Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly

Aim: We take advantage of next generation sequencing-based technology to assess how landscape-level dynamics, biogeographical history and functional factors shape the distribution of genetic diversity in rain forest trees. To achieve this, we explore chloroplast genomic diversity and divergence patterns across multiple, co-distributed species from three major centres of rain forest diversity. Location: Subtropical rain forests in south-eastern Australia: Nightcap–Border Ranges, Dorrigo and Washpool. Methods: We assembled chloroplast genomic data from whole-genome shotgun libraries for 71 species collected across three major centres of rain forest diversity. Chloroplast single nucleotide polymorphisms were used to measure genetic variation within and between multiple populations, species and locations, and we used this information to identify patterns related to landscape-level processes, biogeographical origins and functional characteristics. Results: We identified Nightcap–Border Ranges and Dorrigo as containing multiple refugia and Washpool as primarily a recolonized area. We found that rapidly expanding lineages of Indo-Malesian origin exhibit significantly lower levels of genetic diversity than Gondwanan lineages with longer local histories. Functional traits related to persistence and dispersal were the most important in regulating the distribution of genetic diversity. Main conclusions: The distribution and assembly of species reflect interactions and competition between different floristic elements at different stages of continental occupation. Additionally, given the multiple evolutionary origins and histories of the Australian rain forest flora, it is important to avoid treating rain forest communities as single management units. Usage Notes Chloroplast DNA Fasta alignments of Australian Rainforest plant speciesThis data consists of 70 fasta files. The name of each file is the species name and within each file there are up to three aligned fasta sequences. Each fasta sequence is the consensus sequence after mapping a whole genome shotgun sequencing library to a chloroplast reference. The reference were made from concatenated de novo contigs (see manuscript for details). Each shotgun sequencing library consists of DNA of 6 pooled individuals. Each library represents a particular geographic location. Polymorphisms within a library (or geographic site) are indicated with the use of a IUPAC nucleotide code. Please contact the authors if you would like to use this data.where did all the trees come from fasta.zip

研究目的：本研究借助下一代测序技术，探究景观尺度动态、生物地理历史与功能因子如何塑造雨林树木的遗传多样性分布格局。为此，我们对三大雨林多样性核心分布区内多种共分布物种的叶绿体基因组多样性与分化模式展开分析。
研究区域：澳大利亚东南部亚热带雨林，涵盖奈特卡普-博德山脉（Nightcap–Border Ranges）、多里戈（Dorrigo）与沃什波恩（Washpool）三个区域。
研究方法：我们为采自三大雨林多样性核心区的71个物种构建全基因组鸟枪测序文库的叶绿体基因组数据。以叶绿体单核苷酸多态性（Single Nucleotide Polymorphism, SNP）衡量多个种群、物种及区域间的遗传变异，并借此解析与景观过程、生物地理起源及功能特征相关的分布模式。
研究结果：本研究发现，奈特卡普-博德山脉与多里戈存在多处生物避难所，而沃什波恩主要为再定殖区域。我们观察到，起源于印度-马来亚（Indo-Malesian）地区的快速扩张支系，其遗传多样性水平显著低于拥有更长本地演化历史的冈瓦纳（Gondwanan）支系。与物种存续和扩散相关的功能性状，是调控遗传多样性分布的最关键因子。
主要结论：物种的分布与组成反映了不同演化阶段的植物区系类群在大陆定植过程中的相互作用与竞争。此外，鉴于澳大利亚雨林植物区系存在多种演化起源与历史背景，不应将雨林群落视为单一的管理单元，这一点至关重要。
使用说明：澳大利亚雨林植物叶绿体DNA FASTA比对序列
本数据集包含70个FASTA格式文件，文件名均为对应物种的学名，每个文件内最多包含3条比对后的FASTA序列。每条FASTA序列均为将全基因组鸟枪测序文库比对至叶绿体参考基因组后得到的一致性序列。该参考基因组由拼接的从头组装重叠群（详细信息参见相关论文）构建而成。
每个全基因组鸟枪测序文库包含6个混合个体的DNA样本，每个文库对应一个特定的地理区域。文库（或地理位点）内的多态性位点以IUPAC核苷酸代码标注。若您希望使用本数据集，请联系论文作者。
数据集压缩包：where did all the trees come from fasta.zip