: the five reroductive
 habitat analyzed (marshes, native hedgerow, croplands, roadside ditches
 and grazed paddocks).    
  *Daily_survival_rate: the daily nest survival rate for the model that
 considers the habitat type variable.  
    *Estandar_error: standard error for the daily survival rate
 (DSR) in each habitat type.  
    * LCI: lower confidence interval for the DSR in each habitat
 type.       * UCI: upper
 confidence interval for the DSR in each habitat type. 
      * Brood_parasitism: the percentage
 of nests parasitized by habitat type.  
    * order: the order in which the data were
 plotted.   The present
 dataset (H) was used to plot the daily survival rate and brood parasitism
 percentage against breeding habitat type. 
description: # Saffron-cowled Blackbirds' reduced nest success in Argentina's
 agricultural land highlights the importance of non-agricultural habitat
 for its conservation In
 order to understand the impact of agricultural systems over the endangered
 Saffron-cowled Blackbird populations, we studied its breeding biology
 (clutch size, hatching success, nestling production, and fledgling
 success) and the main parameters that influence nest survival rate in five
 breeding habitat types. During the breeding seasons of 2015 to 2019 we
 located nests and monitored their fate (please refer to methods section in
 the manuscript for detailed methodology). We provide the data set in Excel
 spreadsheet format, with the data used in each analysis, each in a
 separate Excel file for clarity. In addition, we include a single text
 document that contains the scripts used for each analysis in the R R. Each
 graphic analysis is separately with its respective title.Description of
 the data and file structure. GENERAL INFORMATION 1\. Dataset used for the
 study: Blackbirds´ reduced nest success in Argentina's agricultural
 land highlights the importance of non-agricultural habitat for its
 conservation 2\. Study published in Ornithological Applications by
 Pucheta, M.F; Pereda, M.I, and Di Giacomo, A.S. corresponding author
 email: correspondig author institution:
 Centro de Ecología Aplicada del Litoral, CONICET. 3\. Date of data
 collection: 2015-2019 4\. Geographic location of data collection:
 Argentina 5\. Information about funding sources that supported the
 collection of the data: PICT2014–3397, PICT2014–2057, PIP2022-2024,
 Neotropical Bird Club, Neotropical Grassland Conservancy, The Rufford
 Fundation, Young Conservation Leadership Program from BirdLife
 International and Aves Argentinas. SHARING/ACCESS INFORMATION 1\.
 Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain 2\. Links to publications that cite or use the data:
 Pucheta, Maria Florencia; Pereda, Maria Inés; Di Giacomo, Adrián Santiago
 (Forthcoming 2024). Saffron-cowled Blackbirds reduced nest success in
 Argentina's agricultural land highlights the importance of
 non-agricultural habitat for its conservation. Ornithological
 Applications. 3\. Links to other publicly accessible locations of the
 data: None 4\. Links/relationships to ancillary data sets: None 5\. Was
 data derived from another source? No A. If yes, list source(s): NA 6\.
 Recommended citation for this dataset: Pucheta, Maria Florencia; Pereda,
 Maria Inés; Di Giacomo, Adrián Santiago (Forthcoming 2024). Data from:
 Saffron-cowled Blackbirds' reduced nest success in Argentina's
 agricultural land highlights the importance of non-agricultural habitat
 for its conservation. Dryad Digital Repository.
 DATA & FILE OVERVIEW
 1\. File List (nomenclature: abbreviated name of Xanthopsar flavus (xafl)
 + parameters presented in the datase) A) xafl_Nest_Height.xlsx B)
 xafl_Brood_parasitism.xlsx C) xafl_Reproductive_Parameters.xlsx D)
 xafl_Nest_Failure_Causes.xlsx E) xafl_Nest_Survival_for_Mark.xlsx F)
 xafl_Nest_Attempts.xlsx G) xafl_Nest_survival_across_Breeding_Season.xlsx
 H) xafl_Nest_Survival_and_Brood_Parasitism_Graphs A) DATA-SPECIFIC
 INFORMATION FOR: xafl_Nest_Height.xlsx 1\. Number of variables: 2 2\.
 Number of cases/rows: 222 3\. Variable List: \* breeding_habitat: the five
 breeding habitat studied (marsh, roadside, hedgerow, grazed_paddock,
 cropland) \* nest_height: height in centimeters at which each of the nests
 was constructed. 4\. Missing data codes: None B) DATA-SPECIFIC INFORMATION
 FOR: xafl_Brood_parasitism.xlsx 1\. Number of variables: 3 2\. Number of
 cases/rows: 223 3\. Variable List: \* nest_ID:the identity of each nest.
 \* BreedingHabitat: the five breeding habitat analyzed (marsh, roadside,
 hedgerow, grazed_paddock, cropland) \* BroodParasitism: binary variable:
 presence (1) or absence (0) of brood parasitism in each nest. 4\. Missing
 data codes: None C) DATA-SPECIFIC INFORMATION FOR:
 xafl_Reproductive_Parameters.xlsx 1\. Number of variables: 9 2\. Number of
 cases/rows: 107 3\. Variable List: \* Hatching_success:Hatching success
 per nest (number of eggs hatched over the total number of eggs laid). \*
 Breeding_habitat_HS: reproductive habitats types for nests with
 information on hatching success(marsh, roadside, hedgerow, grazed_paddock,
 cropland). \* Year_HS: the corresponding year (2015-2019) of the breeding
 season for which hatching success was calculated. \* Clutch_size:clutch
 size (number of eggs) per nest. \* Breeding_habitat_CS: reproductive
 habitats types for nests with information on clutch size. \* Year_CS: the
 corresponding year (2015-2019) of the breeding season for which clutch
 size was calculated. \* Fledgling_success: fledging success for each nest
 (chicks that successfully flew from the nest over total chicks present in
 the nest). \* Breeding_habitat_FS: reproductive habitats types for nests
 with information on fledgling success. \* Year_FS: the corresponding year
 (2015-2019) of the breeding season for which fledgling success. 4\.
