2026/05/01 by Haylea Power, Mitchell J. O’Brien, Kathy Fuller +4 · 1 voice
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Animal Genetics and Reproduction #Cancer Genomics and Diagnostics #Environmental DNA in Biodiversity Studies
paper · doi:10.1002/edn3.70322
openalex publication_date 2026/05/01 · openalex created_date 2026/06/07 · openalex updated_date 2026/07/23
ABSTRACT Environmental DNA (eDNA) analysis has transformed biodiversity monitoring by enabling rapid, non‐invasive species detection. eDNA is derived from multiple species, cell types, and individuals. The non‐cellular fraction of eDNA may contain a mixture of genotypes from multiple individuals. Standard eDNA sampling and analysis does not allow recovery of individual multi‐locus genotypes from this mixture. Solving this requires two innovations: (1) separating eDNA particles (emCells) belonging to individual organisms from a mixture; (2) generating multilocus genotypes from individual emCells. Having addressed partitioning individual emCells previously, here we tested whether multi‐locus nuclear single nucleotide polymorphism (SNP) genotypes can be reliably generated from lab‐generated and isolated single fish cells as a model for wild emCells. Our workflow “emCell‐Seq,” combines fluorescence‐activated cell sorting (FACS) to isolate environmental metazoan cells (emCells) with multiplex PCR targeting discriminatory nuclear SNPs. Individual zebrafish ( Danio rerio ) cells were created from tissue and pooled into mock emCells samples of known single and mixed source. Pooled samples were sorted by FACS, which isolated individual cells that were genotyped with a panel of 35 SNPs. SNP genotypes from emCells were compared to known genotypes to assess assignment accuracy. For emCells in artificial pool from multiple individuals, 91% ( n = 129) were correctly assigned. No mixed genotypes were obtained. This study provides the first evidence that individual‐level nuclear genotypes can be obtained from isolated fish emCells. Extending these findings to field‐collected emCells will significantly expand the scope ecological analyses enabled by eDNA.