Assessment of methods for DNA extraction from formalin-fixed fish specimens and a population genomic analysis of geographical disjunction in Southern Brook Lamprey (Ichthyomyzon gagei).

Abstract

Conservation efforts are limited for many fishes, and genetic approaches using recent and preserved collections could help address important knowledge gaps. Southern Brook Lamprey, Ichthyomyzon gagei, predominately occur in the southeastern United States, with disjunct populations in Wisconsin. Limited access to fresh tissue and DNA- damaging effects of formalin fixation hinder efforts to define the Wisconsin lamprey. To better understand the relationship of Wisconsin I. gagei populations to those in the southeastern U.S., I (1) identified a method that isolates sufficient quantity and quality DNA from formalin-fixed fish; and (2) used reduced-representation genome sequencing to assess genetic relationships between Southern Brook Lamprey populations from the north and south. Extractions compared DNA concentration, purity, and fragment length between extraction protocols, tissue types and preservation periods, and yielded usable DNA for sequence analysis. Gill tissue from lamprey was used to infer population genetic structure and phylogenetic relationships. A clear genetic difference between northern and southern populations of Southern Brook Lamprey was found, with at least two distinct populations of lamprey within Wisconsin. These results highlight the importance of museum specimens, and demonstrate the presence of a distinct I. gagei-related lineage in Wisconsin that warrants separate conservation management.