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

Zifang Liu; Mary A Kishe; Nestory P Gabagambi; Asilatu H Shechonge; Benjamin P Ngatunga; Katie Smith; Andrew D Saxon; Alan G Hudson; Tyler Linderoth; George F Turner; Rupert A Collins; Martin J Genner

doi:10.1016/j.isci.2023.108669

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

iScience. 2023 Dec 7;27(1):108669. doi: 10.1016/j.isci.2023.108669. eCollection 2024 Jan 19.

Authors

Affiliations

¹ School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK.
² Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania.
³ Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
⁴ W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA.
⁵ School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
⁶ Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.

Abstract

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.

Keywords: Environmental science; Evolutionary biology; Genetics; Techniques in genetics.