Search

Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants. [ABSTRACT FROM AUTHOR]

Premise: The genus Gynoxys and relatives form a species‐rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. Methods: We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif‐based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. Results: Our results indicate that the inclusion of all plastid genome partitions is needed to infer well‐supported phylogenetic trees of the Gynoxoid group. Whole plastome‐based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. Conclusions: The concatenation and combined analysis of all plastid genome partitions and the construction of manually‐curated, motif‐based DNA sequence alignments are found to be instrumental in the recovery of well‐supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome‐level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post‐processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa. [ABSTRACT FROM AUTHOR]

Premise: Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb‐Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. Methods: Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off‐target reads, and 10 fossils were used to calibrate dated trees. Results: Varying numbers of targeted loci and off‐target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm‐wide dating analyses, but many major splitting events date to the Eocene. Conclusions: The Angiosperms353 probe set facilitated the assembly of a large, single‐copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades. [ABSTRACT FROM AUTHOR]

Premise: The woody plant group Memecylon (Melastomataceae) is a large clade occupying diverse forest habitats in the Old World tropics and exhibiting high regional endemism. Its phylogenetic relationships have been previously studied using ribosomal DNA with extensive sampling from Africa and Madagascar. However, divergence times, biogeography, and character evolution of Memecylon remain uninvestigated. We present a phylogenomic analysis of Memecylon to provide a broad evolutionary perspective of this clade. Methods: One hundred supercontigs of 67 Memecylon taxa were harvested from target enrichment. The data were subjected to coalescent and concatenated phylogenetic analyses. A timeline was provided for Memecylon evolution using fossils and secondary calibration. The calibrated Memecylon phylogeny was used to elucidate its biogeography and ancestral character states. Results: Relationships recovered by the phylogenomic analyses are strongly supported in both maximum likelihood and coalescent‐based species trees. Memecylon is inferred to have originated in Africa in the Eocene and subsequently dispersed predominantly eastward via long‐distance dispersal (LDD), although a reverse dispersal from South Asia westward to the Seychelles was postulated. Morphological data exhibited high levels of homoplasy, but also showed that several vegetative and reproductive characters were phylogenetically informative. Conclusions: The current distribution of Memecylon appears to be the result of multiple ancestral LDD events. Our results demonstrate the importance of the combined effect of geographic and paleoclimatic factors in shaping the distribution of this group in the Old World tropics. Memecylon includes a number of evolutionarily derived morphological features that contribute to diversity within the clade. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Observations of floral ontogeny indicated that floral organ initiation in pentapetalous flowers most commonly results in a median-abaxial (MAB) petal during early development, a median-adaxial (MAD) petal being less common. Such different patterns of floral organ initiation might be linked with different morphologies of floral zygomorphy that have evolved in Asteridae. Here, we provide the first study of zygomorphy in pentapetalous angiosperms placed in a phylogenetic framework, the goal being to find if the different patterns of floral organ initiation are connected with particular patterns of zygomorphy. METHODS: We analyzed patterns of floral organ initiation and displays of zygomorphy, extracted from floral diagrams representing 405 taxa in 330 genera, covering 83% of orders (30 out of 36) and 37% of families (116 out of 313) in core eudicots in the context of a phylogeny using ancestral state reconstructions. KEY RESULTS: The MAB petal initiation is the ancestral state of the pattern of floral organ initiation in pentapetalous angiosperms. Taxa with MAD petal initiation represent ∼30 independent origins from the ancestral MAB initiation. There are distinct developmental processes that give rise to zygomorphy in different lineages of pentapetalous angiosperms, closely related lineages being likely to share similar developmental processes. CONCLUSIONS: We have demonstrated that development indeed constrains the processes that give rise to floral zygomorphy, while phylogenetic distance allows relaxation of these constraints, which provides novel insights on the role that development plays in the evolution of floral zygomorphy. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Pentaclethra and Dimorphandra (Leguminosae) have long been considered a possible enigmatic link between caesalpinioids and mimosoids because they both have an imbricate calyx and heteromorphic androecium, floral features that are rare among mimosoids but common among caesalpinioids. This study compared the developing flowers of Dimorphandra mollis and Pentaclethra macroloba to determine whether the shared floral conditions also have the same ontogenetic origin. METHODS: Buds of different sizes and flowers were processed for surface (scanning electron microscopy) and histological (light microscopy) examination. KEY RESULTS: The floral meristem initiates five sepal primordia in a modified helical order in both species. The median sagittal sepal is adaxial. The overlap of the sepals during elongation culminates with the formation of the imbricate calyx. Heteromorphic androecia arise in the intermediate stages of development. In P. macroloba, the fertile pollen-bearing stamens are antesepalous, robust and short, and the anthers carry a robust apical gland; the staminodes are long and white with a vestigial apical gland. In contrast, in D. mollis the fertile pollen-bearing stamens are antepetalous without glands and as long as the staminodes. The staminodes are thinner with an expanded apical region. CONCLUSIONS: The imbricate calyx and the heteromorphic androecium in the studied species originated via distinct pathways, favoring the hypothesis of homoplasy of these conditions. The pathways observed in P. macroloba are more similar to those observed in caesalpinioids than to those observed in mimosoids, indicating that although the floral development differs between the species studied, it supports the basal placement of Pentaclethra among mimosoids. [ABSTRACT FROM AUTHOR]

