Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata.

Since the discovery of Paraburkholderia tuberum, an indigenous South African species and one of the first beta-rhizobia described, several other South African rhizobial Paraburkholderia species have been recognized. Here, we investigate the taxonomic status of 31 rhizobial isolates from the root nodules of diverse South African legume hosts in the Core Cape Subregion, which were initially identified as P. tuberum. These isolates originate from the root nodules of genera in the Papilionoideae as well as Vachellia karroo, from the subfamily Caesalpinioideae. Genealogical concordance analysis of five loci allowed delineation of the isolates into two putative species clusters (A and B). Cluster A included P. tuberum STM678T, suggesting that this monophyletic group represents P. tuberum sensu stricto. Cluster B grouped sister to P. tuberum and included isolates from the Paarl Rock Nature Reserve in the Western Cape Province. Average Nucleotide Identity (ANI) analysis further confirmed that isolates of Cluster A shared high genome similarity with P. tuberum STM678T compared to Cluster B and other Paraburkholderia species. The members of Cluster B associated with a single species of Podalyria, P. calyptrata. For this new taxon we accordingly propose the name Paraburkholderia podalyriae sp. nov., with the type strain WC7.3bT (= LMG 31413T; SARCC 750T). Based on our nodA and nifH phylogenies, P. podalyriae sp. nov. and strains of P. tuberum sensu stricto (including one from V. karroo) belong to symbiovar africana, the symbiotic loci of which have a separate evolutionary origin to those of Central and South American Paraburkholderia strains.

Monophyly, phylogenetic position and the role of hybridization in Schoenoxiphium Nees (Cariceae, Cyperaceae).

Incongruence between gene trees, even within genomes, is often the result of hybridization and/or other processes such as incomplete lineage sorting, and can cause problems for phylogenetic analyses. We show here that the radiation of the Cyperaceae genus Schoenoxiphium involved at least one hybridization event with a closely related species of Carex, as indicated by a recombinant nuclear ITS region shared by all species in the S. rufum clade and C. camptoglochin. Recombinant sequences were confirmed with cloning experiments and recombination analyses. The monophyly of Schoenoxiphium has, in previous analyses, been suspected but not sufficiently supported, possibly due in part to this problem. Our phylogenetic analyses include an appropriate representation of Schoenoxiphium and other related Cariceae species and an extended sampling of the nuclear ITS and plastid marker regions, trnLF and rps16. We demonstrate that Schoenoxiphium is monophyletic, nested within Carex, and that several supported clades exist in Schoenoxiphium.