DOI: 10.5061/dryad.rbnzs7hgh
title: Male song structure predicts offspring recruitment to the breeding population in a migratory bird

description: Bird song is a classic example of a sexually selected trait, but much of
 the work relating individual song components to fitness has not accounted
 for song typically being composed of multiple, often-correlated
 components, necessitating a multivariate approach. We explored the role of
 sexual selection in shaping complex male song of house wrens (Troglodytes
 aedon) by simultaneously relating its multiple components to fitness using
 multivariate selection analysis, which is widely used in insect and anuran
 studies but not in birds. The analysis revealed significant variation in
 the form and strength of selection acting on song across different
 selection episodes, from nest-site defense to recruitment of offspring to
 the breeding population. Males that sang more song typically employed in
 close communication sired more offspring that were subsequently recruited
 to the breeding population than those that sang far-communication song.
 However, this relationship was not consistent across earlier selection
 episodes, as evidenced by non-linear selection acting on these song
 components in other contexts. Collectively, our results present a complex
 picture of multivariate selection on male song structure that would not be
 evident using univariate approaches and suggest possible trade-offs within
 and among song components at different points of the breeding
 season. 
description: # Male song structure predicts offspring recruitment to the breeding
 population in a migratory bird *** This data set includes the files
 relevant to house wren (*Troglodytes aedon*) transcriptome assembly and
 code used in bioinformatic analyses, as well as the files necessary to run
 the paternity analysis, summarize song, and conduct canonical analyses
 integral to our study concerning the sexual selection of male song in
 northern house wrens. Rachael A DiSciullo(1)\*, Anna M Forsman(2), Robert
 R Fitak(2), John Hunt(3), Pirmin Nietlisbach(1), Charles F Thompson(1),
 Scott K Sakaluk(1) (1)Behavior, Ecology, Evolution, and Conservation
 Section, School of Biological Sciences, Illinois State University, Normal,
 Illinois, USA (2)Department of Biology, University of Central Florida,
 Orlando, Florida, USA (3)School of Science, Western Sydney University,
 Penrith, New South Wales, Australia \*corresponding author:
 radisci@ilstu.edu ## Description of the data and file structure ## Files
 for transcriptome assembly NOTE: The md5sum is also given for each file
 except "Bioinformatics and Code.pdf". You can verify that you do
 not have a corrupted file by matching the md5sum for each file given below
 with the output of UNIX terminal commands like "md5 file" or
 "md5sum file". The various file formats are described in
 Appendix 1 immediately following the list of files. FILE: Trinity.fasta
 MD5SUM: 8b07883b45f799ccffef2880844b6342 DESCRIPTION: This file contains
 the transcriptome assembly produced using trinity. FORMAT: FASTA FILE:
 Trinity.SuperTrans.fasta MD5SUM: 96411710a67fbca96f3fcec148f57526
 DESCRIPTION: This file contains the transcriptome assembly after being
 collapsed into SuperTranscripts. FORMAT: FASTA FILE: final.thinned.tsv
 MD5SUM: 5059f31f2abd2d67bf7453b7fc7ae7ca DESCRIPTION: This file contains
 information about the final set of SNPs and associate flanking region that
 was submitted for the final iPLEX assay development. The columns are:
 SuperTranscript, Position, SNP\_ID, SNP\_Set, bTaeGut1.4\_Chrom,
 bTaeGut1.4\_start, bTaeGut1.4\_end, Sequence FORMAT: TSV FILE: HOWR-1.html
 MD5SUM: d559aa104e96b5a28de27f0e92c21c6a DESCRIPTION: The results of all
 the raw read cleaning and adapter removal using the fastp software.
 FORMAT: HTML FILE: HOWR-2.html MD5SUM: d0c8764427adbb32db5cc950467a8e98
 DESCRIPTION: The results of all the raw read cleaning and adapter removal
 using the fastp software. FORMAT: HTML FILE: filtered\_output2.vcf.gz
 MD5SUM: 5e9358c00868215318a0ab5ed1ff2329 DESCRIPTION: This file contains
 all the SNPs identified among the Super Transcripts. It is recommended to
 only use SNPs with the "PASS" label for subsequent analyses.
