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Molecular phylogenetics of Maranta (Marantaceae: Zingiberales): non-monophyly and support for a wider circumscription
Abstract and Figures
Neotropical Maranta has repeatedly emerged as non-monophyletic in molecular phylogenetic studies, but no taxonomic changes have been proposed due to previous weak support for the main clades and overall sparse taxonomic sampling. Our study includes a phylogenetic hypothesis strictly based on molecular evidence, using nuclear ribosomal (nrITS) and plastid (rps16, trnL-F and rpl32-trnL) markers for Maranta and allied genera. Thirty-two species from eight genera were sampled, and maximum likelihood (ML) and Bayesian inference (BI) analyses were carried out. Non-ambiguous indels were scored in both analyses to test their contribution to internal support. Our results confirm that Maranta, as previously delimited, is non-monophyletic, with species of Hylaeanthe, Myrosma and Koernickanthe nested among clades of Maranta. The combined BI analysis without indels was the best resolved, and inclusion of indels increased support only for terminal clades. The sampled species comprise two sister clades, one with Maranta + Hylaeanthe + Myrosma + Koernickanthe and the other with Ctenanthe + Saranthe + Stromanthe. The infrageneric classification proposed by Schumann for Maranta (M. subgenera Maranta and Calateastrum) is partially corroborated by our results, but the remaining subgenera need to be further studied. Based on our strongly supported phylogenetic results, we revise the taxonomy of these genera, expanding the limits of Maranta. We propose two new combinations and a new name for Hylaeanthe in Maranta.
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... Marantaceae R. Brown contains about 30 genera and 550 species, has a pantropical distribution with highest species richness in the Neotropics (Andersson 1998, Fernandes et al. 2022. Molecular phylogenetic studies showed that morphologybased informal groups (Andersson 1981) in the family are not monophyletic, but that there are five well-supported clades (Andersson & Chase 2001, Prince & Kress 2006. ...
In this work, we propose typifications of five names belonging to the genera Ctenanthe and Stromanthe, following the
recommendations of the International Code of Nomenclature for algae, fungi and plants—ICN. Lectotypes are designated
for Ctenanthe dasycarpa, C. setosa and Stromanthe papillosa, and neotypes for S. sellowiana and S. schottiana.
... Automaranta K.Schum., but did not include other subgenera because he considered them too poorly circumscribed (Andersson 1986). His impression was confirmed by the most recent phylogenetic analyses, which pointed out the polyphyletism of Maranta (Fernandes et al. 2023). While ...
A new species of Maranta from the Brazilian Atlantic Forest is described. The new species is most similar to Maranta ruiziana , from which it differs mainly in its bambusoid habit, non starch‐storing rhizome, homotropic leaves, with blade entirely glabrous on both surfaces and leaf margins entire, florescence components with numerous cymules, sepals longer than the corolla tube, and spheroidal fruit. The new species also presents morphological characters seen in Maranta tuberculata , from which is easily distinguished by its fruits. I characterize the new species by its external morphology, provide a distribution map, and perform a preliminary conservation assessment based on the IUCN criteria.
A new species of Maranta (Marantaceae) from Central Brazil is described and illustrated. The species is recognizable due to its small rosulate habit, unbranched aerial shoot, hirtellous bracts with apex acute, sub-brachyblastic cymules, and each bracteole subtending a single flower.
The territory of Pernambuco includes portions of the Caatinga and the Atlantic Forest, which house areas of extreme biological importance that are also rich in Marantaceae species. This study presents a synopsis of the Marantaceae from the state, and was based in the morphological analysis of herbaria specimens and other collected in field excursions carried out from 2013 to 2018. We found 26 species belonging to 10 genera; Maranta (seven spp.) and Goeppertia (five spp.) were the most representative. Ctenanthe casupoides Pertersen and Hylaeanthe hexantha are new records for the state and Goeppertia yoshida-arnsiae, G. widgrenii and Maranta gigantea are considered threated. Ten species are endemic to the Atlantic Forest, and four are restricted to Northeastern Brazil. Regarding the local distribution, we observed that 22 spp. (85%) occur in the lowland semideciduous seasonal forest. Identification keys, comments on geographic distribution and habitats, local distribution maps, and photo plates of the species are provided.