Premise of the study: Morphologically diverse clades are useful for detecting adaptive morphological evolution. Each of their variants may have evolved once or several times, suggesting that their repeated appearance may be due to environmental pressures. The North American Manihot species are an excellent system to detect possible adaptations and to assess the effect of mono- or polyphyly on classification. With 20 species, this group includes growth forms from tuberous herbs to trees. The monophyly of this group and its relationship with the economically important M. esculenta were tested for the first time with complete sampling of North American species. Methods: We carried out maximum likelihood and Bayesian phylogenetic analyses on a matrix of 3662 bp from chloroplast (psbA-trnH, trnL-trnF) and nuclear loci (PEPC and two paralogous copies of G3pdh). We included all North American Manihot species, Manihotoides pauciflora, and published sequences from 34 South American species. Key results: Our results support monophyly of the North American Manihot group. Its taxonomic sections are paraphyletic, and three to four growth forms evolved repeatedly. Manihotoides pauciflora is nested within North American Manihot species. Some PEPC and G3pdh clones grouped with clones of other species and not with clones from their own species. Conclusions: North and South American Manihot species are sister clades. Paraphyly of North American sections suggests that taxonomic revision is warranted. The position of Manihotoides pauciflora confirms that Manihotoides should remain subsumed within Manihot. Most growth forms likely evolved repeatedly in this group. The behavior of PEPC and G3pdhNA clones is probably due to incomplete lineage sorting. [ABSTRACT FROM AUTHOR]

Premise of the study: The understanding of homoplasic structures becomes more relevant when they are complex and define large angiosperm taxa. Inflorescence architecture usually fulfills both features, as happens with Cyperus, a genus with two taxonomical subdivisions characterized either by alternative expressions of Kranz anatomy (C3 or C4) or inflorescence shape (condensed or lax). Those subdivisions are not completely congruent because at least one of these presumed characters has evolved several times. We focused a SEM study on the inflorescence development in species with condensed inflorescences and different photosynthetic anatomy to test the possibility that condensed inflorescences of subgen. Anosporum (C3 anatomy) have evolved independently from those of subgen. Cyperus (C4 anatomy). Methods: Freshly collected inflorescences of C. entrerianus, C. eragrostis, C. oxylepis, and C. incomtus were studied using stereoscopic and scanning electron microscopy. Key results: Condensed inflorescences of Cyperus species with C3 and C4 anatomy had differences in structure and development: (1) mature structure, (2) position of second-order branching initiation in the first developmental stage of the inflorescence, (3) main axis development and elongation, and branching development, (4) types of ramifications, (5) phyllotaxis and symmetry. Conclusions: Results support multiple origins of condensed inflorescences in Cyperus, based especially on differences in timing during development and elongation of the main axis and branches, branching pattern and phyllotaxis. Structure and development may be the key to using inflorescence morphology as an external feature to distinguish large natural groups within Cyperus based on vegetative anatomy. [ABSTRACT FROM AUTHOR]

The study of traits that play a key role in promoting diversification is central to evolutionary biology. Floral nectar spurs are among the few plant traits that correlate with an enhanced rate of diversification, supporting the claim that they are key innova- tions. Slight changes in spur morphology could confer some degree of premating isolation, explaining why clades with spurs tend to include more species than their spurless close relatives. We explored whether the cyathial nectar spur of the Pedilanthus dade (Euphorbia) may also function as a key innovation. We estimated the phylogeny of the Pedilanthus dade using one plastid (niatK) and three nuclear regions (ITS and two G3pdh loci) and used our results and a Yule model of diversification to test the hypothesis that the cyathial spur correlates with an increased diversification rate. We found a lack of statistical support for the key innovation hypothesis unless specific assumptions regarding the phylogeny apply. However, the young age (hence small size) of the group may limit our ability to detect a significant increase in diversification rate. Additionally, our results confirm previous species designations, indicate higher homoplasy in cyathial than in vegetative features, and suggest a possible Central American origin of the group. [ABSTRACT FROM AUTHOR]