 FORMAT: VCF FILE: Bioinformatics Methods and Code DESCRIPTION: This file
 contains supplementary bioinformatics methods and code. FORMAT: PDF ##
 Appendix 1: File Formats Format: FASTA This format represents DNA
 sequences without quality scores. See
 https://en.wikipedia.org/wiki/FASTA\_format for more specific information
 Format: TSV This format stores tabulated data in plain text format Each
 line of this format is a record, with fields, or columns separated by a
 tab ("\\t"). Can be opened in any text editor or spreadsheet
 software, e.g. MS Excel Format: HTML HTML (Hyper Text Markup Language) is
 the format for web pages created for display in browsers. These files Can
 be opened in any web browser. Format: VCF This is the standard format for
 representing genomic variation data. It is a tab-delimited text file that
 also contains a header. All header lines begin with a "#". The
 complete VCF specification can be found at the following link:
 http://samtools.github.io/hts-specs/VCFv4.2.pdf The format represents a
 VCF file that has been compressed (.gz). Most computers can uncompress
 this file into a file by double-clicking automatically. In most unix
 machines, it can easily be unpacked from the command line using: gunzip
 file.vcf.gz ## Files for paternity analysis, summarising song, and
 conducting canonical analyses FILE: DiSciullo\_et\_al\_HOWR\_MSA\_Rcode.R
 DESCRIPTION: This file contains the R code that allows one to conduct the
 paternity analysis, summarise song, and conduct the canonical analyses.
 FILE: ADULTS\_2019-2022.csv DESCRIPTION: This file contains all adult
 house wrens captured or visually sighted on the Mackinaw Study Area from
 the 2019-2022 breeding seasons (April-August). The columns are BANDNO
 (unique number of aluminum band), NEST (nest of capture or sighting), SEX
 (M=male, F=female), DATE (day of year of capture or sighting), COLR (color
 of bands on right leg, top to bottom), COLL (color of bands on left leg,
 top to bottom), NOTES, YEAR FILE: Agena\_Genotyping\_PCR\_Conditions.csv
 DESCRIPTION: This file contains the PCR conditions, and SNP and oligo data
 from the University of Minnesota Genomics Center Agena Bioscience iPLEX
 Genotyping. FILE: DiSciullo\_et\_al\_HOWR\_MSA\_fitness.csv DESCRIPTION:
 This file contains fitness proxy information for the 63 focal males from
 the 2018 breeding season (except recruitment of young, which is determined
 in subsequent breeding seasons). The columns are maleID (unique number of
 aluminum band), nest (nest of capture or sighting), num\_nest\_sites
 (number of nests at which a male was captured or sighted defended),
 time2paired\_ctrl4Msettle (the regression of average male settlement on
 average number of days between male and female settlement), WPYsired
 (number of within-pair young sired), WPYandEPYsired (number of within- and
 extra-pair young sired), num\_sired\_yg\_recruited (number of young
 recruited to the breeding population in 2019 and 2020) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_fitness\_and\_song\_factor.csv DESCRIPTION:
 This file contains fitness proxy information for the 63 focal males and
 the extracted values of the four song factors from the factor analysis.
 The columns are maleID (unique number of aluminum band), nest (nest of
 capture or sighting), num\_nest\_sites (number of nests at which a male
 was captured or sighted defended), time2paired\_ctrl4Msettle (the
 regression of average male settlement on average number of days between
 male and female settlement), WPYsired (number of within-pair young sired),
 WPYandEPYsired (number of within- and extra-pair young sired),
 num\_sired\_yg\_recruited (number of young recruited to the breeding
 population in 2019 and 2020), Close.MLCF1 (factor ML1), Complex.MLCF2
 (factor ML3), Perform.MLCF3 (factor ML2), Far.MLCF4 (factor ML4) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_focal\_male\_nests.csv DESCRIPTION: This
 file contains a list of all nests at which a male was captured or sighted
 defended in the 2018 breeding season. The columns are nest (nest of
 capture or sighting), maleID (unique number of aluminum band), COLR (color
 of bands on right leg, top to bottom), COLL (color of bands on left leg,
 top to bottom) FILE: DiSciullo\_et\_al\_HOWR\_MSA\_genotypes.csv
 DESCRIPTION: This file contains the genotypes for 807 house wrens (104
 males, 84 females [four of whom have no genotype--all loci set to NA], and
 619 offspring [two of whom have no genotype--all loci set to NA]) for the
 paternity analysis. The first column "id" is the unique number
 of aluminum band. All other columns are two alleles of one locus (Name\_1
 and Name\_2). Loci at which genotyping was unsuccessful have NA. FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_MCMCped.csv DESCRIPTION: This file is the