A new species of Maranta (Marantaceae) from the Brazilian Amazon is described and illustrated. This species belongs to Maranta subg. Maranta and has close affinities with M. linearis, from which it differs in its caulescent habit, absent petiole, pulvinus with deciduous tufts of erect trichomes on the adaxial side, very long inflorescence with many florescences, and longitudinally ridged ovary and capsule.
Premise of the Study
We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot‐wide divergence times and rates of species diversification.
Methods
We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.
Key Results
Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large‐scale accelerations in PACMAD‐BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae‐Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non‐coding regions in identifying and supporting short, deep branches.
Conclusions
We provide the first resolved, well‐supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome‐scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
Caamembeca (Polygalaceae) is a genus of 13 species endemic to South America. The genus is morphologically distinctive, e.g. supported by the putative morphologic synapomorphy of paired glands in a stipular position and on the rachis. However, its monophyly has not been robustly tested as only four species have been included in previous phylogenetic analyses. We present a phylogenetic analysis of 11 species based on nrITS, matK, the trnL intron, and trnL-trnF intergenic spacer. Relationships among Caamembeca species are discussed, and three new combinations are made, Caamembeca amazonensis, Caamembeca autranii, and Caamembeca formosa, providing an improved understanding of the genus.
We provide a molecular phylogenetic analysis of the Laelia alliance based on sampling of 20 of an estimated 24 species, and seven plastid regions plus nrITS 1 & 2 analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. Furthermore, we used coded indels to evaluate their effect on the phylogenetic relationships and / or support values (bootstrap and posterior probabilities). Our results confirm the existence of two clades, the long known Laelia (endemic to México at middle to high elevations) and Schomburgkia (a more widely distributed taxon). Both clades were strongly supported by PP values and moderate BS; thus, we preferred to recognize them as separate genera with a reappraised morphology
and taxonomic delimitation. The inclusion of coded indels in the analyses was of great utility; we could identify the probable hybrid origin of L. gouldiana and L. halbingeriana. We propose new combinations to accommodate the taxonomic changes resulting from our study. We transfer L. anceps subsp. anceps, L. anceps subsp. dawsonii, L. aurea, L. mottae, and L. rubescens to Schomburgkia, with the second taxon elevated to species level; the molecular evidence together with previous published work on the morphology, phenology and geography of the group support these decisions. Lastly, the recently described genus Encabarcenia is considered as a synonym of Schomburgkia and, as a result, a new combination is proposed.
Zingiberales is represented in the Brazilian flora by almost 300 species, of which about 100 occur in the Northeast Region of the country. Zingiberales is poorly known in the Atlantic Forest of the state of Pernambuco and this study provides a taxonomic survey of the species found in the forest fragments of Usina São José, Igarassu. The field work was carried out in eight expeditions (from November 2013 to December 2014), as well as visits to herbaria: HST, IPA, PEUFR and UFP. In the studied area were found one species of Costaceae, three of Heliconiaceae and seven of Marantaceae. Heliconia episcopalis and Maranta subterranea are new records to the state. Identification key, descriptions, comments and illustrations are presented.
Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species‐rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo‐Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent.
The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses.
All three Musaceae genera – Ensete, Musa and Musella – originated in northern Indo‐Burma during the early Eocene. Musa species dispersed from ‘northwest to southeast’ into Southeast Asia with only few back‐dispersals towards northern Indo‐Burma.
Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.
Calathea, with an estimated 285 species, is the largest genus of Marantaceae and an important component of Neotropical herbaceous diversity. The genus is also of high importance for horticulture as species are cultivated for their showy, patterned leaves. Previous molecular phylogenetic studies indicated that the genus is polyphyletic, but have not provided a basis for redefining generic limits due to incomplete taxon sampling. To address this problem we analyzed DNA sequence data from three plastid markers (matK with flanking 3' trnK intron, trnL intron and trnL-trnF intergenic spacer) and one nuclear marker (ITS) under a maximum parsimony criterion for a large and representative taxon sample covering all previously proposed infrageneric entities, and representing the full range of morphological variation known in the genus. Our results confirm that Calathea is polyphyletic. One clade, including subgenus Calathea, the C. lanicaulis group, and the genus Sanblasia, is sister to a clade formed by Ischnosiphon and Pleiostachya. The genus Monotagma is placed as sister to this clade. The remaining species form a second strongly supported clade as sister to a clade containing these other genera. Based on these findings Calathea is recircumscribed in a narrow sense and Sanblasia is placed in synonymy. The genus Goeppertia is resurrected and redefined to include all members of the second Calathea clade. Morphological characters defining each genus are provided. A total of 246 new combinations are made.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
Background and Aims Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have
undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology,
and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of
Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot
tree of life.
