DOI: 10.5061/dryad.ffbg79ct1
title: Plasticity and genetic basis of cichlid gill arch anatomy reveal novel roles for Hedgehog signaling

description: Teleost gill arches are exquisitely evolved to maximize foraging
 efficiency, and include structures for the capture, filtering, and
 processing of prey. While both plasticity and a genetic basis for gill
 arch traits have been noted, the relative contribution of genetics and the
 environment in shaping these structures remains poorly understood. East
 African cichlids are particularly useful in this line of study due to
 their highly diverse and plastic feeding apparatus. Here we explore the
 gene-by-environmental effects on cichlid GRs by rearing pure bred species
 and their F3 hybrids in different foraging environments. We find that
 anatomical differences between species are dependent on the environment.
 The genetic architecture of these traits is also largely distinct between
 foraging environments. We did, however, note a few genomic “hotspots”
 where multiple traits map to a common region. One of these, for GR number
 across multiple arches, maps to the ptch1 locus, a key component of the
 Hedgehog (Hh) pathway that has previously been implicated in cichlid oral
 jaw shape and plasticity. Since Hh signaling has not previously been
 implicated in GR development, we explored functional roles for this
 pathway.  Using a small molecule inhibitor in cichlids, as well
 as zebrafish transgenic systems, we demonstrate that Hh levels negatively
 regulate GR number, and are both necessary and sufficient to maintain
 plasticity in this trait. In all these data underscore the critical
 importance of the environment in determining the relationship between
 genotype and phenotype, and provide a molecular inroad to better
 understand the origins of variation in this important foraging-related
 trait.
description: See methods for a full description. The data are largely
 morphological in nature, and include both counts, which were collected
 with the use of a dissecting microscope, and skeletal lengths, which were
 collected from digital images in the software program, Image J. The
 genetic data are presented as genotypes - "AA", "AB",
 and "BB". Polymorphisms were identified and genotyped via
 RAD-seq. 
description: All data are formatted for direct import into R - e.g., each
 sheet many be saved as a .txt or .csv file that may read into R. Missing
 data are represented as "NA". Abbreviations are as follows: Ben
 = benthic foraging treatment, Gli = zebrafish carrying
 the dominant-negative <i>Gli2 </i>transgene, GR = gill raker,
 LF = <em>Labeotropheus fuelleborni</em>, MZ
 = <em>Maylandia zebra,</em> Pel = pelagic foraging treatment
 (note that this treatment is refered to as Lim=limnetic foraging treatment
 in the manuscript; these terms may be used interchangeably), res =
 residual values, Shh = zebrafish carrying
 the <i>Shha </i>activator transgene, SL = standard length, TRC
 = <em>Tropheop sp. </em>"red cheek", WT = wild-type
 zebrafish. The genetic data is organized as a matrix
 [indiviuals x genotype]. The first three cells in each column represent
 (1) the marker name "scaffold_X.########", whereby "X"
 refers to the specific scaffold number and "########" represents
 the base pair on that scaffold where the polymorphism is located, (2) the
 linkage group number, 1-22, and (3) the genetic position in centimorgans,
 cM. The LF allele is A, and the TRC allele is B.