DOI: 10.5061/dryad.rxwdbrvm0
title: Data from: A landscape genetics approach reveals species-specific connectivity patterns for stream insects in fragmented habitats

description: Dispersal is a critical process in ecology and evolution, shaping global
 biodiversity patterns. In stream habitats, which often exist within
 diverse and fragmented landscapes, dispersal ensures population
 connectivity and survival. For aquatic insects in particular, landscape
 features may significantly influence the degree of genetic connectivity
 among populations. Thus, understanding connectivity drivers in such
 populations is essential for the conservation and management of streams.
 We conducted a landscape genetic study using mitochondrial DNA (mtDNA) and
 genome-wide single nucleotide polymorphism (SNP) markers to assess
 functional connectivity of stream insects in a fragmented
 pasture-dominated landscape. We focused on three species with terrestrial
 winged adults: the mayfly Coloburiscus humeralis, the stonefly Zelandobius
 confusus, and the caddisfly Hydropsyche fimbriata. We observed significant
 spatial genetic structure at larger geographical distances (populations
 separated by ~30 and 170 km). However, the effect of landscape factors,
 which were assessed  at fine spatial scales varied among species:
 for C. humeralis SNP data, genetic differentiation was weakly correlated
 with land cover, suggesting greater population connectivity within stream
 channels protected by forested riparian zones compared to fragmented
 streams; for Z. confusus, widespread gene flow indicated high dispersal
 potential across forested and pasture land; while overland dispersal was
 reduced for for H. fimbriata (potentially due to local habitat features),
 this did not seem to hinder broader population connectivity. Our results
 emphasise the importance of assessing landscape features when evaluating
 population connectivity in stream riparian zones, which can greatly
 benefit stream management efforts through enhanced understanding of
 connectivity dynamics.
description: Insect Collection The study sampled aquatic
 insects at 11 sites across three streams in two neighboring catchments on
 Mount Pirongia, New Zealand, selected based on land cover, accessibility,
 and species presence. Sampling occurred at 3–4 sites per stream, spaced at
 least 490 m apart. Three additional stream sites were included at Mount
 Karioi (Wainui Stream), approximately 30 km from the main study area, and
 Mount Taranaki (Katikara & Patea Streams), about 170 km away. All
 streams had perennial flow, boulder/cobble bottoms, and minimal sediment
 deposition. <em>Coloburiscus humeralis</em> and
 <em>Zelandobius confusus </em>nymphs, and
 <em>Hydropsyche fimbriata</em> larvae were collected via
 kick-netting or hand-picking and preserved in 95% ethanol.
 DNA extraction and SNP sequencing DNA
 extraction, sequencing, and SNP genotyping were conducted by Diversity
 Array Technology (DarTseq™) in Australia. DNA was digested with
 the <em>PstI-SphI</em> enzyme pair, selected through a pilot
 study for optimal genome complexity reduction. Custom adapters were used
 for Illumina sequencing, and fragments were amplified via PCR. Amplified
 products were pooled and sequenced using 77 cycles of single-read
 sequencing on the HiSeq2500 (Illumina) platform. Raw reads were processed
 with a proprietary DarT pipeline for filtering, variant calling, and
 genotype generation. Each DNA sample was genotyped in duplicate to assess
 marker reproducibility. SNPs polymorphic across samples were scored as
 binary data: ‘1’ for presence, ‘0’ for absence, and ‘-’ for missing
 data. Additional sequence data information
 All individuals were also sequenced for the
 cytochrome <em>c</em> oxidase subunit I (COI) gene, conducted
 by the Canadian Centre for DNA Barcoding. Each individual sample ID in the
 SNP csv files can be matched to both the raw COI sequence data and the
 sample metadata in the dataset DS-EPTNZNI, published on the Barcode of
 Life Data Systems (BOLD) at dx.doi.org/10.5883/DS-EPTNZNI.
