The San Bernardino flying squirrel (Glaucomys oregonensis californicus) is thought to be the southernmost population of the Humboldt’s flying squirrel (G. oregonensis) and is restricted to the San Bernardino and San Jacinto Mountains in California. However, recent surveys indicate they have been extirpated from the latter locality. In this study, we characterized the intraspecific genetic structure and diversity of G. oregonensis. We amplified and sequenced at least 300 bp of the mitochondrial cytochrome-b gene and 11 nuclear microsatellites to provide baseline genetic data for this species and subspecies, investigate G. oregonensis genetic structure with a focus on the subspecies distributed in California, and finally evaluate the genetic diversity within G. o. californicus. Population and phylogenetic analyses were performed on a total of 147 samples (tissue, hair, and museum specimen) using the Illumina high-throughput sequencing (HTS) platform, thereby bioinformatically coding microsatellite alleles using established pipelines. Our results indicate reduced genetic diversity in G. o. californicus and highlight genetic distinctiveness of the San Jacinto population. In addition, the differences in genetic diversity between the mitochondrial and nuclear markers suggest sex-biased dispersal and historic separation of the species in multiple refugia followed by more recent gene flow among subpopulations in northern California. This study contributes valuable information toward understanding the genetic variation within G. oregonensis, provides information for future conservation decisions for G. o. californicus, and has novel implications for HTS genotyping-by-sequencing.

中文翻译：

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使用高通量测序对洪堡鼯鼠种群遗传分析

圣贝纳迪诺鼯鼠 (Glaucomys oregonensis californicus) 被认为是洪堡鼯鼠 (G. oregonensis) 中最南端的种群，仅限于加利福尼亚州的圣贝纳迪诺和圣哈辛托山脉。然而，最近的调查表明他们已经从后一个地方灭绝。在这项研究中，我们描述了 G. oregonensis 的种内遗传结构和多样性。我们扩增并测序了至少 300 bp 的线粒体细胞色素-b 基因和 11 个核微卫星，为该物种和亚种提供基线遗传数据，研究 G. oregonensis 的遗传结构，重点关注分布在加利福尼亚的亚种，最后评估G. o. 内的遗传多样性 加利福尼亚州。使用 Illumina 高通量测序 (HTS) 平台对总共 147 个样本（组织、头发和博物馆标本）进行种群和系统发育分析，从而使用已建立的管道对微卫星等位基因进行生物信息编码。我们的结果表明 G. o. 的遗传多样性降低。californicus 并突出圣哈辛托种群的遗传独特性。此外，线粒体和核标记之间遗传多样性的差异表明，该物种在多个避难所中存在性别偏见的分散和历史分离，随后是加利福尼亚北部亚群之间最近的基因流动。这项研究为了解 G. oregonensis 的遗传变异提供了有价值的信息，为 G. o. 的未来保护决策提供了信息。加利福尼亚州，