Computational protocol: Landscape Patterns in Rainforest Phylogenetic Signal: Isolated Islands of Refugia or Structured Continental Distributions?

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Protocol publication

[…] We used a taxonomically and geographically comprehensive data set representing ca. 180,000 georeferenced records for 2306 rainforest species, including seasonal monsoon and drier vine forest species . The 1872 free-standing and 434 climbing plant species in the data set represent all of Australia's woody rainforest taxa. Marginal rainforest species (i.e., species that occur mostly on the edges of rainforest in moist and dry sclerophyll and mangrove communities) were excluded from the synthesis presented here. Species selection was comprehensive and provides a complete representation of woody rainforest diversity, but was very conservative in relation to including taxa from other communities. This data set is focused on rainforest species distributions and is not contingent on an a priori definition of rainforest and rainforest community distribution. For analysis, the georeferenced species records were first aggregated to presences in 10×10 km grid cells using the Biodiverse software (). These grid cells represent ‘assemblage’ level data for rainforest species across the continent. The 10×10 km grid cell assemblages were aggregated into 50×50 km cells once it was determined that patterns remained the same across these scales. Some dry vine forest species occur as isolated trees in very low rainfall (non-rainforest) areas. To avoid populating drier (non-rainforest) inland areas with cells and potentially over representing the spatial distribution of rainforest in figures (–), only grid cells with >5 species were included. Higher minimum thresholds resulted in reduced representation of species-poor rainforest in southern regions such as Tasmania and Victoria. [...] Taxonomic checking used currently available and updated online data base resources . All data sets were reconciled with collection records using the Australian Virtual Herbarium (AVH) database , the Angiosperm Phylogeny Group (APG III) classification , the Taxonomic Nomenclature Checker – GRIN , and The Plant List .A phylogenetic supertree was generated using PROTEUS . The procedure, similar to Phylomatic , combines the phylogenetic backbone of seed plants as summarized on the Angiosperm Phylogeny Website with internal phylogenetic structure of families where available and assuming that genera are monophyletic. Although this assumption might prove incorrect for some genera in the future, it is a reasonable and necessary approximation for the purpose of this study. In addition, we were careful to follow the latest family-level phylogenetic classifications and genus concepts in PROTEUS in order to limit the extent of this problem to the best of our knowledge. Where undescribed species within genera were included they were allocated a collection location name so trait values and distribution records could be allocated to them. Conspecific taxa within the original data compilation were all resolved to a single name. Varietal status was merged for combined trait and phylogenetic analyses (not presented) as it was acknowledged these would be absorbed into polytomies. The tree is available in PDF form as .In order to include branch lengths in our analyses of phylogenetic endemism, diversity, and structure, we then transformed this supertree into an ultrametric tree using the bladj function of Phylocom . We acknowledge that the resulting chronogram cannot be compared to a dated tree produced by a relaxed clock analysis of original molecular data, but we believe that the benefits of using approximate branch lengths are greater than using topology alone (e.g., all branch lengths equal to one). However, we were careful to use the estimated ages from the study by Magallón and Castillo (2009) as input landmarks for the bladj function, rather than the default age table provided in Phylocom, which is based on an older, now obsolete study of angiosperm divergence times. Specifically, we used as landmarks the mean crown-group ages for orders and the main clades of angiosperms from the constrained analysis reported in of Magallón and Castillo (2009) . […]

Pipeline specifications

Software tools Biodiverse, Phylomatic, Phylocom
Application Phylogenetics