Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Additional Data

This repository is intended to accompany the final report to the US Fish and Wildlife Service, entitled: Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new microsatellite markers for use in population structure and kinship analyses. We also used DNA from natural mortalities to determine whether non-invasively collected samples could be used to generate enough single nucleotide polymorphisms (SNPs) to perform fine-scale genomic analyses. Whole mitochondrial genomes were assembled, annotated, and used to infer a phylogeny with museum specimens of insulanus collected ~100 years ago from Vancouver Island and other members of the E. ausonides species complex. The results indicated that insulanus suffers from low heterozygosity, a small effective population size (Ne), and low allelic diversity. There was evidence of high levels of inbreeding in some individuals, but inbreeding was uneven across the population. There was no population structure or partitioning by host plant detected. The mitogenomes of extant insulanus were all identical and there was a loss of allelic diversity in modern samples compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management decisions and genetic monitoring. Included in this repository are: Sample metadata for all samples used, including which analysis they were used in (microsatellite, mitogenome, and/or ddRAD), and the BioSample and SRA accessions for sequenced samples desposited with NCBI GenBank under BioProject PRJNA1156227 (IMB_metadata.csv) The VCF file of SNPs produced from ddRAD NovaSeq sequencing (novaseq_IMB_20_depth_Q30_50_missing.vcf) The microsatellite loci used for population genetic analyses (IMB_microsatellite_loci.csv)本仓库旨在配合提交给美国鱼类及野生动物管理局（US Fish and Wildlife Service）的最终报告，报告标题为《狭布岛大理石蝴蝶（Narrowly Endemic Island Marble Butterfly）的保护遗传学与基因组学》。 本研究的目的为采集并分析濒危物种岛大理石蝴蝶（Euchloe ausonides insulanus）的非侵入性DNA样本，以评估种群结构、识别适应潜力、助力人工繁育，并支持迁地保护规划。研究团队使用从蛹便、蜕壳以及自然死亡个体中提取的DNA，开发并验证了13个全新的微卫星（microsatellite）标记，用于种群结构和亲缘关系分析。此外，研究人员还利用自然死亡个体的DNA，探究非侵入性采集的样本是否能够产生足够的单核苷酸多态性（single nucleotide polymorphisms, SNPs）以开展高精度基因组分析。 研究团队组装并注释了完整线粒体基因组，并结合约100年前在温哥华岛采集的岛大理石蝴蝶博物馆标本以及E. ausonides物种复合体的其他成员，构建了系统发育树。结果显示，岛大理石蝴蝶存在杂合度较低、有效种群规模（Ne）偏小以及等位基因多样性匮乏的问题。部分个体表现出高水平近交，但种群内近交程度并不均匀。未检测到基于寄主植物的种群结构或遗传分化。现存岛大理石蝴蝶的线粒体基因组完全一致，且与博物馆标本相比，现代样本的等位基因多样性有所丢失。现存种群与博物馆标本共同构成一个单系群，研究人员还鉴定出多个可用于区分岛大理石蝴蝶与其他亚种的候选诊断等位基因。基于上述结果，研究人员提出了物种管理决策与遗传监测的相关考量方向。 本仓库包含以下内容： 1. 所有所用样本的元数据，包括其应用的分析类型（微卫星、线粒体基因组和/或ddRAD测序），以及已提交至NCBI GenBank、隶属于BioProject PRJNA1156227的测序样本的BioSample和SRA登录号（文件为IMB_metadata.csv） 2. 由ddRAD NovaSeq测序得到的SNP的VCF文件（novaseq_IMB_20_depth_Q30_50_missing.vcf） 3. 用于种群遗传分析的微卫星位点信息（IMB_microsatellite_loci.csv）