Oxalis seeds from the Cape Flora have a spectrum of germination strategies.

PREMISE: Seed germination strategy has profound ecological and evolutionary consequences, with transitions between germination strategies receiving renewed recent attention. Oxalis from the Cape Flora, South Africa, has seeds with two contrasting germination strategies: orthodox and recalcitrant. The morphological gulf between these strategies (and potential intermediate morphologies) has been poorly quantified, with questions regarding their ecological function and evolution. We reconsidered this binary classification, emphasizing potential intermediate states. METHODS: Seed physiological traits were used to assign strategies to 64 Oxalis species. We tested for morphological/phenological signal corresponding to defined strategies with cluster, principal component, K-means clustering and discriminant analyses. RESULTS: We showed that an intermediate germination strategy does exist among Cape Oxalis, with two possible morphological groups within each strategy. These could reflect a continuum of germination states, where an ancestral orthodox strategy evolved toward a maximally recalcitrant peak, with a mosaic of intermediate states reflected in extant taxa. CONCLUSIONS: Environmental factors may affect germination strategy and distribution throughout the Cape because recalcitrant and intermediate species are confined to the winter rainfall region. They occupy specialized niches and may face adverse impacts under predicted climate change (hotter and drier winters), meriting focused future conservation.

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).

Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region. This resulted in 1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb-Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nrDNA cistron from 23 southern African Oxalis species. Despite a wide range of gene trees, the phylogeny based on the LCN genes was very robust, as retrieved through various gene and species tree reconstruction methods as well as concatenation. Cytonuclear discordance was strong. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb-Seq in phylogenetics.