description: # A landscape genetics approach reveals species-specific connectivity
 patterns for stream insects in fragmented habitats
 [https://doi.org/10.5061/dryad.rxwdbrvm0](https://doi.org/10.5061/dryad.rxwdbrvm0) ## Description of the data and file structure #### Dataset Overview This dataset contains the genomic data used for population genetics analyses in the manuscript, to test the rates of gene flow among aquatic insect populations within streams and between streams across three different regions in the North Island of New Zealand: Pirongia, Karioi and Taranaki. The genomic dataset contains three csv files, each with single nucleotide polymorphisms (SNPs) reports for the three studied species: *Coloburiscus humeralis, Zelandobius confusus* and *Hydropsyche fimbriata. * The key features of the csv file include SNP position, frequency of genotypes and SNP markers scored as **binary presence/absence data**: * **"1"** → SNP is present in the sample. * **"0"** → SNP is absent in the sample. * **"-"** → Failed to score (low-quality or missing data). ### Files and variables #### File: ColoburiscusHumeralis\_SNP\_mapping.csv.zip **Description:** Contain a unique csv file with SNPs scores for *Coloburiscus humeralis* individual samples *AlleleID*: Unique identifier for the allele. *CloneID*: Identifier for the clone associated with the SNP. *AlleleSequence*: Full nucleotide sequence of the allele. *TrimmedSequence*: Trimmed version of the allele sequence. *SNP*: SNP mutation. *SnpPosition*: Position of the SNP within the sequence. *CallRate*: Proportion of successful genotype calls for this SNP. *OneRatioRef*: Ratio of homozygous reference alleles. *OneRatioSnp*: Ratio of homozygous SNP alleles. *FreqHomRef*: Frequency of homozygous reference genotype. *FreqHomSnp*: Frequency of homozygous SNP genotype. *FreqHets*: Frequency of heterozygous genotype. *PICRef*: Polymorphic Information Content (PIC) for reference allele. *PICSnp*: Polymorphic Information Content (PIC) for SNP allele. *AvgPIC*: Average Polymorphic Information Content across samples. *AvgCountRef*: Average read count for reference allele. *AvgCountSnp*: Average read count for SNP allele. *RepAvg*: Average repeatability score. *CHDF0M01:* Unique sample identifier and SNP scored as binary presence/absence data: **"1"** if SNP is present in the sample; **"0"** if SNP is absent in the sample; **"-"** if failed to score (low-quality or missing data). All remaining columns starting with CH follow this description. #### File: HydropsycheFimbriata\_SNP\_mapping.csv.zip **Description:** Contain a unique csv file with SNPs scores for *Hydropsyche fimbriata* individual samples *AlleleID*: Unique identifier for the allele. *CloneID*: Identifier for the clone associated with the SNP. *AlleleSequence*: Full nucleotide sequence of the allele. *TrimmedSequence*: Trimmed version of the allele sequence. *SNP*: SNP mutation. *SnpPosition*: Position of the SNP within the sequence. *CallRate*: Proportion of successful genotype calls for this SNP. *OneRatioRef*: Ratio of homozygous reference alleles. *OneRatioSnp*: Ratio of homozygous SNP alleles. *FreqHomRef*: Frequency of homozygous reference genotype. *FreqHomSnp*: Frequency of homozygous SNP genotype. *FreqHets*: Frequency of heterozygous genotype. *PICRef*: Polymorphic Information Content (PIC) for reference allele. *PICSnp*: Polymorphic Information Content (PIC) for SNP allele. *AvgPIC*: Average Polymorphic Information Content across samples. *AvgCountRef*: Average read count for reference allele. *AvgCountSnp*: Average read count for SNP allele. *RepAvg*: Average repeatability score. *HDF0M3:* Unique sample identifier and SNP scored as binary presence/absence data: **"1"** if SNP is present in the sample; **"0"** if SNP is absent in the sample; **"-"** if failed to score (low-quality or missing data). All remaining columns starting with HF follow this description. #### File: ZelandobiusConfusus\_SNP\_mapping.csv.zip **Description:** Contain a unique csv file with SNPs scores for *Zelandobius confusus* individual samples *AlleleID*: Unique identifier for the allele. *CloneID*: Identifier for the clone associated with the SNP. *AlleleSequence*: Full nucleotide sequence of the allele. *TrimmedSequence*: Trimmed version of the allele sequence. *SNP*: SNP mutation. *SnpPosition*: Position of the SNP within the sequence. *CallRate*: Proportion of successful genotype calls for this SNP. *OneRatioRef*: Ratio of homozygous reference alleles. *OneRatioSnp*: Ratio of homozygous SNP alleles. *FreqHomRef*: Frequency of homozygous reference genotype. *FreqHomSnp*: Frequency of homozygous SNP genotype. *FreqHets*: Frequency of heterozygous genotype. *PICRef*: Polymorphic Information Content (PIC) for reference allele. *PICSnp*: Polymorphic Information Content (PIC) for SNP allele. *AvgPIC*: Average Polymorphic Information Content across samples. *AvgCountRef*: Average read count for reference allele. *AvgCountSnp*: Average read count for SNP allele. *RepAvg*: Average repeatability score. *ZCDF0M11:* Unique sample identifier and SNP scored as binary presence/absence data: **"1"** if SNP is present in the sample; **"0"** if SNP is absent in the sample; **"-"** if failed to score (low-quality or missing data). All remaining columns starting with ZC follow this description.