DOI: 10.5061/dryad.m905qfv9k
title: Data from: Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)

description: Historical specimens from museum collections provide a valuable source of
 material also from remote areas or regions of conflict that are not easily
 accessible to scientists today. With this study, we are providing a
 taxon-complete phylogeny of snowfinches using historical DNA from whole
 skins of an endemic species from Afghanistan, the Afghan snowfinch,
 Pyrgilauda theresae. To resolve the strong conflict between previous
 phylogenetic hypotheses, we generated novel mitogenome sequences for
 selected taxa and genome-wide SNP data using from ddRAD sequencing for all
 extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and
 for an extended intraspecific sampling of the sole Central and Western
 Palearctic snowfinch species (Montifringilla nivalis).
description: We extracted DNA from 40 samples of snowfinches from all eight
 species of the three genera (<em>Montifringilla</em>,
 <em>Onychostruthus,</em> and <em>Pyrgilauda</em>)
 and one further sample of the rock sparrow, <em>Petronia
 petronia</em>. All samples were either frozen blood or tissue
 samples preserved in ethanol or preserving buffer except two toe pad
 samples taken from two historical specimens of the Afghan
 snowfinch, <em>P. theresae</em>. We generated whole
 mitochondrial genomes for this species and representatives from the two
 other snowfinch genera using specific protocols for museum material. To
 complete a previous single-marker data set, we amplified a 1079-bp-long
 cytochrome-<em>b</em> fragment for 19 samples using the primer
 combination of O-L14851/ O-H16065 primers. For
 inference of a genome-wide SNP data set were used for double-digest
 restriction site associated DNA sequencing (ddRAD seq). DdRAD seq was
 performed at the Deep Sequencing Facility in the Center for Molecular and
 Cellular Bioengineering (CMCB) Dresden. We used Qubit (Thermo Fisher
 Scientific, Waltham, MA, USA), dsDNA High-Sensitivity (HS) and Broad-Range
 (BR) assays for DNA concentration measurement following the manufacturer’s
 protocol. According to our Qubit measurements, we selected 38 samples with
 sufficient DNA concentrations for ddRAD seq. For sample preparation, 50 ng
 gDNA were double-digested with SbfI and MspI (NEB) for 120 minutes at 37°C
 followed by heat inactivation at 65°C for 20 min. SbfI specific library
 barcodes carrying Truseq-i5 Illumina adapters with cohesive ends were
 ligated to the cohesive ends of the SbfI restriction sites of the digested
 DNA fragments. The same was done for the MspI site with a MspI-specific
 truncated universal TruSeq-i7 adapter. Samples with different P5 Barcodes
 were pooled and purified using XP beads (Beckman Coulter, Krefeld,
 Germany) at a ratio of 1:1 to remove non-ligated adaptors. Libraries were
 equimolarly pooled before sequencing them in single-end mode on an
 Illumina NextSeq 500 system to a read length of 75 bp and a depth of at
 least 1 million reads per sample. We mapped our cleaned
 ddRAD seq read data to three different reference genomes of
 1.) <em>Pyrgilauda ruficollis</em> (NCBI acc. no:
 GCF_017590135.1), 2.) <em>Onychostruthus tazcanowskii</em>
 (NCBI acc. no: GCA_017590055.1) and 3.) to a house sparrow
 (<em>Passer domesticus</em>) genome which was assembled to
 chromosome-level. We used ipyrad v.0.9.42 for data assembly and read
 mapping to the three different reference genomes. We applied a clustering
 threshold of 85% and a minimum sequencing depth for clustering ≥6X. We
 applied default parameter settings of the reference-based ipyrad pipeline
 with a maximum of 8 indels, 0.5 heterozygous sites, 20% SNPs per locus,
 and a minimum of four samples per locus. After these first filtering
 steps, the ipyrad pipeline (Eaton and Overcast, 2020) produced three
 independent VCF output files from mapping against three different
 reference genomes. From each of the VCF files we generated final SNP data
 sets allowing for 0%, 10%, 20% and 30% missing data that were used as
 input data for phylogenetic analysis. For variant calling we used vcftools
 1.1.5 and bcftools v1.8 with a quality value ≥30 applied to separate
 autosomal from Z-chromosomal data sets [which was possible only for the
 data set inferred from alignment to the house sparrow reference genome
 that was annotated to the chromosome level].
