Mark P. Simmons

A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Abstract A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.

Whole-Genome Comparison of Leucine-Rich Repeat Extensins in Arabidopsis and Rice. A Conserved Family of Cell Wall Proteins Form a Vegetative and a Reproductive Clade

We have searched the Arabidopsis and rice (Oryza sativa) genomes for homologs of LRX1, an Arabidopsis gene encoding a novel type of cell wall protein containing a leucine-rich repeat (LRR) and an extensin domain. Eleven and eight LRX (LRR/EXTENSIN) genes have been identified in these two plant species, respectively. TheLRX gene family encodes proteins characterized by a short N-terminal domain, a domain with 10 LRRs, a cysteine-rich motif, and a variable C-terminal extensin-like domain. Phylogenetic analysis performed on the conserved domains indicates the existence of two major clades of LRX proteins that arose before the eudicot/monocot divergence and then diversified independently in each lineage. In Arabidopsis, gene expression studies by northern hybridization and promoter::uidA fusions showed that the two phylogenetic clades represent a specialization into “reproductive” and “vegetative” LRXs. The four Arabidopsis genes of the “reproductive” clade are specifically expressed in pollen, whereas the seven “vegetative” genes are predominantly expressed in various sporophytic tissues. This separation into two expression classes is also supported by previous studies on maize (Zea mays) and tomato (Lycopersicon esculentum)LRX homologs and by information on available rice ESTs. The strong conservation of the amino acids responsible for the putative recognition specificity of the LRR domain throughout the family suggests that the LRX proteins interact with similar ligands.

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

BackgroundKinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved ~350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis) has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships.ResultsWe used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages.ConclusionThe increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage-specific groups contributed to the functional diversification of kinesins. Results from our gene-tree analyses indicate that there was tremendous lineage-specific duplication and diversification of kinesins in eukaryotes. Since the functions of only a few plant kinesins are reported in the literature, this comprehensive comparative analysis will be useful in designing functional studies with photosynthetic eukaryotes.

Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

The amount of missing data in many contemporary phylogenetic analyses has substantially increased relative to previous norms, particularly in supermatrix studies that compile characters from multiple previous analyses. In such cases the missing data are non‐randomly distributed and usually present in all partitions (i.e. groups of characters) sampled. Parametric methods often provide greater resolution and support than parsimony in such cases, yet this may be caused by extrapolation of branch lengths from one partition to another. In this study I use contrived and simulated examples to demonstrate that likelihood, even when applied to simple matrices with little or no homoplasy, homogeneous evolution across groups of characters, perfect model fit, and hundreds or thousands of variable characters, can provide strong support for incorrect topologies when the matrices have non‐random distributions of missing data distributed across all partitions. I do so using a systematic exploration of alternative seven‐taxon tree topologies and distributions of missing data in two partitions to demonstrate that these likelihood‐based artefacts may occur frequently and are not shared by parsimony. I also demonstrate that Bayesian Markov chain Monte Carlo analysis is more robust to these artefacts than is likelihood.

Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology

Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loeseners subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.

Phylogeny and Delimitation of the Celastrales Inferred from Nuclear and Plastid Genes

Abstract A phylogenetic analysis of the Celastrales was performed using nuclear (18S, ITS 1, 26S rDNA) and plastid (atpB, matK, rbcL, trnL-F spacer) genes. In contrast to most previous studies, Celastrales and Malpighiales are resolved as being more closely related to one another than either are to Oxalidales. The Huaceae are well supported as the sister group to Oxalidales, not Celastrales, as had been previously proposed. The Lepidobotryaceae are unambiguously supported as sister to the clade consisting of Celastraceae and Parnassiaceae. The Parnassiaceae are well supported as members of an early branching lineage within Celastraceae, rather than as its sister group. Likewise, Pottingeria appears to be part of an early derived lineage of Celastraceae. Empleuridium is unambiguously supported as a derived member of Celastraceae, as are Brexia, Canotia, Siphonodon, Stackhousia, and Tripterococcus. Bhesa is unambiguously supported as a member of Malpighiales, though its relationships within the order remain unclear. Perrottetia should be transferred out of Celastraceae and into eurosids II, being closely related to Tapiscia and Dipentodon. These results help delimit the Celastrales and Celastraceae as morphologically more homogeneous taxa.

Spurious 99% bootstrap and jackknife support for unsupported clades.

Quantifying branch support using the bootstrap and/or jackknife is generally considered to be an essential component of rigorous parsimony and maximum likelihood phylogenetic analyses. Previous authors have described how application of the frequency-within-replicates approach to treating multiple equally optimal trees found in a given bootstrap pseudoreplicate can provide apparent support for otherwise unsupported clades. We demonstrate how a similar problem may occur when a non-representative subset of equally optimal trees are held per pseudoreplicate, which we term the undersampling-within-replicates artifact. We illustrate the frequency-within-replicates and undersampling-within-replicates bootstrap and jackknife artifacts using both contrived and empirical examples, demonstrate that the artifacts can occur in both parsimony and likelihood analyses, and show that the artifacts occur in outputs from multiple different phylogenetic-inference programs. Based on our results, we make the following five recommendations, which are particularly relevant to supermatrix analyses, but apply to all phylogenetic analyses. First, when two or more optimal trees are found in a given pseudoreplicate they should be summarized using the strict-consensus rather than frequency-within-replicates approach. Second jackknife resampling should be used rather than bootstrap resampling. Third, multiple tree searches while holding multiple trees per search should be conducted in each pseudoreplicate rather than conducting only a single search and holding only a single tree. Fourth, branches with a minimum possible optimized length of zero should be collapsed within each tree search rather than collapsing branches only if their maximum possible optimized length is zero. Fifth, resampling values should be mapped onto the strict consensus of all optimal trees found rather than simply presenting the ≥ 50% bootstrap or jackknife tree or mapping the resampling values onto a single optimal tree.

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data

Non-random distributions of missing data are a general problem for likelihood-based statistical analyses, including those in a phylogenetic context. Extensive non-randomly distributed missing data are particularly problematic in supermatrix analyses that include many terminals and/or loci. It has been widely reported that missing data can lead to loss of resolution, but only very rarely create misleading or otherwise unsupported results in a parsimony context. Yet this does not hold for all parametric-based analyses because of their assumption of homogeneity across characters and lineages, which can lead to both long-branch attraction and long-branch repulsion. Contrived examples were used to demonstrate that non-random distributions of missing data, even without rate heterogeneity among characters and a well fitting model, can provide misleading likelihood-based topologies and branch-support values that are radically unstable based on slight modifications to character sampling. The same can occur despite complete absence of parsimony-informative characters. Otherwise unsupported resolution and high branch support for these clades were found to occur frequently in 22 empirical examples derived from a published supermatrix. Partitioning characters based on the distribution of missing data helped to decrease, but did not eliminate, these artifacts. These artifacts were exacerbated by low quality tree searches, particularly when holding only a single optimal tree that must be fully resolved.

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.