DOI: 10.5061/dryad.3ffbg7b01
title: Data from: Demographic history inferred from an inversion-rich spruce bark beetle genome

description: The demographic history of species inferred from whole-genome data
 provides quantitative insights into key biological parameters such as
 population size changes and divergence times. Reliable estimates often
 require data that have not been affected by selection. Extensive research,
 however, indicates that many species harbour multiple polymorphic
 chromosomal inversions, which often evolve under different selective
 pressures. Consequently, inversions can influence genome-wide patterns of
 variation and subsequent evolutionary inferences. In this study, we used
 genome-wide data from over 300 spruce bark beetle (Ips typographus)
 individuals from 23 populations across Europe to reconstruct their
 demographic history and to investigate the impact of a complex polymorphic
 inversion landscape (covering approximately 28% of the beetle genome) on
 demographic inference. We used two complementary methods, Pairwise
 Sequential Markovian Coalescent (PSMC) and Site Frequency Spectrum
 (SFS)-based modelling, and revealed a Late Pleistocene divergence (~79
 kya) between populations from the southern and northern parts of the
 species’ European range, and a long-term effective population size of
 ~250,000. The southern group underwent significant population expansion
 after this divergence event, whereas the northern group expanded during
 the Holocene (~7 kya). Recent population size estimates suggest that the
 southern group is twice as large as the northern group. Neglecting the
 presence of chromosomal inversions did not significantly affect the model
 selection procedure and resulted in relatively small biases in the
 estimated demographic parameters. This study provides information on the
 historical population dynamics of the spruce bark beetle and improves our
 understanding of the influence of a complex genomic architecture on the
 inference of evolutionary history. 
description: # Data from: Demographic history inferred from an inversion-rich spruce
 bark beetle genome Dataset DOI:
 [10.5061/dryad.3ffbg7b01](https://doi.org/10.5061/dryad.3ffbg7b01) ##
 Description of the data and file structure **Associated publication:**
 *Demographic history inferred from an inversion-rich spruce bark beetle
 genome* **Raw sequencing data availability:** Raw FASTQ files are
 deposited in the NCBI Sequence Read Archive (SRA) and are available under
 BioProject ID PRJNA1013983. ### **General information** This repository
 contains data files and analysis pipelines used for population genomic and
 demographic analyses of *Ips typographus*. The materials include workflows
 for raw sequencing data processing, variant calling, site frequency
 spectrum (SFS) construction, and demographic inference using both
 SFS-based (fastsimcoal2) and Pairwise Sequentially Markovian Coalescent
 (PSMC) based approaches. Processed variant call data (VCF format) and
 scripts are provided to facilitate transparency, reproducibility, and
 reuse of the analyses presented in the associated manuscript. **Reference
 genome information** Sequencing reads were mapped to the *Ips typographus*
 reference genome assembly: Assembly accession: GCA_016097725.1\ Genome
 size: 236.8 Mb Analyses were restricted to 25 autosomal contigs listed
 in: ALL_PSMC_Contigs.txt (see below). 
 
 **Repository file inventory** This repository contains the following
 files and folders: Raw_data_processing.zip VCF.tar BED_files.zip
 SFS_pipeline/ Fastsimcoal_files.zip PSMC_pipeline/ 
 
 ### **File/folder content description** #### **Raw_data_processing.zip**
 Pipeline and scripts for parallelised preprocessing (each contains
 separate README file) of raw sequencing data prior to downstream analyses.
 The workflows are designed for execution in high-performance computing
 (HPC) environments. To view and edit all files within subfolders one can
 use any plain text editor i.e.: Notepad++, nano.  **Directory contents:**
 * **Raw_data_processing_pipeline** - main wrapper pipeline coordinating
 successive preprocessing steps * **parallel_trimming/** - parallel adapter
 trimming and quality filtering of raw sequencing reads *
 **parallel_sorting/** - parallel sorting and indexing of alignment files *
 **parallel_duplicate_removal/** - parallel removal or marking of PCR
 duplicates * **parallel_coverage/** - calculation of genome-wide or
 regional sequencing coverage * **parallel_snp_calling/** - parallel SNP
 calling from processed alignment files * **parallel_genotyping/** -
 genotyping of variants across individuals *
 **parallel_combine_variants/** - merging and combining variant call files
 into final datasets **Input:** Raw sequencing reads (FASTQ files from NCBI
 SRA). **Output:** Processed BAM & VCF files. **Software
 requirements:** FastQC; Trimmomatic, Bowtie2, samtools/bcftools, Picard,
 GATK; 
 
 #### **VCF.tar** Compressed Variant Call Format (VCF) file and
 corresponding index file (.tbi extension) used for population genomic and
 demographic analyses. VCF file structure is according to the VCF v4.2
 specification. File represents variation for the whole genome dataset and
 can be furter filtered using bed files to provide subsets of the data used
 in the publication for downstream analyses. This file resulted from fastq
 files processing, mapping and variant calling and was used for SFS
 construction and population genetic analyses. File with the .tbi extension
 is tabix index file associated with compressed Variant Call Format file. A
 .tbi file contains indexing information that allows software tools to
 rapidly access specific genomic regions within a compressed VCF file
 without reading the entire file sequentially.  To view and edit the files
 one can use any plain text editor i.e.: Notepad++, nano. For further
 bioinformatic analyses we reccommend the following software: bedtools,
 bcftools, GATK, easySFS.  
 
