List of data files and the associated scripts that were used in the statistical tests and result presentations in the paper "Weak sperm differentiation in Darwin's finches".

Data files

Morphometrics.txt: Data file for the measurements of wing length and beak dimensions of Darwin's finches.

  Species: species epithet (suffix "_L" and "_Z" indicate island population, resp. "San Cristobal" and "Santa Cruz")

  Island: Name of island (in Galápagos archipelago)

  AccNo: Accession number (in the DNA bank of Natural History Museum, University of Oslo) that links all data for an individual

  Wing_length: Wing length (mm)

  Beak_length: Beak length (from skull) (mm)

  Beak_height: Beak height (at nostrils) (mm)

  Beak_width: Beak width (at nostrils) (mm)

Sperm_lengths.txt: Data file for the sperm measurements of Darwin's finches.

  Genus: Genus epithet

  Species: Species epithet

  Island: Name of island (in Galápagos archipelago)

  AccNo: Accession number (in the DNA bank of Natural History Museum, University of Oslo) that links all data for an individual

  TSL: Average total sperm length per individual (micrometer)

  HL: Average sperm head length per individual (micrometer)

  ML: Average sperm midpiece length per individual (micrometer)

  TL: Average sperm tail length (midpiece-free distal end of flagellum) per individual (micrometer)

  N: Number of sperm cells measured per individual

  SDTSL: Standard deviation of total sperm lengths per individual (micrometer)

Sperm_length_Thraupidae.txt: Data file for measurements of total sperm length for species in the family Thraupidae (incl. Darwin's finches).

  Species: Species name

  TSL: Total sperm length per individual (micrometer)

  Number: Species number (used for sorting of species in the phylogeny)

Prun64_3miss2mafNoZ_1.vcf.gz: Compressed vcf-file that contains 261 754 bi-allelic SNPs from 64 individuals (50 genomes from our own sequences and 14 genomes downloaded from NCBI-SRA). This is the input file for the phylogenetic PCA and the Admixture analyses. SNPs from the Z chromosome and from contigs smaller than 1000 bases were omitted from the genomes for SNP calling. Further details of SNP calling and filtering are given in the paper. For the PCA we used the program smartpca in the smartsnp package (https://christianhuber.github.io/smartsnp/). For the Admixture analysis we used the program ADMIXTURE (https://doi.org/10.1101/gr.094052.109).

pPCAeigen.txt: Data file with the eigenvalues for 10 principal components from the phylogenetic PCA (Figure 5AB in the paper) of 261 754 SNPs from 64 Darwin's finches.

  SampleID: Sample identity. For the first 50 samples, the first six digits denote the Accession number (in the DNA bank of Natural History Museum, University of Oslo) and the last digits reflect the identity of the sequencing run.

  Population: species name and island ("_L" is "San Cristobal", "_Z" is "Santa Cruz").

  PC1...PC10: Sample scores on the 10 respective Principal Component axes.

pPCA_Eigenvector_variance.xlsx: Output file from the phylogenetic PCA giving the variance explained by each principal component.

  #N: Principal component number ranked after the amount of variance explained

  eigenvalue: the eigenvalue of the component

  %variance: The percent of total variance explained by the component (given for the first 10 components only).

The following seven .txt-files are outputs from the ADMIXTURE analysis (Fig. 5C in the paper) that gives the Q matrix for K=2 to K=8, where "K" is the number of ancestral populations. The variables are:

  ID: sample ID, where the first three letters denote species (first two letters) and island ("B" = "San Cristobal", "Z2 = "Santa Cruz"), and the to digits denote the last two digits in the Accession number (see "pPCAeigen.txt")

  Species: species epithet

  Island: Island in the Galapagos archipelago ("L" = "San Cristobal", "Z" = "Santa Cruz")

  Prob: probability of the sample belonging to an ancestral population

  Variable: name of ancestral population

  Pop: name of population (combination of Species and Island)

qmatrix_2_VAR.txt: Q matrix for K = 2 (2 ancestral populations)

qmatrix_3_VAR.txt: Q matrix for K = 3 (3 ancestral populations)

qmatrix_4_VAR.txt: Q matrix for K = 4 (4 ancestral populations)

qmatrix_5_VAR.txt: Q matrix for K = 5 (5 ancestral populations)

qmatrix_6_VAR.txt: Q matrix for K = 6 (6 ancestral populations)

qmatrix_7_VAR.txt: Q matrix for K = 7 (7 ancestral populations)

qmatrix_8_VAR.txt: Q matrix for K = 8 (8 ancestral populations)

log.errors.txt: output file from the ADMIXTURE analysis giving the crossvalidation errors for each number of ancestral populations ("K"). These values were plotted in Fig 5D in the paper and shows the lowest CV error for K = 5.

