Data for: Re-collected after 55 years: a new species of Bembidion (Coleoptera, Carabidae) from California
Data files
Jul 04, 2023 version files 529.56 KB
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brownorumDataDryad.nex
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README.md
Abstract
A new species of the carabid beetle genus Bembidion Latreille is described from the Central Valley, Los Angeles Basin, and surrounding areas of California. Bembidion brownorum sp. nov. is a distinctive species, a relatively large member of subgenus Notaphus Dejean, and within Notaphus, a member of the Bembidion obtusangulum LeConte species group. It has faint spots on the elytra and a large, convex, rounded prothorax. Of the 22 specimens from 11 localities, all but one were collected more than 55 years ago. Although the collection of the holotype in 2021 at UV light suggests the species is still extant, the lack of other recent specimens suggests the species may have a more restricted distribution than in the past, and its populations may be in decline.
Methods
DNA was extracted using a Qiagen DNeasy Blood and Tissue Kit. Fragments for the four genes were amplified using the Polymerase Chain Reaction on an Eppendorf Mastercycler Pro Thermal Cycler, using TaKaRa Ex Taq and the basic protocols recommended by the manufacturers.
Assembly of multiple chromatograms for each gene fragment and initial base calls were made with Phred (Green and Ewing 2002) and Phrap (Green 1999) as orchestrated by Mesquite's Chromaseq package (Maddison and Maddison 2021a; Maddison and Maddison 2021c), with subsequent modifications by Chromaseq and manual inspection. Multiple peaks at a single position in multiple reads were coded using IUPAC ambiguity codes.
Maximum likelihood analysis was conducted for each gene individually using IQ-TREE and trees from standard bootstrap analysis in IQ-TREE of the concatenated matrix.
Usage notes
This file, intended to be opened in Mesquite (http://www.mesquiteproject.org) contains 4 single-gene matrices as well as a concatenated matrix.