description: # Data from: Museomics help resolving the phylogeny of snowfinches (Aves,
 Passeridae, Montifringilla and allies)
 [https://doi.org/10.5061/dryad.m905qfv9k](https://doi.org/10.5061/dryad.m905qfv9k) This data package includes original data from: Islam, Safiqul et al. (2024). Data from: Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, *Montifringilla* and allies). Molecular Phylogenetics and Evolution, 198, 108135. [https://doi.org/10.1016/j.ympev.2024.108135](https://doi.org/10.1016/j.ympev.2024.108135 "Persistent link using digital object identifier") The package comprises sequence alignments (all in FASTA format aligned with MEGA v 10.1.8) and selected Bayesian tree files for a data set of genome-wide single-nucleotide polymorphisms (SNPs) inferred from ddRAD sequencing of 40 individuals of snowfinches (genera *Montifringilla*, *Onychostruthus* and *Pyrgilauda*), plus one sample of the rock sparrow (*Petronia petronia*). Specimen metadata are provided in supplementary Table S1 (Excel format). Accession numbers of sequence data used for analysis are also provided in the material list in „Islametal_supplementaryTable S1_sample_metadata.xlsx“: Cytochrome-b and mitogenome sequences deposited at GenBank; raw FASTQ files from ddRAD sequencing deposited at European Nucleotide Archive (ENA). Each of the three treefiles represents a consensus treefile from three combined runs with BEAST, MCMC chain length: 50 million generations, trees sampled every 5000 generation, burnin: 30% of sampled trees; the SNP data sets were inferred from mapping to one of the three reference genomes (each with 20% missing data allowed): 1) *Onychostruthus taczanowskii* , 2) *Pygrilauda ruficollis*, 3) *Passer domesticus*. ## Description of the data and file structure Data files included in this package Sample metadata, sequencing success: Filename: Islametal_supplementaryTable S1_sample_metadata.xlsx Table in Excel format providing information on the geographic origin of samples (country, region, locality; n/a= missing information), data availability for sequences (cytochrome-b and whole mitogenomes, GenBank accession numbers; n/a= sample not sequenced) and raw read data from ddRAD sequencing (FASTQ files deposited at European Nucleotide Archive [ENA]; n/a= sample sample not included in ddRAD sequencing); additional information on sequencing success (n/a= sample not included in ddRAD seq, i.e. not analyzed): absolute numbers of raw reads (total and of reads that passed the filter), average reading depth (in base pairs), numbers of reads mapped to each of the three reference genomes (*Passer domesticus*, *Pyrgilauda ruficollis*, *Onychrostruthus tazcanowskii*) and mapping rates for each of the three reference genomes (in %); Mitochondrial data: Filename: Islametal2024_snowfinches_mitogenomes_26ind_16964bp Alignment of 26 mitogenome sequences (newly generated for this study: n= 7; GenBank sequences: n= 19) used for phylogenetic reconstructions; alignment length: 16,964 base pairs; FASTA format, aligned with MEGA v 10.1.8. Filename: Islametal2024_snowfinches_cytochromeb_52ind Alignment of 52 cytochrome-b sequences of snowfinches, rock sparrows and outgroup taxa used for phylogenetic reconstructions; alignment length 1,144 base pair; FASTA format, aligned with MEGA v 10.1.8. Filename: Islametal2024_mitogenome_assembly Annotated mitogenome assembly for three novel snowfinch mitogenomes and  three mitogenome sequences from GenBank for comparison, including aligned sequences of primer pairs used for long-range PCR and sequencing; alignment length: 16,965 base pairs; FASTA format, aligned with MEGA v 10.1.8. Genome-wide SNP data: Filename: Islametal_SNPalignment_Onychostruthus-reference_0%Missing SNP alignment (FASTA) inferred from read mapping to the *Onychostruthus tazcanowskii* reference genome, 0% missing data allowed. Filename: Islametal_SNPalignment_Onychostruthus-reference_10%Missing SNP alignment (FASTA) inferred from read mapping to the *Onychostruthus tazcanowskii* reference genome, 10% missing data allowed. Filename: Islametal_SNPalignment_Onychostruthus-reference_20%Missing