Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes - curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits - remains poorly understood. Here we present a novel, time-stratified extension of the QuaSSE model in which speciation/extinction rate is specified as a static or temporally-shifting Gaussian or skewed-Gaussian function of the diversification trait. We then use simulations to show that the generally imbalanced nature of real phylogenetic trees, as well as their generally greater-than-expected frequency of deep branching events, are typical outcomes when diversification is treated as a dynamic, trait-dependent process. Focusing on four basic models (Gaussian-speciation with and without background extinction; skewed-speciation; Gaussian-extinction), we also show that particular features of the species selection regime produce distinct tree shape signatures and that, consequently, a combination of tree shape metrics has the potential to reveal the species selection regime under which a particular lineage diversified. We evaluate this idea empirically by comparing the phylogenetic trees of plant lineages diversifying within climatically- and geologically-stable environments of the Greater Cape Floristic Region, with those of lineages diversifying in environments that have experienced major change through the Late Miocene-Pliocene. Consistent with our expectations, the trees of lineages diversifying in a dynamic context are less balanced, show a greater concentration of branching events close to the present, and display stronger diversification rate-trait correlations. We suggest that species selection plays an important role in shaping phylogenetic trees but recognize the need for an explicit probabilistic framework within which to assess the likelihoods of alternative diversification scenarios as explanations of a particular tree shape.

中文翻译：

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物种选择机制和系统发育树形

物种选择，即遗传性状在产生谱系间多样化率差异中的作用，为理解性状、多样化和系统发育树形状之间的关系提供了有价值的概念框架。然而，一个重要的挑战是，真正的多样化景观的性质——描述物种水平谱系多样化倾向的曲线或表面——作为一个或多个特征的函数——仍然知之甚少。在这里，我们提出了 QuaSSE 模型的一种新颖的时间分层扩展，其中物种形成/灭绝率被指定为多样化特征的静态或时间移动的高斯或偏斜高斯函数。然后我们使用模拟来表明真实系统发育树的普遍不平衡性质，当多样化被视为一个动态的、依赖于特征的过程时，以及它们普遍高于预期的深层分支事件频率是典型的结果。专注于四个基本模型（高斯物种形成有和没有背景灭绝；偏态物种形成；高斯灭绝），我们还表明物种选择机制的特定特征会产生不同的树形特征，因此，树形的组合指标有可能揭示特定谱系多样化的物种选择机制。我们通过比较在大开普植物区气候和地质稳定环境中多样化的植物谱系的系统发育树，凭经验评估这一想法，随着中新世晚期 - 上新世经历重大变化的环境中的谱系多样化。与我们的预期一致，在动态环境中多样化的谱系树不太平衡，显示出更接近当前的分支事件更集中，并显示出更强的多样化率-性状相关性。我们建议物种选择在塑造系统发育树方面发挥重要作用，但认识到需要一个明确的概率框架，在该框架内评估替代多样化情景的可能性，作为对特定树形的解释。并显示出更强的多样化率-性状相关性。我们建议物种选择在塑造系统发育树方面发挥重要作用，但认识到需要一个明确的概率框架，在该框架内评估替代多样化情景的可能性，作为对特定树形的解释。并显示出更强的多样化率-性状相关性。我们建议物种选择在塑造系统发育树方面发挥重要作用，但认识到需要一个明确的概率框架，在该框架内评估替代多样化情景的可能性，作为对特定树形的解释。