Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest

Background: Refugial populations in Quaternary glaciations are critical to understanding the evolutionary history and climatic interactions of many extant species. Compared with the well-studied areas of Europe and Northern America, refugia of species in eastern Asia remain largely unknown. Here, we investigated the phylogeographic history of a globally important insect pest, the oriental fruit moth Grapholita molesta, in its native range of China.
Results: Genetic structure analyses unveiled three distinct groups and a set of populations with admixture. Approximate Bayesian Computation (ABC) analyses support range expansion of this moth from southwest groups of Yunnan and Sichuan to northern and eastern China. A set of admixed populations was found around these two ancestral groups. This pattern of genetic structure points to two refugia located in the Yunnan region and Sichuan Basin. The split of the two refugia was dated to 329.2 thousand years ago in the penultimate glacial period...., Microsatellite loci genotyped from each individual01_microsatellite_loci_genotyped_from_each_individual.genepopAligned mitochondrial genes from all individuals02_aligned_mitochondrial_genes_from_all_individuals.fasMitochondrial haplotypes used for SplitsTree analysis03_mitochondrial_haplotypes_used_for_SplitsTree_analysis.nexMitochondrial haplotypes used for molecular dating using BEAST04_mitochondrial_haplotypes_used_for_molecular_dating_using_BEAST.fasInputfile for BAPS and STRUCTURE analysesinput_files_of_BAPS_STRUCTURE.rarR script for DAPC analysis09_R_script_for_DAPC_analysis.RFiles for DIYABC analysesfiles for DIYABC analyses.rarCommands used in IMa2 analysis12_commands_used_in_IMa2_analysis.txtScripts and input files used in IBD analysisscripts and input files used in IBD analysis.rar,

研究背景：第四纪冰期（Quaternary glaciations）避难所种群（refugial populations）是解析诸多现存物种（extant species）演化历史与气候交互作用的关键所在。相较于研究较为充分的欧洲与北美地区，东亚地区物种的冰期避难所仍鲜有系统性研究。本研究以全球重要农业害虫——梨小食心虫（Grapholita molesta）为研究对象，在其原生分布范围中国境内开展了谱系地理历史（phylogeographic history）研究。

研究结果：遗传结构分析（genetic structure analyses）揭示了三个显著分化的类群以及一批存在遗传混合的种群。近似贝叶斯计算（Approximate Bayesian Computation, ABC）分析结果支持该蛾类从云南、四川西南部的类群向中国北方及东部地区扩散。在这两个祖先类群周边发现了一批兼具混合遗传背景的种群。此种遗传结构模式表明，该物种存在两处冰期避难所，分别位于云南地区与四川盆地。经推算，两处避难所的分化时间可追溯至倒数第二次冰期（penultimate glacial period），距今约32.92万年。……

附带研究数据文件：
1. 每个个体的微卫星位点基因分型文件：01_microsatellite_loci_genotyped_from_each_individual.genepop
2. 所有个体的比对线粒体基因文件：02_aligned_mitochondrial_genes_from_all_individuals.fas
3. 用于SplitsTree分析的线粒体单倍型文件：03_mitochondrial_haplotypes_used_for_SplitsTree_analysis.nex
4. 用于BEAST分子定年分析的线粒体单倍型文件：04_mitochondrial_haplotypes_used_for_molecular_dating_using_BEAST.fas
5. BAPS与STRUCTURE分析的输入文件压缩包：input_files_of_BAPS_STRUCTURE.rar
6. DAPC分析的R脚本文件：09_R_script_for_DAPC_analysis.R
7. DIYABC分析所需文件压缩包：files for DIYABC analyses.rar
8. IMa2分析使用的命令文件：12_commands_used_in_IMa2_analysis.txt
9. IBD分析所用脚本与输入文件压缩包：scripts and input files used in IBD analysis.rar