 Missing data codes: rows with "n/a" for nests with some
 parameter data not available. D) DATA-SPECIFIC INFORMATION FOR:
 xafl_Nest_Failure_Causes.xlsx 1\. Number of variables: 2 2\. Number of
 cases/rows: 168 3\. Variable List: \* BreedingHabitat: the five breeding
 habitat analyzed (marsh, roadside, hedgerow, grazed_paddock, cropland). \*
 FailureCause: the causes that led to failure in each nest (depredated,
 parasitated, trampling, abandonment, storms). 4\. Missing data codes: None
 E) DATA-SPECIFIC INFORMATION FOR: xafl_Nest_Survival_for_Mark.xlsx 1\.
 Number of variables: 17 2\. Number of cases/rows: 223 3\. Variable List:
 \* NestID: nest identity number \* FirstFound: Julian day of the encounter
 date. \* LastCheck: Julian day of the last date of the nest with contents.
 \* Fate: Final status of the nest: successful (0) or failed (11). \*
 NestAge: days elapsed since the laying of the first egg on day 0. \*
 year2015: dummy variable for the year 2015 (nest of 2015 season are 1,
 nest from another seadon are 0). \* year2016: dummy variable for the year
 2016 (nest of 2016 season are 1, nest from another seadon are 0). \*
 year2017: dummy variable for the year 2017 (nest of 2017 season are 1,
 nest from another seadon are 0). \* year2018: dummy variable for the year
 2018 (nest of 2018 season are 1, nest from another seadon are 0). \*
 Roadside: dummy variable for the roadside habitat. \* Hedgerow: dummy
 variable for the hedgerow habitat. \* GrazedPaddock: dummy variable for
 the grazed paddock habitat. \* Cropland: dummy variable for the cropland
 habitat. \* BroodParasitism: binary variable for brood parasitism
 presence. \* NestHeight: cuantitative variable measured as nest height in
 cm. \* ColonySize: number of total nest in the colony. 4\. Missing data
 codes: None. We used this dataset (E) to calculate the daily survival rate
 (DSR) estimator provided by the nest survival module of the MARK 6.2
 program (White and Burnham 1999). F) DATA-SPECIFIC INFORMATION FOR:
 xafl_Nest_Attempts.xlsx 1\. Number of variables: 4 2\. Number of
 cases/rows: 8 3\. Variable List: \* TimeOfBreeding: the progression of the
 breeding season expressed in fortnights. \* TimeOfBreeding_name: name
 assigned to each fortnight on the x-axis of the graph. \* n: number of
 nest attempts per fortnigh. \* PercentageNestAttemps: percentage of nest
 attempts per fortnight relative to the total nest attempts. 4\. Missing
 data codes: None. This dataset (F) was used to plot nest attempts against
 the progression of the breeding season. G) DATA-SPECIFIC INFORMATION FOR:
 xafl_Nest_survival_across_Breeding_Season.xlsx 1\. Number of variables:
 417 2\. Number of cases/rows: 124 3\. Variable List: \* Breeding_time:
 Progression of the breeding season in days. \* Daily_survival_rate: Daily
 survival rate calculated with MARK for each day within the breeding
 season. \* LCI:Lower confidence interval of the daily survival rate. \*
 UCI:Upper confidence interval of the daily survival rate. 4\. Missing data
 codes: None The present dataset (G) was used to plot the daily survival
 rate against the quadratic trend of the breeding time. H) DATA-SPECIFIC
 INFORMATION FOR: xafl_Nest_Survival_and_Brood_Parasitism_Graphs.xlsx 1\.
 Number of variables: 7 2\. Number of cases/rows: 5 3\. Variable List: \*
 Environment: the five reroductive habitat analyzed (marshes, native
 hedgerow, croplands, roadside ditches and grazed paddocks).
 *Daily_survival_rate: the daily nest survival rate for the model that
 considers the habitat type variable. *Estandar_error: standard error for
 the daily survival rate (DSR) in each habitat type. \* LCI: lower
 confidence interval for the DSR in each habitat type. \* UCI: upper
 confidence interval for the DSR in each habitat type. \* Brood_parasitism:
 the percentage of nests parasitized by habitat type. \* order: the order
 in which the data were plotted. The present dataset (H) was used to plot
 the daily survival rate and brood parasitism percentage against breeding
 habitat type. ## Code/Software We provide the document
 "Puchetaetal2024_rcodes.txt" with the scripts that we correct in
 the Software R 4.1.1.To model the daily survival rate (DSR) of
 Saffron-cowled Blackbird' nests by the different variables of
 interest, we used the nest survival module of the MARK 6.2 program (White
 and Burnham 1999).