Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
Mol Phylogenet Evol. 2010 Mar;54(3):849-56. doi: 10.1016/j.ympev.2009.12.025. Epub 2010 Jan 4.
Variation in substitution rates among evolutionary lineages (among-lineage rate variation or ALRV) has been reported to negatively affect the estimation of phylogenies. When the substitution processes underlying ALRV are modeled inadequately, non-sister taxa with similar substitution rates are estimated incorrectly as sister species due to long-branch attraction. Recent advances in modeling site-specific rate variation (heterotachy) have reduced the impacts of ALRV on phylogeny estimation in several empirical and simulated datasets. However, the addition of parameters to the substitution model reduces power to estimate each parameter correctly, which can also lead to incorrect phylogeny estimation. A potential solution to this problem is to identify the levels of ALRV that negatively impact phylogeny estimation such that molecular markers with non-deleterious levels of ALRV can be identified. To this end, we used analyses of empirical and simulated gene datasets to evaluate whether levels of ALRV identified in a mitochondrial genomic dataset for salamanders negatively impacted phylogeny estimation. We simulated data with and without ALRV, holding all other evolutionary parameters constant, and compared the phylogenetic performance of both simulated and empirical datasets. Overall, we found limited, positive effects of ALRV on phylogeny estimation in this dataset, the majority of which resulted from an increase in substitution rate on short branches. We conclude that ALRV does not always negatively impact phylogeny estimation. Therefore, ALRV can likely be disregarded as a criterion for marker selection in comparable phylogenetic studies.
进化谱系之间的替代率变化（谱系间速率变化或 ALRV）已被报道会对系统发育估计产生负面影响。当对 ALRV 下的替代过程建模不充分时，由于长枝吸引作用，具有相似替代率的非姐妹分类群会被错误地估计为姐妹种。最近在建模特定位置速率变化（异速进化）方面的进展减少了在几个经验和模拟数据集上 ALRV 对系统发育估计的影响。然而，向替代模型添加参数会降低正确估计每个参数的能力，这也可能导致不正确的系统发育估计。解决此问题的一种潜在方法是确定对系统发育估计产生负面影响的 ALRV 水平，以便可以识别具有非有害 ALRV 水平的分子标记。为此，我们使用经验数据集和模拟基因数据集的分析来评估在蝾螈线粒体基因组数据集中鉴定的 ALRV 水平是否会对系统发育估计产生负面影响。我们在保持所有其他进化参数不变的情况下模拟具有和不具有 ALRV 的数据，并比较了模拟和经验数据集的系统发育表现。总体而言，我们发现该数据集的 ALRV 对系统发育估计的影响有限且呈正相关，其中大多数是由于短枝上的替代率增加所致。我们得出结论，ALRV 并不总是对系统发育估计产生负面影响。因此，在类似的系统发育研究中，ALRV 可能可以忽略不计为标记选择的标准。
