Data from: A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific
Data files
Oct 17, 2024 version files 45.50 MB
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CO1_alignment.fasta
56.47 KB
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CO1_BEAST.tre
87.93 KB
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populations.snps.vcf
45.22 MB
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Radseq_BEAST.tre
118.83 KB
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README.md
2.56 KB
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specimen_list.xlsx
12.89 KB
Apr 08, 2025 version files 45.64 MB
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AAL_Haplotypes_DNAsp.nex
14.64 KB
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AccessionReport.txt
1.55 KB
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AOL_Haplotypes_DNAsp.nex
8.27 KB
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CO1_alignment.fasta
56.47 KB
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CO1_BEAST.tre
87.93 KB
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COI_alignment_polished.fasta
56.93 KB
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flatfile.txt
62.18 KB
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populations.snps.vcf
45.22 MB
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Radseq_BEAST.tre
118.83 KB
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README.md
3.17 KB
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specimen_list.xlsx
12.89 KB
Abstract
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.
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 > 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.
Use FigTree v.1.4.3 to visualize the MCC tree