DOI: 10.5061/dryad.hdr7sqvpq
title: Data from: The evolution of using shed snake skin in bird nests

description: Many species of birds use shed snake skin in nest construction, but this
 behavior remains poorly understood. Ecological context is likely key for
 understanding how this unusual, but widespread, behavior evolved. We use
 comparative and experimental approaches to suggest that the evolution of
 this behavior is mediated by nest morphology and predator communities.
 First, we reviewed the literature and found that 78 species from 22
 families have been reported to use shed snake skin in nest construction.
 All but one of these species are passerines and, using comparative
 analyses, we show that this behavior is disproportionately observed in
 cavity-nesting species. Second, we examined a subsample of North American
 species, all of which are reported to use snake skin in nest construction,
 to see if the proportion of nests with snake skin differs between cavity
 and open cup-nesting species. This analysis suggested that the proportion
 of nests with snake skin is roughly 6.5 times higher in cavity than in
 open cup-nesting species. Finally, we used a series of experiments and
 comparisons to test four hypotheses whereby snake skin could award fitness
 benefits (nest predation, nest microbiotas, nest ectoparasites, social
 signaling) and found support for the predation hypothesis. Snake skin
 reduced nest predation in cavity, but not open cup, nests. These unequal
 fitness benefits highlight different ecological conditions between nest
 morphologies and likely explains why, across species, cavity-nesting birds
 show this behavior more frequently compared to open cup-nesting birds.
description: We provide detailed methods, statistical approaches, and results
 for our three analyses of snake skin use in bird nests: (i) comparative
 data, (ii) frequency of use of snake skins in nests, and (iii)
 experimental approaches testing microbiota, ectoparasite, social
 signaling, and predation hypotheses. See Supplement for full descriptions
 of methods.
description: # Data from: The evolution of using shed snake skin in bird nests **Author
 names and contact details:** Vanya G. Rohwer 1
 [[vgr7@cornell.edu](mailto:vgr7@cornell.edu)],  Jennifer L. Houtz 2,4
 [[jhoutz@allegheny.edu\]](mailto:jhoutz@alleghany.edu), Maren N. Vitousek
 2 [[mnv6@cornell.edu\]](mailto:mnv6@cornell.edu), Robyn L. Bailey 3
 [[rb644@cornell.edu\]](mailto:rb644@cornell.edu), Eliot T. Miller 3
 [[etm45@cornell.edu\]](mailto:etm45@cornell.edu) 1\) Cornell University
 Museum of Vertebrates, Department of Ecology and Evolutionary Biology,
 Cornell University, Ithaca, NY, 14850 2\) Department of Ecology and
 Evolutionary Biology, Cornell University, Ithaca, NY, 14850 3\) Cornell
 Lab of Ornithology, Ithaca, NY, 14850 4\) Department of Biology, Allegheny
 College, Meadville, PA, 16335 **Brief summary of study:** This study
 examines a unique breeding behavior in birds: the incorporation of shed
 snake skin into nests. We probe this behavior using both comparative and
 experimental approaches. Briefly, this behavior is largely restricted to
 passerines and species that nest in cavities are reported to use this
 material most often. Experimental approaches revealed that shed snake
 reduced nest predation in cavity, but not open cup nests. This suggests
 that the fitness benefits of using shed snake skin may be unequal across
 nest morphologies, helping to explain why this behavior is most commonly
 observed in cavity nesting species. **Personnel responsible for analyses
 and data collection:** Vanya G. Rohwer: performed experiments, gathered
 data and conducted analyses for predation analyses, nest ectoparasite
 analyses, nest record card analyses, and social signaling analyses.
 Jennifer L. Houtz: performed experiments, gathered data and conducted
 analyses for nest microbiome analyses. Eliot T. Miller: gathered data and
 conducted analyses for comparative analyses. **Summary of files:** Below,
 we describe analyses, data files and their columns, and scripts used in
 analyses. **ANALYSES** are indicated by capitalized bold font, **data
 files** and **scripts** for each analysis are indicated by lower case bold
 font, and *column names* for data files are indicated by italic font.
