DOI: 10.5061/dryad.bnzs7h4p4
title: Microbial composition and diversity across invasive and native spiders in the pacific islands

description: This dataset comprises microbiome sequencing data collected from
 co-occurring native and invasive spider species sampled across three
 distinct locations in the Hawaiian Islands, alongside mainland reference
 populations. The data include gut microbial community profiles cleaned
 using QIIME2 and taxonomically assigned to Amplicon Sequence Variants
 (ASVs) using the SILVA database for annotating bacterial taxonomic groups
 to sequence information. The final dataset consists of an ASV table,
 taxonomic table, metadata file, and phylogenetic tree files that were then
 subjected to downstream processing using phyloseq, where vertically
 transmitted endosymbionts and environmentally acquired microbes were
 separately analyzed to observe differences across invasion status. This
 dataset was used to observe variation in microbial abundance and diversity
 across invasive and native taxa, supporting further investigations into
 the role of microbiota in arthropod adaptation to novel environments.
 Thus, this dataset has potential for reuse in studies of invasion biology,
 microbial ecology, and host-microbe interactions. Ethical considerations
 and site-specific sampling metadata are included to facilitate
 reproducibility and appropriate data reuse.
description: # Microbial composition and diversity across invasive and native spiders
 in the Pacific Islands ## Authors **First Author:** Madison J.
 Pfau,  [mapfau@ucsc.edu](mailto:mapfau@ucsc.edu), University of
 California, Santa Cruz  **Coauthors:** See Dryad Submission for full
 author list  **Corresponding Author:** Rosemary
 Gillespie, [gillespie@berkeley.edu](mailto:gillespie@berkeley.edu),
 University of California, Berkeley #### Description This dataset contains
 high-throughput 16S rRNA sequencing data from the gut microbiomes of
 co-occurring native and invasive spider species sampled from three
 Hawaiian Island sites and mainland reference populations. It supports
 analyses of microbial diversity and host-microbe interactions related to
 invasion biology. #### Contents #### 1. `raw_sequencing_data.zip/` *
 Zipped folder containing demultiplexed FASTQ files for all samples
 (forward and reverse reads), including sequencing blanks  * Low-quality
 and filtered sequences have been removed  * Sequences were processed using
 **QIIME2** and denoised with **DADA2**  * Taxonomic assignment was
 conducted using the **SILVA 16S rRNA database (v138)**  * ASVs were
 clustered at 97% similarity and compiled into `filtered_clustered_ASV.csv`
 #### 2. `filtered_clustered_ASV.csv` * Amplicon Sequence Variant (ASV)
 Count Table * **Rows:** ASV IDs (Feature IDs)  * **Columns:** Sample IDs 
 * **Values:** Abundance of each ASV per sample #### 3.
 `spider_metadata_16S_only.csv` * Sample metadata file  * **Columns
 include:**  * `SampleID`  * `Species Identification` * `Site`  * `Region`
 (island/mainland)  * `Invasion_Status` (native/invasive)  * I7_Index_ID /
 I5_Index_ID: Barcode identifiers for multiplex sequencing. - index /
 index2: Specific nucleotide barcode sequences corresponding to the above
 index IDs. - Additional sequencing preparation details #### Methods
 Summary * DNA was extracted from dissected spider guts  * The 16S rRNA V4
 region was amplified and sequenced on the **Illumina MiSeq platform (2x250
 bp)**  * Sequences were demultiplexed and processed using **QIIME2**  *
 ASVs were generated with **DADA2** and taxonomically assigned via the
 **SILVA database**  * Functional predictions were performed using
 **PICRUSt2**  * Downstream analyses were conducted in R using the
 **`phyloseq`** package, with comparisons of vertically transmitted
 endosymbionts and environmentally acquired microbes #### File Naming
 Conventions * Sample names are coded as:
 `X_[SampleNumber]_[Region]_[Site]_16S`  * All taxonomic annotations follow
 **SILVA v138** conventions **Contact** For questions about the data,
 please contact: **Madison J.
 Pfau**, [mapfau@ucsc.edu](mailto:mapfau@ucsc.edu)}