Nuclear environmental DNA resolves fine-scale population genetic structure in an aquatic habitat

• Published in: iScience Vol. 27; no. 1; p. 108669
• Main Authors: Liu, Zifang, Kishe, Mary A., Gabagambi, Nestory P., Shechonge, Asilatu H., Ngatunga, Benjamin P., Smith, Katie, Saxon, Andrew D., Hudson, Alan G., Linderoth, Tyler, Turner, George F., Collins, Rupert A., Genner, Martin J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.01.2024; Elsevier
• Subjects: Environmental science; Evolutionary biology; Genetics; Techniques in genetics; Genetics; Techniques in genetics; Environmental science; Evolutionary biology
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2023.108669

There is considerable potential for nuclear genomic material in environmental DNA (eDNA) to inform us of population genetic structure within aquatic species. We tested if nuclear allelic composition data sourced from eDNA can resolve fine scale spatial genetic structure of the cichlid fish Astatotilapia calliptera in Lake Masoko, Tanzania. In this ∼35 m deep crater lake the species is diverging into two genetically distinguishable ecomorphs, separated by a thermo-oxycline at ∼15 m that divides biologically distinct water masses. We quantified population genetic structure along a depth transect using single nucleotide polymorphisms (SNPs) derived from genome sequencing of 530 individuals. This population genetic structure was reflected in a focal set of SNPs that were also reliably amplified from eDNA — with allele frequencies derived from eDNA reflecting those of fish within each depth zone. Thus, by targeting known genetic variation between populations within aquatic eDNA, we measured genetic structure within the focal species. [Display omitted] •Intraspecific genetic variation can be identified within aquatic environmental DNA•Allele frequencies in eDNA match those in local source populations•Environmental DNA can be used to quantify population genetic divergence Environmental science; Genetics; Techniques in genetics; Evolutionary biology