Helga Ochoterena

Phylogeny of the herbaceous tribe Spermacoceae (Rubiaceae) based on plastid DNA data

Abstract In its current circumscription, the herbaceous tribe Spermacoceae s.l. (Rubiaceae, Rubioideae) unites the former tribes Spermacoceae s. str., Manettieae, and the Hedyotis–Oldenlandia group. Within Spermacoceae, and particularly within the Hedyotis–Oldenlandia group, the generic delimitations are problematic. Up until now, molecular studies have focused on specific taxonomic problems within the tribe. This study is the first to address phylogenetic relationships within Spermacoceae from a tribal perspective. Sequences of three plastid markers (atpB-rbcL, rps16, and trnL-trnF) were analyzed separately as well as combined using parsimony and Bayesian approaches. Our results support the expanded tribe Spermacoceae as monophyletic. The former tribe Spermacoceae s. str. forms a monophyletic clade nested within the Hedyotis–Oldenlandia group. Several genera formerly recognized within the Hedyotis–Oldenlandia group are supported as monophyletic (Amphiasma Bremek., Arcytophyllum Willd. ex Schult. & Schult. f., Dentella J. R. Forst. & G. Forst., Kadua Cham. & Schltdl., and Phylohydrax Puff), while others appear to be paraphyletic (e.g., Agathisanthemum Klotzsch), biphyletic (Kohautia Cham. & Schltdl.), or polyphyletic (Hedyotis L. and Oldenlandia L. sensu Bremekamp). Morphological investigations of the taxa are ongoing in order to find support for the many new clades and relationships detected. This study provides a phylogenetic hypothesis with broad sampling across the major lineages of Spermacoceae that can be used to guide future species-level and generic studies.

Amino acid vs. nucleotide characters: challenging preconceived notions

The 567-terminal analysis of atpB, rbcL, and 18S rDNA was used as an empirical example to test the use of amino acid vs. nucleotide characters for protein-coding genes at deeper taxonomic levels. Nucleotides for atpB and rbcL had 6.5 times the amount of possible synapomorphy as amino acids. Based on parsimony analyses with unordered character states, nucleotides outperformed amino acids for all three measures of phylogenetic signal used (resolution, branch support, and congruence with independent evidence). The nucleotide tree was much more resolved than the amino acid tree, for both large and small clades. Nearly twice the percentage of well-supported clades resolved in the 18S rDNA tree were resolved using nucleotides (91.8%) relative to amino acids (49.2%). The well-supported clades resolved by both character types were much better supported by nucleotides (98.7% vs. 83.8% average jackknife support). The faster evolving nucleotides with a smaller average character-state space outperformed the slower evolving amino acids with a larger average character-state space. Nucleotides outperformed amino acids even with 90% of the terminals deleted. The lack of resolution on the amino acid trees appears to be caused by a lack of congruence among the amino acids, not a lack of replacement substitutions.

Palynological characters and their phylogenetic signal in Rubiaceae

In the 1990s Rubiaceae became a hot spot for systematists, mainly due to the comprehensive treatment of the family by Robbrecht in 1988. Next to the exploration of macromolecular characters to infer the phylogeny, the palynology of Rubiaceae finally received the attention it deserves. This article aims to present a state-of-the-art analysis of the systematic palynology of the family. The range of varíation in pollen morphology is wide, and some of the pollen features are not known from other angiosperm taxa; e.g., a looplike or spiral pattern for the position of apertures in pantoaperturate grains. We compiled an online database at the generic level for the major pollen characters and orbicule presence in Rubiaceae. An overview of the variation is presented here and illustrated per character: dispersal unit, pollen size and shape, aperture number, position and type, sexine ornamentation, nexine pattern, and stratification of the sporoderm. The presence/absence and morphological variation of orbicules at the generic level is provided as well. The systematic usefulness of pollen morphology in Rubiaceae is discussed at the (sub)family, tribal, generic, and infraspecific levels, using up-to-date evolutionary hypotheses for the different lineages in the family. The problems and opportunities of coding pollen characters for cladistic analyses are also treated.

