DOI: 10.5061/dryad.jn14s
title: Data from: Population-level consequences of complementary sex determination in a solitary parasitoid

description: Background: Sex determination mechanisms are known to be evolutionarily
 labile but the factors driving transitions in sex determination mechanisms
 are poorly understood. All insects of the Hymenoptera are haplodiploid,
 with males normally developing from unfertilized haploid eggs. Under
 complementary sex determination (CSD), diploid males can be produced from
 fertilized eggs that are homozygous at the sex locus. Diploid males have
 near-zero fitness and thus represent a genetic load, which is especially
 severe under inbreeding. Here, we study mating structure and sex
 determination in the parasitoid Cotesia vestalis to investigate what may
 have driven the evolution of two complementary sex determination loci in
 this species. Results: We genotyped Cotesia vestalis females collected
 from eight fields in four townships in Western Taiwan. 98 SNP markers were
 developed by aligning Illumina sequence reads of pooled DNA of eight
 different females against a de novo assembled genome of C. vestalis. This
 proved to be an efficient method for this non-model species and provides a
 resource for future use in related species. We found significant genetic
 differentiation within the sampled population but variation could not be
 attributed to sampling locations by AMOVA. Non-random mating was detected,
 with 8.1% of matings between siblings. Diploid males, detected by flow
 cytometry, were produced at a rate of 1.4% among diploids. Conclusions: We
 think that the low rate of diploid male production is best explained by a
 CSD system with two independent sex loci, supporting laboratory findings
 on the same species. Fitness costs of diploid males in C. vestalis are
 high because diploid males can mate with females and produce infertile
 triploid offspring. This severe fitness cost of diploid males combined
 with non-random mating may have resulted in evolution from single locus
 CSD to CSD with two independent loci.
description: Reference genome
 sequence of Cotesia vestalis: scaffolds and contigsNo genome information
 was available for C. vestalis. In order to build a draft reference genome
 and to develop SNP assays, we sequenced the entire genome of C. vestalis
 on a single lane of paired-end sequences (2x100 bp) on an Illumina HiSeq
 2000 (Illumina Inc., U.S.A.) instrument. The SNP discovery panel consisted
 of eight C. vestalis females, one from each of eight fields.Before
 assembly, Illumina reads were trimmed using an in-house Perl script that
 trims the sequence as soon as two consecutive bases have a quality score
 lower than 20. Reads that after trimming had a length smaller than 50 bp
 were removed from the analysis. To obtain C. vestalis sequence contigs to
 be used as a pseudo-reference genome, we performed a de novo assembly on
 the 133 million 100 bp reads using SOAPDENOVO version 1.05 [37]. The
 assembly was done using a k-mer size of 45 and k-mers that were seen only
 once were removed (option –d). After contig construction, scaffolding was
 performed using intra-scaffold closure (option –F) and a minimum length
 for scaffolding of 50 bp. The total size of the assembly was 152 Mb with a
 contig N50 size of 761 bp and a scaffold N50 size of 2400
 bp.de
 Boer_Cotesia vestalis scaffold
 sequences.scafSeqCotesia vestalis SNP
 information and sequencesFrom our list of
 putative SNPs across the C. vestalis genome, we selected 100 SNPs for
 genotyping assay development. We first selected the 200 largest scaffolds;
 they varied in length from 17-58Kb and contained a total of 7,878 SNPs. We
 then removed SNPs with a minor allele frequency (MAF) &lt;0.2, SNPs that
 had another SNP within 50 bp up- or downstream, and SNPs with more than 2
 alleles. The remaining SNPs were binned in MAF bins of 0.2-0.3 (1,908
 SNPs), 0.3-0.4 (1,605 SNPs) and 0.4-0.5 (1,156 SNPs). Per MAF bin, SNPs
 were ranked by SNP quality score. We then selected the SNPs with the
 highest quality scores, picking 20 SNPs with a MAF between 0.2-0.3 and 40
 each with a MAF between 0.3-0.4 and 0.4-0.5, all on different scaffolds.
 All selected SNPs had a quality score of more than 200 (based on
 SAMTOOLS), and an average read depth of 61. High-throughput genotyping
 assays based on allele-specific forward primers were developed for these
 100 SNP sequences at KBioscience (now LGC Genomics, Hoddesdon,
 U.K.).de
 Boer_SNP info and sequences.xlsxGenototypes of C
 vestalis females at 98 SNPsSNP genotypes of 139
 Cotesia vestalis females collected in Western Taiwan at 98 polymorphic
 SNPsde
 Boer_genotype matrix C
 vestalis.xlsxPutative SNPs discovered
 in genome of Cotesia vestalisIndividual paired-end
 reads were aligned against the artificial Cotesia vestalis reference
 genome obtained from the de novo genome assembly using BWA. The resulting
 BAM file was then used for the identification of putative SNPs using
 SAMTOOLS and varFilter from the samtools.pl utility. We only considered
 nucleotide substitutions and ignored small indels. SNPs were filtered that
 had a mapping quality higher than 20, a minimum read depth of 3 and a
 maximum read depth of 90 (3x the average read depth, a strategy to avoid
 orthologous SNPs, e.g. in multi copy genes.de Boer_putative
 SNPs.xlsx