DOI: 10.5061/dryad.w0vt4b905
title: Data from: Genome-wide support for incipient Tula orthohantavirus species within a single rodent host lineage

description: Evolutionary divergence of viruses is most commonly driven by
 co-divergence with their hosts or through isolation of transmission after
 host-shifts. It remains mostly unknown, however, whether divergent
 phylogenetic clades within named virus species represent functionally
 equivalent byproducts of high evolutionary rates or rather incipient virus
 species. Here, we test these alternatives with genomic data from two
 widespread phylogenetic clades in Tula orthohantavirus (TULV) within a
 single evolutionary lineage of their natural rodent host, the common vole
 Microtus arvalis. We examined voles from 42 locations in the contact
 region between clades for TULV infection by RT-PCR. Sequencing yielded 23
 TULV Central North and 21 TULV Central South genomes which differed by
 14.9-18.5% at the nucleotide and 2.2-3.7% at the amino acid level without
 evidence of recombination or reassortment. Geographic cline analyses
 demonstrated an abrupt (&lt;1 km wide) transition between the
 parapatric TULV clades in continuous landscape. This transition was
 located within the Central mitochondrial lineage of M. arvalis and genomic
 SNPs showed gradual mixing of host populations across it. Genomic
 differentiation of hosts was much weaker across the TULV Central North to
 South transition than across the nearby hybrid zone between two
 evolutionary lineages in the host. We suggest that these parapatric TULV
 clades represent functionally distinct, incipient species which are likely
 differently affected by genetic polymorphisms in the host. This highlights
 the potential of natural viral contact zones as systems for investigating
 of the genetic and evolutionary factors enabling or restricting the
 transmission of RNA viruses.
description: Genotyping of host nuclear DNA Genome-wide
 nuclear DNA (nucDNA) was used to infer the genetic structure of hosts via
 Genotyping by Sequencing (GBS) (Elshire et al., 2011). We sequenced at
 least five individuals per sampling site across the Central transect
 whenever possible, for a total of 200 individuals. Sequencing was carried
 out by LGC Biosearch Technologies (Berlin, Germany) using Illumina NovaSeq
 6000 and PstI/MspI as restriction enzymes. We combined our dataset with
 GBS data of 216 additional individuals from the Porcelain transect
 (Saxenhofer et al., 2022) processed under the same conditions. This
 separate dataset consisted of voles from the Central and Eastern lineage
 as well as admixed individuals and served as a reference for the
 assignment of the newly genotyped 200 individuals to the evolutionary
 lineages. SNP calling was performed for all 416 individuals together using
 the GBS v2 pipeline (Tassel 5) (Glaubitz et al., 2014) with the
 <em>M. arvalis</em> genome (BioProject ID: PRJNA737461, Gouy
 et al., submitted) as reference. We utilized default parameters, except
 requiring a minimum of five reads to identify a unique tag.. We only
 retained bi-allelic SNPs and called genotypes if individuals had a read
 depth of at least five at the locus. After SNP calling, we removed all
 loci with complex indels, a minor allele frequency of less than 5%, more
 than 20% missing data or observed heterozygosity greater than 50%, which
 may indicate loci that contain paralogs merged together (White et al.,
 2013). Individuals with more than 50% missing data were also removed
 (seven individuals, all from Saxenhofer et al. (2022)). We performed a
 LD-KNNi imputation in TASSEL 5 (Glaubitz et al., 2014) for remaining
 missing data based on the most common state of the allele across the 10
 closest genetic neighbors, calculated across the 30 SNPs with the highest
 LD towards the missing site and keeping Ns in case of ties. A total of
 12.8% of data were missing in the dataset of 409 individuals, of those
 99.93% were imputed. Sites which still contained missing data after
 imputation were discarded. To address potential batch effects of combining
 two independent GBS datasets, six of the 200 sequenced individuals were
 replicates of samples from Saxenhofer et al. (2022). One of the replicates
 was among the seven samples which failed quality control, leaving a total
 of five effective replicates. We performed all analyses of host population
 structure with the original data set before imputation, a second dataset
 after imputation of missing data and a third, very stringently filtered
 data set in which we removed any loci from our analysis at which SNPs
 differed between the originals and replicates. We found minor quantitative
 differences between the three datasets but identical qualitative patterns
 across all analyses.
description: # Genome-wide support for incipient Tula orthohantavirus species within a
 single rodent host lineage 
 Raw data belonging to: Labutin, A. and Heckel, G. (2024) Genome-wide
 support for incipient Tula orthohantavirus species within a single rodent
 host lineage. Virus Evolution Metadata for tab
 "Central_Porcelain_keys.txt" Column entry and explanation:
 Flowcell: Identifier of the Flowcell containing this sample Lane: Number
 of lane for sequencing the sample Barcode: Unique Barcode within the
 Flowcell for identifying the sample FullSampleName: Same as DNASample
 LibraryPlateID: Identifier for every library plate Row: Identifier of
 Flowcell row of each sample Col: Identifier of Flowcell column of each
 sample Enzyme: Restriction enzymes used for the digestion of genomic DNA
 during GBS Note: The keyfile is necessary for assembly and SNP calling of
 the RAW GBS data of the corresponding Manuscript, found in SRA links:
 and
 . The files
 from both repositories are required.