The evolutionary distinctiveness and phylogenetic position of Marantaceae within the Zingiberales is strongly supported, yet relatively little phylogenetic research has been conducted on members of Marantaceae. Phylogenetic analyses of plastid DNA sequence data (matK and 3' intergenic spacer region, and the trnL-F intergenic spacer region) for 80 ingroup taxa representing 27 genera were conducted under parsimony criteria. Results identify five major clades and support significant realignments in tribal and "group" circumscriptions. Four non-monophyletic genera, Calathea, Marantochloa, Phrynium, and Schumannianthus are identified. Although significant work remains to identify relationships of the major lineages within Marantaceae and to redefine several problematic genera, we propose a working classification that better reflects the inferred evolutionary history of the family.
The Marantaceae (530 spp.) are one of the most species rich families within the order Zingiberales which incites the search for evolutionary factors favoring speciation. A positive influence on their divergence is ascribed to their unique explosive pollination mechanism which has been proposed to be a key innovation. To test this hypothesis phylogenies of the two major African clades (Sarcophrynium and the Marantochloa clade) were established based on data from nuclear (ITS, 5S) and chloroplast (trnL/trnL-F) DNA for an almost complete taxon sample. The phylogeny was used to parsimoniously reconstruct morphological and ecological traits and geographic distribution patterns. The resulting molecular relationships of the genera are congruent with the existing family phylogeny. As in previous studies the species Ataenidia conferta is nested within Marantochloa so that a new circumscription of Marantochloa is proposed leading to the new name Marantochloa conferta . Hybridization events, adaptation to different pollinators, and Pleistocene climatic fluctuations are hypothesized evolutionary factors fostering speciation in the African clades. The explosive pollination mechanism might have played an important role in optimizing the mating system but did certainly not force speciation directly through mechanisms of reproductive isolation.
Eight genera and approximately 55 species of Marantaceae occur in Asia. Until recently these were the most poorly understood members of the family, but over the last few years much progress have been made in understanding their alpha taxonomy and distribution. Generic delimitation and phylogenetic relationships between genera, however, remain unclear. We analysed phylogenetic relationships in Asian Marantaceae using maximum parsimony and Bayesian analysis of plastid (rps16 intron) and nuclear [internal transcribed spacer (ITS)1 and 5S-non-transcribed spacer (NTS)] DNA sequence data. The results show that two Asian genera, Halopegia and Stachyphrynium, are well-defined monophyletic entities that should be maintained in their current form. Schumannianthus virgatus is sister to Halopegia and should be transferred to a genus of its own. Phacelophrynium, Monophrynium and Cominsia are nested within a paraphyletic Phrynium. Within this large clade, a number of geographically focused monophyletic species groups can be identified, in some cases corroborated by flower and fruit characters not previously emphasized in taxonomic studies, but these do not provide a useful framework for a revised generic classification. A revised generic classification of Asian Marantaceae is supplied, including the description of a new genus Indianthus Suksathan & Borchs. to which S. virgatus is transferred. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 381–395.
Intron sequences of the chloroplast generps16 from 46 species were used to examine phylogenetic relationships indicated by nrDNA ITS sequence variation in the tribeSileneae (Caryophyllaceae, Caryophylloideae). This region has previously not been utilized for phylogenetic purposes but the results presented here suggest that it is a consistent and valuable complement to the ITS sequences. Therps16 intron trees are largely congruent with the ITS trees. All the major hypotheses suggested by the ITS data are supported, often at similar bootstrap levels. The joint usage ofrps16 intron and ITS sequences provides a powerful tool for resolving many of the difficult taxonomic issues in the tribeSileneae.
Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single-copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32-trnL((UAG)), trnQ((UUG))-5'rps16, 3'trnV((UAC))-ndhC, ndhF-rpl32, psbD-trnT((GGU)), psbJ-petA, 3'rps16-5'trnK((UUU)), atpI-atpH, and petL-psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.
Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character
independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data,
maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models
for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification
of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters
are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially
serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach
to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence
data), likelihood ratio tests, and Bayesian analyses.
Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations; in particular, there are more posterior probability values in the range 0.85-1 than expected by theory. Therefore, our results corroborate the findings of others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
Many empirical studies have revealed considerable differences between nonparametric bootstrapping and Bayesian posterior probabilities
in terms of the support values for branches, despite claimed predictions about their approximate equivalence. We investigated
this problem by simulating data, which were then analyzed by maximum likelihood bootstrapping and Bayesian phylogenetic analysis
using identical models and reoptimization of parameter values. We show that Bayesian posterior probabilities are significantly
higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be
made more often. These errors are strongly accentuated when the models used for analyses are underparameterized. When data
are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also
conservative in this respect, but less so.
We describe a new species of Schomburgkia, S. vandenbergiana, from northeastern Brazil and provide a phylogenetic analysis and a summary of its conservation status. Our phylogenetic analyses indicate that S. vandenbergiana is most likely related to S. undulata and S. gloriosa. The species with dark purple flowers, S. elata, S. splendida, S. undulata and S. vandenbergiana, did not form a clade, and this trait seems to have multiple independent origins. Based on small flower size and number of keels on the disc of the lip, the new species is morphologically more similar to S. heidii, a species native to Colombia and Venezuela, but it differs in the shorter sepals and lip and erose clinandrium margin. The new species should be classified as endangered (EN) based on the IUCN criteria B1ab(i)+2ab(ii).
The Trichocentrum cepula complex comprises three species, T. caatingaense, T. cepula and T. sprucei, endemic to tropical forests east of the Andes in South America. The delimitation of these species has been diversely interpreted due to the extensive morphological variation in the complex. We applied an integrative approach to achieve a better understanding of these biological units, using geometric morphometrics, cytogenetic analysis (chromosome counts and CMA/DAPI banding) and molecular phylogenetics (ITS and rpl32-trnL). An initial morphometric analysis using the pre-identified specimens into three taxa suggested that T. sprucei is distinct from the other two, which show some overlap. A subsequent analysis of the labellum, including only T. caatingaense and T. cepula organized in six pseudo-populations, suggested the existence of four morphological groups. All analysed specimens presented 2n = 36 chromosomes, CMA⁺/DAPI⁻ terminal bands and CMA⁻/DAPI⁺ pericentromeric bands, which varied in number across species, localities or even individuals from the same locality. The notable variation in DAPI⁺ pericentromeric bands may be related to transposable elements that could also be a factor influencing the wide morphological variation in the flowers. In the phylogenetic analysis, the specimens belonging to T. caatingaense formed a strongly supported clade sister to the rest, whereas the specimens belonging to T. cepula and T. sprucei emerged together, with their relationships tending to be determined by geographic proximity. The evidence we generated suggests that treating the Brazilian populations of this species complex under a single name, T. cepula, provides more taxonomic stability and utility, thus the necessary taxonomic changes are implemented.
This study summarizes the taxonomy of the species of Maranta from northeastern Brazil. While 20 names have been proposed in the region, only 13 are accepted. We provide two new records, M. rugosa and M. polystachya , and five new species are described, of which M. bahiensis and M. villosovaginata are endemic to Bahia, M. chrysogina to Ceará, M. vieirae to Maranhão, and M. lorifolia occurs in Bahia and Espírito Santo. Maranta noctiflora , M. parvifolia , M. phrynioides , and M. rupicola L. have distributions outside of the study area, while M. anderssoniana and M. hatschbachiana are synonymized. Our final checklist includes 21 species, which represent more than half of the species in the genus, highlighting northeastern Brazil as a center of diversity for Maranta . Among the species listed, M. lorifolia , M. tuberculata , and M. zingiberina are thought to be endangered (EN), while M. gigantea is likely critically endangered (CR). Finally, this study provides informal conservation statuses, descriptions, distribution maps, and an identification key to the species. Typifications for M. subterranea and M. polystachya are also provided.
