Plotting a future for Amazonian canga vegetation in a campo rupestre context - Supplementary data

These are the supplementary data for our study on biogeography and conservation of the flora of <i>campo rupestre</i> vegetation in Brazil. We compared the differences in plant species composition and lineage distribution of <i>campos rupestres</i> in the Amazonian Carajás (Pará state) and easter Brazil (Minas Gerais and Bahia states). The study is published in the journal Plos One. <br><br><br>The supplementary data is described as follow:<br><b>S1 Fig</b> shows the flow chart of methods used in our analyses. Red symbols represent the sites with canga substrate (inedited database produced for this paper). Blue symbols represent sites with quartzite substrate and lilac symbol sites with mixed substrate (both canga and quartzite), produced for Zappi et al (2017) paper (https://doi.org/10.3389/fpls.2017.02141).<br><b>S2 Fig</b> shows the SOS values for our sites. SOS values express clades with differential over-representation of certain lineages in a set of sites, versus lineages with over-representation elsewhere (see Borregaard et al. 2014). This analysis was made with '<i>nodiv</i>' R package (https://doi.org/10.1111/2041-210X.12283).<br><br><b>S3 Fig </b>is the graph with the results of the rarefaction, extrapolation and Angiosperm species richness estimation of <i>campo rupestre </i>in Carajás. These analyses were made on software EstimateS (https://doi.org/10.1111/ecog.00814)<br><b>S4 Fig</b> brings the phylogenetic tree of all species from the campos rupestres in both Carajás and Espinhaço range in PDF format. This tree was generate in iTol (https://itol.embl.de) using the <b>S2 Text</b> file available here.<br><br><b>S1 Text</b> is the script used for all analyses done in R environment (note that some analyses were made in different software like Phylocom and EstimateS, as described in the paper).<br><b>S2 Text</b> is the dated phylogenetic tree showing evolutive relationships between all species present in our database. This tree was created in the software Phylocom based on the megatree 'R20160415.new', which is provided by Gastauer and Meira-Neto (2017) in their datapaper (https://doi.org/10.1590/0102-33062016abb0306).<br><b>S1 Table</b> contains the data matrix showing the presence of plant species in each of the 14 individual sites on mountaintops in Carajás (Pará state), which was used in the multivariate analysis, rarefaction and richness estimation for the area.<br><br><b>S2 Table</b> contains the data matrix showing the presence of plant species for each of the 14 Carajás sites plus the 14 sites of <i>campo rupestre</i> of easter Brazil (Minas Gerais and Bahia states - see Zappi et al. 2017 paper), which was used in the biogeographical comparison at national level.<br><b>S3 Table </b>brings the raw results of the rarefaction, extrapolation and species richness estimation of campo rupestre in Carajás. These analyses were made on software EstimateS (https://doi.org/10.1111/ecog.00814).<br>

本数据集为我们针对巴西岩原草原（campo rupestre）植被区系的生物地理学与保护生物学研究的补充数据。本研究对比了亚马逊卡拉加斯（帕拉州）与巴西东部（米纳斯吉拉斯州和巴伊亚州）的岩原草原的植物物种组成与谱系分布差异。本研究已发表于《PLOS ONE》期刊。

补充数据说明如下：
**S1图**展示了本研究分析所用方法的流程图。红色符号代表含铁结壳基质（canga substrate）样地（为本研究构建的未正式发表数据库）；蓝色符号代表石英岩基质样地，淡紫色符号代表混合基质（含铁结壳与石英岩）样地，数据来源于Zappi等人2017年的研究（https://doi.org/10.3389/fpls.2017.02141）。
**S2图**展示了本研究样地的SOS值（SOS values）。SOS值用于表征在特定样地组中某些演化支出现过度富集，而其他谱系则在其余样地中呈现富集的情况（详见Borregaard等人2014年的研究）。本分析通过*nodiv* R包完成（https://doi.org/10.1111/2041-210X.12283）。
**S3图**为卡拉加斯地区岩原草原的物种稀疏分析（rarefaction）、外推分析（extrapolation）以及被子植物物种丰富度估算结果的可视化图表。本分析通过EstimateS软件完成（https://doi.org/10.1111/ecog.00814）。
**S4图**为PDF格式的卡拉加斯与埃斯皮尼亚苏山脉（Espinhaço range）两地岩原草原所有物种的系统发育树。本树通过iTol在线工具（https://itol.embl.de）构建，所用数据来自本文附带的S2文本文件。

**S1文本**为R语言环境下所有分析所用的脚本文件（请注意，部分分析如论文所述，通过Phylocom、EstimateS等其他软件完成）。
**S2文本**为带时间标定的系统发育树，展示了本研究数据库中所有物种间的演化关系。本树通过Phylocom软件构建，所用的巨型系统发育树'R20160415.new'由Gastauer与Meira-Neto于2017年在其数据论文中提供（https://doi.org/10.1590/0102-33062016abb0306）。

**S1表**为数据矩阵，展示了帕拉州卡拉加斯地区14处山顶样地的植物物种存在情况，该矩阵用于本区域的多元分析、物种稀疏分析与物种丰富度估算。
**S2表**为数据矩阵，涵盖了卡拉加斯地区的14处样地以及巴西东部（米纳斯吉拉斯州与巴伊亚州，详见Zappi等人2017年的研究）的14处岩原草原样地的植物物种存在情况，该矩阵用于国家级尺度的生物地理学对比分析。
**S3表**包含了卡拉加斯地区岩原草原的物种稀疏分析、外推分析以及物种丰富度估算的原始结果。本分析通过EstimateS软件完成（https://doi.org/10.1111/ecog.00814）。