Mark Pitkin Simmons

Colorado State University | CSU · Department of Biology

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundation...

We present the best sampled phylogenetic analysis of Celastrales, with respect to both character and taxon sampling, and use it to present a natural classification of the order. Parnassiaceae are highly supported as sister to Celastraceae; we recognize both families as distinct. Pottingeria is highly supported as a member of Celastraceae. We recogn...

Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-...

We examined the impact of successive alignment quality‐control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target‐sequence‐capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemp...

coalescent methods offer an alternative to the concatenation (supermatrix) approach for inferring phylogenetic relationships from genome-scale datasets. Given huge datasets, broad congruence between contrasting phylogenomic paradigms is often obtained, but empirical studies commonly show some well supported conflicts between concatenation and coale...

Phylogenomic analyses of ancient rapid radiations can produce conflicting results that are driven by differential sampling of taxa and characters as well as the limitations of alternative analytical methods. We re-examine basal relationships of palaeognath birds (ratites and tinamous) using recently published datasets of nucleotide characters from...

In two-step coalescent analyses of phylogenomic data, gene-tree topologies are treated as fixed prior to species-tree inference. Although all gene-tree conflict is assumed to be caused by lineage sorting when applying these methods, in empirical datasets much of the conflict can be caused by estimation error. Weakly supported and even arbitrarily r...

New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries. Home to some of the best-preserved ecosystems on the planet and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region, it is a globally recognized centre of biological and cultural diver...

Farmers and traders have developed a system of names to refer to different qat (Catha edulis) cultivars, using stem color as the primary trait to differentiate them. In this study, we tested if the named cultivars from Ethiopia, Kenya, and Yemen represent genetic clusters. We also quantified clonal reproduction and tracked the geographic dispersal...

DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciph...

Compensatory mutations are crucial for functional RNA because they maintain RNA configuration and thus function. Compensatory mutation has traditionally been considered to be a two-step substitution through the GU-base-pair intermediate. We tested for an alternative AC-mediated compensatory mutation (ACCM). We investigated ACCMs by using a comprehe...

Contemporary phylogenomic studies frequently incorporate two‐step coalescent analyses wherein the first step is to infer individual‐gene trees, generally using maximum‐likelihood implemented in the popular programs PhyML or RAxML. Four concerns with this approach are that these programs only present a single fully resolved gene tree to the user des...

Background and aims: Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying...

Genomic datasets sometimes support conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (=concatenation) approach, several methods...

Species richness is greatest in the tropics, and much of this diversity is concentrated in mountains. Janzen proposed that reduced seasonal temperature variation selects for narrower thermal tolerances and limited dispersal along tropical elevation gradients [Janzen DH (1967) Am Nat 101:233-249]. These locally adapted traits should, in turn, promot...

Genomic datasets sometimes support unconventional or conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (= concatenation) approa...

In summary (“two-step”) coalescent analyses of empirical data, researchers typically apply the bootstrap to quantify branch support for clades inferred on the optimal species tree. We tested whether site-wise bootstrap analyses provide consistently more conservative support than gene-wise bootstrap analyses. We did so using data from three empirica...

Appendix S1 Description of the statistical analyses of the RNA sequencing data, comparing effects of treatments, species and organs. Figure S1 Biomass production and Se and S accumulation by Stanleya pinnata and S. elata. The plants were grown from seed on agar with 0 or 20 μm sodium selenate. Figure S2 Overview of differential expression between...

Associate editors are typically given minimal guidance when they are hired by editors-in-chief of scientific journals. Ten rules (or guidelines) are presented for associate editors based on the author’s experience as an associate editor for three evolutionary journals. First, accept invitations to edit manuscripts that are outside your comfort zone...

To obtain better insight into the mechanisms of selenium hyperaccumulation in Stanleya pinnata, transcriptome-wide differences in root and shoot gene expression levels were investigated in S. pinnata and related nonaccumulator Stanleya elata grown with or without 20 μM selenate. Genes predicted to be involved in sulfate/selenate transport and assim...

Premise of the study: Qat (Catha edulis, Celastraceae) is a woody plant species cultivated for its stimulant alkaloids. Qat is important to the economy and culture in large regions of Ethiopia, Kenya, and Yemen. Despite the importance of this species, the wild origins and dispersal of cultivars have only been described in often contradictory histo...

