Additional file 1:

EST clones for which significant divergence was detected between embryos or juveniles of dwarf and normal whitefish. List of all EST clones for which significant divergence of gene expression was detected for dwarf and normal whitefish (33 and 502 EST clones for the Embryo and Juvenile datasets). EST clone and annotation, the Log2-fold change of dwarfs relative to normals and the FDR adjusted Permutation p-value (significance criterion in this study) are given.

Format: XLS Size: 80KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Regulatory changes between juvenile dwarf and normal whitefish in a common environment. Similarity of regulatory changes between dwarf and normal whitefish at different life history stages in controlled common environments. All comparisons are based on the same strains (Lake Témiscouata "dwarf" and Lake Aylmer "normal" respectively). 108 EST clones that display significant differentiation in gene expression in whole juvenile fish (this study) were previously found to be differentially expressed in muscle tissue from adult fish [21]. When genes are represented by several EST clones these are grouped according to their annotation (accession number and gene name) and patterns of gene expression. "up" or "down" regulation describes the direction of the change of gene expression in the dwarf whitefish relative to normal whitefish. Biological functions are as given in Derome et al. [21]. EM = energetic metabolism; IR = immune response; OB = oxygen binding; OF = other function; PS = protein synthesis; RPD = reproduction; MCR = muscle contraction regulation; PM = protein metabolism. Despite the fact that different tissues were used, 31 out of 45 genes show congruent directions of significant regulatory changes in juvenile and adult fish (last column), which points towards ubiquitous patterns of expression divergence at juvenile and adult stages in a common laboratory environment.

Format: DOC Size: 74KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional file 3:

Regulatory changes between juvenile dwarf and normal whitefish at candidate adaptive traits. Comparison of significant regulatory changes between juvenile dwarf and normal whitefish with patterns observed at candidate adaptive traits. Derome et al. [20] and St-Cyr et al. [22] analysed gene expression in white muscle and liver tissue of adult fish from species pairs in natural lakes (dwarfs and normals from Cliff Lake and Indian Pond) and identified candidate adaptive traits based on patterns of parallel divergence. 96 EST clones that match candidate adaptive traits displayed significant patterns of divergence in whole juvenile dwarf and normal whitefish in this study (Lake Témiscouata "dwarf" and Lake Aylmer "normal" respectively). Column contents correspond with Additional file 2 [see Additional file 2], with an additional column describing regulatory changes found by St-Cyr et al. [22] for adult fish liver tissue and the following additional biological functions as described in St-Cyr et al. [22]: DT = detoxification; LM = lipid metabolism; BT = blood and transport; GLF = germ-line formation; PD = Protein degradation. A minus (-) indicates that gene expression divergence was not tested or detected in the corresponding adult tissue. Ten out of 26 genes clones show regulatory changes in the controlled environment that are congruent with the patterns observed in candidate adaptive traits in independent dwarf normal pairs in natural lakes. Eight of these ten genes are related to energy metabolism, which shows that regulatory changes between dwarf and normal whitefish related to this function are more constant across different environments, tissues and life history stages than those related to other functions.

Format: DOC Size: 63KB Download file

This file can be viewed with: Microsoft Word Viewer