Abstract Objective Fish abundance and growth are regulated by a combination of bottom‐up and top‐down forces, but many management techniques depend more heavily on the latter. Here, we evaluated whether intersystem variation in nutrient loading and bottom‐up forces play more dominant roles in the control of abundance and growth of species across similar lakes than intra‐ and interspecific compensatory effects. We aimed to assess whether patterns of abundance and growth are consistent among fish species across lakes. Methods We tested this by evaluating pairwise comparisons of catch‐per‐unit‐effort, condition, and length‐at‐age data for 11 common warmwater fish species from 184 mesotrophic and eutrophic glacial lakes in Indiana, United States. We characterized the environmental conditions of each lake using limnological measurements (e.g., chlorophyll‐ a concentration and surface temperature), lake morphology descriptions (e.g., depth and size), catchment characteristics (e.g., percent agricultural land cover), and nutrient load modeling using the Long‐Term Hydrologic Impact Analysis model. Taking a meta‐analysis approach, we used effect size calculation from pairwise correlations among lakes to identify environmental and community impacts on species abundance, condition, and length at age. Result We demonstrated that there were positive associations among most species comparisons (i.e., multiple species experiencing relatively fast growth in the same lake). Evaluations of environmental conditions among systems suggested that differences in estimated phosphorus input and the limnological measurements of total phosphorus, Secchi depth, and chlorophyll‐ a concentration were good predictors of length at age and catch per unit effort for fish. Conclusion Our results indicated that there is a strong and consistent influence of environmental conditions and bottom‐up processes in determining species abundance and growth. This suggests that bottom‐up forces and environmental conditions linked to nutrient loading likely determine the upper boundary of fish abundance and growth in these lakes.
Differences in genomic architecture between populations, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco-evolutionary dynamics is in freshwater fishes, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n = 345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed in walleye assigned to Lake Winnipeg. These patterns exist despite the potential for high gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptive divergence between the two lakes despite gene flow. However, a specific adaptive role for the putative inversion could not be tested with the present data. Our study illuminates the importance of genomic architecture consistent with local adaptation in freshwater fishes. Furthermore, our results provide additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.
Abstract Delineating population structure helps fishery managers to maintain a diverse “portfolio” of local spawning populations (stocks), as well as facilitate stock‐specific management. In Lake Erie, commercial and recreational fisheries for Walleye Sander vitreus exploit numerous local spawning populations, which cannot be easily differentiated using traditional genetic data (e.g., microsatellites). Here, we used genomic information (12,264 polymorphic loci) generated using restriction site‐associated DNA sequencing to investigate stock structure in Lake Erie Walleye. We found low genetic divergence (genetic differentiation index F ST = 0.0006–0.0019) among the four Lake Erie western basin stocks examined, which resulted in low classification accuracies for individual samples (40–60%). However, more structure existed between western and eastern Lake Erie basin stocks ( F ST = 0.0042–0.0064), resulting in greater than 95% classification accuracy of samples to a lake basin. Thus, our success in using genomics to identify stock structure varied with spatial scale. Based on our results, we offer suggestions to improve the efficacy of this new genetic tool for refining stock structure and eventually determining relative stock contributions in Lake Erie Walleye and other Great Lakes populations.
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Abstract Interpretation of high‐throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site‐associated sequencing (RAD‐seq) data sets, which are increasingly being used for molecular ecology. To determine the influence PCR clones and the bioinformatic handling of clones have on genotyping, we evaluate four RAD‐seq data sets. Data sets were compared before and after clones were removed to estimate the number of clones present in RAD‐seq data, quantify how often the presence of clones in a data set causes genotype calls to change compared to when clones were removed, investigate the mechanisms that lead to genotype call changes and test whether clones bias heterozygosity estimates. Our RAD‐seq data sets contained 30%–60% PCR clones, but 95% of RAD‐tags had five or fewer clones. Relatively few genotypes changed once clones were removed (5%–10%), and the vast majority of these changes (98%) were associated with genotypes switching from a called to no‐call state or vice versa. PCR clones had a larger influence on genotype calls in individuals with low read depth but appeared to influence genotype calls at all loci similarly. Removal of PCR clones reduced the number of called genotypes by 2% but had almost no influence on estimates of heterozygosity. As such, while steps should be taken to limit PCR clones during library preparation, PCR clones are likely not a substantial source of bias for most RAD‐seq studies.
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems.
