We assess the phylogenetic information in trnK intron at the ordinal level using the Caryophyllales and compare it with that derived from matK. The trnK gene is split into two exons by an intron that ...includes the matK gene. The plastid trnK is a tRNA gene encoding Lysine(UUU), whereas the matK gene is a putative group II intron maturase. The two regions are usually coamplified, and trnK intron is partially sequenced but its sequences are often excluded from phylogenetic reconstruction at deep historic levels. This study shows that the two regions are comparable in proportion of variable sites, possess a comparable pattern of substitution rates per site, and display similar phylogenetic informativeness profiles and per‐site informativeness. Phylogenetic analyses show strong congruence between phylogenetic trees based on matK and trnK intron partitioned datasets from 45 genera representing 30 of the 34 recognized Caryophyllales families. The trnK intron alone provides a relatively well‐resolved topology for the order. Combining the trnK intron with matK sequence data resulted in six most parsimonious trees, differing only in the placement of Claytonia (Portulacaceae) within the noncore group. A well‐supported major basal split in the order into core and noncore Caryophyllales with Rhabdodendraceae, Simmondsiaceae, and Asteropeiaceae as sister to remaining core lineages is evident in partitioned and combined analyses. The placement of these three families has been disputable, impacting the overall backbone topology of the Caryophyllales. This study demonstrates the cost effectiveness of using the trnK intron along with matK (both substitutions and insertions/deletions) at deeper phylogenetic level.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Molecular phylogenetics has revolutionized our understanding of the Caryophyllales, and yet many relationships have remained uncertain, particularly at deeper levels. We have performed parsimony and ...maximum likelihood analyses on separate and combined data sets comprising nine plastid genes (∼12,000 bp), two nuclear genes (∼5000 bp), and the plastid inverted repeat (∼24,000 bp), giving a combined analyzed length of 42,006 bp for 36 species of Caryophyllales and four outgroups. We have recovered strong support for deep‐level relationships across the order. Two major subclades are well supported, the noncore and core Caryophyllales;Rhabdodendronfollowed bySimmondsiaare sisters to the core Caryophyllales,LimeumandStegnospermaare successive sisters to the “globular inclusion” clade,Gisekiais a distinct lineage well separated fromRivinawithin the “raphide” clade, andRivinaand Phytolaccaceae are disparate lineages, withRivinasister to Nyctaginaceae. The placement ofSarcobatusand relationships within the portulacaceous cohort remain problematic. Within the latter,Halophytumis sister to Basellaceae and Didiereaceae, and the clade comprisingPortulaca,Talinum, and Cactaceae is well supported. Classical hypotheses argued that the early Caryophyllales had evolved in open, dry, marginal environments at a time when pollinators were scarce, and, as such, the ancestral caryophyllid flower was wind pollinated with an undifferentiated perianth. We reevaluated these hypotheses in light of our phylogeny and find little support for anemophily as the ancestral condition; however, the early caryophyllid flower is suggested to have possessed an undifferentiated perianth. A subsequent minimum of nine origins of differentiated perianth is inferred. We discuss the evidence for independent origins of differentiated perianth and highlight the research opportunities that this pattern offers to the field of evolutionary developmental genetics.
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BFBNIB, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The recent call to reconstruct a detailed picture of the tree of life for all organisms has forever changed the field of molecular phylogenetics. Sequencing technology has improved to the point that ...scientics can now routinely sequence complete plastid/mitochondrial genomes and thus, vast amounts of data can be used to reconstruct phylogenies. These data are accumulating in DNA sequence repositories, such as GenBank, where everyone can benefit from the vast growth of information. The trend of generating genomic-region rich datasets has far outpaced the expasion of datasets by sampling a broader array of taxa. We show here that expanding a dataset both by increasing genomic regions and species sampled using GenBank data, despite the inherent missing DNA that comes with GenBank data, can provide a robust phylogeny for the plant order Caryophyllales (angiosperms). We also investigate the utility of trnK intron in phylogeny reconstruction at relativley deep evolutionary history (the caryophyllid order) by comparing it with rapidly evolving matK. We show that trnK intron is comparable to matK in terms of the proportion of variable sites, parsimony informative sites, the distribution of those sites among rate classes, and phylogenetic informativness across the history of the order. This is especailly useful since trnK intron is often sequenced concurrently with matK which saves on time and resources by increasing the phylogenetic utility of a single genomic region (rapidly evolving matK/trnK). Finally, we show that the inclusion of RNA edited sites in datasets for phylogeny reconstruction did not appear to impact resolution or support in the Gnetales indicating that edited sites in such low proportions do not need to be a consideration when building datasets. We also propose an alternate start codon for matK in Ephedra based on the presense of a 38 base pair indel in several species that otherwise result in pre-mature stop codons, and present 20 RNA edited sites in two Zamiaceae and three Pinaceae species.
Ph. D.
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