使用家族遗传数据进行岛屿生物地理分析:DAISIEprep包
Joshua W Lambert1, Lizzie Roeble2, Théo Pannetier3
1Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands.
Molecular phylogenetics and evolution
|March 11, 2025
概括
新的软件DAISIEprep简化了岛屿生物地理模型的遗传学数据的提取和可视化. 这个R包通过克服进化推断中的数据结构挑战来帮助宏观进化和生态研究.
科学领域:
- 生态生态学 生态生态学
- 进化生物学 进化生物学
- 生物地理学 生物地理学 生物地理学
背景情况:
- 分子系谱越来越多地用于推断进化,生态和生物地理过程.
- 遗传学分析中的新型数据结构可能会对研究人员构成障碍.
- 通过物种化,移民和灭绝 (DAISIE) 的岛屿动态组合模型需要特定的遗传学数据格式.
研究的目的:
- 介绍DAISIEprep,一个旨在促进宏观进化和生物地理模型数据提取和可视化的R包.
- 解决与DAISIE等模型所需的非常规数据结构相关的用户挑战.
- 为岛屿生物地理研究提供可复制和用户友好的族系遗传数据的准备.
主要方法:
- DAISIEprep处理来自岛屿组合的分子遗传数据.
- 该软件提取了岛上殖民者的数据,并解释了各种不确定性 (生物地理,拓学,分类学).
- 它允许灵活地纳入缺失的物种或整个岛屿谱系.
主要成果:
- DAISIEprep以宏观进化和生物地理推理模型可解释的格式生成和可视化数据.
- 该软件包提供了用于数据提取和不确定性处理的简单算法.
- 它支持包括不完整的数据,如缺失的物种或谱系.
结论:
- DAISIEprep提高了岛屿生物地理研究的遗传学数据的可访问性和可用性.
- 该软件简化了数据准备,使研究人员能够解决岛屿进化和生态学的复杂问题.
- 这些工具对使用DAISIE的研究人员和分析岛屿物种遗传学数据集的研究人员来说是有价值的.
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