DOI: 10.5061/dryad.83bk3j9z1
title: Song and genetic divergence within a subspecies of white-crowned sparrow (Zonotrichia leucophrys nuttalli)

description: ​Animal culture evolves alongside genomes, and the two modes of
 inheritance—culture and genes—interact in myriad ways. For example, stable
 geographic variation in culture can act as a reproductive barrier, thereby
 producing genetic divergence between “cultural populations.” White-crowned
 sparrows (Zonotrichia leucophrys) are a well-established model species for
 bird song learning and cultural evolution, as they have distinct,
 geographically discrete, and culturally transmitted song types (i.e., song
 dialects). In this study, we tested the hypothesis that divergence between
 culturally transmitted songs drives genetic divergence within Nuttall’s
 white-crowned sparrows (Z. l. nuttalli). In accordance with sexual
 selection theory, we hypothesized that cultural divergence between mating
 signals both preceded and generated genetic divergence.We characterized
 the population structure and song variation in the subspecies and found
 two genetically differentiated populations whose boundary coincides with a
 major song boundary at Monterey Bay, California. We then conducted a song
 playback experiment that demonstrated males discriminate between songs
 based on their degree of divergence from their local dialect. These
 results support the idea that discrimination against non-local songs is
 driving genetic divergence between the northern and southern populations.
 Altogether, this study provides evidence that culturally transmitted bird
 songs can act as the foundation for speciation by sexual selection.
description: # Song and genetic divergence within a subspecies of white-crowned sparrow
 (*Zonotrichia leucophrys nuttalli*) [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.83bk3j9z1) These are white-crowned
 sparrow (*Zonotrichia leucophrys*) data from Luo et al. 2024. The data are
 in three parts: genetic data, song recordings and trait data, and playback
 experiment data. The genetic data include two peripatric white-crowned
 sparrow subspecies (*Z. l. nuttalli* and *Z. l. pugetensis*), and the song
 and playback experiment data are just from *Z. l. nuttalli*.
 **Corresponding author information:** Amy Luo
 [aluo@vols.utk.edu](mailto:aluo@vols.utk.edu) Department of Ecology and
 Evolutionary Biology University of Tennessee, Knoxville This dataset
 includes three components: genetic data, song data, and playback
 experiment results. For the genetic and song data, genetic or acoustic
 dissimilarity was calculated between all samples. These dissimilarities
 were used to map geographic boundaries between groups, so there are files
 containing coordinates for each sample. There is also a second song
 dataset used to run a PCA. The last file contains results of a playback
 experiment that was run to determine whether males discriminated between
 songs with varying degrees of acoustic dissimilarity. ## List of files
 This is a brief list of all the files in this dataset. For more details on
 each file, see the last section of this document, "Descriptions of
 data." * dropped_samples_maf05_missloc80.recode.vcf. Genetic data.
 Filtered single nucleotide polymorphisms (SNPs) data with 26977 loci from
 263 individuals derived from genotype-by-sequencing (GBS) reads. *
 Fst_matrix.csv. Genetic data. Pairwise Fst values between all sampled
 localities. * genetic_sample_coordinates.csv. Geographic data for genetic
 samples. GPS points where each genetic sample was collected. This sheet
 includes all samples in dropped_samples_maf05_missloc80.recode.vcf and the
 samples that were dropped in the filtering process. *
 song_dissimilarity_dataset_recordings. Song data. Folder with the 175
 songs (each wav file contains one song) comprising the song dissimilarity
 dataset. * song_dissimilarity_sampling_coordinates.csv. Geographic data
 for song data. GPS points where each song in the song dissimilarity
 dataset was recorded. * song_trait_dataset.csv. Song data. Second song
 dataset. Trait measurements of the 113 songs used in the PCA. *
 playback_experiment_raw_data.xlsx. The raw data from the playback
 experiment. ## Usage notes * The csv and xlsx files are spreadsheets that
 can be accessed with, for example,
 [LibreOffice](https://www.libreoffice.org). * wav files in the
 song_dissimilarity_dataset_recordings folder can be opened with any
 software created to play music or bioacoustics recordings, though we
 viewed them in [Audacity](https://www.audacityteam.org). * vcf files can
 be viewed in text editors like [Sublime
 Text](https://www.sublimetext.com). vcf files, including the one in this
 dataset, are often large. They may take a moment to load. ##
 Sharing/Access Information Some of the songs in the song dissimilarity
 dataset were extracted from recordings on
 [Xeno-Canto](https://xeno-canto.org) ## Descriptions of data All the data
 are from the West Coast of the United States, in the coastal scrub habitat
 of these two subspecies of white-crowned sparrow. The genetic data were
 collected in 2004, 2005, and 2014. Songs from the song dissimilarity
 dataset were recorded 2010-2022, and songs from the song trait dataset
 were recorded 2004-2014. The playback experiment was run in the spring of
 2022. ### Details on genetic data
 **dropped_samples_maf05_missloc80.recode.vcf** Includes 251 individuals
 from *Z. l. nuttalli*, *Z. l. pugetensis*, and their hybrids. It also
 includes 12 individuals from outgroups, which are two other white-crowned
 sparrow subspecies (*Z. l. gambellii* and *Z. l. oriantha*) and the
 closely-related golden-crowned sparrow (*Z. atricapilla*). Biallelic SNPs
 were called using the STACKS pipeline. To produce
 dropped_samples_maf05_missloc80.recode.vcf, we filtered out SNPs with a
 minor allele frequency of less than five percent and individuals missing
 over 80 percent of loci. **Fst_matrix.csv** Using the filtered data, we
 calculated the pairwise Fst between all the localities sampled, including
 *Z. l. pugetensis*, *Z. l. nuttalli* and their hybrid zone. We used the
 hierfstat package in R to calculate these values, which compare genetic
 variation within and between populations. Each cell in the matrix contains
 the pairwise dissimilarity between the localities in that row and column;
 higher values indicate high between-population variation, relative to
 within-population variation. **genetic_sample_coordinates.csv** Contains
 three columns: * **key:** The ID of the genetic sample. * **lat:**
 Latitude. * **lon:** Longitude. ### Details on song data
 **song_dissimilarity_dataset_recordings** Contains wav files that were
 used to calculate acoustic dissimilarity across song dialects using a
 dynamic time warping algorithm implemented in the warbleR package in R.
