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..., ,