Assessing population impacts of low-use lock-and-dam structures on the Alabama River: fish hard-part microchemistry and genetics

Abstract

Two techniques, hard-part microchemistry and genetics, were used in a coordinated effort to determine the impacts of low-use lock-and-dam structures on riverine fish species of varying migratory nature and capability. These approaches were selected to investigate population connectivity from different temporal perspectives: microchemistry – shorter term (over a fish’s lifetime) and genetics – long-term (over multiple generations in a fish population). The first technique, fish hard-part microchemistry, has evolved into a powerful tool for fisheries managers, allowing one to quantify natal habitat, population connectivity, and individual movement patterns. To assess these objectives in a river system modified by the construction of dams, hard-part micro-elemental composition was quantified using Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS) for individuals of each species collected during 2017-2019. Species and structures were: Paddlefish (dentary bones), Smallmouth Buffalo (otoliths), and Largemouth Bass (otoliths). Location of capture within the study area was used to assign each fish to a population group. These locations were specific river sections that were separated by the three low-use lock-and-dam structures on the Alabama River, as well as major tributaries. Seasonal water samples were obtained from 15 sites throughout the study area during 2017-2018 to allow comparison of trace element conditions in water to those incorporated into fish hard-parts. Concentrations of Sr, Ba, Mn, Mg, and Ca were quantified. Water elemental signatures were spatially variable but temporally consistent throughout the study area, and were reflected in fish hard-part structure element-to-calcium ratios in core, age-0, edge, and whole-transect ablations. In particular, hard-part Sr:Ca ratios differed significantly among river sections for all three species. Additionally, discriminant function analyses (DFAs), determined how accurately multivariate element signatures could classify a fish back to its river section of capture. Paddlefish yielded the highest level of accuracy (55-74%; errors nearly always assigning individuals to an adjacent river section), followed by Largemouth Bass (39-48%), and Smallmouth Buffalo, (37-47%). Differences in classification accuracy among species are likely due to a combination of factors, including differences in habitat type preferred by each species, varying life-history strategies, differences in the hard-part structures analyzed, and human influences (i.e., stocking and/or transport).

The second approach, population genetic analyses, were performed on a subset of the same fish collected for microchemistry analysis (i.e., for Paddlefish and Smallmouth Buffalo), representing fish from each river section, tributaries to the Alabama River, and neighboring watersheds. Genotyping-by-sequence techniques (GBS) identified 1,889 and 3,737 single nucleotide polymorphisms (SNPs) post filtering in Paddlefish and Smallmouth Buffalo, respectively, which were then used to estimate population diversity indices and conduct differentiation analyses. Analysis of molecular variance (AMOVA), discriminant analysis of principal components (DAPC), Bayesian clustering, and pairwise comparisons of FST values concluded that Paddlefish and Smallmouth Buffalo did not show strong evidence for genetic divergence among river sections.

When considering the combined results of these two approaches, the “potential” for population isolation trends to continue in some river sections exists based on microchemistry if no mitigation actions are taken. However, genetic analyses indicate that currently these dams have either not been present long enough, or that there is enough mixing/population connectivity occurring to prevent genetic divergence across river sections. Some limited mixing is believed to occur across lock-and-dam structures for Paddlefish and Smallmouth Buffalo, with fish movement highly restricted to passage during high water events at a crested spillway at the lowermost dam, or through lock structures.