Papers by Kenneth Oberlander
European journal of taxonomy, Jun 30, 2023
Zenodo (CERN European Organization for Nuclear Research), Aug 30, 2022
American Journal of Botany
PremiseIt is well‐known that whole genome duplication (WGD) has played a significant role in the ... more PremiseIt is well‐known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best‐known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid‐rich geophyte Oxalis, at both organ and cellular scales.MethodsWe measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy‐variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry.ResultsWe found substantial variation and no consistent ploidy‐related siz...
A phylogenetic tree with additional discrete-data of leaflet anatomical traits observed in southe... more A phylogenetic tree with additional discrete-data of leaflet anatomical traits observed in southern African Oxalis. A single ITS phylogenetic tree from the BEAST posterior distribution for southern African Oxalis taxa. The discrete data of 15 additional leaflet anatomical traits as noted in the results section of this article. (TIF 6750Â kb)
Discrete and continuous leaflet anatomical data for southern African Oxalis. The discrete and con... more Discrete and continuous leaflet anatomical data for southern African Oxalis. The discrete and continuous data of all studied leaflet anatomical traits. Captions of columns for discrete data include character state descriptions and captions of columns for continuous data include units (when applicable). (XLSX 143Â kb)
Background Plant-endophyte symbioses often revolve around nitrogen metabolism, and involve varyin... more Background Plant-endophyte symbioses often revolve around nitrogen metabolism, and involve varying degrees of intimacy. Although evidence for vertical inheritance of nitrogen-fixing endophytic bacteria is increasing, it is confined mostly to crop plants, and to date no such system has been reported for geophytes. Methods Bacterial endophytes associated with Oxalis, the most species-rich geophytic genus form the Cape Flora in southern Africa was studied. Culturable endophytes were isolated from surface-sterilized vegetative and reproductive plant organs for six host species at three locations. Colonies of microbes on various artificial media were morphotyped, enumerated and identified using sequence data. Filter exclusion experiments were conducted to determine if endophytes were vertically transmitted to seeds, determine if mucilage plays a role to actively attract microbes from the soil and to assess microbial richness isolated from the mucilage of Oxalis seedlings. Fluorescent mic...
Additional file 5: Table S2. A key to all species names relating to Fig. 2.
Additional file 4: Table S1. Properties of bacterial endophytes isolated from Oxalis host plants,... more Additional file 4: Table S1. Properties of bacterial endophytes isolated from Oxalis host plants, as described in literature [57â 67].
Additional file 2: Figure S2. Phylogenetic consensus tree constructed with universal 16S region s... more Additional file 2: Figure S2. Phylogenetic consensus tree constructed with universal 16S region sequences for endophytic bacteria isolated from Cape Oxalis (boldface font) and representative GenBank BLAST results. Colour boxes indicate the most likely species identifications of Oxalis isolates. B. megaterium and B. aryabhattai that had unresolved relationships based on the consensus tree.
MRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene... more 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
Alignment of the plastome of 25 southern African Oxalis accession
MP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions... more 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
For a description of the contents of "RawReads_OxalisHybSeq.gz" please see "RawRea... more For a description of the contents of "RawReads_OxalisHybSeq.gz" please see "RawReads_OxalisHybSeq.doc
Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome s... more Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12
Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome s... more Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12
Final low-copy nuclear probe sequences (output of step 11 of Sondovač
FASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs... more FASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs (step 7 of Sondovač
Bayesian inference majority rule consensus tree of the plastome of 25 southern African Oxalis acc... more 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
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their... more 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
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Papers by Kenneth Oberlander