Phylogenetic endemism and ancestral area inference reveal historical refugia in the Greater Cape Floristic Region

Aim: Refugial areas and habitats are thought to have played a key role in facilitating both the emergence and persistence of floristic diversity in the Greater Cape Floristic Region (GCFR) of South Africa. While refugial areas may be identified using a diversity of biological proxies (e.g., narrow-range endemism; paleoendemism), there is a shortage of studies in the GCFR that apply these approaches at the species level and in a comparative manner across multiple clades.

Location: GCFR, South Africa.

Time Period: Cenozoic.

Major Taxa Studied: Protea, Leucadendron, Pentameris, Restionoideae.

Methods: We quantify and compare the spatial distribution of phylogenetic endemism (PE) in four Cape-centric plant clades, two clades of shallow-rooted graminoids (Poales) and two of deep-rooted shrubs (Proteales). For each clade, we also quantify the phylogenetic effect on PE (PPE), a metric describing the contribution of evolutionarily distinctive species (paleoendemics) to PE. Spatial moving average regression models are used to assess the influence of climate stability and topography on the distributions of PE and PPE. Finally, we use ancestral area inference to complement these analyses, on the premise that refugial areas are more likely to be resolved as ancestral.

Results: Both PE and PPE are concentrated in the southwestern GCFR, a pattern consistent with the long-term climate stability and steep relief of this mountainous region. In addition, ancestral area inference resolves the southwestern GCFR as a likely area of origin for all clades examined. Spatial patterns of PE and PPE nevertheless vary between clades, with PE centres more diffusely and broadly distributed in Proteales than in Poales.

Main Conclusions: Our study indicates that stable climate and topography have played an important refugial role in shaping patterns of diversity and endemism in the GCFR, but that functionally distinct clades (i.e., shallow-rooted graminoids versus deep-rooted shrubs) differ in terms of the location and dispersion of areas that have served as historical refugia. We attribute this variation to trait-dependent differences in their climate sensitivity.

Methods
See manuscript related to this dataset for a detailed description of the methodology.

研究目的：学界普遍认为，避难所区域与生境在南非大开普植物区（Greater Cape Floristic Region, GCFR）的植物区系多样性起源与维持过程中发挥了关键作用。尽管可通过多种生物代用指标（如窄分布特有性、古特有性）识别避难所区域，但目前GCFR内尚未有研究在物种层面应用此类方法，并开展跨多进化支的比较分析。
研究区域：南非大开普植物区。
研究时段：新生代。
研究类群：帝王花属（Protea）、银叶树属（Leucadendron）、五蕊草属（Pentameris）、帚灯草亚科（Restionoideae）。
研究方法：本研究对4个以开普地区为核心的植物进化支的系统发生特有性（phylogenetic endemism, PE）空间分布进行量化与比较，其中包括2个浅根草本类群（禾本目, Poales）与2个深根灌木类群（山龙眼目, Proteales）。同时，本研究对每个进化支的PE系统发生效应（phylogenetic effect on PE, PPE）进行量化——该指标用于描述演化独特物种（古特有种）对PE的贡献度。本研究采用空间移动平均回归模型，评估气候稳定性与地形对PE及PPE分布的影响。最后，本研究基于"避难所区域更可能被解析为祖先区域"的前提，利用祖先区域推断法对上述分析进行补充。
研究结果：PE与PPE均集中分布于GCFR西南部，该分布格局与该山区长期的气候稳定性及陡峭地形特征相符。此外，祖先区域推断结果显示，GCFR西南部是本次研究所涉及所有进化支的潜在起源地。不过不同进化支的PE与PPE空间格局存在差异：山龙眼目类群的PE分布中心相较于禾本目类群更为弥散和广泛。
主要结论：本研究表明，稳定的气候与地形在塑造GCFR的多样性与特有性格局中发挥了重要的避难所功能，但功能分化的进化支（即浅根草本类群与深根灌木类群）在历史避难所的位置与分布范围上存在差异。本研究将这种差异归因于类群间气候敏感性的性状依赖型差异。
补充方法：详细研究方法请参阅本数据集关联的研究论文。