Introduction: Catha edulis (qat, khat, mirra) is a woody plant species that is grown and consumed in East Africa and Yemen for its stimulant alkaloids cathinone, cathine and norephedrine. Two Celastraceae species, in addition to qat, have been noted for their stimulant properties in ethnobotanical literature. Recent phylogenetic reconstructions pl...

Maytenus species are distributed in the New World from Argentina to the U. S. A. The genus delimitation has been controversial, especially in relation to the inclusion of Gymnosporia. Maytenus has been treated in a broad sense such that it was considered widely distributed in tropics and subtropics worldwide. Even in its current restricted circumsc...

Based on phylogenetic analyses using rDNA and plastid sequence data, and the examination of morphological characters, we infer that Pleurostylia, as currently delimited, is a polyphyletic group. Pleurostylia serrulata and two newly described species from Africa are part of the New World Crossopetalum lineage. By contrast, Pleurostylia s. s. consist...

An important goal of the angiosperm systematics community has been to develop a shared approach to molecular data collection, such that phylogenomic data sets from different focal clades can be combined for meta-studies across the entire group. Although significant progress has been made through efforts such as DNA barcoding, transcriptome sequenci...

Identifying the extant sister group to the remaining angiosperms has been a subject of long debate, for which the primary currently competing hypotheses are that Amborella alone is sister or that the clade (Amborella, Nymphaeales) is sister. Both Xi et al. (Syst. Biol., 2014, 63, 919) and Goremykin et al. (Syst. Biol., 2015, 64, 879) identified Amb...

Both traditional as well as 10 more recent methods of coding characters from exons of protein-coding genes are reviewed. The more recent methods collectively blur the distinction between nucleotide and amino-acid coding and enable investigators to carefully quantify the effects of different sources of phylogenetic signal as well as their potential...

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP-EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with man...

The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may...

Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete...

Dot-plots comparing the L. fauriei plastid genome to those of six other Myrtales species. (TIF)

Supplementary matrix: The full alignment of 73 protein-coding genes from 10 used species (NEXUS format). (NEX)

Primers used for gap closure in L. fauriei. (DOCX)

The Sanger sequence verification of the rpl2 gene from species with and without the intron. (A) The boundary sequences of two exons: the dash lines represents the elliptical intron sequences; the sequence from the maple shade is from first exon and from the green shade is from the second intron. The Sanger sequencing chromatograms with first exon a...

PCR products indicating rpl2 intron absence in Lagerstroemia. MA = L. macrocarpa, FL = L. floribunda, INT = L. intermedia, GU = L. guilinensis, FA = L. fauriei, VE = L. venusa, CAU = L. caudata, LI = L. limii, SUB = L. subcostata, IND = L. indica, PA = L. parvifolia, PU = Punica granatum, LY = Lythrum salicaria, CU = Cuphea hyssopifolia, OEN = Oeno...

Lengths of plastid genomes and repetitive regions. A. Plastid genome size comparison among seven Myrtales species (1 = Lagerstroemia fauriei, 2 = Oenothera argillicola, 3 = Angophora costata, 4 = Corymbia eximia, 5 = Eucalyptus aromaphloia, 6 = Stockwellia quadrifida, 7 = Syzygium cumini, with species listed according to their distance). B. All rep...

Lengths of exons and introns in intron-containing genes from the plastid genome of L. fauriei. (DOCX)

Ten highest sites of non-coding regions with respect to their potential phylogenetic signal. (DOCX)

Divided genes (longer than 1.5kb) into short regions and their parsimony-informative distribution. (DOCX)

The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in stand-alone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome seq...

We leverage genomic resources from 43 angiosperm species to develop enrichment probes useful for collecting textasciitilde500 loci from non-model taxa across the diversity of angiosperms. By taking an anchored phylogenomics approach, in which probes are designed to represent sequence diversity across the group, we are able to efficiently target loc...

Efforts to subject one’s own pet hypotheses to severe tests, to attempt to falsify them, are always warranted. The likelihood that one will impose unrealistically high standards is quite low. The same cannot be said for the standards that scientists set for the work of their opponents…. As unseemly as factionalism in science may be, it does serve a...

