Pedigree analysis and estimates of effective breeding size characterize sea lamprey reproductive biology.

The sea lamprey (Petromyzon marinus) is an invasive species in the Great Lakes and the focus of a large control and assessment program. Current assessment methods provide information on the census size of spawning adult sea lamprey in a small number of streams, but information characterizing reproductive success of spawning adults is rarely available. We used RAD-capture sequencing to genotype single nucleotide polymorphism (SNP) loci for ~1600 sea lamprey larvae collected from three streams in northern Michigan (Black Mallard, Pigeon, and Ocqueoc Rivers). Larval genotypes were used to reconstruct family pedigrees, which were combined with Gaussian mixture analyses to identify larval age classes for estimation of spawning population size. Two complementary estimates of effective breeding size (N b), as well as the extrapolated minimum number of spawners (N s), were also generated for each cohort. Reconstructed pedigrees highlighted inaccuracies of cohort assignments from traditionally used mixture analyses. However, combining genotype-based pedigree information with length-at-age assignment of cohort membership greatly improved cohort identification accuracy. Population estimates across all three streams sampled in this study indicate a small number of successfully spawning adults when barriers were in operation, implying that barriers limited adult spawning numbers but were not completely effective at blocking access to spawning habitats. Thus, the large numbers of larvae present in sampled systems were a poor indicator of spawning adult abundance. Overall, pedigree-based N b and N s estimates provide a promising and rapid assessment tool for sea lamprey and other species.

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics.

Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site-associated DNA sequencing (RAD-Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00-0.018) were concordant with previous microsatellite-based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age-1 and age-2 families of full and half-siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non-native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.

An automated approach to Litchfield and Wilcoxon's evaluation of dose-effect experiments using the R package LW1949.

The authors developed a package, LW1949, for use with the statistical software R to automatically carry out the manual steps of Litchfield and Wilcoxon's method of evaluating dose-effect experiments. The LW1949 package consistently finds the best fitting dose-effect relation by minimizing the chi-squared statistic of the observed and expected number of affected individuals and substantially speeds up the line-fitting process and other calculations that Litchfield and Wilcoxon originally carried out by hand. Environ Toxicol Chem 2016;35:3058-3061. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

Population synchrony of a native fish across three Laurentian Great Lakes: evaluating the effects of dispersal and climate.

Climate and dispersal are the two most commonly cited mechanisms to explain spatial synchrony among time series of animal populations, and climate is typically most important for fishes. Using data from 1978-2006, we quantified the spatial synchrony in recruitment and population catch-per-unit-effort (CPUE) for bloater (Coregonus hoyi) populations across lakes Superior, Michigan, and Huron. In this natural field experiment, climate was highly synchronous across lakes but the likelihood of dispersal between lakes differed. When data from all lakes were pooled, modified correlograms revealed spatial synchrony to occur up to 800 km for long-term (data not detrended) trends and up to 600 km for short-term (data detrended by the annual rate of change) trends. This large spatial synchrony more than doubles the scale previously observed in freshwater fish populations, and exceeds the scale found in most marine or estuarine populations. When analyzing the data separately for within- and between-lake pairs, spatial synchrony was always observed within lakes, up to 400 or 600 km. Conversely, between-lake synchrony did not occur among short-term trends, and for long-term trends, the scale of synchrony was highly variable. For recruit CPUE, synchrony occurred up to 600 km between both lakes Michigan and Huron (where dispersal was most likely) and lakes Michigan and Superior (where dispersal was least likely), but failed to occur between lakes Huron and Superior (where dispersal likelihood was intermediate). When considering the scale of putative bloater dispersal and genetic information from previous studies, we concluded that dispersal was likely underlying within-lake synchrony but climate was more likely underlying between-lake synchrony. The broad scale of synchrony in Great Lakes bloater populations increases their probability of extirpation, a timely message for fishery managers given current low levels of bloater abundance.

Temporal trends of young-of-year fishes in Lake Erie and comparison of diel sampling periods.

We explored temporal trends of young-of-year (YOY) fishes caught in bottom trawl hauls at an established offshore monitoring site in Lake Erie in fall during 1961-2001. Sampling was conducted during morning, afternoon, and night in each year. Catches per hour (CPH) of alewife (Alosa pseudoharengus) YOY were relatively low and exhibited no temporal trend. This result was consistent with the species' intolerance to Lake Erie's adverse winter water temperatures. Gizzard shad (Dorosoma cepedianum) YOY decreased sharply after 1991, which was consistent with recent oligotrophication of the lake. Following the establishment in 1979 and rapid increase of white perch (Morone americana) YOY, white bass (Morone chrysops) and freshwater drum (Aplodinotus grunniens) YOY decreased. Trout-perch (Percopsis omiscomaycus) YOY decreased during 1986-1991, but recovered to previous levels during 1991-2001. The recovery coincided with the resurgence of mayflies (Ephemoptera) in the lake. CPH of spottail shiner (Notropis hudsonius) and emerald shiner (N. atherinoides) YOY exhibited no temporal trend between 1961 and the late 1970s to early 1980s. CPH of yellow perch (Perca flavescens) YOY decreased during 1961-1988, and walleye (Sander vitreum) YOY increased overall during the time series. These observations were consistent with published studies of adults in the region. CPH of 4 of the 10 species of YOY considered were greatest during night. CPH for walleye YOY was higher in the morning than in the afternoon, but there was no significant difference between night and morning abundances. The results suggest that (1) CPH of YOY fishes may be a useful monitoring tool for Lake Erie, and (2) offshore monitoring programs that do not include night sampling periods may underestimate recruitment for several common species.

Effects of selected polybrominated diphenyl ether flame retardants on lake trout (Salvelinus namaycush).

Polybrominated diphenyl ether (PBDE) flame-retardants have been identified as an emergent contaminants issue in many parts of the world. In vitro analyses were conducted to test the hypothesis that selected PBDEs congeners affect viability, apoptosis, and necrosis of thymocytes from laboratory-reared lake trout (Salvelinus namaycush). At current environmental levels (< 1 mg/L), effects of the tested PBDEs on thymocytes were negligible. However, at 100 mg/L, major effects were seen for congener brominated diphenyl ether 47 (BDE-47) and minor effects were seen for congener BDE-99.

In vitro toxicity and interactions of environmental contaminants (Arochlor 1254 and mercury) and immunomodulatory agents (lipopolysaccharide and cortisol) on thymocytes from lake trout (Salvelinus namaycush).

The immunotoxicity of chemical combinations commonly encountered by the lake trout (Salvelinus namaycush) immune system was the focus of this study. It was hypothesised that combinations of an environmental contaminant (mercuric chloride or Aroclor 1254) and an immunomodulatory agent (bacterial endotoxin or cortisol) might interact to produce a greater toxicity than that of the environmental contaminant alone at concentrations typically encountered in piscine blood and other tissues. Thus lake trout thymocytes were isolated and treated with mercuric chloride or Aroclor 1254 in the presence and absence of cortisol or lipopolysaccharide. Incubations were performed for 6 or 20 h at 4 degrees C or 10 degrees C. Lipopolysaccharide did not affect the toxicity of either contaminant. In contrast, cortisol enhanced the toxicity of both environmental contaminants. Hence, stressors that lead to increased cortisol production, but not lipopolysaccharide directly, may increase the toxicity of mercury and Aroclor 1254 to lake trout thymocytes.