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.
ASTRAL_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq
ASTRAL 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_OxalisHybSeq
ASTRAL 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_OxalisHybSeq
MP-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_OxalisHybSeq
MP-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_OxalisHybSeq
STAR 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_OxalisHybSeq
Bootstrapped 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_OxalisHybSeq
MRP 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_OxalisHybSeq
MRP 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_OxalisHybSeq
Bootstrapped 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_OxalisHybSeq
Bayesian inference gene trees of 727 low-copy nuclear genes of 25 southern African Oxalis accessions and Oxalis corniculata.
RAxMLGeneTrees_OxalisHybSeq
Maximum likelihood gene trees of 727 low-copy nuclear genes of southern African Oxalis accessions and Oxalis corniculata.
plastome_MrBayesMajorityRuleConsensusTree_OxalisHybSeq
Bayesian 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_OxalisHybSeq
Bayesian 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_OxalisHybSeq
FASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs (step 7 of Sondovač)
probeSequences_OxalisHybSeq
Final low-copy nuclear probe sequences (output of step 11 of Sondovač)
Assembly_LCNloci_OxalisHybSeq
Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)
Assembly_plastome_OxalisHybSeq
Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)
Assembly_nrDNAcistron_OxalisHybSeq
Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)
alignment_concatenatedLCNloci_OxalisHybSeq
Alignment of 727 concatenated low-copy nuclear genes of 25 southern African Oxalis accessions
alignment_plastome_OxalisHybSeq
Alignment of the plastome of 25 southern African Oxalis accessions
alignment_nrDNAcistron_OxalisHybSeq
Alignment of the nrDNA cistron of 25 southern African Oxalis accessions
RawReads_OxalisHybSeq
For a description of the contents of "RawReads_OxalisHybSeq.gz" please see "RawReads_OxalisHybSeq.doc"