 output from the MCMC model. The column names are id (unique number of
 aluminum band of the 619 offspring), dam (social.mother of the offspring
 as supplied in the model), sire (the most likely sire from the model),
 prob (posterior probability of assignment of father to offspring) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_phenotypes.csvDESCRIPTION: This file
 contains the phenotypes for 807 house wrens (104 males, 84 females, and
 619 offspring for the paternity analysis. The columns are id (unique
 number of aluminum band), sex (Male, Female, or NA if offspring),
 social.father (unique number of aluminum band of father who tended to
 offspring in the nest), social.mother (unique number of aluminum band of
 mother who tended to offspring in the nest), offspring (0=adult,
 1=offspring), nest (nest of social family), notes, long (average x
 coordinate of all nests at which the male was captured or sighted), lat
 (average y coordinate of all nests at which the male was captured or
 sighted), link.father (unique identified to connect social.father value in
 the same row to id value of the male in another row), link.mother (unique
 identified to connect social.mother value in the same row to id value of
 the male in another row) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_putative\_parents.csv DESCRIPTION: This file
 is the output from the MCMC model with the social father information
 added. The column names are id (unique number of aluminum band of the 619
 offspring), nest (nest of social family), social.mother (unique number of
 aluminum band of mother who tended to offspring in the nest), dam
 (social.mother of the offspring as supplied in the model), social.father
 (unique number of aluminum band of father who tended to offspring in the
 nest), sire (the most likely sire from the model), prob (posterior
 probability of assignment of father to offspring), match.fat.90 (TRUE if
 social.father=fat.90, else FALSE), fat.90 (unique number of aluminum band
 of sire when prob &gt;0.9, else "unk" for unknown) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_Raven\_Pro\_selections.csv DESCRIPTION: This
 file contains the concatenated output from Raven Pro 1.6 selection files,
 to summarise song parameters. The column names are maleID (unique number
 of aluminum band), recording (name of .wav recording file), day (day of
 year on which recording was gathered), duration (length of the recording
 in min), name (initials of individual who recorded the file), nest (active
 nest at which the recording was gathered), status (breeding stage
 [pre=pre-pairing]), fem (Y=female was sighted during the recording, N=no
 female was sighted during the recording, unk=unknown if the female was
 present during the recording), scored (date the recording file was
 quantified in Raven Pro 1.6), `Begin Time (s)` (time in sec that the
 selection begins), `End Time (s)`(time in sec that the selection ends),
 `BW 90% (Hz)`(the difference between the frequencies [Hz] that divide the
 selection into two frequency intervals that contain 5% and 95% of the
 energy), `notes to self`, section (intro=introduction section,
 terminal=terminal section), element (name of the note; all uppercase
 letters are notes in the introduction and all lowercase letters are notes
 in the terminal section), introNum (overall number of the introduction
 sections within the file, labelled sequentially), termNum, (overall number
 of the terminal sections within the file, labelled sequentially), songNum
 (overall number of the song within a file including intro-only,
 terminal-only, or intro+terminal [full-song], labelled sequentially),
 introOnly (Y=song is only composed of introduction section notes, blank
 otherwise), termOnly (Y=song is only composed of terminal section notes,
 blank otherwise) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_rel\_recr\_eigenvalues.CSV DESCRIPTION: This
 file contains the extracted values of the four song factors (Close.MLCF1,
 Complex.MLCF2, Perform.MLCF3, Far.MLCF4), the relative recruitment
 (rel.recr), and the indivdual scores for each eigenvector of the canonical
 analysis comparing song factors to recruitment (m1, m2, m3, m4). The
 column names are Close.MLCF1, Complex.MLCF2, Perform.MLCF3, Far.MLCF4,
 rel.recr, m1, m2, m3, m4. FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_rel\_time2pair\_eigenvalues.CSV DESCRIPTION:
 This file contains the extracted values of the four song factors
 (Close.MLCF1, Complex.MLCF2, Perform.MLCF3, Far.MLCF4), the relative
 time-to-pairing (rel.time2pair), and the indivdual scores for each
 eigenvector of the canonical analysis comparing song factors to
 time-to-pairing (m1, m2, m3, m4). The column names are Close.MLCF1,
 Complex.MLCF2, Perform.MLCF3, Far.MLCF4, rel.time2pair, m1, m2, m3, m4.
