Simulating South American biodiversity The emergence, distribution, and extinction of species are driven by interacting factors—spatial, temporal, physical, and biotic. Rangel et al. simulated the past 800,000 years of evolution in South America, incorporating these factors into a spatially explicit dynamic model to explore the geographical generation of diversity. Their simulations, based on a paleoclimate model on a 5° latitude-longitude scale, result in shifting maps of speciation, persistence, and extinction (or cradles, museums, and graves). The simulations culminate in a striking resemblance to contemporary distribution patterns across the continent for birds, mammals, and plants—despite having no target patterns and no empirical data parameterizing them. Science, this issue p. eaar5452 Mechanistic simulations of climate dynamics, speciation, and adaptive evolution yield realistic geographical patterns of biodiversity. INTRODUCTION Individual processes that shape geographical patterns of biodiversity are increasingly understood, but their complex interactions on broad spatial and temporal scales remain beyond the reach of analytical models and traditional experiments. To meet this challenge, we built a spatially explicit, mechanistic model that simulates the history of life on the South American continent, driven by modeled climates of the past 800,000 years. Operating at the level of geographical ranges of populations, our simulations implemented adaptation, geographical range shifts, range fragmentation, speciation, long-distance dispersal, competition between species, and extinction. Only four parameters were required to control these processes (dispersal distance, evolutionary rate, time for speciation, and intensity of competition). To assess the effects of topographic heterogeneity, we experimentally smoothed the climate maps in some treatments. RATIONALE The simulations had no target patterns. Instead, the study took a fundamental approach, relying on the realism of the modeled ecological and evolutionary processes, theoretical derivations of parameter values, and the climatic and topographic drivers to produce meaningful biogeographical patterns. The model encompassed only the Late Quaternary (last 800,000 years), with its repeated glacial-interglacial cycles, beginning at a time when South America was already populated with a rich biota, comprising many distinct lineages. Nonetheless, current consensus holds that the contemporary flora and vertebrate fauna of South America include numerous lineages that have undergone rapid diversification during the Quaternary, particularly in the Andes. In our model, over the course of each simulation, a complete phylogeny emerged from a single founding species. On the basis of the full historical records for each species range, at each 500-year interval, we recorded spatial and temporal patterns of speciation (“cradles”), persistence (“museums”), extinction (“graves”), and species richness. RESULTS Simulated historical patterns of species richness, as recorded by maps of the richness of persistent (museum) species, proved quite successful in capturing the broad features of maps of contemporary species richness for birds, mammals, and plants. Factorial experiments varying parameter settings and initial conditions revealed the relative impact of the evolutionary and ecological processes that we modeled, as expressed in spatial and temporal patterns of cradles, museums, graves, and species richness. These patterns were most sensitive to the geographical location of the founding species and to the rate of evolutionary adaptation. Experimental topographic smoothing confirmed a crucial role for climate heterogeneity in the diversification of clades, especially in the Andes. Analyses of temporal patterns of speciation (cradles) and extinction (graves) emerging from the simulations implicated Quaternary glacial-interglacial cycles as drivers of both diversification and extinction on a continental scale. CONCLUSION Our biogeographical simulations were constructed from the bottom up, integrating mechanistic models of key ecological and evolutionary processes, following well-supported, widely accepted explanations for how these processes work in nature. Despite being entirely undirected by any target pattern of real-world species richness and covering only a tiny slice of the past, surprisingly realistic continental and regional patterns of species richness emerged from the model. Our simulations confirm a powerful role for adaptive niche evolution, in the context of diversification and extinction driven by topography and climate. Observed species richness versus modeled (simulated) richness. Upper map: Contemporary South American bird richness (2967 species). Lower map: Simulated spatial pattern for the cumulative richness of persistent (museum) species, arising from the model. The map show results averaged over all parameter values for an Atlantic Rainforest founder, excluding the climate-smoothing experimental treatments. Simulated species richness is highly correlated with observed species richness for birds (r2 = 0.6337). Individual processes shaping geographical patterns of biodiversity are increasingly understood, but their complex interactions on broad spatial and temporal scales remain beyond the reach of analytical models and traditional experiments. To meet this challenge, we built a spatially explicit, mechanistic simulation model implementing adaptation, range shifts, fragmentation, speciation, dispersal, competition, and extinction, driven by modeled climates of the past 800,000 years in South America. Experimental topographic smoothing confirmed the impact of climate heterogeneity on diversification. The simulations identified regions and episodes of speciation (cradles), persistence (museums), and extinction (graves). Although the simulations had no target pattern and were not parameterized with empirical data, emerging richness maps closely resembled contemporary maps for major taxa, confirming powerful roles for evolution and diversification driven by topography and climate.

