Species discovery and delimitation in ground beetles of the subgenus Trepanedoris: matrices and trees

We infer species boundaries in small ground beetles of the genus Bembidion, presenting the discoveries made by a class of students in an experiential learning course at Oregon State University. Focusing on the Bembidion connivens group of subgenus Trepanedorisoutside of California, we integrate data from external structure and male genitalia, DNA sequences of one mitochondrial gene and six nuclear genes, and geographic distribution. We analyze the DNA data using Bayesian multispecies coalescent methods to help infer reproductive communities or species; SPEEDEMON tended to split species more than what our integrated approach inferred, whereas DELINEATE tended to lump more than synthetic inference. We infer 12 species in North America outside of California, including four new species. The files in this archive include a Mesquite NEXUS file containing DNA data matrices and inferred trees, Supplementary Tables including localities of specimens and GenBank accession numbers of analyzed DNA s..., , # Species discovery and delimitation in ground beetles of the subgenus Trepanedoris: matrices and trees

Dataset DOI: [10.5061/dryad.9cnp5hqx1](10.5061/dryad.9cnp5hqx1)

## Description of the data and file structure

Most DNA data was collected by extracting DNA from specimens collected into 95% ethanol; the DNA was then subjected to PCR and Sanger sequencing, with the resulting chromatgrams processed using the Chromaseq package of Mesquite ([http://chromaseq.mesquiteproject.org](http://chromaseq.mesquiteproject.org)). 

Most phylogenetic trees contained in the file are from maximum likelihood analyses in IQ-TREE version 2.2.2.7.  One phylogenetic tree is the maximum clade credibility tree from a STACEY version 1.3.1 analysis conducted within BEAST version 2.7.6.

### Files and variables

#### File: Supplementary_Figures.pdf

**Description:** Two figures showing intermediate results in the DELINEATE analysis

#### File: Maddison_et_al._Trepanedoris_Matrices_And_Trees.v2.nex

**Descripti..., ,

本研究针对步甲属（Bembidion）小型步甲类群开展物种边界界定，呈现俄勒冈州立大学体验式学习课程中某班级学生团队的研究成果。本研究聚焦加州以外的Trepanedoris亚属Bembidion connivens类群，整合外部形态结构与雄性外生殖器数据、1个线粒体基因及6个核基因的DNA序列数据，以及地理分布信息。本研究采用贝叶斯多物种溯祖分析法处理DNA数据，以辅助推断繁殖社群或物种；相较于本研究的整合推断框架，SPEEDEMON倾向于拆分更多物种，而DELINEATE则倾向于合并更多类群。本次研究在加州以外的北美区域共界定出12个物种，其中包含4个新物种。本归档文件包含1个含DNA数据矩阵与推断系统树的Mesquite NEXUS格式文件，以及包含标本采集地与分析所用DNA序列GenBank登录号的补充附表（原文此处存在截断）。
# Trepanedoris亚属步甲的物种发现与界定：数据矩阵与系统树
数据集DOI：10.5061/dryad.9cnp5hqx1

## 数据与文件结构说明
绝大多数DNA数据通过采集于95%乙醇中的标本提取DNA获得，随后通过PCR扩增与Sanger测序完成测序，所得测序峰图采用Mesquite的Chromaseq工具包进行处理（http://chromaseq.mesquiteproject.org）。
文件中的绝大多数系统发育树基于IQ-TREE 2.2.2.7版本的最大似然法分析所得；另有1棵系统发育树为基于BEAST 2.7.6环境下运行STACEY 1.3.1版本分析得到的最大类群置信度树。

### 文件与变量
#### 文件：Supplementary_Figures.pdf
**说明：** 包含2张展示DELINEATE分析中间结果的示意图

#### 文件：Maddison_et_al._Trepanedoris_Matrices_And_Trees.v2.nex
**说明：** （原文此处存在截断）