It has recently been concluded that phylogenomic data from 310 nuclear genes support the clade of (Amborellales, Nymphaeales) as sister to the remaining angiosperms and that shortcut coalescent phylogenetic methods outperformed concatenation for these data. We falsify both of those conclusions here by demonstrating that discrepant results between t...

Past studies have identified herbivory as a likely selection pressure for the evolution of hyperaccumulation, but few have tested the origin(s) of hyperaccumulation in a phylogenetic context. We focused on the evolutionary history of selenium (Se) hyperaccumulation in Stanleya (Brassicaceae). Multiple accessions were collected for all Stanleya taxa...

When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences followed by branch swapping, or usi...

Haydenia M. P. Simmons (Celastraceae) is an illegitimate name because it is a later homonym of Haydenia Seward (Cyatheaceae). The genus is renamed Haydenoxylon M. P. Simmons and the three included species are renamed Haydenoxylon gentryi (Lundell) M. P. Simmons, H. haberianum (Hammel) M. P. Simmons, and H. urbanianum (Loes.) M. P. Simmons. The name...

The use of Next Generation Sequencing (NGS) techniques to identify microsatellite markers has replaced more time intensive methods such as molecular cloning. The main advantage of NGS over traditional methods of identifying microsatellite markers is the generation of many more sequences with less effort. It is possible to design primers from unenri...

The greater power of parametric methods over parsimony is frequently observed in empirical phylogenetic analyses by providing greater resolution and higher branch support. This greater power is provided by several different factors, including some that are generally regarded as disadvantageous. In this study we used both empirical and (modified) si...

Selenium (Se) hyperaccumulation, the capacity to concentrate the toxic element Se above 1000 mg·kg(-1)·dry mass, is found in relatively few taxa native to seleniferous soils. While Se hyperaccumulation has been shown to likely be an adaptation that protects plants from herbivory, its evolutionary history remains unstudied. Stanleya (Brassicaceae) i...

We applied simple 4-taxon simulations with 3-way character conflict or a hard polytomy to check for false positive branch support, with a focus on the bootstrap and recently introduced likelihood-based phylogenetic-inference programs. Given that there are only three possible bifurcating topologies, discrepancies among methods identified in this stu...

Abstract— A new species of Celastraceae, Maytenus megalocarpa, is described and illustrated. The species is known from only a small number of collections from eastern Brazil, in the Atlantic Rainforest of Bahia and Minas Gerais states. It is considered endangered given the rapid deforestation of this biome. The species is readily distinguished fro...

Eucosma Hübner is the largest genus in Tortricidae, currently comprising 298 described species. Its circumscription and those of the closely related genera Pelochrista Lederer, Phaneta Stephens and Epiblema Hübner have long been matters of confusion. Prior to the mid-1920s, assignment to any of these genera was largely arbitrary due to a lack of cl...

Broad-scale patterns of species diversity have received much attention in the literature, yet the mechanisms behind their formation may not explain species richness disparities across small spatial scales. Few taxa display high species diversity on either side of Wallace's Line and our understanding of the processes causing this biogeographical pat...

Disjunct distributions in poorly defined taxa can serve as indicators that the members of the isolated ranges are polyphyletic, as has been previously demonstrated in many plant families. Such taxa should be prioritized for inclusion in phylogenetic analyses so that at least one member from each isolated range should be sampled together with other...

A supermatrix of 272 terminals from Rubiaceae tribe Spermacoceae that were scored for up to 10 gene regions (two nrDNA, eight plastid) was used as an empirical example to quantify sources of error in heuristic parametric (Bayesian MCMC and maximum likelihood) phylogenetic analyses. The supermatrix includes dramatic disparities in which terminals we...

RNA silencing, or RNA interference (RNAi) in metazoans mediates development, reduces viral infection and limits transposon mobility. RNA silencing involves 21-30 nucleotide RNAs classified into microRNA (miRNA), exogenous and endogenous small interfering RNAs (siRNA), and Piwi-interacting RNA (piRNA). Knock-out, silencing and mutagenesis of genes i...