 #### **BED_files.zip** This archive contains files defining genomic
 regions used for filtering, masking, and partitioning the genome,
 especially for defining genomic regions by including / excluding
 inversions. To view and edit the files one can use any plain text editor
 i.e.: Notepad++, nano. For further bioinformatic analyses we reccommend
 the following software: bedtools, bcftools, GATK. **Contents:** *
 **ALL_PSMC_Contigs.txt** - plain text file, contains list of contigs
 included in PSMC analyses * **PSMC_INVERSIONS.bed** - plain text file in
 bed format, contains genomic coordinates of inversion regions used for
 filtering * **ALL_25_PSMC_contigs.bed** - plain text file in bed format,
 file defining contigs used for whole genome dataset *
 **ALL_25_PSMC_contigs_No_inversions.bed** - plain text file in bed format,
 file defining genomic coordinates of 25 contigs with inversion removed *
 **ALL_25_PSMC_contigs_No_inversions_no_genes_no_repeats.bed** - plain text
 file in bed format, file defining genomic coordinates of 25 contigs
 excluding inversions, genes, and repeats *
 **ALL_25_PSMC_contigs_Inversions_no_genes_no_repeats.bed** - plain text
 file in bed format, file defining genomic coordinates of 25 contigs
 including only inverted regions, excluding genes and repetitive elements *
 **Small_colinear.bed** - plain text file in bed format, file defining
 genomic coordinates of regions representing small colinear segments in the
 associated publication * **Small_colinear_sorted.bed** - plain text file
 in bed format, file defining genomic coordinates of small colinear
 segments in the associated publication, sorted version of
 Small_colinear.bed * **ALL_25_PSMC_contigs_SMALL_no_genes_no_repeats.bed**
 - plain text file in bed format, file defining genomic coordinates of
 small colinear segments in the associated publication, excluding genes and
 repeats 
 
 #### **SFS_pipeline** Pipeline for constructing observed site frequency
 spectra (SFS) from data (plain text files with .obs extension). To view
 and edit the file one can use any plain text editor i.e.: Notepad++, nano.
 For further bioinformatic analyses we reccommend using the following
 software: bedtools, bcftools, GATK, easySFS.  Observed SFS (.obs) files
 represent joint minor allele frequency spectra where: * rows and columns
 represent allele frequency bins across analysed populations * each matrix
 cell represents the number of SNPs observed in a given frequency class
 Units: number of SNPs per frequency bin. Two population groups were
 defined for demographic inference: * Northern population (Nor) –
 individuals originating from Sweden, Norway and Finland - Southern
 population (Sou) – individuals originating from Italy, Austria, Germany
 and Czech Republic 
 
 #### **Fastsimcoal_files.zip** Input files for demographic inference
 using **fastsimcoal2**, organized in folders by genomic partitions. Used
 to test demographic models under different genomic partitions to assess
 effects of inversions and genome subsets. To view and edit the file one
 can use any plain text editor i.e.: Notepad++, nano. For further
 bioinformatic analyses we recommend using the following software:
 fastsimcoal2. ##### **Top-level directories and contents:** *
 **whole-genome/** - contains files used for full-genome analyses *
 **inversions-only/**  - contains files used for analyses restricted to
 inverted regions * **no-inversions/**  - contains files used for analyses
 excluding inversions * **no-inversions-small/**  - contains files used for
 analyses of smaller subset of non-inverted regions ##### **Each folder
 contains:** * observed site frequency spectrum files (in two different
 file formats) required by fastsimcoal2 to run a given demographic model.
 Naming convention for the files (for example
 NorSouC25INV_jointMAFpop1_0.obs  NorSouC25INV_MSFS.obs) is: * Nor -
 northern population * Sou - southern population * C25 - dataset restricted
 to 25 contigs used in demographic analyses * INV - genomic partition
 including just inversion regions * Demographic model directories
 corresponding to different demographic scenarios: IM/, IMDE/, ISO/,
 ISODE/, SC/, SCDE/.  * IM - isolation with constant migration model * IMDE
 - isolation with constant migration model and single, instant demographic
 event (expansion or contraction) * ISO - isolation model * ISODE
 - isolation model and single, instant demographic event (expansion or
 contraction) * SC - secondary contact model * SCDE - secondary contact
 model and single, instant demographic event (expansion or contraction) *
 Each model subdirectory contains steering files required by fastsimcoal2
 to run simulations * .tpl - plain text file with template defining the
 demographic model * .est - plain text file with starting parameters for
 the model 
 
 #### **PSMC_pipeline** **Description:** Pipeline for demographic
 inference using Pairwise Sequentially Markovian Coalescent (PSMC). To view
 and edit the file one can use any plain text editor i.e.: Notepad++, nano.
 For further bioinformatic analyses we reccommend using the following
 software: bedtools, bcftools, GATK, psmc. 
 
 ### **Notes on reuse** * File paths in scripts require adaptation to
 local directory structures. 
 
 ### **Contact** For questions regarding the dataset or analysis
 pipelines, please contact the corresponding author of the associated
 publication. 
 
 ### Access information Publicly accessible locations of the raw
 sequencing data: * National Centre for Biotechnology Information Sequence
 Read Archive BioProject ID PRJNA1013983