A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus.

Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.

Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish.

Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 µm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2-0.6 µm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.

Assessing the effects of historical exposure to endocrine-active compounds on reproductive health and genetic diversity in walleye, a native apex predator, in a large riverine system.

In this combined field and laboratory study, we assessed whether populations of native walleye in the Upper Mississippi River experienced altered genetic diversity correlated with exposure to estrogenic endocrine-active compounds (EACs). We collected fin-clips for genetic analysis from almost 600 walleye (13 sites) and subsampled 377 of these fish (6 sites) for blood and reproductive organs. Finally, we caged male fathead minnows at 5 sampling sites to confirm the presence of estrogenic EACs. Our findings indicate that male walleye in four river segments produced measurable concentrations of plasma vitellogenin (an egg-yolk protein and, when expressed in male fish, a biomarker of acute estrogenic exposure), a finding consistent with the presence of estrogenic EACs and consistent with published historical data for at least three of these study sites (Grand Rapids, St. Paul, and Lake City on Lake Pepin). Patterns of vitellogenin induction were consistent for native walleye and caged fathead minnows. No widespread occurrence of histopathological changes, such as intersex was found compared with published reports of intersex at the furthest downstream study site. To assess possible effects of estrogenic exposure on the genetic diversity of walleye populations at the study sites, we DNA-fingerprinted individual fish using 10 microsatellite loci. Genetic differences were observed between populations; however, these differences were consistent with geographic distance between populations, with the largest observed difference in genetic diversity found between fish upstream and downstream of St. Anthony Falls (and/or Lock and Dam 1 of the Mississippi River), traditionally a historical barrier to upstream fish movement. Although the persistent occurrence of endocrine disruption in wild fish populations is troubling, we did not detect degradation of reproductive organs in individual walleye or alteration in genetic diversity of walleye populations.

Mixed-source reintroductions lead to outbreeding depression in second-generation descendents of a native North American fish.

Reintroductions are commonly employed to preserve intraspecific biodiversity in fragmented landscapes. However, reintroduced populations are frequently smaller and more geographically isolated than native populations. Mixing genetically, divergent sources are often proposed to attenuate potentially low genetic diversity in reintroduced populations that may result from small effective population sizes. However, a possible negative tradeoff for mixing sources is outbreeding depression in hybrid offspring. We examined the consequences of mixed-source reintroductions on several fitness surrogates at nine slimy sculpin (Cottus cognatus) reintroduction sites in south-east Minnesota. We inferred the relative fitness of each crosstype in the reintroduced populations by comparing their growth rate, length, weight, body condition and persistence in reintroduced populations. Pure strain descendents from a single source population persisted in a greater proportion than expected in the reintroduced populations, whereas all other crosstypes occurred in a lesser proportion. Length, weight and growth rate were lower for second-generation intra-population hybrid descendents than for pure strain and first-generation hybrids. In the predominant pure strain, young-of the-year size was significantly greater than any other crosstype. Our results suggested that differences in fitness surrogates among crosstypes were consistent with disrupted co-adapted gene complexes associated with beneficial adaptations in these reintroduced populations. Future reintroductions may be improved by evaluating the potential for local adaptation in source populations or by avoiding the use of mixed sources by default when information on local adaptations or other genetic characteristics is lacking.

Full life-cycle assessment of gene flow consistent with fitness differences in transgenic and wild-type Japanese medaka fish (Oryzias latipes).

Transgenic fish in development for aquaculture could escape from farms and interbreed with wild relatives in the nearby environment. Predicting whether escapes would result in transgene introgression is a major challenge in assessing environmental risks of transgenic fish. Previous studies have simulated gene flow from transgenic fish using mathematical modeling of fitness traits to predict the relative selective value of transgenic genotypes. Here, we present the first study of gene flow over the full life cycle in openly-breeding populations of transgenic animals, along with measurement of fitness traits. We conducted two invasion experiments in which we released two lines of growth-enhanced transgenic fish (T67 and T400), Japanese medaka (Oryzias latipes), into populations of wild-type (W) medaka in structured mesocosms. After several generations, the frequency of transgenic fish varied across replicates in the first invasion experiment (6 months), but the frequency of transgenic fish decreased in the second experiment (19 months). We also measured selected fitness traits in transgenic and wild-type medaka because these traits could be used to predict the relative selective value of a genotype. We found that: T400 males were more fertile than W males; offspring of W females lived longer than those with transgenic mothers; and W and T67 females reached sexual maturity sooner than T400 females. In contrast with other research that reported larger transgenic males had a mating advantage, we found that W males obtained more matings with females than T males; genetic background effects may account for our differing results as we compared W and T fish derived from different strains. The decreasing frequency of transgenic fish in the second invasion experiment suggests that transgenic fish had a selective disadvantage in the experimental environment. Our finding of transgenic advantage of some fitness traits and wild-type advantage in others is consistent with our invasion experiment results.

Effects of maternally transferred organochlorine contaminants on early life survival in a freshwater fish.

Laboratory research has shown that female fish can pass toxic organochlorines (OCs) from their bodies to their eggs, killing their offspring if sufficient quantities are transferred. We conducted a controlled incubation study using gametes from a wild, OC-contaminated walleye (Sander vitreus) population (Bay of Quinte, Lake Ontario, Canada) in order to assess among-female variation in offspring early life survival in relation to ova concentrations of planar OCs (polychlorinated dibenzo-p-dioxins and furans and planar polychlorinated biphenyls) and a suite of other maternal and ova characteristics. Equal volumes of ova from each female were fertilized, pooled, and incubated together as an experimental cohort. Relative survival of each female's offspring was estimated as the proportion of surviving larvae (at approximately 5 d posthatch) that she contributed to the cohort as determined by microsatellite DNA parentage assignment. Total planar OC concentration (expressed as toxic equivalency of 2,3,7,8-tetrachlorodibenzo-p-dioxin) of ova was positively related to maternal age and size and to ova lipid content. However, early life survival did not decline with increasing ova planar OC concentrations. Similarly, we observed no significant relationships between early life survival and ova thiamine content, ova fatty acid composition, or maternal age or size. Early life survival was more strongly correlated with date of spawn collection, thyroid hormone status of the ova, and ovum size. Maternally transferred planar OCs do not appear to negatively influence female reproductive success in this walleye population.

Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea.

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Aland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran's I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100-150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.