We examined phylogenetic relationships and patterns of stem structural evolution in Eleocharis subgenus Limnochloa, an ecologically and economically important group of tropical to temperate-growing sedges, whose stems serve as the primary photosynthetic organs. We used maximum parsimony, likelihood, and Bayesian inference to develop phylogenetic trees and stochastic mapping and a Markov one-rate model to develop character history reconstructions of stem architecture. A complex history of stem shape evolution characterized by a high degree of homoplasy and rapid rates of change (an average of 13 transitions per character history for about 25 species) was identified across subgenus Li,nnochloa. Character states transition much more frequently in some lineages than others, but tend to follow a consistent directional pattern of evolutionary change. Our data also suggest that changes in stem shape and anatomy may be associated with speciation events in the subgenus (Pagel's κ = 0.3503, P = 0.04579) and may have some adaptive significance. The potential adaptive roles of stem structural traits are unclear, but may be elucidated by further studies. This work serves as a starting point for future evolutionary studies of stem shape and structure in monocots and provides important background knowledge for further studies of ecological adaptations of Eleocharis. [ABSTRACT FROM AUTHOR]

The unique properties of tree building in Arecaceae strongly constrain their architectural lability. Potentially compensating for this limitation, the extensive diversification of leaf anatomical structure within palms involves many characters whose alternate states may confer disparate mechanical or physiological capabilities. In the context of a recent global palm phylogeny, we analyzed the evolution of 10 such lamina anatomical characters and leaf morphology of 161 genera, conducting parsimony and maximum likelihood ancestral state reconstructions, as well as tests of correlated evolution. Lamina morphology evolves independently from anatomy. Although many characters do optimize as synapomorphic for major clades, anatomical evolution is highly homoplasious. Nevertheless, it is not random: analyses indicate the recurrent evolution of different cohorts of correlated character states. Notable are two surface layer (epidermis and hypodermis) types: (I) a parallel-laminated type of rectangular epidermal cells with sinuous anticlinal walls, with fibers present in the hypodermis and (2) a cross-laminated type of hexagonal cells in both layers. Correlated with the cross-laminated type is a remarkable decrease in the volume fraction of fibers, accompanied by changes in the architecture and sheath cell type of the transverse veins. We discuss these and other major patterns of anatomical evolution in relation to their biomechanical and ecophysiological significance. [ABSTRACT FROM AUTHOR]

The cacti have undergone extensive specialization in their evolutionary history, providing an excellent system in which to address large-scale questions of morphological and physiological adaptation. Recent molecular phylogenetic studies suggest that (I) Pereskia, the leafy genus long interpreted as the sister group of all other cacti, is likely paraphyletic, and (2) Cactaceae are nested within a paraphyletic Portulacaceae as a member of the "ACPT" dade (Anacampseroteae, Cactaceae, Portulaca, and Talinuin). We collected new data on the vegetative anatomy of the ACPT dade and relatives to evaluate whether patterns in the distributions of traits may provide insight into early events in the evolutionary transition to the cactus life form. Many traits had high levels of homoplasy and were mostly equivocal with regard to infraclade relationships of ACPT, although several characters do lend further support to a paraphyletic Pereskia. These include a thick stem cuticle, prominent stem mucilage cells, and hypodermal calcium oxalate druses, all of which are likely to be important traits for stem water storage and photosynthesis. We hypothesize that high lability of many putative "precursor" traits may have been critical in generating the organismal context necessary for the evolution of an efficient and integrated photosynthetic stem. [ABSTRACT FROM AUTHOR]

The four o'clock family (Nyctaginaceae) has a number of genera with unusual morphological and ecological characters, several of which appear to have a "tendency" to evolve repeatedly in Nyctaginaceae. Despite this, the Nyctaginaceae have attracted little attention from botanists. To produce a phylogeny for the Nyctaginaceae, we sampled 5 1 species representing 25 genera (of 28-31) for three chloroplast loci (ndhF, rps16, rpl16, and nrITS) and included all genera from North America. Parsimony, likelihood, and Bayesian methods were used to reconstruct the phylogeny for the family. The family is neotropical in origin. A radiation of woody taxa unites Pisonia and Pisoniella with the difficult tropical genera Neea and Guapira, which also form a clade, though neither appears to be monophyletic. This group is sister to a clade containing Bougainvillea, Belemia, and Phaeoptilum. A dramatic radiation of genera occurred in the deserts of North America. The tribe Nyctagineae and its subtribes are paraphyletic, due to over-reliance on a few homoplasious characters, i.e., pollen morphology and involucre presence. Two notable characters associated with the desert radiation are cleistogamy and edaphic endemism on gypsum soils. We discuss evolutionary trends in these traits in light of available data about self-incompatibility and gypsum tolerance in Nyctaginaceae. [ABSTRACT FROM AUTHOR]

Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142–166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed. [ABSTRACT FROM AUTHOR]