Eremitis, Pariana, and Parianella are herbaceous bamboos (tribe Olyreae) included in the subtribe Parianinae, which is characterized by the presence of fimbriae at the apex of the leaf sheaths and exclusively spiciform synflorescences. We analyzed 43 samples of herbaceous and woody bamboos in order to infer relationships within the Parianinae, based on combined data from the nuclear ribosomal internal transcribed spacer (ITS) and plastid DNA (rpl32-trnL and trnD-trnT spacers). Bayesian inference, maximum likelihood, and maximum parsimony methods were applied, and macro- and micromorphological aspects were also analyzed, including the ectexine patterns of pollen grains. Parianinae is represented by three well-supported lineages in our analyses: (1) Parianella, endemic to southern Bahia, Brazil; (2) Pariana sensu stricto with a broad distribution in southern Central America and northern South America, especially in the Amazon region; and (3) Eremitis, endemic to the Brazilian Atlantic Forest, from the states of Pernambuco to Rio de Janeiro, including one species previously described as a member of Pariana. Our molecular phylogeny showed that Pariana, as historically circumscribed, is not monophyletic, by recovering Pariana sensu stricto as strongly supported and sister to Eremitis + Pariana multiflora, with Parianella sister to the Pariana-Eremitis clade. Morphological features of their synflorescences and differences in ectexine patterns characterize each lineage. Based on all these characters and the phylogenetic results, Pariana multiflora, endemic to the state of Espírito Santo, Brazil, is transferred to Eremitis.
The genus Haumania (Marantaceae) consists of three described species of perennial climbers endemic to the tropical lowland rainforest in Central Africa. To unravel their phylogenetic relationship to each other, we used variation among DNA sequences of two nuclear ribosomal (nr) and four plastid (p) markers in five to seven accessions per species sampled across their respective distribution range. Maximum parsimony and Bayesian analyses were applied. All datasets and analyses corroborated the monophyly of the genus. Within the genus, individuals of the species H. danckelmaniana and H. leonardiana were each monophyletic. Individuals of H. liebrechtsiana, however, were paraphyletic. They clustered into two distinct geographic clades (Gabon and Democratic Republic of Congo), with the Gabonese clade being most closely related to the individuals of H. danckelmaniana. The latter might be due to introgression in areas of distributional overlap between these two species, as shown in earlier phylogeographic studies. A recent hybridisation event between H. danckelmaniana and H. liebrechtsiana is documented here in a single individual by incongruence in the nr and p dataset. Overall, the study provides support for H. leonardiana being sister to all other species of this genus. To confirm the absence of hybridisation in H. leonardiana further sampling is proposed in the respective areas of distributional overlap with its sister species.
A new species of Maranta subg. Maranta, M. gigantea, is described and illustrated. This is known from the submontane Atlantic Forest in the states of Pernambuco and Alagoas (Brazil). Based on the zingiberoid growth form it is morphologically similar to M. anderssoniana and M. zingiberina, differing mainly in the shape of the leaf blade (lanceolate to oblong or ovate respectively vs. narrow-lanceolate) and number of calli in the callose staminode (one prominent callus vs. two prominent calli). It is further differentiated from M. anderssoniana by being larger plants (up to 1.8 m tall vs. up to 1.0 m tall), with a tomentose leaf sheath (vs. sericeous), larger corolla tube length (9−12 mm long vs. 5−6 mm long), asymmetrically elliptical corolla lobes (vs. asymmetrically oblong) and larger outer staminodes (minor 12−15 × 6.5−8 mm vs. 10−11 × 5.5−6 mm and major 13−16 × 8.5 × 10.5 mm vs. 10−12 × 8−9.2 mm). Due to its narrow distribution, it is classified as critically endangered.
Heliconia (Heliconiaceae, order Zingiberales) is among the showiest plants of the Neotropical rainforest and represent a spectacular co-evolutionary radiation with hummingbirds. Despite the attractiveness and ecological importance of many Heliconia, the genus has been the subject of limited molecular phylogenetic studies. We sample seven markers from the plastid and nuclear genomes for 202 samples of Heliconia. This represents ca. 75% of accepted species and includes coverage of all taxonomic subgenera and sections. We date this phylogeny using fossils associated with other families in the Zingiberales; in particular we review and evaluate the Eocene fossil Ensete oregonense. We use this dated phylogenetic framework to evaluate the evolution of two components of flower orientation that are hypothesized to be important for modulating pollinator discrimination and pollen placement: resupination and erect versus pendant inflorescence habit. Our phylogenetic results suggest that the monophyletic Melanesian subgenus Heliconiopsis and a small clade of Ecuadorian species are together the sister group to the rest of Heliconia. Extant diversity of Heliconia originated in the Late Eocene (39 Ma) with rapid diversification through the Early Miocene, making it the oldest known clade of hummingbird-pollinated plants. Most described subgenera and sections are not monophyletic, though closely related groups of species, often defined by shared geography, mirror earlier morphological cladistic analyses. Evaluation of changes in resupination and inflorescence habit suggests that these characters are more homoplasious than expected, and this largely explains the non-monophyly of previously circumscribed subgenera, which were based on these characters. We also find strong evidence for the correlated evolution of resupination and inflorescence habit. The correlated model suggests that the most recently common ancestor of all extant Heliconia had resupinate flowers and erect inflorescences. Finally, we note our nearly complete species sampling and dated phylogeny allow for an assessment of taxonomic history in terms of phylogenetic diversity. We find approximately half of the currently recognized species, corresponding to fully half of the corresponding phylogenetic diversity, have been described since 1975, highlighting the continued importance of basic taxonomic research and conservation initiatives to preserve both described and undiscovered species of Heliconia.
