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?
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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 ...
适应性渐渗（adaptive introgression）指通过杂交获取有利遗传变异，此类变异因与有益性状相关联而受到自然选择的青睐。这些从近缘物种继承的渐渗后适应性等位基因，可使杂交谱系适应新的环境变化或开拓全新的生态位。本研究通过基因组分析，对盗蛛（kleptoparasitic spider）兰银斑蛛（Argyrodes lanyuensis）的物种形成模式展开研究，并在中国台湾-菲律宾过渡带检测适应性渐渗的遗传证据。利用高度多态性单核苷酸多态性（single nucleotide polymorphism, SNP），本研究证实，在更新世早中期，台湾岛花莲种群与菲律宾（含兰屿）种群分化形成了当前物种。通过近似贝叶斯计算（Approximate Bayesian Computation）与随机森林（Random Forests）筛选得到的最优定殖模型，支持物种形成过程中存在瓶颈效应，该结论得到后续观测数据的支撑……，mt-COI数据集：我们通过minimap2（Heng Li, 2018）从限制性位点关联DNA测序（restriction-site associated DNA sequencing, RAD-seq）标记中，提取了2个花莲样本与2个绿岛样本的mt-COI基因序列。将这些序列与Responte等人（2021）已发表的4条mt-COI单倍型序列（存于GenBank，编号MN881069.1、MN881070.1、MN881071.1、MN881072.1）以及1个外类群物种彩虹银斑蛛（Argyrodes rainbowi，MW549752.1）的序列进行比对。最终，我们使用MAFFT（Katoh, K. & Standley, D. M., 2013）对8条内类群mt-COI序列与1条外类群序列完成比对。我们采用溯祖树模型（Kingman, J. F. C., 1982）与无相关对数正态松弛时钟模型（Drummond et al., 2006）作为BEAST软件的先验参数。设置基于蜘蛛线粒体替换速率估计得到的ucld.mean值为0.0112 位点⁻¹（Bidegaray-Batista & Arnedo, 2011; Kuntner et al., 2013），并将ucld.stdv的标准差设为0.01。我们运行马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）链共5×10⁸代，每1×1…… ## **COI数据集:** "**COI_alignment.fasta**"为比对格式FASTA文件，包含内类群物种兰银斑蛛（Argyrodes lanyuensis）的序列：2个花莲样本与2个绿岛样本的RAD-seq标记提取序列、Responte等人（2021）已发表的4条GenBank登录的mt-COI单倍型序列（MN881069.1、MN881070.1、MN881071.1、MN881072.1），以及1个外类群物种彩虹银斑蛛（Argyrodes rainbowi，MW549752.1）的序列。 "**COI.trees**"与"**COI_consensus_tree**"为BEAST基于溯祖模型构建的系统发育树与共识树。我们设置无相关对数正态松弛时钟与蜘蛛线粒体替换速率估计值作为校准分化时间的先验参数。 "**flatfile.txt**"与"**AccessionReport.tsv**"源自NCBI提交系统，包含本研究中采集自绿岛与花莲的兰银斑蛛单倍型序列信息。 ### **RAD-seq数据集:** "**Lan1.vcf**"与"**Lan2.vcf**"共包含130个个体……