 Scripts have in-line annotations. **PREDATION ANALYSES** This analysis
 experimentally tests if the effect of shed snake skin in reducing nest
 predation differs between cavity and open cup nests. Data for this
 experiment come from artificial nests. **R script: predation.R** This is
 the R script used for nest predation analyses. **Data file:
 predation.csv** *nest_id*: unique identifier for each nest in this
 experiment. *type*: describes nest type used in this experiment as either
 cavity or cup. *treatment*: EXP nests received 20-30 cm of shed snake
 skin; CON nests received no shed snake skin. *treatmentczeo*: binary
 coding for EXP and CON nests where EXP=1 and CON=0. *fate_1dep_0suc*:
 binary coding for nest survival where 1=nests that were depredated and
 0=nests that were not depredated and assigned as successful.
 *days_till_dep*: the number of days between the start of the experiment
 and when a nest was depredated; 14 days represents successful nests.
 *height*: a continuous variable for cup nests only; height is measured in
 inches above the ground; all nest boxes were placed 4-5 meters above the
 ground. **NEST ECTOPARASITE ANALYSES** This analysis experimentally tests
 for differences in the number of ectoparasites in cavity nests with or
 without shed snake skin. The species used in this analyses, Tree Swallow
 and Eastern Bluebird, do not normally use shed snake skin in nest
 construction. **R script: ectoparasites.R** This is the R script used for
 nest ectoparasite analyses. **Data file: ectoparasites.csv** *nest_id*:
 unique identifier for each nest in this experiment. *clutch_size*: number
 of eggs in nest. *ss*: the treatment column. Did the nest receive 20-30 cm
 of shed snake skin: Yes or No; in other words yes=EXP (nest received snake
 skin), no=CON (nest did not receive snake skin). *species*: EABL=Eastern
 Bluebird, TRES=Tree Swallow. *first_egg_date*: date the first egg was
 laid. *day_of_year*: date the first egg was laid converted to day of year
 calendar (where January 1st = day 1). *nest_survive_support_parasites*:
 sorting column; if a nest survived past nestling day 4 it is coded as
 “yes” and included in our analysis. Nests that did not survive beyond
 nestling day 4 were coded as “no” and not included in our analysis.
 *numb_fleas*: this column summarizes the total number of fleas found in
 nest dissections. *numb_ticks*: this column summarizes the total number of
 ticks found in nest dissections. *numb_big_blowfly*: this column
 summarizes blowfly larvae in their 3rd and older larval instars and
 pupated larvae. *total_blowflies*: this column summarizes numbers of all
 blowfly larvae found within a nest. **NEST RECORD CARD ANALYSES
 (proportion of snake skin use in nests among cavity- vs cup-nesting
 species)** This analysis examines for differences in the proportion of
 (unmanipulated) nests containing shed snake skin between open cup and
 cavity nesting birds, all of which have been reported to use shed snake
 skin in nest construction. All data for this analysis come from nest
 record cards at the Western Foundation of Vertebrate Zoology. **R script:
 nest_record_cards.R** This is the R script used to analyze nest record
 cards. **Data file: nest_record_cards.csv** *species*: Focal species of
 bird. *total_cards*: The total number of scanned nest record cards (1 card
 per nest) we examined and includes nests with and without descriptions of
 nesting materials. *usable_cards*: The number of cards that included a
 description of nesting materials. This column represents the total number
 of cards we used to calculate the frequency of snake skin use for a given
 species. *cards_with_SS*: The number of cards that included shed snake or
 reptile skin in the description of nesting materials. *frequency*: This
 column gives the frequency that a species was reported to use shed snake
 skin in nest construction and was calculated as:
 (cards.with.SS/usable.cards). *nest_type*: This column summarizes if a
 species nests in cavities or constructs a cup nest. **SOCIAL SIGNALING
 ANALYSES** This analysis compares clutch sizes between (unmanipulated)
 nests with and without shed snake skin, among species all of which have
 been reported to use shed snake skin in nest construction. All data for
 this analysis come from nest record cards at the Western Foundation of
 Vertebrate Zoology. **R script: social_signaling.R** This is the R script
 used for social signaling analyses. **Data file: social_signaling.csv**
 This spreadsheet contains three columns per species: “catalog_species
 code”, “snake_skin_species code”, and “clutch_size_species code”. The
 species codes are as follows: SLSP = Slaty Spinetail; BEWR = Bewick’s
 Wren; BLGR = Blue Grosbeak; GCFL=Great Crested Flycatcher; HOWR=House
 Wren; TUTI=Tufted Titmouse. As an example for one species, SLSP (Slaty
 Spinetail): *catalog_SLSP*:  This column provides the unique ID# from the
 Western Foundation of Vertebrate Zoology for each nest.
