Data from: Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (Hypericaceae)

In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that “the present is the key to the past”. Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the present distribution of extant species. Yet, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account “ecological connectivity” through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem-lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, while the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an integrative approach to historical biogeography —that combines sources of evidence as diverse as paleontology, ecology, and phylogenetics— could help us obtain more accurate reconstructions of ancient evolutionary history. It also reveals the confounding effect different rates of extinction across regions have in biogeography, sometimes leading to ancestral areas being erroneously inferred as recent colonization events.在宏演化（macroevolution）等难以开展实验的研究领域，科学家通常借助当前观测数据检验针对历史事件的假说，并以"将今论古"作为核心前提。例如，生物地理学家便沿用这一前提，从现存物种的当前分布格局中重建祖先分布区。然而，在高灭绝速率情景下，当前观测到的生物多样性可能无法代表历史生物多样性，这可能导致生物地理重建结果出现偏差。本研究提出一种新方法，将化石记录所提供的时间、空间与环境信息纳入生物地理推断（biogeographic inference）中，以此作为灭绝生物多样性组分的直接证据。首先，对经化石记录校准的系统发育（phylogeny）树各节点的祖先分布区进行推断时，需限定其包含该化石的地理分布范围；其次，本研究利用化石分布与古气候数据，重建祖先支系随时间变化的气候偏好与潜在分布范围，并以此构建考虑跨时间尺度生态连通性（ecological connectivity）的生物地理模型。为验证该方法的有效性，我们针对大型被子植物属金丝桃属（Hypericum）重建了生物地理历史——该属的化石记录可追溯至早新生代（Early Cenozoic）。与此前基于现存物种分布的重建结果不同，本研究结果显示，金丝桃属的茎支系（stem-lineages）在冠群（crown-group）分化前便已分布于全北区（Holarctic），且该属的地理分布在新生代的气候波动中始终保持相对稳定。该属的地理迁移依赖白令陆桥（Beringia）这类气候廊道（climatic corridors）的存在，而赤道热带带则充当了气候屏障，阻碍金丝桃属支系进入南半球温带区域。本研究表明，整合古生物学、生态学与系统发育学（phylogenetics）等多类证据的历史生物地理学整合方法，可帮助我们更精准地重建古老的演化历史。同时，该研究还揭示了不同区域灭绝速率差异对生物地理学研究的混淆效应（confounding effect），有时会导致祖先分布区被错误地推断为近期定殖事件。