DOI: 10.5061/dryad.9w0vt4bnn
title: Data from: Recent range expansion and genomic admixture in a kleptoparasitic spider, Argyrodes lanyuensis: A case of adaptive introgression on isolated small island of the Taiwan-Philippine transition zone?

description: Adaptive introgression involves the acquisition of advantageous genetic
 variants through hybridization, which subsequently are favored by natural
 selection due to their association with beneficial traits. These
 post-introgression adaptive alleles inherited from related species may
 allow the hybrid lineage to adapt to new environmental changes or exploit
 novel ecological niches. Here, we analyzed speciation patterns of the
 kleptoparasitic spider Argyrodes lanyuensis through genomic analyses and
 tested for genetic evidence of adaptive introgression at the
 Taiwan-Philippines transition zone. Using highly polymorphic SNPs, our
 study demonstrated that speciation occurred when the Hualien (on Taiwan
 Island) and Philippine (including the Orchid Island) lineages separated
 during the early to mid-Pleistocene. The best colonization model suggested
 by Approximate Bayesian Computation and Random Forests supported an
 inference of a bottleneck during speciation, an interpretation reinforced
 by observation of lower FST values and reduced genetic diversity of the
 Philippine+Orchid Island lineage. We found the highest support for the
 occurrence of introgression on the youngest island (Green Island) of the
 Taiwan-Philippines transition zone based on ABBA-BABA test. Additionally,
 we have identified a putative adaptive locus under balancing selection on
 Green Island, suggesting evolution by adaptive introgression in a
 newly-formed niche (or novel geographical context). Our study highlights a
 possible rare case of introgression at the Taiwan-Philippines transition
 zone under balancing selection, that could be an evolutionary response to
 a unique climatological zone lying between the tropical climate of the
 Philippines and the subtropical climate of Hualien, Taiwan.
description: <strong>mt-COI dataset:</strong><br>We extract
 the mt-COI gene sequences of 2 Hualien samples and 2 Green Island samples
 from our RAD markers by minimap2 (Heng Li, 2018). We aligned these
 sequences with four previously published mt-COI haplotype sequences of
 Responte et al., (2021) available in Genbank (MN881069.1, MN881070.1,
 MN881071.1, MN881072.1) and one outgroup species <em>Argyrodes
 rainbowi </em> (MW549752.1). In total, we aligned eight mt-COI
 sequences from the ingroup and one additional outgroup species using mafft
 (Katoh, K., & Standley, D. M., 2013).<em> </em>We
 implemented the coalescent tree model (Kingman, J. F. C., 1982) and the
 uncorrelated lognormal relaxed clock model (Drummond et al., 2006) as
 priors in BEAST. A ucld.mean of 0.0112 site-1, derived from the
 mitochondrial substitution rate estimates in spiders (Bidegaray-Batista
 & Arnedo, 2011; Kuntner et al., 2013), and used a standard
 deviation of ucld.stdv = 0.01. We ran the MCMC chain for 5 x
 10<sup>8</sup> generations with tree sampling frequency per 1
 x 10<sup>4</sup> generations in three replicates. Burn-in was
 determined using Tracer v.1.7.1 (Rambaut et al., 2018), in which the first
 10 percent of the trees were discarded (Rambaut et al., 2018). The maximum
 clade credibility (MCC) tree was summarized in TreeAnnotator (Drummond et
 al., 2012) and visualized using FigTree (Rambaut, 2014).
 <strong>RAD-seq dataset:</strong>
 We used the Multiplex Shotgun Genotyping (MSG; Andolfatto et al.,
 2011) with modifications from our in-house protocol to prepare the
 high-throughput sequencing libraries. After size selection using Pippin
 Prep with a 1.5% agarose gel cassette, the size selected fragments
 (300-450 bp) were amplified using the Phusion High Fidelity PCR kit (NEB,
 USA). Then, we purified the DNA libraries using AMPure XP magnetic beads
 (Beckman, USA) following the manufacturer’s instructions.  We have
 multiplexed 130 samples and were sequenced using the Illumina Nova-seq
 6000 in a sequencing facility (Genomics Co. Ltd., Taiwan). We
 demultiplexed Illumina raw reads using the process_radtags program from
 stacks manual version 2.4 (Catchen et al., 2013) to clean and trim the
 sequences. The combined forward and reverse reads from PEAR version 0.9.6
 (Zhang et al., 2014) were aligned with the <em>A.
 miniaceu</em>s reference genome using the Burrows-Wheeler Alignment
 (BWA) tool (Li & Durbin, 2009).
description: ## **COI Dataset:** "**COI_alignment.fasta**", an alignment
 fasta includes ingroup species, *Argyrodes lanyuensis, *from two Hualien
 samples and two Green Island samples extracted from RAD markers, four
 previously published mt-COI haplotype sequences of Responte et al., (2021)
 available in Genbank (MN881069.1, MN881070.1, MN881071.1, MN881072.1), and
 one outgroup species, *Argyrodes rainbowi *(MW549752.1)
 "**COI.trees**" and "**COI_consensus_tree**" are the
 Phylogenetic trees and the consensus tree performed by BEAST under the
 coalescent model. We set the uncorrelated lognormal relaxed clock and the
 mitochondrial substitution rate estimates in spiders as priors to
 calibrate divergence time. "**flatfile.txt**" and
 "**AccessionReport.tsv**" are received from the NCBI submission
 system, containing Argyrodes lanyuensis haplotypes that we collected from
 Green Island and Hualien in this artical. ### **RAD-seq Dataset:**
 "**Lan1.vcf**" and "**Lan2.vcf**" contain a total of
 130 individual *Argyrodes lanyuensis* from three separate landmasses of
 Taiwan, and 14 localities (6 islands) from the Philippines. The RAD-seq
 assembly exported loci that are shared in at least 50% of the total
 samples. We kept a total of 23,989 loci for the 50% coverage in the Lan1
 dataset. This configuration is composed of all SNPs per locus, which
 produced 59,080 SNPs. For the Lan2 dataset, we assembled a more
 conservative matrix by retaining only one unlinked SNP per locus, which
 produced 9,187 SNPs. The "**Lan3.vcf**" dataset assembled all
 SNPs for *Argyrodes lanyuensis* samples and the outgroup, which produced a
 total of 69,411 SNPs. "**RAD_seq_Coalescent_rep.trees**" and
 "**RAD_seq_Yule_rep.trees**" are the three repeat trees of each
 model performed by the BEAST, Coalescent, and Yule processes. 
 "**SNAPP_fossil_lower_limit.trees**",
 "**SNAPP_fossil_upper_limit.trees**" and
 "**SNAPP_taiwan_age_combined.trees**", are the three divergence
 time calibration schemes tested by SNAPP using the multispecies coalescent
 model. "**RASP_result**" is the standard output from Reconstruct
 Ancestral State in Phylogenies.
 "**DIYABC_Group1_scenarios_headerRF.txt**" and
 "**DIYABC_Group2_scenarios_headerRF.txt**", are the two assigned
 population scenarios for Approximate Bayesian Computation (ABC) with
 supervised machine learning method, Random Forest (DIYABC).
 "**DIYABC_Lan2_snp_filtered.snp**" is the filtered SNPs dataset
 to fit the input qualify by the DIYABC, at least one genotyped individual
 per population for each locus. In total of 2,616 SNPs were retained.
 "**CLUMPAK_STRUCTURE_summary.pdf**" is the summary of *K*
 cluster by CLUMPAK website using the Delta K approach.