Calathea subgenus Pseudophrynium series Polystachyae was proposed to accommodate a single species, Calathea polystachya. This species is herein transferred to Maranta, recognizing the wide morphological re-delimitation of this genus.
Terrestrial rhizomatous herbs, sometimes lianescent and high-climbing, very variable in development of aerial shoots. Leaves distichous, segregated into sheath, petiole proper (often missing), pulvinus and blade; blade with a strong midrib and thin, parallel and closely set lateral veins, these ± sigmoid, fusing marginally, interconnected by closely set, parallel transverse veinlets. Inflorescence terminal or lateral, simple or a ± complex synflorescence; inflorescence unit (florescence) a usually spiciform or capitate thyrse with distichous or spiral spathes (“bracts”) subtending ± elaborate flower clusters composed of 1-several (rarely numerous) 2-flowered cymules (1-flowered in Monotagma and Monophrynium), each with a prophyll on the dorsal side at base, sometimes also with a scale-like interphyll on the ventral side and 1 or 2 ± dorsal bracteoles (additional “lateral bracteoles” in one species of Calathea). Flowers perfect, epigynous, pentacyclic, heterochlamydeous, completely asymmetric (the 2 flowers of a pair being mirror images); sepals distinct; petals, androecial elements, and style fused to form a floral tube (“corolla tube”) greatly variable in length. Outer androecial whorl rarely missing, usually of 1 or 2 staminodes, which are usually petaloid and showy, but sometimes acicular, or ± rudimentary; inner androecial whorl of 3 members, 1 fertile monothecic stamen (often with a petaloid appendage), 1 hood-shaped staminode (staminodium cucullatum), and 1 conspicuously firm and fleshy staminode (staminodium callosum); the inner staminodes basally fused to form a firm and fleshy staminal tube which ± exceeds the level where the corolla lobes separate from the floral tube. Ovary 3-carpellate and 3-locular, but 2 locules often empty and compressed; fertile locule(s) 1-ovulate with the anatropous ovule inserted at base; septa with completely sunken septal nectaries. Style fused basally with the floral tube, in mature untriggered flowers the style enclosed in the hood of the cucullate staminode, bent backwards and held under tension; when released by a pollinator, snapping forward and curling up in a circinate or (Thalia) helical fashion; stigmatic surface restricted to the inner side of a funnel-shaped depression in the apex of the style. Fruit usually a loculicidal capsule, more rarely berry-like (Sarcophrynium, Thaumatococcus), or caryopsislike (Thalia). Seeds rather large (3–20 mm), without endosperm at maturity, embryo horseshoe-shaped, embedded in copious starchy perisperm; perisperm with a simple or forked, central canal running from base to the level of the embryo bend, or slightly further.
Ribosomal DNA (rDNA) is the region of the genome coding for the RNA component of ribosomes. The ubiquity and conservation of rDNA sequences has made these DNA regions important tools for reconstructing phylogenetic relationships. In eukaryotes, rDNA sequences may be found in the nucleus and organelles. However, mitochondrial and chloroplast rDNA are more like those of their prokaryote ancestors than those of their eukaryote hosts. Eukaryotic nuclear rDNA is tandemly organized, with copy numbers up to the order of 104. Each repeat unit consists of the genes coding for the small subunit (16–18S), large subunit (23–28S) and the 5.8S nuclear rDNA. These coding regions are separated from each other by spacers (see Fig. 14.1).
