Computational protocol: The Role of Edaphic Environment and Climate in Structuring Phylogenetic Pattern in Seasonally Dry Tropical Plant Communities

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Protocol publication

[…] We compiled data from 13 floristic surveys in the Caatinga Phytogeographical Domain, NE Brazil, with information on Raunkiaerian life forms of species (; ). These studies were selected from a thorough literature survey of plant diversity on the Caatinga Phytogeographical Domain that identified 131 surveys with site-based floristic or phytosociological information []. From this larger dataset we selected all lists that sampled the general flora of each site (i.e. those that included plants of all habits, from woody to herbaceous species) and that included Raunkiaer’s life-form for each species. We then created a database of all species reported in these studies, excluding exotic species and species assigned only to genus or family level. We assumed that species with a cf. status (i.e. species identified with a certain degree of uncertainty) were correctly identified. Ferns and Lycophytes were also excluded from the analysis, because they represent very old clades, which would bias the phylogenetic metrics, and are a species-poor component in Caatinga.We classified all reported life forms according to the five main Raunkiaer [] categories: (1) phanerophytes, which have buds that are well above the ground during the dry season; (2) chamaephytes, which have buds close to the ground; (3) hemicryptophytes, which have buds at the ground level; (4) cryptophytes, which have buds below ground; and (5) therophytes, which are annual plants that complete their life-cycle, reproduce and die during a single rainy season. We used Raunkiaer categories because they are based on life history features that are closely aligned with adaptation to the ecological conditions highlighted in our study. When one of the studies reported a life-form using a category different from those originally proposed by Raunkiaer (e.g. succulent and climbers), we reclassified species back into one of the Raunkiaerian categories. Aerophytes, epiphytes and hemiparasites were reclassified as phanerophytes. Cacti and succulents were reclassified as chamaephytes or phanerophytes depending on the size of adult plants. Climbers were reclassified as phanerophytes, chamaephytes or therophytes, depending on their senescence in the dry season. In these studies, a few species were not classified into any Raunkiaer category. In these cases, we assigned species to Raunkiaer categories based on personal field experience or consultation with other taxonomic specialists. When more than one life form was associated with a single species (e.g. a species was reported as chamaephyte in one site, but phanerophyte in another), we considered that the life form with buds less protected was applicable for the species (in this case, a phanerophyte).Because the Caatinga is a semi-arid region, we considered climatic variables related to temperature and precipitation as potentially significant ecological drivers of species distributions. We obtained five climatic variables for each site from the global climate model WorldClim [] using DIVA GIS 7.3 software []: annual mean temperature, annual precipitation, precipitation seasonality, precipitation of the wettest quarter, and precipitation of the driest quarter. In order to take into account variation in edaphic environments on species distributions, we classified each site as sedimentary, crystalline, or inselberg (; ), depending on the type of edaphic environment reported by the authors of the study. [...] We obtained a phylogenetic tree for all plant species in our database using the online mega-tree Phylomatic, a phylogenetic database and software toolkit for the assembly of phylogenetic trees []. Phylogenetic relationships among species from different families were estimated from the current Phylomatic tree (R20100701). The backbone of the Phylomatic tree is the phylogenetic relationships among Angiosperm Phylogeny Group orders []. Phylomatic generates a supertree assembled by hand, rather than by an automated supertree algorithm, and conflicting branching patterns were resolved subjectively. Phylomatic outputs are intended to represent a pragmatic approximation of the true phylogeny of seed plants []. Branch lengths were based on minimum ages of nodes determined for families and higher orders from fossil data []. We placed undated nodes in the tree evenly between dated nodes with the branch length adjustment algorithm in Phylocom []. This algorithm took the phylogeny generated by Phylomatic, fixed the root node at 137 million years before present (i.e., the age of the eudicots clade) and fixed other nodes for which we had age estimates from Wikström et al. []. Phylomatic then sets all other branch lengths by placing the nodes evenly between dated nodes, and between dated nodes and terminals []. This has the effect of minimizing variance in branch length, within the constraints of dated nodes. Phylomatic thus produces a pseudo-chronogram that can be useful for estimating phylogenetic distance (in units of time) between taxa for analysis of phylogenetic community structure. [...] We decomposed the variation of phylogenetic diversity between climate and edaphic environment components to evaluate their relative roles in constraining the plant community structure. We followed the procedure described in Legendre & Legendre [] to calculate the portion of the variation of each diversity measure (Y) that is attributed to climate variables (X) and to edaphic environment (W). We first did an ANCOVA, regressing Y against X and W. The resulting value of R2 determined the portion of variation [a + b + c] related to climate [a], to soil type [c], and to both variables [b]. We did a multiple regression of Y against X, from which the resulting value of R2 determined [a + b]. We did a linear regression of Y against W, from which the resulting value of R2 determines [b + c]. Then, the portion [b] was obtained by the equation [b] = [a + b] + [b + c]–[a + b + c] [].We did phylogenetic analyses using R software [], and ANCOVAs and multiple regressions using SAS for Windows 9.4 (SAS Institute Inc., Cary, NC, USA). We tested for phylogenetic signal in life forms with the ‘phylo.signal.disc’ function, which was developed ad hoc by E.L. Rezende (pers. comm.) and corresponds to the ‘fixed tree, character randomly reshuffled model’ proposed by Maddison and Slatkin []. We calculated MPD, MNTD, and their respective SES using the ‘picante’ package (version 0.2–0; []). All calculations for the spatial analyses (i.e. Moran’s I and spatial filters) were conducted in SAM version 4.0 []. […]

Pipeline specifications

Software tools DIVA-GIS, Phylomatic, Phylocom, PHYSIG, Picante
Application Phylogenetics