Phylogenetic relationships of the genera of Theaceae based on morphology

This work represents the first phylogenetic analysis of all genera belonging to the plant family Theaceae (sensu lato). The study is based on 60 morphological characters derived from herbarium specimens and an extensive literature review of 37 genera (including the outgroup). In contrast to the results from molecular data, Theaceae is here found to consist of one clade in which the recognition of two families or subfamilies would leave Theaceae s.s. paraphyletic. Within that clade, Ternstroemiaceae is supported as monophyletic and includes Adinandra, Anneslea, Archboldiodendron, Balthasaria, Cleyera, Eurya, Euryodendron, Ficalhoa, Freziera, Symplococarpon, Ternstroemia and Visnea. The paraphyletic Theaceae s.s. includes Apterosperma, Camellia, Dankia, Gordonia, Pyrenaria, Schima, and Stewartia. Tetrameristaceae (Pentamerista and Tetramerista) are supported as a monophyletic family, with Pellicieraceae (Pelliciera) as sister group, and that clade is sister to the rest of the taxa. Bonnetiaceae (Archytaea and Bonnetia) and Kielmeyeroideae of the Clusiaceae (Caraipa, Haploclathra, Kielmeyera, Mahurea, Marila, and Neotatea) are also supported as monophyletic. Given the differences between the results obtained from morphological and molecular data, we consider that there is still a need for further research, including combined analyses.

Conflict between Amino Acid and Nucleotide Characters

Slowly evolving characters, such as amino acids and replacement substitutions, have generally been favored over faster evolving characters for inferring phylogenetic relationships. However, amino acids constitute composite characters and, because of the degenerate genetic code, are subject to convergence. Based on an analysis of atpB and rbcL in 567 seed plants, we show that silent substitutions may be more phylogenetically informative than replacement substitutions and that artifacts caused by composite characters and/or convergence cause clades on amino acid trees to conflict with nucleotide trees and independent evidence. These findings indicate that coding nucleotide sequences only as amino acid characters for phylogenetic analysis provides little benefit and may yield misleading results.

Homology in coding and non-coding DNA sequences: a parsimony perspective

Putative synapomorphy assessment (primary homology assessment) is distinct for DNA strings having a codon structure (hereafter, coding DNA) versus those lacking it (hereafter, non-coding DNA). The first requires the identification of a reading frame and of usually few in-frame insertions and deletions. In non-coding DNA, where length variation is much more common, putative synapomorphy assessment is considerably less straightforward and highly depends on the alignment method. Appreciating the existence of evolutionary constraints, alignments that consider patterns associated with specific putative evolutionary events are favored. Once the sequences have been aligned, the postulated putative evolutionary events need to be coded as an additional step. In order for the alignments and the alignment coding to be falsifiable, they should be carried out using justified and explicitly formulated criteria. Alternative coding methods for the most common patterns present in alignments of non-coding DNA are discussed here. Simpler putative synapomorphy assessment will not always correlate to more reliable phylogenetic information because simplicity does not necessarily correlate to the degree of homoplasy. The use of non-coding DNA can result in more laborious coding, but at the same time in more corroborated hypotheses, mirroring their accuracy for phylogenetic inference.

Molecular phylogeny, origin and taxonomic implications of the tribe Cacteae (Cactaceae)

