Genome-wide markers test the status of two putative species of North American bumble bees

Accurate species delimitation is critical to identifying the conservation status of species. Molecular species delimitation methods have revealed previously unrecognized cryptic species across the taxonomic spectrum. However, studies vary in the molecular markers selected, analytical approaches used, and taxon sampling, which sometimes results in conflicting conclusions. We tested a two-species hypothesis of the Bombus occidentalis complex using nuclear (ultraconserved elements, UCE) and mitochondrial (cytochrome c oxidase I, COI) markers to infer maximum likelihood and Bayesian phylogenies for the taxa. We extracted tissue and sequenced 102 specimens from across the geographic range of the species complex. Through our analyses, we concluded that the complex actually represents two species, B. occidentalis and B. mckayi. Here, we include the raw sequences for the UCE and COI analyses and the final newick-formatted trees from the analyses. , UCE methods: Methods generally followed those in Branstetter et al. (2021). We extracted DNA from the mid and hind legs of specimens using a Zymo Quick-DNA Miniprep Plus extraction kit and stored extracts in -80°C freezers at PIRU. Specimens were collected between 1956 and 2017, with one specimen from 1920. We used a Tapestation 4150 automated electrophoresis system (Agilent, 5301 Stevens Creek Blvd., Santa Clara, CA 95051, USA) to measure the size of DNA fragments extracted from the specimens and Qubit 3.0 to quantify DNA concentrations. The size of fragments varied among specimens due to their variable ages, collection methods, and storage histories. We sheared the DNA fragments to target fragment sizes of 400 to 600 base pairs using a Q800R2 acoustic sonicator (Qsonica, Newtown, CT, U.S.A.). We varied shearing times from 0 seconds to 120 seconds with a 10-second on, 10-second off pulsing pattern. Samples with small fragment sizes were sheared for less time and samples with large frag..., , # Data from: Genome-wide markers test the status of two putative species of North American bumble bees [https://doi.org/10.5061/dryad.z612jm6nw](https://doi.org/10.5061/dryad.z612jm6nw) ## Description of the data and file structure The goal of this study was to clarify the species status of *Bombus occidentalis* and *B. mckayi* by expanding on the phylogenetic analyses that were previously done, which focused on only one mitochondrial gene (cytochrome c oxidase I, COI) and included few specimens from a limited portion of the geographic range. Results of phylogenetic studies vary based on the molecular markers selected, analytical approaches used, and taxon sampling, which sometimes results in conflicting conclusions. Phylogenetic studies that focus on a single gene are criticized for misrepresenting the evolutionary history of species because nuclear and mitochondrial genomes, and even some genes within them, may have different evolutionary patterns. *B. occidentalis* was once an abu..., ,精准的物种界定对于确定物种的保护现状至关重要。分子物种界定方法已在各类分类群中揭示了此前未被认知的隐存物种。然而，不同研究在选取分子标记、采用分析方法以及类群采样方面存在差异，有时会得出相互矛盾的结论。本研究针对西方熊蜂（Bombus occidentalis）复合群的双物种假说展开验证，利用核基因组标记（超保守元件，ultraconserved elements, UCE）与线粒体基因组标记（细胞色素c氧化酶I，cytochrome c oxidase I, COI），对该类群构建最大似然法与贝叶斯系统发育树。我们从该物种复合群的整个地理分布范围内采集了102份标本并提取组织进行测序。通过分析，我们确认该复合群实际包含两个物种：西方熊蜂（B. occidentalis）与麦凯熊蜂（B. mckayi）。本文附带了用于UCE与COI分析的原始序列，以及分析得到的最终newick格式（newick-formatted）系统发育树。 UCE实验方法： 实验方法总体参考Branstetter等人2021年的研究方案。我们使用Zymo Quick-DNA Miniprep Plus提取试剂盒从标本的中足与后足中提取DNA，并将提取物保存于PIRU实验室的-80℃冰箱中。标本采集时间跨度为1956年至2017年，另有1份标本采集于1920年。 我们使用Tapestation 4150自动化电泳系统（安捷伦，地址：美国加利福尼亚州圣克拉拉市史蒂文斯溪大道5301号，邮编95051）检测提取得到的DNA片段大小，并用Qubit 3.0定量DNA浓度。由于标本的保存年限、采集方式与存储历史存在差异，不同标本的DNA片段大小有所不同。我们使用Q800R2声波破碎仪（Qsonica，美国康涅狄格州纽敦市）将DNA片段剪切至400至600碱基对的目标片段长度。破碎时长设置为0秒至120秒，采用10秒开启、10秒关闭的脉冲模式。片段较小的样本缩短破碎时长，片段较大的样本则…… # 数据来自：全基因组标记验证北美两种疑似熊蜂物种的分类地位 [https://doi.org/10.5061/dryad.z612jm6nw](https://doi.org/10.5061/dryad.z612jm6nw) ## 数据与文件结构说明 本研究旨在通过拓展此前的系统发育分析，澄清西方熊蜂（B. occidentalis）与麦凯熊蜂（B. mckayi）的物种分类地位。此前的研究仅聚焦于单个线粒体基因（细胞色素c氧化酶I，COI），且仅采集了地理分布范围内有限区域的少量标本。系统发育研究的结果会因选取的分子标记、采用的分析方法以及类群采样的不同而存在差异，有时甚至会得出相互矛盾的结论。仅聚焦于单个基因的系统发育研究常被诟病无法准确反映物种的进化历史，因为核基因组与线粒体基因组，乃至基因组内的部分基因，可能具有不同的进化模式。西方熊蜂（B. occidentalis）曾是……