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