 *snake_skin_SLSP*:  This column summarizes if snake skin was reported in
 the nest (yes or no). *clutch_size_SLSP*:  This column provides clutch
 size data from nest record cards for each nest.   **COMPARATIVE ANALYSES**
 These analyses explore intraspecific variation in the proportion of nests
 that contain snake skin, using a subset of North American species, all of
 which have been reported to use snake skin in nest construction. **R
 script: script_corHMM_plusExtras.R** This is the R script that all
 comparative analyses are conducted with the following data files. **Data
 file: Stage2_Hackett_MCC_no_neg.tre** This is the tree file used in our
 comparative analyses; the tree comes from BirdTree.org, Jetz et al. 2012.
 **Data file: cavities.csv** This file is a csv of the "cavities"
 worksheet from van der Hoek 2017’s database of cavity nesting birds.
 Columns are as follows: *Order*: Order to which individual bird species
 belongs. *Family:* Family to which individual bird species belongs.
 *Name*: Common English name of species. *Scientific Name*: Scientific name
 of species. *Size (cm)*:* * Size range of cavities used for breeding.
 *Cavity nester type*: categorical variable describing if a species
 excavates their nesting cavity, uses existing cavities, etc. *Reference*:
 Sources used by van der Hoek 2017. *Obligate or Facultative*: categorical
 variable describing if a species always nest in cavities (i.e., obligate).
 *Occasional*: Sorting column indicating if a species nest “occasionally”
 in cavities. *Excavated*: Sorting column indicating species that excavate
 their cavities. *Decay-formed*: Sorting column indicating species that
 nest in natural, decay-formed cavities (i.e., cavity formed naturally by a
 rotten tree limb). *Excavator species*: Indicates potential species/groups
 of birds that initially excavated cavities that non-excavating species
 use. *Status*: Categorical variable assessing population health (i.e.,
 vulnerable, threatened, etc.). *Nearctic*: Geographic area a species is
 found. *Palearctic*: Geographic area a species is found. *Neotropical*:
 Geographic area a species is found. *Afrotropical*: Geographic area a
 species is found. *Oriental*: Geographic area a species is found.
 *Australasia*: Geographic area a species is found. **Data file:
 fixed.csv** This file summarizes 79 mismatches in taxonomy between the
 cavities data set (described above) and eBird taxonomy. Columns are as
 follows: *db.name*: Scientific name reported for a species in van der Hoek
 (2017)’s cavities datafile. *change.to*: Scientific name reported for the
 same species but using the eBird taxonomy. *direct.to.ebird*: Mismatches
 in species status between taxonomies. **Data file: fixedCavities.csv**
 This file largely mirrors the "cavities" database from van der
 Hoek 2017 (above) except mismatches in species names between taxonomies
 are now fixed. Column names follow those described above for datafile
 “cavities.csv” with the following additions: *ebird.name*: Scientific name
 recognized by eBird. *jetz.name*: Scientific name recognized by Jetz et
 al. 2012.   **Data file: currentJetzEbird3Feb2019.csv** This file helps
 reconcile conflicting taxonomies between: BirdTree.org (Jetz et al. 2012),
 the International Ornithological Congress’s world bird list (IOC), and
 eBird. *jetz.etm.assigned*: Avian taxonomy from Jetz et al. 2012.
