Restriction site‐associated DNA sequencing generates high‐quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China

Abstract

Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high-quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site-associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure-species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty-seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure-species Asian carps in the United States and China.

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…This method is popular and has been used in many studies since its inception (Figure S1). RAD sequencing has been used, particularly in fish, to identify population divergence (Boehm, Waldman, Robinson, & Hickerson, 2015; Ferchaud & Hansen, 2016; Larson et al., 2014), for SNP identification in polyploid fish (Hohenlohe, Amish, Catchen, Allendorf, & Luikart, 2011; Ogden et al., 2013; Palti et al., 2014), in phylogeographic studies (Macher et al., 2015; Reitzel, Herrera, Layden, Martindale, & Shank, 2013), for QTL analysis (Gagnaire, Normandeau, Pavey, & Bernatchez, 2013; Houston et al., 2012; Yoshizawa et al., 2015), for linkage mapping (Brieuc, Waters, Seeb, & Naish, 2014; Henning, Lee, Franchini, & Meyer, 2014), in hybridization studies (Hand et al., 2015; Lamer et al., 2014; Pujolar et al., 2014), for exploration of genome architecture and evolution (Brawand et al., 2014; Kai et al., 2014; Waples, Seeb, & Seeb, 2016), and in phylogenetic analyses (Gonen, Bishop, & Houston, 2015; Wagner et al., 2013). This methodology should be particularly suited to phylogeographic studies as the inference power from large numbers of markers may identify patterns that are not easily visible in traditional analyses based on relatively few loci (Davey et al., 2011).…”

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

“…Genotyping analysis of 57 species‐specific SNPs developed by Lamer et al. (2014) identified B1 as a hybrid; however, transcriptomic data suggested B1 was a second‐generation backcross with bighead carp (Figure 3). A similar situation occurred between S1 (second‐generation backcross with silver carp) and S2 (pure silver carp), whose transcriptomic analysis suggests S1 should be a post‐first‐generation backcross with silver carp.…”

“…Within the native ranges, reproduction isolation may be maintained by spatial or temporal isolation rather than pre‐ or postzygotic barriers (Mayr, 1970). This study provides an insight into hybridization and introgression of bigheaded carps, which supports the prediction that bigheaded carps in the MRB are likely to form a hybrid swarm (Lamer et al., 2014). This introgressive hybridization may result from a shift to a more homogenous reproductive environment in the MRB which lacks extrinsic factors that are required for the restriction of gene flow between species (Seehausen, Takimoto, Roy, & Jokela, 2008).…”

Physiological consequences of hybridization: early generation backcrossing decreases performance in invasive bigheaded carps

“…ability to obtain prey or avoid predation). Thus, quantifying nutritional status can provide insights into hybrid performance relative to their parents and may provide critical information for invasive species that hybridize, such as bighead carp, Hypophthalmichthys nobilis, and silver carp, Hypophthalmichthys molitrix (hereafter, bigheaded carps; Lamer et al 2010Lamer et al , 2014Lamer et al , 2015.…”

“…Previous research has suggested that bigheaded carps may negatively affect invaded habitats (Irons et al 2007;Sass et al 2010;Calkins et al 2012;Sass et al 2014). Bigheaded carps have hybridized in native and non-native habitats, with an estimated 44% of individuals in the MRB existing as hybrids (Lamer et al 2010(Lamer et al , 2014(Lamer et al , 2015. Physiological performance of hybrids relative to their parents is unknown, and quantifying differences could have significant implications for better understanding and managing these invaders.…”