DOI: 10.5061/dryad.4qrfj6qch
title: Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load

description: Meiotic drive supergenes are complexes of alleles at linked loci that
 together subvert Mendelian segregation resulting in preferential
 transmission. In males, the most common mechanism of drive involves the
 disruption of sperm bearing one of a pair of alternative alleles. While at
 least two loci are important for male drive- the driver and the target-
 linked modifiers can enhance drive, creating selection pressure to
 suppress recombination. In this work, we investigate the evolution and
 genomic consequences of an autosomal, multilocus, male meiotic drive
 system, Segregation Distorter (SD) in the fruit fly, Drosophila
 melanogaster. In African populations, the predominant SD chromosome
 variant, SD-Mal, is characterized by two overlapping, paracentric
 inversions on chromosome arm 2R and nearly perfect (~100%) transmission.
 We study the SD-Mal system in detail, exploring its components,
 chromosomal structure, and evolutionary history. Our findings reveal a
 recent chromosome-scale selective sweep mediated by strong epistatic
 selection for haplotypes carrying Sd, the main driving allele, and one or
 more factors within the double inversion. While most SD-Mal chromosomes
 are homozygous lethal, SD-Mal haplotypes can recombine with other,
 complementing haplotypes via crossing over, and with wildtype chromosomes
 via gene conversion. SD-Mal chromosomes have nevertheless accumulated
 lethal mutations, excess non-synonymous mutations, and excess transposable
 element insertions. Therefore, SD-Mal haplotypes evolve as a small,
 semi-isolated subpopulation with a history of strong selection. These
 results may explain the evolutionary turnover of SD haplotypes in
 different populations around the world, and have implications for
 supergene evolution broadly.
description: We sequenced haploid embryos using the following scheme: we
 crossed <em>SD-Mal/CyO </em>stocks to homozygous
 <em>ms(3)K81</em> males and allowed them to lay eggs
 overnight. We inspected individual embryos under a dissecting scope for
 evidence of development and then isolated them for whole genome
 amplification using the REPLI-g Midi kit from Qiagen (catalog number
 150043) and tested for the presence of <em>Sd-RanGAP
 </em>using PCR. We prepared sequencing libraries for Illumina
 sequencing with TruSeq PCR free 350bp.  To trim reads, we used Trimgalore
 v0.3.7 and the parameters:<em> q 28 --length 20 --paired -a
 GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a2 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
 --phred33 --fastqc --retain_unpaired -r1 21 -r2 21 --dont_gzip --length
 20.</em> Trimmed reads are available in SRA (Bioproject PRJNA649752,
 SRA accession numbers in Table S1). We sequenced a total of 10
 <em>SD-Mal</em> genomes.  For
 the Nanopore library, we extracted High-Molecular-Weight DNA from ~200
 frozen female <em>SD-ZI125/SD-ZI125</em> virgins, extracted
 DNA using a standard phenol-chloroform method and spooled DNA using
 capillary tubes. We constructed a library with ~1 ug DNA using RAD004 kit
 and the ultra-long read sequencing protocol. We sequenced the library
 using R9.4 flow cells and called bases with the ONT Albacore Sequencing
 Pipeline Software version v2.2.10. For SNP calling, we
 mapped the Illumina reads from our <em>SD-Mal</em> libraries
 and the 20 <em>SD<sup>+</sup></em> libraries from
 the <em>DPGP3</em> dataset to <em>D.
 melanogaster</em> (BDGP6) genome (ftp://ftp.ensembl.org/pub/release-88/fasta/drosophila_melanogaster/dna/; last accessed 6/25/20) using BWA mem (v0.7.9a). We removed duplicated reads with Picard (2.0.1) and applied the GATK (3.5) “best practices” pipeline for SNP calling. We did local realignment and base score recalibration using SNPs data from DPGP1 ensembl release 88 (ftp://ftp.ensembl.org/pub/release-88/variation/vcf/drosophila_melanogaster/; last accessed 6/25/20). To call SNPs and indels, we used HaplotypeCaller and performed joint genotyping for each of the five genotypes using GenotypeGVCFs. SNPs filtered with following parameters: 'QD &lt; 2.0 || FS &gt; 60.0 || MQ &lt; 40.0 || MQRankSum &lt; -12.5 || ReadPosRankSum &lt; -8.0'. We annotated SNPs as synonymous or nonsynonymous using SNPeff  with the integrated <em>D. melanogaster </em>database (dmel_r6.12) database and parsed these annotations with SNPsift . To classify the SNPs as ‘shared’ between <em>SD-Mal</em>, <em>SD<sup>+</sup>In(2L)t</em> and <em>SD<sup>+</sup>In(2R)NS</em>, or ‘private’ to each one of them, we used BCFtools intersect (v1.6). Please see the manuscript for complete methods.
description: Please see README.md for instructions for how to reproduce all
 figures and analyses.