 *IOC_7.3*: Avian taxonomy from IOC. *ebird_v2017_18Aug2017*: Avian
 taxonomy from eBird. *marshall.notes*: taxonomy notes column from master
 taxonomist, Marshall Ilif. **Data file: ebird_taxonomy_v2022.csv** This
 file is eBird’s avian taxonomy data file. *TAXON_ORDER:* A numerical value
 assigned to each species; used for sorting. *CATEGORY*: Categorical
 variable describing species status (i.e., “species” = species, “issf” =
 subspecies, “spuh” = species group only (i.e., ducks), etc.).
 *SPECIES_CODE*: 6-letter code for each species within eBird.
 *PRIMARY_COM_NAME:* Common name assigned to species. *SCI_NAME*:
 Scientific name assigned to species. *ORDER1:* Order to which species
 belong. *FAMILY*: Family to which species belong. *SPECIES_GROUP*:
 Grouping variable by species category (i.e., all Rhea species are assigned
 “Rheas”, all Duck species are assigned “Ducks”, etc.). *REPORT_AS*:
 Species code for subspecies that lack official species status. **Data
 file: HBW3.0-ebirdv2018match4Feb2019.csv** This data file helps reconcile
 differences in taxonomy between Handbook of Birds of the World (HBW)/eBird
 (Clements) and Avibase. *orig_sort*: Sorting column based on numerical
 value. *AvibaseID*: Unique identifier for each bird species within the
 Avibase taxonomy. *Avibase_latin_name*: Scientific name for bird species
 as assigned in Avibase. *cat_hbw*: Categorical variable describing species
 status between Avibase and Clements taxonomy (i.e., grp = group (as in
 “Ducks”), sp = species (as in “Northern Pintail”), etc.). *TAXON_nid*:
 Unique numerical identifier for each bird species. *hbw_latin*: Scientific
 name for species assigned in Handbook of Birds of the World (HBW).
 *hbw_english_for_eBird*: Common name for species assigned in HBW.
 *HBW-Clem*: taxonomic congruency between HBW and Clements taxonomy.
 *match*: sorting column indicating matches in taxonomic congruency between
 HBW and Clements taxonomy. *clements_latin*: Scientific name for species
 assigned by Clements. *clements_english*: English names for species
 assigned by Clements. *eBird code*: unique, species identifiers in eBird
 taxonomy. *cat_Clements*: species status within Clements taxonomy (i.e.,
 grp = group, sp = species, hybr = hybrid, etc.). *cl_sort*: unique
 identifier for sorting Clements taxonomy. *species (HBW or Clements)*:
 sorting column to identify species recognized by HBW or Clements (1 =
 recognized species). **Data file: fromVanya23Mar2023.csv** This file
 summarizes data for all the species reported to use shed snake skin in
 bird nests. *Species*: Common English names of birds. *Scientific names*:
 Scientific names of birds. *Family*: Family to which birds belongs.
 *Suboscines/Oscines*: categorical variable; both clades belong to the
 Passeriformes order and are distinguished by how they learn/inherit their
 songs. *nest type*: Categorical variable describing the type of nest
 constructed by each species. *placement of skin*: Categorical variable
 describing where shed snake skin is placed within a nest. *type of skin*:
 Categorical variable describing source of skin (snake or lizard). *sex
 building nest*: If known, which member of the pair builds the nest (male,
 female, both). *estimate of frequency of skin use:* If provided in the
 literature, the frequency of nests within a species reported to use snake
 skin. *source*: Literature documenting use of snake skin for each species.