 Each wav file contains an individual song. The acoustic dissimilarity was
 used to estimate the presence and strength of cultural boundaries across
 the *Z. l. nuttalli* range.
 **song_dissimilarity_sampling_coordinates.csv** Contains coordinates for
 the songs in song_dissimilarity_dataset_recordings, with these variables:
 * **site:** The locality and dialect of the recording. *
 **genetic_group:** The genetic population of the male that sang the song,
 as determined by the genetic analyses in this study. * **male:** The ID of
 the singer. * **song:** The ID of the song. * **lat:** Latitude. *
 **lon:** Longitude. * **year:** The year that the song was recorded.
 **song_trait_dataset.csv** Includes all the songs and measurements used to
 run the song trait PCA. Each row contains the traits for one song, and the
 variables are as listed below: * **bird:** The ID of the male that sang
 the song. * **band:** The USGS Bird Banding Lab band number. Some of the
 birds were banded before recording. If they were, this column contains
 their band number. * **group:** The genetic group of the singer, as
 determined by the genetic analyses in this study. There is a northern
 population, southern population, and an area in which the two populations
 meet and admix. * **song_length:** Length of the entire song, in seconds.
 * **whistle_length:** Length of the introductory whistle, in seconds. All
 white-crowned sparrow songs start with a whistle note. *
 **avg_com_length:** Average length of each complex note, in seconds. Not
 all song dialects have complex notes, but many have one or multiple
 complex notes. This measure is the average length of each complex note,
 when there are multiple. * **trill_length:** Length of the trill, in
 seconds. Most, but not all, songs have trills, or rapid simple notes. This
 is the length of the *entire* trill. * **avg_trill_dur:** Average length
 of each trill note, in seconds. This is the average length of *each* trill
 note in the trill. * **trill_rate:** Notes per second in the trill. *
 **song_bandwd:** Frequency bandwidth of the entire song (difference
 between maximum and minimum frequencies), in Hz. * **com_bandwd:**
 Frequency bandwidth of the complex notes (difference between maximum and
 minimum frequencies), in Hz. * **trill_bandwd:** Frequency bandwidth of
 the trill (difference between maximum and minimum frequencies), in Hz. *
 **song_max_f:** Maximum frequency of the entire song, in Hz. *
 **song_min_f:** Minimum frequency of the entire song, in Hz. *
 **com_max_f:** Maximum frequency of the complex notes, in Hz. *
 **com_min_f:** Minimum frequency of the complex notes, in Hz. *
 **trill_max_f:** Maximum frequency of the trill, in Hz. * **trill_min_f:**
 Minimum frequency of the trill, in Hz. * **whistle_dom_f:** Dominant
 frequency of the introductory whistle, in Hz. * **term_buzz_length:**
 Length of the terminal buzz, in seconds. Not all song dialects have a
 terminal buzz. ### Details on the playback experiment data Each male was
 given three song stimulus treatments, given three-minute playback periods,
 and up to 15 males were tested at each site (two sites each in the
 northern population, southern population, and admixture zone). All the
 data from this experiment are in playback_experiment_raw_data.xlsx. Below
 is a description of the sheets in this file. The "raw_data"
 sheet contains the dataset used for analysis. Two localities
 ("site") were tested in each genetic population/admixture zone
 ("genetic_group"). Each male is represented in three rows,
 showing the results from each treatment. "order" indicates the
 position of the treatment in the sequence of three stimuli. In the
 treatment column, "same_group" is a song from the same genetic
 population but not the local dialect, and "different_group" is a
 song from the other population. For males at the admixed sites, songs from
 a different group were drawn from either the northern or southern
 population, as indicated in "admix_treatment". The variables are
 listed below: * **genetic_group:** The genetic group of the focal male. *
 **site:** The location of the experimental trial, and also the dialect of
 the focal male. * **date:** Date that the male was tested. * **order:**
 Whether the treatment was played first, second, or third. * **treatment:**
 The name of the treatment, which is the relationship between the focal
 male and the stimulus dialect. * **fst:** Fst, a population-level measure
 of genetic distance between the focal male's locality and the
 stimulus' origin locality * **songs:** The number of times the male
 sang in response to the stimulus during the playback period. *
 **flights:** The number of times the male flew over or at the speaker. *
 **distance:** The average distance between the male and the speaker, in
 meters, during the playback period. * **post_distance:** The average
 distance between the male and the speaker, in meters, for three minutes
 after the playback period. The "distance" sheet contains the
 individual distance estimates at every 10 or 20 second interval. Distances
 were estimated at 10 second intervals during the playback period and 20
 second intervals in the post-playback period, then averaged across the
 measurement period. These averages are the values found in
 "raw_data" Columns C-T are the distance estimates during the
 playback period, and columns U-AC are the distance estimates during the
 post-playback period. The "toss" and "toss_distances"
 sheets are the same as "raw_data" and "distances",
 respectively. These trials were not used in the analysis because of some
 error in the field (e.g., setting up on a territorial border between two
 males or possibly testing the same male twice on different days).