Data from: Heterogeneity in breeding productivity is driven largely by factors affecting nestlings and young fledglings in an imperiled migratory passerine
Data files
Nov 22, 2024 version files 2.08 MB
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gwwa_21nov2024.zip
2.07 MB
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README.md
7.94 KB
Abstract
Identifying factors that drive variation in vital rates among populations is a prerequisite to understanding a species’ population biology and, ultimately, to developing effective conservation strategies. This is especially true for imperiled species like the golden-winged warbler (Vermivora chrysoptera) that exhibit strong spatial heterogeneity in demography and respond differently to conservation interventions. Habitat management actions recommended for breeding grounds conservation include timber harvest, shrub shearing, and prescribed fire that maintain or create early successional woody communities. Herein, we assessed variation in the survival of nests [n=145] and fledglings [n=134] at 17 regenerating timber harvests sites within two isolated populations in Pennsylvania that differed in productivity and response to habitat management. Although overall survival of nests and fledglings was higher in the eastern population than the central population, this was only true when the nest phases and fledgling phases were considered wholly. Indeed, survival rates of nestlings and recently fledged young (1-5 days post-fledging) were lower in the central population, whereas eggs and older fledglings (≥ 6 days post-fledging) survived at comparable rates in both populations. Fledglings in the central population were smaller (10% lower weight) and begged twice as much as those in the eastern population, suggesting food limitation may contribute to lower survival rates. Fledgling survival in the central population, but not eastern, also was a function of habitat features (understory vegetation density [+] and distance to mature forest [-]) and individual factors (begging effort [-]).Our findings illustrate how identifying how survival varies across specific life stages can elucidate potential underlying demographic drivers, such as food resources in this case. In this way, our work underscores the importance of studying and decomposing stage-specific demography in species of conservation concern.
README
Description of subfolders:
The "INPfiles" folder refers to MARK input files described below
The "MARKfiles" folder refers to MARK (.DBF and .FPT) files to implement the input files mentioned above.
Note that each .INP file (input file) has two MARK (.DBF and .FPT) files to implement the analysis in program MARK.
The following are descriptions of the variables present in each analysis
##########################
lifestages_eggsurvival
/* day 1 = Julian date 134 for Pocs and day 1 = Julian date 141 for PA Wilds */
/* nesting season is 46 days in Pocs and 47 days in PA Wilds */
/* therefore, # occasions = 47 */
/* six values: i, j, k, f, n, and region ('pa wilds' vs 'poconos' where 0 = poconos) */
# so, when you open this file, you'll see the three monitoring variables (i, j, and k) followed by
# fate ("f"; 1/0), number ("n"; always 1), and region.
lifestages_nestlingsurvival
/* day 1 = Julian date 134 for Pocs and day 1 = Julian date 141 for PA Wilds */
/* nesting season is 46 days in Pocs and 47 days in PA Wilds */
/* therefore, # occasions = 47 */
/* six values: i, j, k, f, n, and region ('pa wilds' vs 'poconos' where 0 = poconos) */
lifestages_fledglings1to5survival
/* 5 occasions */
/* each observation includes a 5 day detection history, n, and region */
/* 2 regions (pa wilds vs poconos - 0 = poconos) */
/* I did not run 'region' as a group effect - I ran as a covariate */
lifestages_fledglings6to30survival
/* 25 occasions */
/* each observation includes a 25 day detection history, n, and region */
/* 2 regions (pa wilds vs poconos - 0 = poconos) */
/* I did not run 'region' as a group effect - I ran as a covariate */
## These are all variable definitions for fledgling survival files:
Var1 study area (pa wilds vs poconos - 0 = poconos)
Var2 year (0 = first year); poconos: 2014-15, pa wilds: 2016-17
Var3 mass at time of banding (g)
Var4 fledge date (ordinal)
Var5 distance fledgling moved before day 1 (m)
Var6 distance fledgling moved before day 2 (m)
Var7 distance fledgling moved before day 3 (m)
Var8 distance fledgling moved before day 4 (m)
Var9 distance fledgling moved before day 5 (m)
Var10 fledgling begging on day 1 (0-5; 0 = 0%, 5 = 100%)
Var11 fledgling begging on day 2 (0-5; 0 = 0%, 5 = 100%)
Var12 fledgling begging on day 3 (0-5; 0 = 0%, 5 = 100%)
Var13 fledgling begging on day 4 (0-5; 0 = 0%, 5 = 100%)
Var14 fledgling begging on day 5 (0-5; 0 = 0%, 5 = 100%)
Var15 mean basal area (m2/ha)
Var16 mean percent unvegetated cover
Var17 mean percent nonherbaceous cover
Var18 mean percent herbaceous cover
Var19 mean number of snags
Var20 mean percent lateral vegetation density
Var21 mean percent vertical density
Var22 mean percent early-successional within 150m
Var23 mean percent hardwood swamp within 150m