SNP alignment (FASTA) inferred from read mapping to the *Onychostruthus tazcanowskii* reference genome, 20% missing data allowed. Filename: Islametal_SNPalignment_Onychostruthus-reference_30%Missing SNP alignment (FASTA) inferred from read mapping to the *Onychostruthus tazcanowskii* reference genome, 30% missing data allowed. Filename: Islametal_SNPalignment_Pyrgilauda-reference_0%Missing SNP alignment (FASTA) inferred from read mapping to the *Pyrgilauda ruficollis* reference genome, 0% missing data allowed. Filename: Islametal_SNPalignment_Pyrgilauda-reference_10%Missing SNP alignment (FASTA) inferred from read mapping to the *Pyrgilauda ruficollis* reference genome, 10% missing data allowed. Filename: Islametal_SNPalignment_Pyrgilauda-reference_20%Missing SNP alignment (FASTA) inferred from read mapping to the *Pyrgilauda ruficollis* reference genome, 20% missing data allowed. Filename: Islametal_SNPalignment_Pyrgilauda-reference_30%Missing SNP alignment (FASTA) inferred from read mapping to the *Pyrgilauda ruficollis* reference genome, 30% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-autosomes_0%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only autosomal SNP data, 0% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-autosomes_10%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only autosomal SNP data, 10% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-autosomes_20%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only autosomal SNP data, 20% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-autosomes_30%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only autosomal SNP data, 30% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-Zchromosome_0%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only Z-chromosome SNP data, 0% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-Zchromosome_10%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only Z-chromosome SNP data, 10% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-Zchromosome_20%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only Z-chromosome SNP data, 20% missing data allowed. Filename: Islametal_SNPalignment_Passer-reference-Zchromosome_30%Missing SNP alignment (FASTA) inferred from read mapping to the house sparrow (*Passer domesticus*) reference genome, only Z-chromosome SNP data, 30% missing data allowed. Tree files: Filename: Islametal_snowfinchesOT_20missing_50Mio3runscombined_TREE Consensus treefile from three combined runs with BEAST, MCMC chain length: 50 million generations, trees sampled every 5000 generation, burnin: 30% of sampled trees; inferred from mapping to the *Onychostruthus taczanowskii* genome, unthinned data, 20% missing data allowed (matrix size: 39,952 bp; alignment: filename= Islametal_SNPalignment_Onychostruthus-reference_20%Missing). Filename: Islametal_snowfinchesPR_20missing_50Mio3runscombined_TREE Consensus treefile from three combined runs with BEAST, MCMC chain length: 50 million generations, trees sampled every 5000 generation, burnin: 30% of sampled trees; inferred from mapping to the *Pyrgilauda ruficollis* genome, unthinned data, 20% missing data allowed (matrix size: 40,695 bp; alignment: filename= Islametal_SNPalignment_Pyrgilauda-reference_20%Missing). Filename: Islametal_snowfinchesPasserautosomes_20missing_50Mio3runscombined_TREE Consensus treefile from three combined runs with BEAST, MCMC chain length: 50 million generations, trees sampled every 5000 generation, burnin: 30% of sampled trees; inferred from mapping to the *Passer domesticus* genome, unthinned autosomal data, 20% missing data allowed (matrix size: 30,550 bp; alignment: filename= Islametal_SNPalignment_Passer-reference-autosomes_20%Missing). ## Sharing/Access information Other publicly accessible locations of the data: Accession numbers of sequence data used for analysis are provided in the material list in „SupplementaryTable S1_sample_metadata.xlsx“: Cytochrome-b and mitogenome sequences deposited at GenBank; raw FASTQ files from ddRAD sequencing deposited at European Nucleotide Archive (ENA).