 FILE: DiSciullo\_et\_al\_HOWR\_MSA\_song\_and\_bout.csv DESCRIPTION: This
 file contains the summarised sequences of notes for each song within a
 file and when (in sec) the song starts and ends within the file, for
 song-type renaming and bout number labelling. The columns are recording
 (name of .wav recording file), songNum (overall number of the song
 including intro-only, terminal-only, or intro+terminal [full-song] within
 the file, labelled sequentially), song (notes of the song, separated by
 spaces), min.start (time in sec in the recording when the song started),
 max.end (time in sec in the recording when the song ended), intersong.post
 (time between consecutive songs (n and n+1) in sec), bout.label (X=bout
 ends here [intersong.post&gt;30sec]) FILE:
 DiSciullo\_et\_al\_HOWR\_MSA\_song\_and\_bout\_manual\_edit.csv
 DESCRIPTION: This file contains the summarised sequences of notes for each
 song within a file and when (in sec) the song starts and ends within the
 file, as well as the manually entered song-type condensing steps and the
 bout number. The column names are recording (name of .wav recording file),
 songNum (overall number of the song including intro-only, terminal-only,
 or intro+terminal [full-song] within the file, labelled sequentially),
 song (notes of the song, separated by spaces), song.squish (song with
 repeated notes removed), song.squish.syll (song.squish with syllables
 identified but true order of note and syllable presentation maintained),
 song.squish.syll.conden (condensed version of song.squish.syll with extra
 notes removed and song-type defined as note and syllable presentation
 order, regardless of number of times a note or syllable was repeated
 [including half presentations of 2-note syllables]), min.start (time in
 sec in the recording when the song started), max.end (time in sec in the
 recording when the song ended), intersong.post (time between consecutive
 songs (n and n+1) in sec), bout.label (X=bout ends here
 [intersong.post&gt;30sec]), bout.num (sequential number of bout within
 a recording) FILE: DiSciullo\_et\_al\_HOWR\_MSA\_song\_parameters.csv
 DESCRIPTION: This file contains the summarised song parameters for use in
 the factor analysis. The column names are recording (name of .wav
 recording file), nest (active nest at which the recording was gathered),
 status (breeding stage [pre=pre-pairing]), maleID (unique number of
 aluminum band), total\_songNum (total number of songs/recording),
 avg\_notesD\_per\_song (average number of distinct notes/song/recording)
 avg\_total\_notes\_per\_song (average total number of
 notes/song/recording), avg\_song\_duration (average song
 duration/recording), avg\_element\_rate (average number of
 notes/song/recording), avg\_bandwidth (average 90% frequency bandwidth of
 notes/song/recording), avg\_intro\_duration (average duration of the
 introduction section/recording), avg\_term\_duration (average duration of
 the terminal section/recording), avg\_term\_rate (average number of notes
 in the terminal section only/song/recording), total\_bout (total number of
 bouts/recording), avg\_rate\_within\_bout (average number songs/sec within
 a bout per recording), n.distinct.songtype (total number of distinct
 songs/recording), prop.unique.songtype (proportion of all songs within the
 recording that are distinct), consistency (1 minus the number of changes
 between successive song-types divided by the total number of songs sung)
 FILE: DiSciullo\_et\_al\_HOWR\_MSA\_strategy.csv DESCRIPTION: This file
 contains the mating strategy used by each of the 63 focal males. The
 columns are strategy (seq=sequentially monogamous, mon=singly monogamous,
 pol=socially polygynous) FILE: DiSciullo\_et\_al\_HOWR\_MSA\_time2pair.csv
 DESCRIPTION: This file contains the infomration necessary to calculate the
 time-to-pairing proxy that accounts for day of year. The column names are
 nest (active nest at which the recording was gathered), earliest.M.settle
 (earliest possible day of year the male added &gt;=50% sticks),
 latest.M.settle (latest possible day of year the male added &gt;=50%
 sticks), avg.M.settle (average of earliest.M.settle and latest.M.settle),
 earliest.F.settle (earliest possible day of year the female added soft
 lining material), latest.F.settle (latest possible day of year the female
 added soft lining material), avg.F.settle (average of earliest.F.settle
 and latest.F.settle), time2pair (difference between avg.F.settle and
 avg.M.settle), maleID (unique number of aluminum band), COLR (color of
 bands on right leg, top to bottom), COLL (color of bands on left leg, top
 to bottom) FILE: NS\_x.csv DESCRIPTION:This file contains the extracted
 values of the four song factors for each of the 63 focal males for
 canonical analysis. FILE: NS\_y.csv DESCRIPTION: This file contains the
 five fitness proxies for each of the 63 focal males for canonical
 analysis. ## Sharing/Access information Links to other publicly accessible
 locations of the data: All raw sequencing data can be obtained through the
 NCBI BioProject database, under accession PRJNA631786 *
 https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA631786 The computer
 code and commands used to generate the transcriptome results are available
 at Bob Fitak's GitHub page. Thanks for promoting data-sharing!!! Bob
 Fitak 04/11/2023 * https://github.com/rfitak/HouseWren\_Transcriptome