Delimiting species without monophyletic gene trees
Delimiting species without monophyletic gene trees
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DOI：
10.1080/10635150701701091
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发表时间：
2007-12-01
影响因子：
6.5
通讯作者：
Carstens, Bryan C.
中科院分区：
文献类型：
--
作者：
Knowles, L. Lacey;Carstens, Bryan C.
遗传数据经常用于划分物种，其中物种地位是根据排他性标准确定的，例如互惠单系。不仅有许多从这些数据中推断出的边界与其他来源（如形态学）不一致的经验例子，特别是最近衍生的物种，而且种群遗传理论也清楚地表明，由于遗传阈值没有明确考虑到物种形成的时间如何影响遗传分化模式，因此物种状态不可避免地会产生偏差。这项研究代表了基因数据如何用于划分物种的根本转变。基因树和物种历史之间的关系是概率建模的，而不是将基因树等同于物种树或基于某种遗传阈值的物种状态。在这里，我们表明，用于计算互单系概率的相同理论也可用于划分物种，尽管广泛存在不完整的谱系排序。初步模拟研究的结果表明，最近衍生的物种可以在物种形成后实现互惠单系的必要时间之前很久就被准确识别出来。该研究还表明了抽样的重要性，无论是对基因座还是对个体。尽管对基于聚结的方法有效的条件进行了彻底的调查，即相对于物种有效种群大小的分化时间如何影响准确的物种划分，但结果与最近其他旨在推断物种关系的研究一致，表明尽管缺乏单系基因树，物种分化的信号仍然存在并且可以提取。使用明确的基于模型的方法还避免了两个主要的物种划分问题，即当遗传阈值与遗传数据一起应用时，物种检测中的固有偏差源于物种形成的时间和方式，以及未能考虑到遗传过程的高度随机方差。本文讨论了基于聚结的方法的实用性和敏感性；最值得注意的是，基于模型的方法对于确定不完全分类的基因谱系是否与单独的物种谱系一致是必不可少的，并且这种推断需要精确的模型参数化（即，相对于所声称的物种的潜在分化时间的实际有效种群规模范围）。这是本研究的目标（和动机），遗传数据可能被有效地用作补充其他来源的数据诊断物种，而不是排除其他证据的物种划分，这将需要明确考虑谱系分裂的时间动态对遗传数据的影响。
Genetic data are frequently used to delimit species, where species status is determined on the basis of an exclusivity criterium, such as reciprocal monophyly. Not only are there numerous empirical examples of incongruence between the boundaries inferred from such data compared to other sources like morphology-especially with recently derived species, but population genetic theory also clearly shows that an inevitable bias in species status results because genetic thresholds do riot explicitly take into account how the timing of speciation influences patterns of genetic differentiation. This study represents a fundamental shift in how genetic data might be used to delimit species. Rather than equating gene trees with a species tree or basing species status on some genetic threshold, the relationship between the gene trees and the species history is modeled probabilistically. Here we show that the same theory that is used to calculate the probability of reciprocal monophyly can also be used to delimit species despite widespread incomplete lineage sorting. The results from a preliminary simulation study suggest that very recently derived species can be accurately identified long before the requisite time for reciprocal monophyly to be achieved following speciation. The study also indicates the importance of sampling, both with regards to loci and individuals. Withstanding a thorough investigation into the conditions under which the coalescent-based approach will be effective, namely how the timing of divergence relative to the effective population size of species affects accurate species delimitation, the results are nevertheless consistent with other recent studies (aimed at inferring species relationships), showing that despite the lack of monophyletic gene trees, a signal of species divergence persists and can be extracted. Using an explicit model-based approach also avoids two primary problems with species delimitation that result when genetic thresholds are applied with genetic data-the inherent biases in species detection arising from when and how speciation occurred, and failure to take into account the high stochastic variance of genetic processes. Both the utility and sensitivities of the coalescent-based approach outlined here are discussed; most notably, a model-based approach is essential for determining whether incompletely sorted gene lineages are (or are not) consistent with separate species lineages, and such inferences require accurate model parameterization (i.e., a range of realistic effective population sizes relative to potential times of divergence for the purported species). It is the goal (and motivation of this study) that genetic data might be used effectively as a source of complementation to other sources of data for diagnosing species, as opposed to the exclusion of other evidence for species delimitation, which will require an explicit consideration of the effects of the temporal dynamic of lineage splitting on genetic data.