DOI: 10.5061/dryad.hqbzkh1dz
title: Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait

description: Despite considerable progress in recent decades in dissecting the genetic
 causes of natural morphological variation, there is limited understanding
 of how variation within species ultimately contributes to species
 differences. We have studied patterning of the non-sensory hairs, commonly
 known as “trichomes,” on the dorsal cuticle of first-instar larvae of
 Drosophila. Most Drosophila species produce a dense lawn of trichomes, but
 a subset of dorsal trichomes were lost in D. sechellia and D. ezoana due
 entirely to regulatory evolution of the shavenbaby (svb) gene. Here we
 describe intraspecific variation in dorsal trichome patterns of
 first-instar larvae of D. virilis that is similar to the trichome pattern
 variation identified previously between species. We found that 67% of this
 difference is explained by a QTL that contains svb and that svb expression
 correlates with trichome variation within D. virilis . Despite using an
 experimental design with reasonable power to detect a second locus
 accounting for the remainder of the variance in trichome number, only a
 single QTL could be mapped, suggesting that multiple other loci each make
 a small contribution to trichome patterning. Thus, the genetic
 architecture of intraspecific variation and interspecific differences
 exhibit similarities and differences that may reflect differences between
 short-term and long-term evolutionary processes.
description: The order of the existing <i>D. virilis </i>genome
 (r1.2) scaffolds on Muller arms was proposed by Schaeffer et al.
 (Schaeffer et al. 2008). Therefore, to simplify presentation of QTL
 results, we concatenated scaffolds following the assignments provided in
 Supplementary Table 24 of (Schaeffer et al. 2008) to generate a
 Muller-element pseudo-assembly. We then used recomninant inbred lines
 to estimate ancestry using MSG (Andolfatto et al. 2011) and calculated
 linkage scores (r<sup>2</sup>) between neighboring markers in
 this pseudo-assembly. We identified several locations where neighboring
 chromosomal regions did not appear to be co-inherited, most likely
 resulting from incorrect genome assembly,  estimated the locations of
 these incorrect assembly locations and re-joined fragments at the ends
 showing higher linkage to generate the following genome:
 <em>Dvir.Genome.MullerArms.10iv15.fa</em>
 The reference pseudo-assembly was updated with sequencing reads
 (SAMN16729993) from the Mexico <em>D. virilis </em>line
 (15010–1051.48) using methods described previously (Andolfatto et al.
 2011) to generate the following genome:
 <em>Dvir.Mexico.msg.updated.MullerArms.10iv15.fa</em> We used these two genomes as parental genomes to estimate ancestry for 96 recombinant inbred lines (SAMN16729994-SAMN16730089). The full ancestry files for all 96 lines are provided in two files:  <em>ancestry-probs-par1.tsv</em> <em>ancestry-probs-par2.tsv</em> These ancestry probability files were thinned using <em>pull_thin_tsv.py</em> (https://github.com/dstern/pull_thin) with the configuration file <em>pt.cfg </em>to generate the following thinned ancestry files that can be directly imported with <em>virpheno.csv </em>into Rqtl using read.cross.msg (https://github.com/dstern/read_cross_msg) <em>ancestry-probs-par1.tsv.sorted.pulled.converted.thinned.f2_rqtl</em> <em>ancestry-probs-par2.tsv.sorted.pulled.converted.thinned.f2_rqtl</em> <em>ancestry-probs-par2.tsv.sorted.csv</em>