Data from: Evaluating the accuracy of biodiversity changes through geological times: from simulation to solution

Estimating biodiversity and its variations through geologic time is a notoriously difficult task, due to several taphonomic and methodological effects that make the reconstructed signal potentially distinct from the unknown, original one. Through a simulation approach, we examine the effect of a major, surprisingly still understudied, source of potential disturbance: the effect of time discretization through biochronological construction, which generates spurious coexistences of taxa within discrete time intervals (i.e., biozones), and thus potentially makes continuous- and discrete-time biodiversity curves very different. Focusing on the taxonomic-richness dimension of biodiversity (including estimates of origination and extinction rates), our approach relies on generation of random continuous-time richness curves, which are then time-discretized to estimate the noise generated by this manipulation. A broad spectrum of data-set parameters (including average taxon longevity and biozone duration, total number of taxa, and simulated time interval) is evaluated through sensitivity analysis. We show that the deteriorating effect of time discretization on the richness signal depends highly on such parameters, most particularly on average biozone duration and taxonomic longevity because of their direct relationship with the number of false coexistences generated by time discretization. With several worst-case but realistic parameter combinations (e.g., when relatively short-lived taxa are analyzed in a long-ranging biozone framework), the original and time-discretized richness curves can ultimately show a very weak to zero correlation, making these two time series independent. Based on these simulation results, we propose a simple algorithm allowing the back-transformation of a discrete-time taxonomic-richness data set, as customarily constructed by paleontologists, into a continuous-time data set. We show that the reconstructed richness curve obtained this way fits the original signal much more closely, even when the parameter combination of the original data set is particularly adverse to an effective time-discretized reconstruction.

通过地质时间尺度估算生物多样性及其变化向来是一项极具挑战性的工作，这是因为多种埋藏学（taphonomic）与方法论层面的影响因素，会导致重建得到的生物多样性信号与未知的原始信号存在显著差异。本研究通过模拟实验方法，探究了一个此前鲜少被关注的重要潜在干扰源的影响：生物年代学（biochronological）构建过程中的时间离散化效应。该效应会在离散时间区间（即生物带（biozone））内产生分类群（taxa）的虚假共存现象，进而可能使得连续时间与离散时间的生物多样性曲线出现显著差异。本研究聚焦生物多样性的分类丰富度维度（包含起源速率与灭绝速率的估算），其方法为先生成随机连续时间丰富度曲线，再对其进行时间离散化处理，以此量化该操作所产生的噪声。我们通过敏感性分析（sensitivity analysis）评估了涵盖平均分类群寿命、生物带时长、总分类群数量以及模拟时间区间在内的多组数据集参数。研究表明，时间离散化对丰富度信号的负面影响高度依赖于上述参数，其中尤以平均生物带时长与分类群寿命最为关键——这二者直接与时间离散化所产生的虚假共存数量相关。在若干极端但符合实际的参数组合下（例如在长时生物带框架下分析寿命较短的分类群），原始丰富度曲线与经时间离散化处理后的曲线之间的相关性可能极低，甚至趋近于零，致使这两个时间序列相互独立。基于上述模拟结果，我们提出了一种简单算法，可将古生物学家常规构建的离散时间分类丰富度数据集逆向转换为连续时间数据集。研究显示，通过该方法得到的重建丰富度曲线能够更精准地匹配原始信号，即便原始数据集的参数组合对时间离散化重建极为不利，该算法依然有效。