This study aimed to test the phylogenetic relationships of the tribe Cacteae, the generic circumscription within the tribe, in particular, the monophyly of the genus Ferocactus, and to provide a biogeographical hypothesis about the origin of Cacteae. The analysis included 135 species from all of the 27 accepted genera and four outgroup species. Five chloroplast regions were sequenced, aligned, and coded postulating gaps, simple sequence repeats (SSRs), and inversions as potential synapomorphies, and their contributions to phylogenetic reconstruction were evaluated. The phylogenetic analyses recovered 63% of the genera as monophyletic. The contribution of rpl16, trnL-F and psbA to the phylogenetic signal was higher than in the two more slowly evolving genes (rbcL, matK), but the gaps and SSRs supported some of the genera. This result differs from those of previous phylogenetic studies in which less than 35% of the genera were recovered as monophyletic. In this work, Astrophytum and Echinocactus were re-circumscribed with five and four species, respectively. Turbinicarpus was found to be polyphyletic; 11 species correspond to Turbinicarpus s.str., whereas a highly supported clade corresponded to Rapicactus, and three species need further study. Contrary to its current circumscription, Ferocactus was not supported as monophyletic because it is polyphyletic concerning Glandulicactus, Leuchtenbergia, Stenocactus and Thelocactus. We recognize this group of genera as the Ferocactus clade in which the species share the presence of scales in the pericarpel and ribbed stems, whether tuberculated or not. The Cacteae seem to have originated in the Sierra Madre Oriental and then dispersed to the Mexican Plateau, where radiation and diversification occurred at the boundaries of the Miocene–Pliocene Epoch. The development of the Mexican Plateau and the Trans-Mexican Volcanic Belt may have favoured the isolation of the Cacteae. A taxonomic diagnosis is presented for the tribe Cacteae and 18 genera that we now recognize.

Foliar and Petiole Anatomy of Tribe Hamelieae and Other Rubiaceae1

Abstract In this study, foliar and petiole anatomy of several genera was compared to determine whether there are characteristics that can be used to reevaluate the circumscription and taxonomic position of Hamelieae (Rubiaceae). Our sample included a total of 36 species, which were sectioned using conventional embedding and staining methods. From these species, 23 represented six of the seven genera of Hamelieae sensu Robbrecht; Syringantha Standl. was included in order to reevaluate its putative inclusion within Hamelieae. For comparative purposes, the sample also included representative species of tribes Psychotrieae (Rubioideae), the Portlandia informal group (Cinchonoideae), and Gardenieae (Ixoroideae). Our results indicated that foliar and petiole anatomy contained taxonomic information that can be used in systematic studies. Members of Hamelieae shared the following characters: cuticle more than 3 µm, dorsiventral mesophyll, a single palisade parenchyma cell layer, loose spongy parenchyma, raphides, tannins, and vascular tissue of types I, II, or III in the midrib and petiole. Plocaniophyllon Brandegee is unique in having fibers associated with major and minor veins. The petiole vascular tissue has an open arc shape in all studied species except in Randia L., which has a closed cylinder. Hamelieae, Syringantha, and Psychotria L. have raphides, one layer of palisade parenchyma cells, and loose spongy parenchyma, while the other taxa have druses, two layers of palisade parenchyma cells, and compact spongy parenchyma. Bouvardia Salisb. is unique, showing both raphides and druses. Our results show that comparative foliar and petiole anatomy may provide additional characters to be considered in taxonomic and phylogenetic studies within Rubiaceae. There was anatomical support for the inclusion of Syringantha within Hamelieae, while the presence of raphides and the mesophyll attributes suggest an understanding of why Hamelieae was morphologically treated as a member of Rubioideae.

A PHYLOGENETIC ANALYSIS OF THE CASCABELA–THEVETIA SPECIES COMPLEX (PLUMERIEAE, APOCYNACEAE) BASED ON MORPHOLOGY1

Abstract A parsimony cladistic analysis based on 55 morphological characters was performed for the Cascabela Raf.–Thevetia L. species complex (Apocynaceae), including 22 terminals, sampling at least one species of each genus in Plumerieae sensu Endress and Bruyns. The consensus of the 12 most parsimonious trees (length = 164, consistency index = 0.50, retention index = 0.75) can be correlated to three previous subtribal classifications. The topology supports the monophyly of the Cascabela–Thevetia species complex, but it is not conclusive to whether Cascabela should be recognized as a genus or as a subgenus of Thevetia. Because there are two important and easy-to-diagnose characters supporting each clade (digitiform suprastaminal appendages and embryos not compressed in Cascabela; reniform fruits and segmented endocarp in Thevetia), the recognition of two genera is preferred here. Therefore, the new combination C. pinifolia (Standl. & Steyerm.) Alvarado-Cárdenas & Ochot.-Booth is proposed. Keys and synoptic descriptions for the two genera and their species are provided.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

PREMISE OF THE STUDY The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. METHODS We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. KEY RESULTS Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. CONCLUSIONS Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.