A novel phylogenetic regionalization of phytogeographical zones of southern Africa reveals their hidden evolutionary affinities

Abstract

Aim Although existing bioregional classification schemes often consider the compositional affinities within regional biotas, they do not typically incorporate phylogenetic information explicitly. Because phylogeny captures information on the evolutionary history of taxa, it provides a powerful tool for delineating biogeographical boundaries and for establishing relationships among them. Here, we present the first vegetation delineation of the woody flora of southern Africa based upon evolutionary relationships.Location Southern Africa. MethodsWe used a published time-calibrated phylogenetic tree for 1400 woody plant species along with their geographical distributions and a metric of phylogenetic beta diversity to generate a phylogenetic delineation of the woody vegetation of southern Africa. We then explored environmental correlates of phylogenetic turnover between them, and the evolutionary distinctiveness of the taxa within them. ResultsWe identified 15 phylogenetically distinct biogeographical units, here referred to as phyloregions. The largest phyloregion broadly overlaps with Savanna vegetation, while the phyloregion overlapping with the south-western portion of the Fynbos biome is the most evolutionarily distinct. Potential evapotranspiration and mean annual temperature differ significantly among phyloregions and correlate with patterns of phylogenetic beta diversity between them. Our phylogeny-based delimitation of southern Africa's woody vegetation broadly matches currently recognized phytogeographical classifications, but also highlights parts of the Namib Karoo and Greater Limpopo Transfrontier Park as distinct, but previously under-recognized biogeographical units. Main conclusionsOur analysis provides new insights into the structure and phylogenetic relationships among the woody flora of southern Africa. We show that evolutionary affinities differentiate phyloregions closely resembling existing vegetation classifications, yet also identify 'cryptic' phyloregions that are as evolutionarily distinct as some of the recognized African vegetation types.

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

“…Existing African plant DNA barcodes have helped resolve the systematics of ecologically and economically important taxa, including rosewoods (Hassold et al, ), acacias (Boatwright, Maurin, & Bank, ; Kyalangalilwa, Boatwright, Daru, Maurin, & Bank, ), aloes (Daru et al, ; Manning, Boatwright, Daru, Maurin, & Bank, ), and the Combretaceae (Gere et al, ; Jordaan, Wyk, & Maurin, , ; Maurin, Chase, Jordaan, & Bank, ). Researchers in the field of community phylogenetics (also called phylogenetic community ecology), have used African plant DNA barcodes to understand plant community responses to herbivory (Yessoufou et al, ), classify biogeographical regions of Southern Africa (Daru, Bank, et al, ), and to assess the evolutionary history of African cycads (Yessoufou, Bamigboye, Daru, & Bank, ), underground trees (geoxyles) (Maurin et al, ) and thorny savanna plant assemblages (Charles‐Dominique et al, ). Increasing the taxonomic and geographic coverage of DNA barcodes for African plants will enrich our understanding of these species, communities, and ecosystems.…”

Unravelling the evolutionary origins of biogeographic assemblages

“…Following Daru et al. (), we used a dated molecular phylogenetic tree for the woody flora of southern Africa from Maurin et al. () to generate a classification of phyloregions representing the major vegetation types in southern Africa.…”

“…In a second step, we used the “elbow” method of Salvador and Chan () to “cut” the dendrogram and determined the optimal number of meaningful clusters (phyloregions) using the “elbow” function in the R package GMD (Zhao, Valen, Parker, & Sandelin, ). Last, we described the relationships among the resulting phylogenetically delimited clusters (“phyloregions”; Daru et al., ) using hierarchical dendrogram of dissimilarity and non‐metric multidimensional scaling (NMDS) ordination, which represents the original distance matrix in a few (usually 2 or 3) dimensions with a minimum loss of information. A full description of how phyloregions were delimited is included in Daru et al.…”

International Barcode of Life: Focus on big biodiversity in South Africa

“…For more than a decade, South African researchers have been among the global leaders in the DNA barcoding, molecular systematics, and community phylogenetics of plants (Kyalangalilwa et al 2013;Charles-Dominique et al 2016;Daru et al 2016;Bezeng et al 2017). This strength is again apparent at the 7th Conference, in which abstracts about plants of Africa feature prominently, alongside other plant-focused contributions from around the globe.…”