CodeML results for each of the five models for detection of positive selection and each of the six genes. For each gene, the ML model is highlighted in grey. The number of positively selected sites (PSS) identified using the naive empirical Bayes (NEB) and Bayes empirical Bayes (BEB) methods are listed for each gene. l = −log likelihood ratio. The...

Alternative amino acids found to be under positive selection in CodeML using BEB. The locations of the replacements are indicated in parentheses (U = region with unassigned function, Pw = Piwi, Pz = PAZ, DUF = domain of unknown function, Hc = Helicase superfamily c-terminal domain, Hcd = Helicase dimerization domain, Dc = DExD/H-like helicase, Db =...

The phylogeny of Celastraceae subfamilies Cassinoideae (120 species in 17 genera in both the Old and New World tropics and subtropics) and Tripterygioideae (39 species in seven genera) was inferred using plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) loci together with morphological characters. Subfamily Cassinoideae include those Celastrace...

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) sampl...

The study of three island groups of the palm tribe Trachycarpeae (Arecaceae/Palmae) permits both the analysis of each independent radiation and comparisons across the tribe to address general processes that drive island diversification. Phylogenetic relationships of Trachycarpeae were inferred from three plastid and three low-copy nuclear genes. Th...

Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ base...

Figure S1. Parsimony strict consensus trees of all the sequence data summarized to show only the inter-generic relationships and Pritchardia from different island chains. Parsimony jackknife support values above, and likelihood bootstrap values below each branch of each gene individually, the plastid partition, and the simultaneous analysis.

Figure S4. The individual plastid gene trees and the plastid simultaneous-analysis estimated for Pritchardia species delimitation with jackknife branch support values above and bootstrap values below each branch.

Table S1. Mutually exclusive character states were used to test if gene flow had ceased between the sampled populations using population aggregation analysis for each of the three datasets listed in columns with spaces between each of the independent lineages. In the sequence dataset, terminals with missing data for diagnostic characters were arbit...

Figure S2. Parsimony simultaneous analysis and strict consensus tree of all the 105 terminals sampled for nucleotide data with parsimony jackknife values shown.

Figure S3. The individual nuclear gene trees estimated for Pritchardia species delimitation as shown in the parsimony strict consensus with parsimony jackknife values above and likelihood bootstrap values below each branch.

The phylogeny of Celastraceae tribe Euonymeae (≈ 230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculi...

The phylogeny of Celastraceae subfamilies Cassinoideae (120 species in 17 genera in both the Old and New World tropics and subtropics) and Tripterygioideae (39 species in seven genera) was inferred using plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) loci together with morphological characters. Subfamily Cassinoideae include those Celastrace...

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 l...

Abstract—Maytenus s. l. (including Gymnosporia) is a morphologically diverse genus of about 300 species that is widely distributed in the tropics and subtropics of both the Old and New Worlds. Its delimitation has been extensively debated and despite the segregation of Gymnosporia, Maytenus s. s. remains a heterogeneous, polyphyletic group. To deli...

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 pse...

Pritchardia (loulu palm) is the seventh largest flowering plant genus in the Hawaiian archipelago, and many species are of high conservation concern. The island radiation has produced many cryptic species complexes across fine ecological gradients. Microsatellite primers were optimized to investigate genetic diversity of Pritchardia martii (Gaudich...

The potential application of DNA barcodes of plastid (matK, trnH. psbA, petD, and rbcL) and nuclear (internal transcribed spacer (ITS) of rDNA) DNA regions was investigated for 25 Hedyotis taxa. The ITS showed the best species discrimination by resolving 23 of the species as exclusive lineages with no shared alleles between any of the 24 distinct s...

Tripterygium wilfordii Hook.f., known as Leigongteng (Thunder God Vine) in traditional Chinese medicine, has attracted much attention for its applications in relieving autoimmune disorders such as rheumatoid arthritis and systemic lupus erythematosus, and for treating cancer. Molecular analyses of the ITS and 5S rDNA sequences indicate that T. hypo...

We used random sequences to determine which alignment methods are most susceptible to aligning sequences so as to create artifactual resolution and branch support in phylogenetic trees derived from those alignments. We compared four alignment methods (progressive pairwise alignment, simultaneous multiple alignment of sequence fragments, local pairw...