Geographic patterns of intra- and interspecific diversity of riverine fish species in the Italian Northern Apennines and Ligurian Alps

Abstract: Understanding the intricate dynamics of biodiversity within and across riverine ecosystems, influenced by geological history and environmental factors, is crucial for effective conservation and management strategies. Italy, particularly the Ligurian region, harbors diverse freshwater fish communities and populations shaped by unique geological and hydrological conditions. Here, we investigated the suitability of environmental DNA (eDNA) metabarcoding to identify inter- and intraspecific diversity patterns of riverine fish populations in drainage basins on both sides of the main drainage divide (MDD) between the Adriatic and Ligurian river basins in Northern Italy. We collected 96 aquatic eDNA samples across 48 riverine sites, amplified them using a cytochrome b primer pair, and denoised the sequences to retrieve amplicon sequence variants (ASVs). We calculated communities’ phylogenetic distance with betaMPD based on genetic distances derived from the ASVs, combined them with conductance-based landscape metrics, and applied generalized dissimilarity models to assess spatial genetic structure. Our results reveal genetic differentiation among populations of several fish species, with some displaying clustering patterns across the main drainage divide and isolation by distance patterns. Overall, taxon richness was higher on the Adriatic side (12.82 ± 3.57; 26 unique taxa) than on the Ligurian side of the MDD (8.35 ± 3.66 SD, 25 unique taxa), but the other way around for ASV richness across all species (Ligurian side: 51.94 ± 25.79, 308 unique ASV, Adriatic side: 68.00 ± 32.97, 274 unique ASV). Our findings highlight the effectiveness of eDNA metabarcoding in uncovering various facets of diversity, shedding light on hidden genetic diversity among ASVs, and revealing significant spatial genetic structuring in freshwater fish populations across multiple species. This dataset contains the raw sequencing data and bioinformatic code for a study investigating environmental DNA (eDNA) metabarcoding patterns of riverine fish populations across the main drainage divide (MDD) between the Adriatic and Ligurian river basins in Northern Italy. We collected 96 aquatic eDNA samples across 48 riverine sites (Spring 2021 and 2022). Samples were amplified using a cytochrome b primer pair and sequenced on an Illumina MiSeq. Methodology Summary: Target: Teleost Fish. Marker: ~420 bp fragment of the Cytochrome b gene. Primers: Modified from Hänfling et al. (2016). Sequencing: Illumina MiSeq (2x250 bp). Bioinformatics: Pipeline implemented in Shell and R (DADA2, DECIPHER). Dataset Contents: This repository provides the raw data and scripts required to reproduce the analysis: Raw Sequencing Data: Demultiplexed FASTQ files (R1/R2) for 2021 and 2022 libraries. Demultiplexing Metadata: Tag-to-sample mapping files (.xlsx) containing primer and tag sequences (within the corresponding library folder). Field Metadata: Sample collection details (dates, coordinates, environmental variables). Reference Database: The custom trained DECIPHER classifier (.rds) used for taxonomic assignment. Code/Scripts: The complete bioinformatic pipeline (Shell and R scripts) used to process the raw data into ASV tables. Publication Status: This data supports a manuscript currently under review at Ecology and Evolution (Kirschner & Vance et al.). Intermediate processed data (e.g., final ASV tables) are also available as Supplementary Material in the published manuscript.