DOI: 10.5061/dryad.fr27m
title: Data from: Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

description: Adaptive phenotypic plasticity, the ability of an organism to change its
 phenotype to match local environments, is increasingly recognized for its
 contribution to evolution. However, few empirical studies have explored
 the molecular basis of plastic traits. The East African cichlid fish
 Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its
 pharyngeal jaw apparatus, a structure that is widely seen as an
 evolutionary key innovation that has contributed to the remarkable
 diversity of cichlid fishes. It has previously been shown that in response
 to different diets, the pharyngeal jaws change their size, shape and
 dentition: hard diets induce an adaptive robust molariform tooth phenotype
 with short jaws and strong internal bone structures, while soft diets
 induce a gracile papilliform tooth phenotype with elongated jaws and
 slender internal bone structures. To gain insight into the molecular
 underpinnings of these adaptations and enable future investigations of the
 role that phenotypic plasticity plays during the formation of adaptive
 radiations, the transcriptomes of the two divergent jaw phenotypes were
 examined. Our study identified a total of 187 genes whose expression
 differs in response to hard and soft diets, including immediate early
 genes, extracellular matrix genes and inflammatory factors. Transcriptome
 results are interpreted in light of expression of candidate genes—markers
 for tooth size and shape, bone cells and mechanically sensitive pathways.
 This study opens up new avenues of research at new levels of biological
 organization into the roles of phenotypic plasticity during speciation and
 radiation of cichlid fishes.
description: geometric morphometric
 landmarks of A_alluaudi LPJsThis file contains x and
 y co-ordinates of A. alluaudi lower pharyngeal jaws (LPJ) used in
 geometric morphometrics analyses, and calculations of area and centroid
 size (Figure 3a-c, Table S3). Co-ordinates are in millimeter scale, as set
 using the 'scale' function in ImageJ. Specimen names correspond
 those assigned in Table S1.geometric morphometrics
 data.txtlinear morphometric
 measurements of A_alluaudi LPJsThis file describes the
 linear measurements, and weight measurements made of lower pharyngeal jaws
 (LPJ), and standard lengths of the A. alluaudi specimens, as used in
 statistical analyses of LPJ size (Figure 3a-b, Table S3). Linear
 measurements are in mm and weight measurements are in mg. Specimen names
 correspond those assigned in Table S1.linear morphometrics
 data.xlsxCandidate gene
 expression using qRT-PCR on A_alluaudi LPJsThis file contains the
 relative expression values of candidate genes, amplifying cDNA from lower
 pharyngeal jaws (LPJ) of the A. alluaudi specimens. The reported values
 have been scaled against normalisation factors (NF) that were calculated
 from 2 housekeeeping genes. These expression values were subjected to
 statistical analyses that are reported in Figure 4 a-c and Table S4.
 Specimen names correspond those assigned in Table S1.qRT-PCR
 results.xlsFasta files of RNA-seq
 contigs generated from A_alluaudi LPJsThis file contains
 .fasta files, generated through assembly of RNA-seq transcripts, derived
 from A. alluaudi specimens used in our study. These .fasta files were used
 for differential expression (DE) analyses and BLAST queries, the results
 of which are depicted in Figure 5 and Tables S5. In tables S6 and S7,
 these .fasta sequences were used as queries against the human genome, and
 significant hits were then used for relative enrichment analyses in
 DAVID.RNA-seq
 transcripts.fasta