DOI: 10.5061/dryad.905qfttvb
title: Network dynamics revealed from eDNA highlight seasonal variation in urban mammal communities

description: Urban ecosystems are expanding rapidly, significantly altering natural
 landscapes and impacting biodiversity. Here we explore seasonal variation
 in mammal diversity using environmental DNA (eDNA) from soil samples
 collected during winter and summer across 21 urban parks in Detroit,
 Michigan. We estimated gamma (regional), alpha (local), and beta
 (compositional change) diversity to determine if seasonal shifts,
 reflecting winter scarcity and summer abundance in mammal community
 composition and human activity, could be detected using eDNA. We expected
 that larger parks would exhibit greater diversity and higher seasonal
 turnover, consistent with the species-area relationship (SAR), and
 hypothesised that increased summer resource availability would lead to
 decreased network density as species disperse more broadly. We found that
 urban parks show subtle, park-specific changes in community composition
 influenced by both ecological and anthropogenic factors, with species
 including striped skunk, brown rat, and groundhog responsible for the
 observed seasonal variation. Consistent with the SAR, larger parks
 supported higher species richness and diversity. Ecological network
 analysis, focusing on metrics such as clustering coefficient and network
 density, revealed a decrease in the overall connectivity and cohesiveness
 of species interactions from winter to summer, supporting our hypothesis
 of broader species dispersal during resource-rich periods. Notably, human
 DNA was prevalent in all parks, alongside detections of pig and cow eDNA,
 potentially reflecting human disturbance and anthropogenic food
 inputs. Our findings underscore the efficacy of eDNA analysis in
 capturing urban mammal community dynamics, the impact of human activities
 on biodiversity, and its potential as a valuable tool for urban ecological
 research. Ultimately, enhancing monitoring capacity aids in conservation
 and urban planning efforts that will promote human-wildlife coexistence
 and preserve the socio-ecological benefits stemming from biodiversity
 across cityscapes.
description: # Network dynamics revealed from eDNA highlight seasonal variation in
 urban mammal communities Dataset DOI:
 [10.5061/dryad.905qfttvb](10.5061/dryad.905qfttvb) ## Description of the
 data and file structure This dataset contains environmental DNA (eDNA)
 metabarcoding results from soil samples collected across 21 urban parks in
 Detroit, Michigan. The data represent vertebrate species detections across
 two seasons (Winter and Summer), aimed at evaluating spatial and seasonal
 variation in mammal community composition and biodiversity in urban green
 spaces. ### Files and variables #### File:
 Detroit\_eDNA\_master\_dataJH.csv **Description:**  ##### Variables *
 Park: Name of the Detroit urban park * Sample_ID: Unique identifier for
 each DNA sample (camera trap-season-extraction replicate) * ID: Park
 sublocation (camera trap) * Season: Sampling winter or summer *
 Extraction_replicate: Three extraction replicates were made from each soil
 sample * Identity: Best match taxonomic assignment from BLAST *
 ASV: Amplicon Sequence Variant ID assigned via DADA2 pipeline *
 Common: Common name of detected species from  * Readcount: Number of reads
 assigned to the ASV in the sample after removal of contamination *
 Extraction_date_dmy: Date of DNA extraction (day-month-year format) *
 final.weight..g.: Weight of sample used in extraction (grams) *
 Nanodrop_conc_ng.uL: DNA concentration measured with Nanodrop (ng/μL) for
 quality control * Nanodrop_260.280: Nanodrop purity ratio (260/280) for
 quality control * Sequence: DNA sequence of the ASV * sseqid: Subject
 sequence ID from the BLAST reference database * pident: Percent identity
 from sequence alignment * length: Alignment length * mismatch: Number of
 mismatches in alignment * gapopen: Number of gap openings in alignment *
 qstart: Query start position * qend: Query end position * sstart: Subject
 sequence start * send: Subject sequence end * evalue: BLAST statistics for
 alignment confidence. Estimates the number of matches expected by chance;
 lower values indicate more significant hits. * bitscore: BLAST statistics
 for alignment confidence. Reflects the alignment quality; higher scores
 indicate better sequence similarity. * superkingdom: Taxonomic
 classification * phylum: Taxonomic classification * class: Taxonomic
 classification * order: Taxonomic classification * family: Taxonomic
 classification * genus: Taxonomic classification * species: Taxonomic
 classification ## Access information Other publicly accessible locations
 of the data: * NA Data was derived from the following sources: *
 Sequencing was conducted at the Yale Center for Genomic Analysis and
 prepared using cutadapt, DADA2, and BLAST as stated in Methods.