The complex distributions of morphological character states in the Indo-Pacific palm tribe Areceae (Arecaceae; Arecoideae) are potentially challenging for the delimitation of its genera. In the first exhaustive sampling of all 65 genera of the Areceae, we examined relationships of two of the tribe's most problematic genera, Heterospathe and Rhopaloblaste, using portions of the low-copy nuclear genes phosphoribulokinase (PRK) and RNA-polymerase II subunit B (RPB2). Both genera fell within a highly supported clade comprising all Areceae genera, but are clearly unrelated. Rhopaloblaste was strongly supported as monophyletic and is most closely related to Indian Ocean genera. Heterospathe was resolved with strong support within a clade of western Pacific genera, but with the monotypic Alsmithia nested within it. Ptychosperma micranthum, which has previously been included in both Heterospathe and Rhopaloblaste, is excluded from these and from Ptychosperma, supporting its recent placement in a new genus Dransfieldia. Morphological comparisons indicate that the crownshaft is putatively synapomorphic for the Areceae with numerous reversals within the clade and some independent origins elsewhere. The putative diagnostic characters of Heterospathe show high levels of homoplasy, and the genus can only be distinguished by a suite of characters, whereas Rhopaloblaste is more clearly defined. Our results have implications not only for the two genera in focus, but have also been influential for the new classification of the Areceae. [ABSTRACT FROM AUTHOR]

Unisexual flower morphology was examined within a phylogenetic context in order to identify developmental transitions associated with the multiple origins of dioecy in flowering plants. Historically, two categories of unisexual flowers have been recognized: type 1 flowers exhibit rudiments of the nonfunctional organ type, while type II flowers bear no vestigial sexual organs. Mapping of these flower types onto a composite phylogeny shows that type II morphology is homoplasious and has resulted from at least four distinct evolutionary developmental pathways. The historical assignment of unisexual flowers into only two morphological types has masked important developmental and evolutionary dynamics. [ABSTRACT FROM AUTHOR]

* Premise of the study: To estimate genetic structure, chloroplast loci containing length-variable regions were developed for two legumes, Acmispon argophyllus and A. dendroideus . * Methods and Results: Primers for 14 chloroplast loci containing repeat regions were developed from the chloroplast genome sequence of the legume Lotus japonicus and tested in Acmispon. Nine loci exhibited polymorphism in Acmispon, with up to six alleles per locus. Gene diversity ranged from 0 to 0.775 in A. argophyllus and 0.142 to 0.766 in A. dendroideus. The primers also amplified in other Acmispon species. Sequencing of the fragments revealed discordance between fragment sizes and underlying sequence for three loci containing complex repeat regions. * Conclusions: Although genotypes were easily generated and sized, sequencing may be more informative of genetic variation in loci with complex repeat regions. These loci exhibit substantial variation and should be useful for understanding genetic structure associated with seed dispersal in Acmispon . [ABSTRACT FROM AUTHOR]

• Premise of the study: Most orchid species native to the Macaronesian islands reflect immigration from western Europe or North Africa followed by anagenesis. The only putative exception is the butterfly orchids (Platanthera) of the Azores, where three species apparently reflect at least one cladogenetic speciation event. This multidisciplinary study explores the origin, speciation, phenotypic, and genotypic cohesion of these Azorean species and their mainland relatives.• Methods: Plants of Platanthera from 30 localities spanning all nine Azorean islands were compared with those of four continental European relatives for 38 morphometric characters; substantial subsets were also analyzed for plastid microsatellites, and for nrITS of both the orchids and their mycorrhizae.• Key results: Although the three Azorean and four mainland species are all readily distinguished morphometrically using several floral characters, and hybridization appears rare, divergence in ITS and especially plastid sequences is small. Despite occupying similar laurisilva habitats, the Azorean species differ radically in the identities and diversity of their mycorrhizal partners; specialism apparently increases rarity.• Conclusions: Although morphological evidence suggests two invasions of the islands from NW Africa and/or SW Europe, ITS data imply only one. As the molecular data are unable to distinguish among the potential mainland ancestors, two scenarios of relationship are explored that imply different ancestors. Both scenarios require both anagenetic and cladogenetic speciation events, involving homoplastic shifts in overall flower size and (often substantial) changes in the relative dimensions of individual floral organs. Limited genotypic divergence among the three species compared with greater phenotypic divergence suggests comparatively recent speciation. Mycorrhizae may be the most critical factor dictating the respective ecological tolerances, and thus the relative frequencies, of these species. The recent IUCN Red-List amalgamation of Azorean Platanthera taxa into a single species urgently requires reappraisal, as P. micrantha is an excellent indicator species of seminatural laurisilva forest and P. azorica is arguably Europe's rarest orchid., (© 2014 Botanical Society of America, Inc.)