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.

Department of Biology Hobart and William Smith Colleges 213 Eaton Hall Geneva NY 14456 USA

Department of Botany and Plant Pathology Oregon State University 2082 Cordley Hall Corvallis OR 97331 USA

Department of Botany and Zoology Stellenbosch University Private Bag X1 Matieland 7602 South Africa

Department of Botany Faculty of Science Charles University Prague Benátská 2 128 01 Prague Czech Republic

Department of Conservation Ecology and Entomology Stellenbosch University Private Bag X1 Matieland 7602 South Africa

Institute of Botany The Czech Academy of Sciences Zámek 1 252 43 Průhonice Czech Republic

USDA Forest Service Pacific Northwest Research Station 3200 SW Jefferson Way Corvallis OR 97331 USA

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EU436922, HQ664602, JF937588, NC_015141, NC_016736