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.

• MeSH
• Phylogeny MeSH
• Genetic Variation * MeSH
• Genetic Markers * MeSH
• Genome MeSH
• Genotyping Techniques methods   MeSH
• Oxalidaceae classification   genetics   MeSH
• Sequence Analysis, DNA MeSH
• Transcriptome MeSH
• Publication type
• Journal Article MeSH
• Evaluation Study MeSH
• Geographicals
• Africa, Southern MeSH

BACKGROUND: The southern African Oxalis radiation is extremely morphologically variable. Despite recent progress in the phylogenetics of the genus, there are few morphological synapomorphies supporting DNA-based clades. Leaflet anatomy can provide an understudied and potentially valuable source of information on the evolutionary history and systematics of this lineage. Fifty-nine leaflet anatomical traits of 109 southern African Oxalis species were assessed in search of phylogenetically significant characters that delineate clades. RESULTS: A combination of 6 leaflet anatomical traits (stomatal position, adaxial epidermal cells, abaxial epidermal cells, mesophyll, sheath around vascular tissue, degree of leaflet conduplication) clearly support various clades defined by previous DNA-based phylogenetic work. Other, mostly continuous leaflet anatomical traits were highly variable and showed less phylogenetic pattern. CONCLUSIONS: Major and unexpected findings include the transition from ancestral hypostomatic leaflets to adaxially-located stomata in the vast majority of southern African Oxalis, the loss of semi-swollen AB epidermal cells and the gain of swollen adaxial and abaxial epidermal cells in selected clades, and multiple changes from ancestral bifacial mesophyll to isobilateral or homogenous mesophyll types. The information gathered in this study will aid in the taxonomic revision of this speciose member of the Greater Cape Floristic Region and provide a basis for future hypotheses regarding its radiation.

• MeSH
• Biological Evolution MeSH
• Plant Vascular Bundle cytology   MeSH
• Gene Duplication MeSH
• Phenotype MeSH
• Phylogeny * MeSH
• Quantitative Trait, Heritable MeSH
• Plant Leaves anatomy & histology   cytology   genetics   MeSH
• Mesophyll Cells cytology   MeSH
• Oxalidaceae anatomy & histology   genetics   MeSH
• Plant Stomata cytology   MeSH
• Trichomes cytology   MeSH
• Publication type
• Journal Article MeSH