DOI: 10.5061/dryad.4mw6m90fn
title: Data from: Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river

description: Hybridization between coastal cutthroat trout (Oncorhynchus clarkii
 clarkii) and steelhead (O. mykiss) was assessed in the Smith River,
 California. Individuals were categorized as pure or as one of 10 hybrid
 classes using 30 ‘diagnostic’ single-nucleotide polymorphisms positioned
 on 26 separate chromosomes. Most of the individuals examined (n = 876),
 were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213),
 and 29 individuals were identified as having hybrid ancestry. Among
 hybrids, first generation hybrids (n = 15) and coastal cutthroat trout
 backcrosses (n = 12) were the most common. No individuals were identified
 as backcrosses to SH, suggesting the presence of genetic or behavioral
 mechanisms constraining such backcrosses, or the growth and survival of
 their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead
 origin, suggesting that hybridization was driven primarily by sneak-mating
 of male coastal cutthroat trout with female steelhead. Evaluation of
 classical phenotypic characters for coastal cutthroat trout and steelhead
 (i.e., jaw slash, maxillary length, and hyoid teeth) were not reliable by
 themselves for identification of either pure parental fish or hybrids. In
 contrast, analysis with geometric morphometrics revealed distinctive body
 shapes for pure coastal cutthroat trout and steelhead, and the combination
 of classical traits and geometric morphology was mostly accurate in
 distinguishing them. However, first generation hybrids and backcrosses
 overlapped completely with parental types, highlighting challenges in
 hybrid identification using phenotypic traits.
description: This data was collected by sampling coastal cutthroat trout and
 steelhead in the Smith River. Fish were captured using night netting, hook
 and line, electrofishing, and weirs from mid-May through August 2013. A
 tissue sample, photograph, and fork length measurement were collected from
 874 fish. Phenotypic characteristics of jaw slash color intensity,
 maxillary length compared to posterior margin of eye, and presence of
 hyoid teeth were also recorded for each fish in the field. We generated
 genotypes for 96 single-nucleotide polymorphisms (SNPs) using
 TaqMan<sup>TM</sup> 5’ nuclease assays (Applied Biosystems
 Inc.) and 96.96 Dynamic Genotyping Arrays (Fluidigm Corporation), with
 imaging on an EP1 instrument l (Fluidigm). Genotypes were manually called
 using the SNP Genotyping Analysis Software (3.0.2, Fluidigm). NewHybrids
 was configured to assign fish to ten hybrid classes characterized by the
 expected frequencies of loci having 0, 1, or 2 alleles originating from
 each parental type.  Body morphologies of CCT, SH, and
 their hybrids were compared using landmark-based geometric morphometrics.
 Landmark locations were as follows: 1) tip of snout; 2) anterior margin of
 eye; 3) posterior margin of eye; 4) posterior end of operculum; 5)
 posterior end of maxillary; 6) origin of pectoral fin; 7) origin of pelvic
 fin; 8) origin of anal fin; 9) anterior attachment of ventral membrane of
 caudal fin; 10) base of middle caudal rays; 11) anterior attachment of
 dorsal membrane of caudal fin; 12) origin of adipose fin; 13) origin of
 dorsal fin; and 14) posterior end of the neurocranium. To ensure landmark
 placement did not migrate, and to adjust for imperfect digitizing, each
 fish was landmarked twice and results of the digitizing events were
 averaged. All morphometric analyses were performed in Morpho J.