DOI: 10.5061/dryad.1c59zw40r
title: Data from: A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific

description: Aim We assessed the population genetic structure of the kleptoparasitic
 spider Argyrodes bonadea across the Southwestern Pacific
 islands. Our aim is to evaluate the impact of overseas distances and, in
 particular, the Kerama gap, as potential drivers of genetic
 differentiation. If no relationship exists, then we assume dispersal
 following adaptive change as alternative non-vicariant mechanism that
 generates divergence. Location Southwestern Pacific Islands. Taxon
 Argyrodes bonadea. Methods We used mitochondrial Cytochrome Oxidase 1
 (CO1) gene sequences and Restriction Site-associated DNA Sequencing
 (RAD-seq) for our analyses. Results Two strongly supported lineages, an
 Amami-Okinawa Lineage (AOL) and an Austral-Asia Lineage (AAL), correspond
 to two separate clades, roughly divided by the Kerama Gap, in phylogenetic
 trees estimated here. However, species delimitation led to the
 interpretation of only a single species present. The AOL exhibits complex,
 geographically structured host web spider species specificity, wherein the
 Amami population utilizes Cyrtophora, but AOL samples in Okinawa
 associate exclusively with Nephila—and yet all broadly
 distributed AAL populations show no evidence of host web spider species
 specificity. Main Conclusion The population boundary between AOL and AAL
 likely results from local adaptation to novel hosts—instead of isolation
 by the Kerama Gap—following long-distance dispersal and range expansion.
 Our results suggest kleptoparasitic spiders have the capacity to overcome
 permanent deep-sea barriers and colonize distant landmasses. Whereas
 peripheral populations (AOL) demonstrate the capacity for specialization
 to a single host, which may have contributed to genetic differentiation
 and isolation, the broadly distributed AAL persists and has successfully
 expanded its geographical range as a host generalist, which may contribute
 to ongoing gene flow inferred in this study.
description: Use FigTree v.1.4.3 to visualize the MCC tree
description: # Data from: Dispersal and host-driven genetic divergence: a phylogenomic
 case of Argyrodes bonadea (Araneae, Theridiidae) ## Data files ### 1.
 Specimen list The list includes 112 samples used for CO1 and RAD-seq
 analyses. The areas covered by our sample collection include Palawan and
 Surigao, Philippines; Queensland in Australia; the major Ryukyu island
 groups of Yaeyama, Miyako (includes Irabu and Ikema), Okinawa, and Amami
 in Southern Japan; Taitung, Taiwan. Argyrodes bonadea were found
 co-inhabiting the webs of different hosts such as Nephila, Argiope, and
 Cyrtophora, Cyclosa, and as well as Nihonhimea as observed during the
 fieldwork from 2007 to 2020. ### 2. VCF Stacks v2.0 was used to assemble
 the raw RAD-seq sequences then we merged the forward and reverse strands
 using Paired-End read merger. The paired strands were aligned to Argyrodes
 miniaceus genome draft sequenced via Hi-seq 2500 platform as the reference
 with the aid of a standard alignment program Burrows-Wheeler Aligner
 (BWA). The gstacks program processes the aligned data and calls SNPs using
 the population-wide data per locus as executed in ref_map.pl. The
 population program filters the data, calculates the population genetics
 statistics and produces different data formats to be used for the
 downstream analyses. We defined population as a set of individuals per
 island. Loci were filtered out at 50% occupancy rate to include locus that
 is present in at least half of the total individuals in a population. ###
 3. Maximum Clade Credibility Tree We used the Multi-Locus data set
 (ML_SNPs data) from our RAD-seq libraries to generate the MCC tree. GTR
 was the best fit model based on the jModelTest2 v.2.1.1. We used the
 uniform flat prior with Markov Chain Monte Carlo (MCMC) chain length of 1
 x 10^9 and sampled trees were saved every 1 x 10^3. The generated XML file
 was run in BEAST v.1.10.4 then the trace file results were visualized in
 Tracer v.1.7.1 to determine the Effective Sample Size (ESS &gt; 200) and
 discard the first 10% of the sampled trees as burn-in. The final MCC tree
 was generated in TreeAnnotator v.1.8.4.This can be visualized using
 FigTree v.1.4.3. Maximum Clade Credibility (MCC)tree of the 82 CO1
 sequences generated in TreeAnnotator 1.8.4 (Rambaut & Drummond, 2010),
 and visualized it using FigTree 1.4.3 (Rambaut, 2014).The original XML
 file was generated in BEAUTi 1.10.4 (Drummond et al., 2012)then run in
 BEAST 1.10.4 (Drummond et al., 2012.) ### 4. Alignment Fasta file of the
 82 CO1 sequences manually aligned using Geneious Pro 6.03.\
 "COI_alignment_polished.fasta" is the manually polished COI
 alignment, retaining all 65 sequences. ### 5. NCBI Assession Report and
 Flatfile We submitted the haplotypes to NCBI, providing the Accession
 Report as a metadata summary and the Flatfile as the complete record with
 nucleotide sequences. Change Log ========== ### Version 3 – 2025-04-08 *
 Added description of the updated alignment, NCBI accession report, and
 flatfile in the README. ### Version 2 – 2024-10-30 * Updated the alignment
 files, NCBI accession report, and flatfile. ### Version 1 – 2024-10-17 *
 Initial release.