ASTRAL_speciesTree_fromMrBayesGeneTrees_OxalisHybSeqASTRAL species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.ASTRAL_speciesTree_fromRAxMLGeneTrees_OxalisHybSeqASTRAL species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.MP-EST_speciesTree_fromMrBayesGeneTrees_OxalisHybSeqMP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.MP-EST_speciesTree_fromRAxMLGeneTrees_OxalisHybSeqMP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.STAR_speciesTree_fromMrBayesGeneTrees_OxalisHybSeqSTAR species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.STAR_bootstrappedSpeciesTree_fromRAxMLGeneTrees_OxalisHybSeqBootstrapped STAR species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.MRP_supertree_fromMrBayesGeneTrees_OxalisHybSeqMRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.MRP_supertree_fromRAxMLGeneTrees_OxalisHybSeqMRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.concatenatedLCNloci_bootstrapped_RAxML_OxalisHybSeqBootstrapped maximum likelihood tree based on concatenation of 727 low-copy nuclear genes of 25 southern African Oxalis accessions. Oxalis corniculata was used as outgroup.MrBayesGeneTrees_OxalisHybSeqBayesian inference gene trees of 727 low-copy nuclear genes of 25 southern African Oxalis accessions and Oxalis corniculata.RAxMLGeneTrees_OxalisHybSeqMaximum likelihood gene trees of 727 low-copy nuclear genes of southern African Oxalis accessions and Oxalis corniculata.plastome_MrBayesMajorityRuleConsensusTree_OxalisHybSeqBayesian inference majority rule consensus tree of the plastome of 25 southern African Oxalis accessions and Oxalis latifolia. The alignment was partitioned into protein-, tRNA-, and rRNA-coding as well as intron/spacer (i.e., non-coding) regions.nrDNAcistron_MrBayesMajorityRuleConsensusTree_OxalisHybSeqBayesian inference majority rule consensus tree of the nrDNA cistron of 25 southern African Oxalis accessions and Oxalis corniculata. The nrDNA alignment was partitioned into 18S, ITS1, 5.8S, ITS2 and 26S.geneious_deNovoAssembly_OxalisHybSeqFASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs (step 7 of Sondovač)probeSequences_OxalisHybSeqFinal low-copy nuclear probe sequences (output of step 11 of Sondovač)Assembly_LCNloci_OxalisHybSeqAlignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)Assembly_plastome_OxalisHybSeqAlignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)Assembly_nrDNAcistron_OxalisHybSeqAlignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)alignment_concatenatedLCNloci_OxalisHybSeqAlignment of 727 concatenated low-copy nuclear genes of 25 southern African Oxalis accessionsalignment_plastome_OxalisHybSeqAlignment of the plastome of 25 southern African Oxalis accessionsalignment_nrDNAcistron_OxalisHybSeqAlignment of the nrDNA cistron of 25 southern African Oxalis accessionsRawReads_OxalisHybSeqFor a description of the contents of "RawReads_OxalisHybSeq.gz" please see "RawReads_OxalisHybSeq.doc"

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.