Var24 mean percent mature forest within 150m
Var25 mean percent sapling stand within 150m
Var26 mean percent shrubland within 150m
Var27 mean percent thinned stand within 150m
Var28 distance (m) to nearest early-successional stand, day 1
Var29 distance (m) to nearest early-successional stand, day 2
Var30 distance (m) to nearest early-successional stand, day 3
Var31 distance (m) to nearest early-successional stand, day 4
Var32 distance (m) to nearest early-successional stand, day 5
Var33 distance (m) to nearest hardwood swamp, day 1
Var34 distance (m) to nearest hardwood swamp, day 2
Var35 distance (m) to nearest hardwood swamp, day 3
Var36 distance (m) to nearest hardwood swamp, day 4
Var37 distance (m) to nearest hardwood swamp, day 5
Var38 distance (m) to nearest mature forest, day 1
Var39 distance (m) to nearest mature forest, day 2
Var40 distance (m) to nearest mature forest, day 3
Var41 distance (m) to nearest mature forest, day 4
Var42 distance (m) to nearest mature forest, day 5
Var43 distance (m) to nearest sapling (pole) stand, day 1
Var44 distance (m) to nearest sapling (pole) stand, day 2
Var45 distance (m) to nearest sapling (pole) stand, day 3
Var46 distance (m) to nearest sapling (pole) stand, day 4
Var47 distance (m) to nearest sapling (pole) stand, day 5
Var48 distance (m) to nearest shrubland, day 1
Var49 distance (m) to nearest shrubland, day 2
Var50 distance (m) to nearest shrubland, day 3
Var51 distance (m) to nearest shrubland, day 4
Var52 distance (m) to nearest shrubland, day 5
Var53 distance (m) to nearest thinned stand (eg, shelterwood), day 1
Var54 distance (m) to nearest thinned stand (eg, shelterwood), day 2
Var55 distance (m) to nearest thinned stand (eg, shelterwood), day 3
Var56 distance (m) to nearest thinned stand (eg, shelterwood), day 4
Var57 distance (m) to nearest thinned stand (eg, shelterwood), day 5
## These are all variable definitions for nest survival files:
Var1 year (0 = first year); poconos: 2014-15, pa wilds: 2016-17
Var2 number of 1-2 m tall shrubs within 5 m of the nest
Var3 number of >2 m tall shrubs within 5 m of the nest
Var4 number of saplings within 5 m of the nest
Var5 basal area (m2/ha)
Var6 percent leaf litter cover within 1 m of the nest
Var7 percent grass cover within 1 m of the nest
Var8 percent bare ground cover within 1 m of the nest
Var9 percent forb cover within 1 m of the nest
Var10 percent woody cover within 1 m of the nest
Var11 percent vine cover within 1 m of the nest
Var12 percent rubus cover within 1 m of the nest
Var13 number of snags within 11.3 m of the nest
Var14 mean shrub height within 11.3 m of the nest
Var15 mean sapling height within 11.3 m of the nest
Var16 percent grass cover within 11.3 m of the nest
Var17 percent forb cover within 11.3 m of the nest
Var18 percent rubus cover within 11.3 m of the nest
Var19 percent vine cover within 11.3 m of the nest
Var20 percent shrub cover within 11.3 m of the nest
Var21 percent sapling cover within 11.3 m of the nest
Var22 percent canopy cover within 11.3 m of the nest
###########################################################
## Guide to all of the inp/MARK files in this study:
Objectives were to assess:
1) variation in survival rates across key life stages (egg, nestling, and fledgling)
2) effects of breeding phenology and micro-habitat on NEST survival
3) influence of individual, phenological, micro-habitat, and stand-scale variables on FLEDGLING survival
## There are 12 MARK analyses
# Objective 1 has 4 analyses (and, thus, four .INP files):
i. "lifestages_eggsurvival"; only has one covariate (region aka "Var1")
ii. "lifestages_nestlingsurvival"; only has one covariate (region aka "Var1")
iii. "lifestages_fledglings1to5survival"; only has one covariate (region aka "Var1") but we test many age-specific survival patternsso there are many models
iv. "lifestages_fledglings6to30survival"; only has one covariate (region aka "Var1")
# Objective 2 has 2 analyses (and, thus, two .INP files):
v. "pawilds_nestsurvival"; Var1-22; see above
vi. "poconos_nestsurvival"; Var1-22; see above
# Objective 3 has 6 analyses (and, thus, six .INP files):
vii. "pawilds_fledglingsurvival_individual"; year (Var2), mass (Var3), fledgedate (Var4), distmoved (Var5-9), and begging (Var10-14)
viii. "pawilds_fledglingsurvival_microhabitat"; basal (Var15), unveg (Var16), nonherb (Var17),herb (Var18), snag (Var19), latdensity (Var20), vertdensity (Var21)
ix. "pawilds_fledglingsurvival_standscale"; Var22-57; see above
x. "poconos_fledglingsurvival_individual";year (Var2), mass (Var3), fledgedate (Var4), distmoved (Var5-9), and begging (Var10-14)
xi. "poconos_fledglingsurvival_microhabitat"; basal (Var15), unveg (Var16), nonherb (Var17),herb (Var18), snag (Var19), latdensity (Var20), vertdensity (Var21)
xii. "poconos_fledglingsurvival_standscale"; Var22-57; see above
####################
Helpful note: if MARK throws this warning:
Return value from WinExec = #
See this link: http://www.phidot.org/forum/viewtopic.php?f=2&t=2394
Methods
Herein are all MARK input files (which contain the analysis data), README file, and MARK .DBF and .FPT files which contain the analyses.