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?

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 observ..., mt-COI dataset: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 Argyrodes rainbowi  (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). 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 108 generations with tree sampling frequency per 1 x 1..., , ## **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 ...