The multispecies coalescent over-splits species in the case of geographically widespread taxa

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic–nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically-distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using ge..., , , , # Data from: The multispecies coalescent over-splits species in the case of geographically widespread taxa

Dataset DOI: [10.5061/dryad.7hs34mj](10.5061/dryad.7hs34mj)

## Description of the data and file structure

This repository contains data files for:

**Chambers EA & Hillis DM. (2020) The multispecies coalescent over-splits species in the case of geographically widespread taxa.** ***Systematic Biology 69(1):184–193***, **[DOI](https://doi.org/10.1093/sysbio/syz042).**

This paper re-examines species delimitation in the American milksnake species complex (*Lampropeltis triangulum*). All raw data and input files can be found on Dryad.

## DRYAD FILES: DATA FILES

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### Naming Conventions

* **TAXONOMY**: Files are named according to taxonomic groups contained with them.
* **trigentalt** Includes samples belonging to triangulum, gentilis, and alterna.
* **trigent** Includes samples belonging to L. triangulum and gentilis.
* **DATASETS**: Files for analyses are named according ...

近年来，诸多物种界定（species delimitation）研究仅依赖基于多物种溯祖模型（multispecies coalescent, MSC）开展的有限遗传数据分析，且此类研究的结果常被视为支持分类学修订的决定性证据。然而，绝大多数基于MSC的物种界定方法均存在广为人知却常未被满足的前提假设。若不加甄别地使用这类基于遗传数据的研究方法（未充分考量采样设计、先验分组的影响、距离隔离、质核不匹配以及种群结构等因素），可能会导致物种划分过度细分。
本文认为，在诸多常见的生物学场景中，研究者需对这些局限性保持格外谨慎，尤其是针对那些已被充分研究、地理变异显著且呈邻域分布的物种复合群。我们以历史上存在争议的物种类群——美国奶蛇（Lampropeltis triangulum复合群）为研究对象，结合相关数据对上述观点展开探讨，相关数据来自：《广布类群中多物种溯祖模型导致物种过度细分》。

# 数据来源：《广布类群中多物种溯祖模型导致物种过度细分》
数据集DOI: [10.5061/dryad.7hs34mj](10.5061/dryad.7hs34mj)

## 数据与文件结构说明
本仓库包含以下研究的配套数据文件：
**Chambers EA 与 Hillis DM. (2020) 广布类群中多物种溯祖模型导致物种过度细分。** 《系统生物学（Systematic Biology）》69(1):184–193，**DOI**: https://doi.org/10.1093/sysbio/syz042。
本研究重新审视了美国奶蛇物种复合群（*Lampropeltis triangulum*）的物种界定问题。所有原始数据与分析输入文件均可在Dryad数据库获取。

## DRYAD数据库文件：数据文件
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### 命名规则
* **分类学命名**：文件根据其包含的分类群命名。
* **trigentalt** 包含隶属于triangulum、gentilis与alterna的样本。
* **trigent** 包含隶属于L. triangulum与gentilis的样本。
* **数据集**：用于分析的文件命名规则如下……