Past environmental changes have shaped the evolutionary and ecological diversity of extant organisms. Specifically, climatic fluctuations have made environmental conditions alternatively common or rare over time. Accordingly, most taxa have undergone restriction of their distribution to local refugia during habitat contraction, from which they could expand when suitable habitat became more common. Assessing how past restrictions in refugia have shaped species distributions and genetic diversity has motivated much research in evolutionary biology and biogeography. But there is still lack of clear synthesis on whether and how the taxonomic, functional and phylogenetic composition of extant multispecies assemblages retains the imprint of past restriction in refugia. We devised an original eco-evolutionary model to investigate the temporal dynamics of a regional species pool inhabiting a given habitat today, and which have experienced habitat reduction in the past. The model includes three components: (i) a demographic component driving stochastic changes in population sizes and extinctions due to habitat availability, (ii) a mutation and speciation component representing how divergent genotypes emerge and define new species over time, and (iii) a trait evolution component representing how trait values have changed across descendents over time. We used this model to simulate dynamics of multispecies assemblages that occupied a restricted refugia in the past and could expand their distribution subsequently. We characterized the past restriction in refugia in terms of two parameters representing the ending time of past refugia, and the extent of habitat restriction in the refugia. We characterized extant patterns of taxonomic, functional and phylogenetic diversity depending on these parameters. We found that extant relative abundances reflect the lasting influence of more recent refugia on demographic dynamics, while phylogenetic composition reflects the influence of more ancient habitat change. Extant functional diversity depends on the interplay between diversification dynamics and trait evolution, offering new options to jointly infer current trait adaptation and past trait evolution dynamics.

中文翻译：

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过去栖息地面积减少对现有生物分类，功能和系统发育组成的影响

过去的环境变化影响了现存生物的进化和生态多样性。具体而言，随着时间的推移，气候波动使环境条件变得普遍或罕见。因此，大多数类群在生境收缩过程中受到局限在局部避难所中的分配，当合适的生境变得更加普遍时，它们可以从中扩展。评估过去避难所的限制如何影响物种分布和遗传多样性，已经激发了许多有关进化生物学和生物地理学的研究。但是，关于现存的多物种组合的分类学，功能和系统发育组成是否以及如何保留过去对避难所的限制的印象，仍然缺乏清晰的综合。我们设计了一个原始的生态进化模型，以研究当今居住在给定栖息地中并且过去经历过栖息地减少的区域物种库的时间动态。该模型包括三个组成部分：（i）人口因素，这些因素驱动种群数量和灭绝的随机变化（由于栖息地的可用性）；（ii）突变和物种组成，代表不同基因型如何出现并随时间定义新物种；（iii）特质进化组件，表示特质值在整个子代中随时间变化的方式。我们使用该模型来模拟过去占据有限避难所的多物种组合的动力学，并且可以随后扩展它们的分布。我们通过两个参数来表征过去避难所的限制条件，这些参数代表过去避难所的结束时间，以及避难所中栖息地限制的程度。我们根据这些参数对分类学，功能和系统发育多样性的现有模式进行了表征。我们发现现存的相对丰度反映了最近避难所对人口动态的持久影响，而系统发育组成反映了更古老的生境变化的影响。现有的功能多样性取决于多元化动态与性状进化之间的相互作用，为共同推断当前性状适应和过去性状进化动态提供了新的选择。功能和系统发育多样性取决于这些参数。我们发现现存的相对丰度反映了最近避难所对人口动态的持久影响，而系统发育组成反映了更古老的生境变化的影响。现有的功能多样性取决于多元化动态与性状进化之间的相互作用，为共同推断当前性状适应和过去性状进化动态提供了新的选择。功能和系统发育多样性取决于这些参数。我们发现现存的相对丰度反映了最近避难所对人口动态的持久影响，而系统发育组成反映了更古老的生境变化的影响。现有的功能多样性取决于多元化动态与性状进化之间的相互作用，为共同推断当前性状适应和过去性状进化动态提供了新的选择。