Data from: Detecting diversification rates in relation to preservation and tectonic history from simulated fossil records

For mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically-controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record towards the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per-capita, three-timer, and capture-mark-recapture metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and capture-mark-recapture metrics produced more accurate rate estimates, per-capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

就现生哺乳动物而言，山地是全球分布的多样生态系统，但物种丰富度与地形复杂度（topographic complexity）之间的紧密关联，并非化石记录中一贯存在的特征。基于化石产出数据，北美西部山间区域的生物多样性及多样化速率（diversification rates）随时间发生变化，在18 Ma至14 Ma期间的全球变暖与区域构造活动（tectonic activity）加剧阶段出现显著增长。然而，我们从化石记录中可靠推断起源速率（origination rates）与灭绝速率（extinction rates）的能力，会受到保存历史（preservation history）变化的影响。为探究保存作用对多样化速率估算的影响，本研究基于4种备选多样化假说（diversification hypotheses）与6种保存情景（preservation scenarios）模拟了化石记录。多样化假说涵盖受构造活动调控的物种形成脉冲（speciation pulses）；保存情景则基于常见趋势（例如，距现今越近的岩石记录（rock record）越丰富），或源自化石产出数据与大陆岩石记录（continental rock record）。针对每种情景，本研究采用3种标准方法——单个体速率法（per-capita）、三计时器法（three-timer）与标记重捕法（capture-mark-recapture）指标——估算起源、灭绝及多样化速率，并评估模拟化石记录准确还原真实多样化动力学（diversification dynamics）的能力。尽管保存概率存在波动且整体偏低，但在部分情景中，模拟化石记录仍保留了真实速率的信号。3种指标在不同保存情景下的表现并不一致：三计时器法与标记重捕法指标能生成更精准的速率估算结果，而单个体速率法则更擅长还原起源速率的真实变化。当模拟记录受到保存状况剧烈波动的影响时，所有指标均会出现起源与灭绝速率的虚假峰值（spurious peaks）。这些模拟结果表明，即便北美化石记录的保存状况存在波动，中新世（Miocene）中期与构造活动相关的升高多样化速率，仍有可能在化石记录中显现。要评估物种形成与灭绝动力学背后的终极机制，必须依托地质历史时期的实证资料。