Prune1st2000_GQ30NoMissNoZ.vcf.gz: compressed vcf-file that was the input file for the SNAPP analysis. SNAPP v. 1.6.1 (https://doi.org/10.1093/molbev/mss086) is an add-on package for the program BEAST2 v.2.7.3 (https://doi.org/10.1371/journal.pcbi.1006650). We used two individuals from each of the five ancestral populations identified by the Admixture analysis to reduce the computational load. We also employed stricter filtering (than for the PCA and Admixture analysis) to ensure high quality SNPs (details given in the paper).

Fig6_MaxCladeCredibility_tree.tre: The tree file visualized in Fig 6A in the paper. The tree file can be visualized with the FigTree software (http://github.com/rambaut/figtree/).

tree2.tre: The single MCC tree from Figure 6A for the construction of the phenogram in Figure 6B. The tree file can be visualized with the FigTree software (http://github.com/rambaut/figtree/).

TSL_5groups.csv: Trait file, giving the average total sperm length for the five ancestral populations identified by the Admixture analysis, used for construction of the phenogram in Figure 6B in the paper.

HedgesG.txt: Data file for the construction of Figure 7. Data for population pairs outside Galapagos originate from a previous paper (https://doi.org/10.1093/evolut/qpae154).

  PairNo: Running number for the population pairs

  Taxon: Species or genus name for the population pair

  *Group": Identifier for Darwin's finch population pairs (= "Galapagos") or other population pairs (= "NONGalapagos")

  DivTime_year: estimated divergence time for the population pair (years)

  Gen_time: generation time (years), data extracted from https://doi.org/10.1111/cobi.13486 and the GenLength column in their Supplementary Table 4).

  EPY: proportion of extrapair young

  Hedgesg: the divergence in total sperm length between the two population as calculated by the "Hedges' g" metric from the data in "Sperm_lengths.txt".

3paral_runs_combinedLog.txt: Combined log file from 3 parallel SNAPP runs for the MCC tree (Figure 6A in paper). The log files were combined using LogCombiner (a utility program within BEAST2), and can be read and checked in Tracer v 1.7.2 (http://beast.bio.ed.ac.uk/Tracer). This procedure was used to ensure that the effective sample sizes of all model parameters were >200 for each completed run.

  Sample: sample number for each tree (every 25 000. tree sampled)

  posterior: model parameter "posterior"

  likelihood: mode parameter "likelihood"

  prior: model parameter "prior"

  lambda: model parameter "lambda"

  treeHeightLogger: model parameter "treeHeightLogger"

  clockRate: model parameter "clockRate"

individuals5grps.txt: defines the individuals used in the SNAPP analysis.

  species: name of groups of species used in the SNAPP analysis

  individual: Sample identity, refers to the "SampleID" variable in "pPCAeigen.txt".

Constraints.txt: defines the constraints for the time divergence estimates in the SNAPP analysis.

Analytical code

script.R: the R script used for data processing, statistical analyses and figure construction. We used R v. 4.4.2 (https://www.r-project.org/)

SmartPCA.txt: script for the PCA analysis of SNPs. The script requires loading VCFtools v. 0.1.16 (https://doi.org/10.1093/bioinformatics/btr330), BCFtools v. 1.17 (https://doi.org/10.1093/gigascience/giab008) and EIGENSOFT v. 7.2.1 (https://bear-apps.bham.ac.uk/applications/2020a/EIGENSOFT/7.2.1-foss-2020a/).

Prep_Run_admixture.txt: script for running ADMIXTURE. The script requires loading VCFtools v. 0.1.16 (https://doi.org/10.1093/bioinformatics/btr330), plink v. 1.90 (https://www.cog-genomics.org/plink/), and Admixture v. 1.3.0 (https://doi.org/10.1101/gr.094052.109).

Prep_and_run_snapp.txt: script to prepare the vcf-file ("Prune1st2000_GQ30NoMissNoZ.vcf") for SNAPP and run SNAPP in BEAST2.

snapp.xml: the input script file (following the snapp_prep.rb script in https://doi.org/10.1093/sysbio/syy006) to run SNAPP in BEAST2.