Macroevolutionary and biogeographical studies commonly apply multiple models to test state‐dependent diversification. These models track the association between states of interest along a phylogeny, although many of them do not consider whether different clades might be evolving under different evolutionary drivers. Yet, they are still commonly applied to empirical studies without careful consideration of possible lineage diversification heterogeneity along the phylogenetic tree. A recent biogeographic study has suggested that orogenic uplift of the southern Andes has acted as a species pump, driving diversification of the lizard family Liolaemidae (307 described species), native to temperate southern South America. Here, we argue against the Andean uplift as main driver of evolution in this group. We show that there is a clear pattern of heterogeneous diversification in the Liolaemidae, which biases state‐ and environment‐dependent analyses in, respectively, the GeoSSE and RPANDA programs. We show here that there are two shifts to accelerated speciation rates involving two clades that have both been classified as having “Andean” distributions. We incorporated the Geographic Hidden‐State Speciation and Extinction model (GeoHiSSE) to accommodate unrelated diversification shifts, and also re‐analyzed the data in RPANDA program after splitting biologically distinct clades for separate analyses, as well as including a more appropriate set of models. We demonstrate that the “Andean uplift” hypothesis is not supported when the heterogeneous diversification histories among these lizards is considered. We use the Liolaemidae as an ideal system to demonstrate potential risks of ignoring clade‐specific differences in diversification patterns in macroevolutionary studies. We also implemented simulations to show that, in agreement with previous findings, the HiSSE approach can effectively and substantially reduce the level of distribution‐dependent models receiving the highest AIC weights in such scenarios. However, we still find a relatively high rate (15%) of distribution‐dependent models receiving the highest AIC weights, and provide recommendations related to the set of models included in the analyses that reduce these rates by half. Finally, we demonstrate that trees including clades following different dependent‐drivers affect RPANDA analyses by producing different outcomes, ranging from partially correct models to completely misleading results. We provide recommendations for the implementation of both programs.

中文翻译：

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在宏观进化研究中考虑谱系多样化异质性有多重要？蜥蜴科Liolaemidae的教训

宏观进化论和生物地理学研究通常采用多种模型来检验依赖状态的多元化。这些模型沿着系统发育追踪目标状态之间的关联，尽管其中许多模型并未考虑不同进化枝可能是否在进化不同进化枝。但是，它们仍然普遍用于经验研究，而没有仔细考虑沿系统发生树的谱系多样化异质性。最近的一项生物地理研究表明，安第斯山脉南部的造山带起了物种泵的作用，推动了蜥蜴科Liolaemidae（307个已描述物种）的多样化，该物种原产于南美洲南部温带。在这里，我们反对安第斯山脉的崛起是该群体进化的主要动力。我们显示，在Liolaemidae中，存在明显的异质多样化模式，这分别在GeoSSE和RPANDA程序中偏向于依赖于状态和环境的分析。我们在这里表明，加速物种形成速率有两个转变，涉及两个进化枝都被归类为“安第斯”分布。我们并入了地理隐藏状态物种灭绝模型（GeoHiSSE），以适应不相关的多样化转变，并且在将生物学上不同的进化枝分开进行单独分析之后，还重新分析了RPANDA程序中的数据，并包括了一组更合适的模型。我们证明，当考虑到这些蜥蜴之间的异质多样化历史时，“安第斯山隆升”假说不受支持。我们使用Liolaemidae作为理想的系统来证明在宏观进化研究中忽略进化枝特定差异的潜在风险。我们还进行了仿真，以表明与以前的发现相一致，HiSSE方法可以有效，显着地降低这种情况下获得最高AIC权重的依赖于分布的模型的水平。但是，我们仍然发现具有较高AIC权重的依赖于分布的模型的比率较高（15％），并提供了与分析中包含的模型集相关的建议，这些模型将这些比率降低了一半。最后，我们证明了树木（包括进化枝跟随不同的依赖驱动程序）会通过产生不同的结果来影响RPANDA分析，从部分正确的模型到完全误导的结果。我们为实施这两个计划提供建议。