Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America.
PLoS One. 2010 Jul 23;5(7):e11781. doi: 10.1371/journal.pone.0011781.
Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the gamma statistic.
Using simulations under varying conditions, I examine the sensitivity of gamma to the distribution of the most recent branching times. Using an exploratory data analysis tool for lineages through time plots, tree deviation, I identified trees with a significant gamma statistic that do not appear to have the characteristic early accumulation of lineages consistent with an early, rapid rate of cladogenesis. I further investigated the sensitivity of the gamma statistic to recent diversification by examining the consequences of failing to simulate the full time interval following the most recent cladogenic event. The power of gamma to detect rate decrease at varying times was assessed for simulated trees with an initial high rate of diversification followed by a relatively low rate.
The gamma statistic is extraordinarily sensitive to recent diversification rates, and does not necessarily detect early bursts of diversification. This was true for trees of various sizes and completeness of taxon sampling. The gamma statistic had greater power to detect recent diversification rate decreases compared to early bursts of diversification. Caution should be exercised when interpreting the gamma statistic as an indication of early, rapid diversification.
系统发育假说越来越多地被用于阐明多样化率变化的历史模式。假设检验通常通过将观测到的分支时间向量与零假设（纯出生期望）进行比较来进行。一种流行的推断物种形成率降低的方法，即可能表明早期多样化爆发，然后是多样化率降低的方法是伽马统计。
使用不同条件下的模拟，我检查了伽马对最近分支时间分布的敏感性。通过使用谱系时间图的探索性数据分析工具（树偏差），我确定了具有显著伽马统计量的树，这些树似乎没有与早期快速分支发生率一致的早期谱系积累的特征。我进一步通过检查未能模拟最近分支事件后完整时间间隔对伽马统计的敏感性来研究伽马统计对最近多样化的敏感性。对于最初具有较高多样化率然后相对较低率的模拟树，评估了伽马检测不同时间处率降低的能力。
伽马统计对最近的多样化率非常敏感，不一定能检测到早期的多样化爆发。这对于各种大小和分类群采样完整性的树都是如此。与早期多样化爆发相比，伽马统计在检测最近的多样化率降低方面具有更大的能力。在将伽马统计作为早期快速多样化的指示时应谨慎。
