ASAP: assemble species by automatic partitioning
ASAP: assemble species by automatic partitioning
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DOI：
10.1111/1755-0998.13281
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发表时间：
2020-11-20
影响因子：
7.7
通讯作者：
Achaz, Guillaume
中科院分区：
文献类型：
--
作者：
Puillandre, Nicolas;Brouillet, Sophie;Achaz, Guillaume
本文介绍了一种基于单位点序列比对（即条形码数据集）构建物种划分的新方法——自动划分装配物种（ASAP）。ASAP的效率足以在几分钟内将数据集分成10(4)个序列的假定物种。虽然基于进化理论，ASAP是一种分层聚类算法的实现，它只使用成对遗传距离，避免了系统发育重建的计算负担。重要的是，ASAP提出了一种新的评分系统来划分物种，这种评分系统不使用种内多样性的生物学先验洞察力。ASAP是一个独立的程序，既可以通过图形网络界面使用，也可以下载并编译供本地使用。我们已经评估了它与其他三个程序（ABGD， PTP和GMYC）在10个真实的COI条形码数据集上的能力，这些数据集代表了不同程度的挑战（从小而简单的案例到大而复杂的数据集）。我们还使用蒙特卡罗模拟多物种聚合框架来评估ASAP和其他程序的优缺点。通过这些分析，我们证明ASAP有潜力成为分类学家的主要工具，因为它可以在完整的图形探索界面中快速提出相关物种假设，作为综合分类过程的第一步。
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10(4) sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.