AC0405080910_final_genotypes_with_tagging_data

Individual genotype and observational dat

halibut_genepop

File containing all genotypes. File in Genepop format. Locus names are formatted with an underscore between the RADtag name and SNP position

supplemental_material_199_sex_assays

Results of two TaqMan assays linked to sex

supplemental_materials_alignments

Alignments between Pacific halibut loci and 1) Atlantic halibut linkage map, 2) turbot genome, and 3) half-smooth tongue sole genome

Posterior probability distribution (PPD) for estimated effective number of migrants (2NM) between species for the coastal and Salish Sea populations.

<p>Species are coded by two letters: Sa–<i>S</i>. <i>auriculatus</i>, Sc–<i>S</i>. <i>caurinus</i>, Sm–<i>S</i>. <i>maliger</i>. The PPD highest peak values are posted above the distribution.</p

Hybrid proportions by region and species.

<p>Hybrid proportions by region and species.</p

Hybridization between Yellowstone Cutthroat Trout and Rainbow Trout Alters the Expression of Muscle Growth-Related Genes and Their Relationships with Growth Patterns

<div><p>Hybridization creates novel gene combinations that may generate important evolutionary novelty, but may also reduce existing adaptation by interrupting inherent biological processes, such as genotype-environment interactions. Hybridization often causes substantial change in patterns of gene expression, which, in turn, may cause phenotypic change. Rainbow trout (<i>Oncorhynchus mykiss</i>) and cutthroat trout (<i>O</i>. <i>clarkii</i>) produce viable hybrids in the wild, and introgressive hybridization with introduced rainbow trout is a major conservation concern for native cutthroat trout. The two species differ in body shape, which is likely an evolutionary adaptation to their native environments, and their hybrids tend to show intermediate morphology. The characterization of gene expression patterns may provide insights on the genetic basis of hybrid and parental morphologies, as well as on the ecological performance of hybrids in the wild. Here, we evaluated the expression of eight growth-related genes (MSTN-1a, MSTN-1b, MyoD1a, MyoD1b, MRF-4, IGF-1, IGF-2, and CAST-L) and the relationship of these genes with growth traits (length, weight, and condition factor) in six line crosses: both parental species, both reciprocal F1 hybrids, and both first-generation backcrosses (F1 x rainbow trout and F1 x cutthroat trout). Four of these genes were differentially expressed among rainbow, cutthroat, and their hybrids. Transcript abundance was significantly correlated with growth traits across the parent species, but not across hybrids. Our findings suggest that rainbow and cutthroat trout exhibit differences in muscle growth regulation, that transcriptional networks may be modified by hybridization, and that hybridization disrupts intrinsic relationships between gene expression and growth patterns that may be functionally important for phenotypic adaptations.</p></div

Significant ANCOVAs (pseudo-<i>F</i> and <i>P</i>-value) and Spearman rank correlation coefficients (<i>r</i>_<i>s</i>) between trait and transcript abundance across parent species and across hybrids within each time point.

<p>The traits are: percent Yct genome (% Yct), condition factor (K), length (L), and weight (W).</p><p>*Significant <i>r</i>_<i>s</i> following the false discovery rate procedure for 16 simultaneous tests (FDR adjusted <i>α</i> = 0.015).</p><p>Significant ANCOVAs (pseudo-<i>F</i> and <i>P</i>-value) and Spearman rank correlation coefficients (<i>r</i>_<i>s</i>) between trait and transcript abundance across parent species and across hybrids within each time point.</p

Population size parameter estimates (q) for <i>S</i>. <i>auriculatus</i>, <i>S</i>. <i>caurinus</i>, and <i>S</i>. <i>maliger</i> and between coastal and Salish Sea populations.

<p>The 95% CI are indicated with bars.</p

Ancestry coefficient (Q) from <i>structure</i> analysis for each individual to one of three genetic groups (k = 3).

<p>Each vertical bar represents a single individual and the colors shows the proportion of ancestry to each genetic group. The three genetic clusters are represented by purple as <i>S</i>. <i>auriculatus</i>, blue as <i>S</i>. <i>caurinus</i> and red as <i>S</i>. <i>maliger</i>. The results for each individual are arranged vertically by morphological species and population: 1 = <i>S</i>. <i>auriculatus</i> (coast), 2 = <i>S</i>. <i>auriculatus</i> (Salish Sea), 3 = <i>S</i>. <i>caurinus</i> (coast), 4 = <i>S</i>. <i>caurinus</i> (Salish Sea), 5 = <i>S</i>. <i>maliger</i> (Salish Sea), 6 = <i>S</i>. <i>maliger</i> (Salish Sea); A and B are <i>S</i>. <i>caurinus</i> hybrid whole specimens from SPS, and C is the <i>S</i>. <i>caurinus</i> putative hybrid whole specimen from CPS. The samples are approximately sorted from left to right on the figure by geography north to south.</p