Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow

Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection, and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergen..., We collected Neodiprion lecontei and N. pinetum mid- to late-instar larval colonies from Lexington, Kentucky and surrounding areas. To confirm sex (and therefore ploidy), we reared the larvae to adults in the lab using standard lab protocols. The adults were either preserved in 100% ethanol (stored at -20 °C) or flash frozen and stored at -80 °C. To avoid sampling close relatives, we selected one individual from each larval colony (each colony typically represents a group of siblings). In total, we sampled 20 N. lecontei females and 18 N. pinetum females. We extracted DNA from head and thorax tissue with a Qiagen DNeasy Blood & Tissue Kit. We followed the standard manufacturer protocol for insects, including an optional RNase A step. DNA concentration was measured with a Quant-iT dsDNA High-Sensitivity fluorescence assay (Invitrogen). A single library was prepared using a Tn5 tagmentation protocol following Bendall (2020). Whole-genome resequencing was performed with 150bp paired-en..., , # Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow

[https://doi.org/10.5061/dryad.fxpnvx128](https://doi.org/10.5061/dryad.fxpnvx128)

## Description of the data and file structure

To perform all analyses, run scripts provided in each folder in the order indicated in the folder name. Each folder has its own README file providing details specific to that analysis.

NOTE: for all bash scripts (*.sh), you will have to modify them to run on your cluster. However, the program commands should work as long as you are using the same version of the program (program versions indicated in the Materials and Method section of the manuscript).

### Files and variables

#### File: MolEcol\_scripts.zip

**Description:**

In the first folder (\"01.get_windowed_statistics\"), each summary statistic and genome feature has a separate folder containing all scripts and input files necessary to generate the statis...