 **Data file: snakeSppToFix.csv** This file summarizes 20 species reported
 to use shed snake skin (from above data file “fromVanya23Mar2023.csv”)
 where taxonomies between HBW and Jetz et al. 2012 are inconsistent. This
 data file has only a single column to ID the species that need updates to
 their names. *x:* A column summarizing species with mismatches in
 taxonomy. **Data file: snakeSppFixed.csv** This file provides the updated
 taxonomies for the 20 species reported in “snakeSppToFix.csv”. *orig:*
 Initial taxonomy that was inconsistent with Jetz et al. 2012. *new*:
 Corrected taxonomy for these 20 species. **MICROBIOME ANALYSES** This
 analysis explores how the nest microbiome differs across a) unmanipulated
 nests of multiple bird species that vary in their nest type, b) different
 nest types in a single species (American Robin), and c) nests of Eastern
 Bluebirds and Tree Swallows that had snake skins experimentally placed in
 the nest.   **QIIME2 script: microbiome_qiime2_code.txt** This file
 contains the code that is used in terminal/command line in QIIME2 (v
 2021.11) for the first half of microbiome analyses. **R script:
 microbiome.R** This is the R script that is used after the QIIME2 steps
 for the remainder of the nest microbiome analyses.   **Data files for
 microbiome analyses in QIIME2:**   **FASTQ microbiome sequences** These
 are the raw demultiplexed forward and reverse sequences for each
 microbiome sample are available as fastq.gz files. These are uploaded to
 QIIME2 using the microbiome_sequence_manifest.csv file.   **Data file:
 microbiome_sequence_manifest.csv** This is the manifest file that matches
 the file names of the raw FASTQ sequences to the sample names for
 importing them into QIIME2. Columns are as follows: *sample-id*: sample
 name that corresponds to samples names in the microbiome metadata file
 "microbiome.csv" that is used in QIIME2 and R analyses.
 *absolute-filepath*: where the user will input the absolute filepath name
 for each sequence. *direction*: direction of the read (forward or
 reverse). **Data files for microbiome analyses in R:** **Data file:
 unrarefied_ASV_table.csv** This is the amplicon sequence variant (ASV)
 table that is outputted from QIIME2 and uploaded to R using the phyloseq
 package. Each column represents a sample name. *ASVID*: unique code
 assigned to each ASV. **Data file: taxonomy_microbiome.csv** This is the
 taxonomy assigned to each ASV that is outputted from QIIME2 and uploaded
 to R using the phyloseq package. *ASVID*: unique code assigned to each
 ASV. *Taxon*: microbial taxonomic assignments (phylum to genus) for each
 ASV **Data file: tree_microbiome.nwk** This is the microbial rooted tree
 that is outputted from QIIME2 and uploaded to R using the phyloseq
 package. **Data file: microbiome.csv** This is the metadata for each
 microbiome sample (rows are sample names that correspond to names of
 sequences found in the "microbiome_sequence_manifest.csv" file).
 Columns are as follows: *sample_name*: sample name that corresponds to raw
 sequences within the "microbiome_manifest.csv" file. *nest*:
 unique identifier for each nest in this experiment.
 *incubation_time_point*: early (EI) or late (LI) incubation stage at the
 time sample was collected. *treatment_incubation_timepoint*: combination
 of treatment of snake skin (EXP) or control (CON) for nests in the snake
 skin placement experiment and early (EI) or late (LI) incubation stage at
 the time the sample was collected. *date_extracted*: date that DNA was
 extracted from the swab. *sample_or_control*: indicates if the sample is a
 real sample or a negative control (used for decontamination step in R).
 *quant_reading*: DNA quantification (ng/ul) (used for decontamination step
 in R). *site*: field site where the nest was located. *species*: bird
 species of the nest where the swab was taken. *experiment*:
 "species_swab" refers to nests that were only swabbed once
 without any snake skin manipulation; "snake_skin_experiment"
 refers to Eastern Bluebird and Tree Swallow nests that were part of the
 snake skin manipulation experiment. *treatment*: treatment of snake skin
 (EXP) or control (CON) for nests in snake skin placement experiment
 *nest_type*: summarizes if a species nests in cavities or constructs a cup
 nest. *placement*: where the nest was physically placed by the birds.
 *egg_number*: number of eggs within the nest where the swab was taken.
 *swab_date*: date that the sample was collected. *date_found*: date that
 the nest was found.