中文翻译：

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对生物多样性的生态和进化建模：生物地理摇篮、博物馆和坟墓

模拟南美生物多样性 物种的出现、分布和灭绝是由空间、时间、物理和生物等相互作用因素驱动的。兰格尔等人。模拟南美洲过去 800,000 年的进化，将这些因素纳入空间明确的动态模型，以探索多样性的地理生成。他们的模拟基于 5° 纬度-经度尺度的古气候模型，导致物种形成、持久性和灭绝（或摇篮、博物馆和坟墓）地图的变化。模拟结果与当代鸟类、哺乳动物和植物在整个大陆的分布模式惊人相似——尽管没有目标模式，也没有经验数据对其进行参数化。科学，这个问题 p。eaar5452 气候动力学、物种形成、和适应性进化产生了现实的生物多样性地理模式。引言 塑造生物多样性地理格局的个体过程越来越被理解，但它们在广泛的空间和时间尺度上的复杂相互作用仍然超出了分析模型和传统实验的范围。为了应对这一挑战，我们建立了一个空间明确的机械模型，模拟南美大陆上的生命历史，由过去 80 万年的模拟气候驱动。在种群地理范围的水平上运行，我们的模拟实现了适应、地理范围转移、范围分裂、物种形成、远距离扩散、物种之间的竞争和灭绝。只需要四个参数来控制这些过程（分散距离、进化速度、物种形成时间和竞争强度）。为了评估地形异质性的影响，我们通过实验对某些处理中的气候图进行了平滑处理。基本原理 模拟没有目标模式。相反，该研究采用了一种基本方法，依靠建模生态和进化过程的真实性、参数值的理论推导以及气候和地形驱动因素来产生有意义的生物地理模式。该模型仅包含第四纪晚期（过去 800,000 年），其重复的冰期-间冰期循环始于南美洲已经拥有丰富的生物群，包括许多不同的谱系。尽管如此，目前的共识认为，南美洲的当代动植物群包括许多在第四纪期间经历了快速多样化的谱系，特别是在安第斯山脉。在我们的模型中，在每次模拟过程中，从单一创始物种中出现了完整的系统发育。在每个物种范围的完整历史记录的基础上，每隔 500 年，我们记录了物种形成（“摇篮”）、持久性（“博物馆”）、灭绝（“坟墓”）和物种的时空模式丰富。结果 物种丰富度的模拟历史模式，如持久（博物馆）物种丰富度地图所记录的，证明在捕捉当代鸟类、哺乳动物和植物物种丰富度地图的广泛特征方面非常成功。不同参数设置和初始条件的因子实验揭示了我们建模的进化和生态过程的相对影响，如摇篮、博物馆、坟墓和物种丰富度的空间和时间模式所表达的。这些模式对创始物种的地理位置和进化适应率最为敏感。实验地形平滑证实了气候异质性在进化枝多样化中的关键作用，尤其是在安第斯山脉。对模拟中出现的物种形成（摇篮）和灭绝（坟墓）的时间模式的分析表明，第四纪冰期-间冰期循环是大陆范围内多样化和灭绝的驱动因素。结论 我们的生物地理模拟是自下而上构建的，整合关键生态和进化过程的机械模型，遵循得到充分支持、广泛接受的关于这些过程在自然界中如何运作的解释。尽管完全不受现实世界物种丰富度的任何目标模式的指导，并且只覆盖了过去的一小部分，但模型中出现了令人惊讶的大陆和区域物种丰富度模式。我们的模拟证实了在地形和气候驱动的多样化和灭绝的背景下，适应性生态位进化的强大作用。观察到的物种丰富度与模型（模拟）丰富度。上图：当代南美鸟类丰富度（2967 种）。下图：模型产生的持久性（博物馆）物种累积丰富度的模拟空间模式。该地图显示了大西洋雨林创始人所有参数值的平均结果，不包括气候平滑实验处理。模拟的物种丰富度与观察到的鸟类物种丰富度高度相关 (r2 = 0.6337)。人们越来越了解塑造生物多样性地理格局的各个过程，但它们在广泛的空间和时间尺度上的复杂相互作用仍然超出了分析模型和传统实验的范围。为了应对这一挑战，我们建立了一个空间明确的机械模拟模型，在南美洲过去 800,000 年的模拟气候驱动下，实现了适应、范围变化、分裂、物种形成、扩散、竞争和灭绝。实验地形平滑证实了气候异质性对多样化的影响。模拟确定了物种形成（摇篮）、持久性（博物馆）和灭绝（坟墓）的区域和事件。虽然模拟没有目标模式，也没有用经验数据参数化，但新兴的丰富度地图与主要分类群的当代地图非常相似，证实了由地形和气候驱动的进化和多样化的强大作用。