Maranta (Maranta arundinacea L.) can be considered as a non-conventional raw material for starch. The objective of this work was to characterize the maranta starch. These starch granules had spherical and elongated geometries with average size of 56.60 μm. The maranta starch presented B-type crystal, revealed by x-ray spectra, and gelatinization temperature of 65.5°C as determined by thermal (differential scanning calorimetry) analysis. Maranta starch suspensions have a pseudoplastic behavior which was well described using a power law model. Storage and loss moduli increased drastically during gelatinization process, corroborating with differential scanning calorimetry results. In general, maranta starch could have numerous applications in the food industry.
Chase, M. W. & Hills, H. H.: Silica gel: An ideal material for field preservation of leaf samples for DNA studies. ‐ Taxon 40: 215–220. 1991. ‐ ISSN 0040‐0262.
Silica gels an inexpensive and reliable substance to preserve field‐collected leaves for molecular studies of variation in DNA. A method for its utilization is explained, and results are presented, comparing total cellular DNA samples extracted from a set of fresh and silica‐gel dried samples of the same species, as well as examining the efficiency of endonuclease restriction and intactness of DNA from of a set of field‐collected leaves preserved with silica gel.
Maranta is a neotropical genus usually found in moist and shaded habitats in pluvial to semideciduous forests and Cerrado, with diversity center in central Brazil. A new species from Mato Grosso, M. rugosa J. M. A. Braga & S. Vieira, is described and illustrated. The new species is somewhat similar to M. parvifolia Petersen with which it is compared.
Four new species are described, viz. Ischnosiphon bahiensis (Brazil), I. ursinus (French Guiana and Rio Negro Basin), I. crassispicus (vicinity of Manaus), and I. fusiformis (NE Peru). New data on ecology, morphology, or distribution are presented for I. inflatus Anderss., I. enigmaticus Anderss., I. centricifolius Anderss., I. gracilis (Rudge) Koern., I. helenae Anderss., I. macarenae Anderss., I. polyphyllus (P. & E.) Koern., and I. surumuensis Loes. The typification of I. arouma (Aubl.) Koern. is briefly discussed.
Maranta subgen. Maranta includes species related to M. arundinacea L. It is characterized by aerial shoots with a strong monopodial tendency, absence of root tubers, simple inflorescences or few-branched, often diffuse synflorescences, florescences with few, herbaceous spathes, and comparatively large, distinctly pedicellate flowers. There are occasional exceptions to all these characters. Most species are partial selfers, only two or three being allogamous. Sixteen species are recognized, eight of which are new: M. linearis, M. sobolifera, M. lindmanii, M. zingiberina, M. incrassata, M. rupicola, M. amazonica, and M. tuberculata. The new species are described, and all species are defined and discussed, data being given about distribution and habitat. Growth habit and rhizome structure are essential taxonomic characters, but leaf shape and indument distribution are more useful characters for routine identification. Of the species referred to subgen. Automaranta by Schumann in Das Pflanzenreich, three are excluded: M. cordata, M. pohliana, and M. foliosa.
Relationships of Marantaceae were estimated from nucleotide sequence variation in the rps16 intron (plastid DNA) and from morphological characters. Fifty-nine species (21 genera) formed the ingroup, and 12 species (12 genera) of other Zingiberales formed the outgroup. There is no support for the traditional subdivision of Marantaceae into a triovulate and a uniovulate tribe or the informal groups previously proposed. The so-called Donax group forms a paraphyletic grade that is basal within Marantaceae. Thalia appears as the distal branch of this grade, but its position is not supported in jackknife analysis. The so-called Calathea group is monophyletic in all shortest trees but not supported with greater than 50% jackknife. The genus Calathea appears to be paraphyletic. The Maranta and Phrynium groups are clearly polyphyletic. Maranta, Koernickanthe, and genera of the Mymsma group, all neotropical, form a strongly supported monophyletic group. The sister of this group is the palaeotropical genus Halopegia. Koernickanthe is nested within Maranta, as this genus is traditionally circumscribed. The African genera Ataenidia and Marantochloa form a strongly supported clade in which Ataenidia is the sister group to Marantochloa. Based on phylogeny it is concluded that Africa, in spite of being much poorer in species, is the most likely ancestral area of Marantaceae
The delimitation of the neotropical genera of the Marantaceae has been revised, using evidence mainly from the morphology of inflorescences and flowers. It is concluded that the generic concepts of Schumann in “Das Pflanzenreich”, often questioned by 20th century American authors, are essentially sound, but that his grouping of the genera into two tribes is quite artificial. Main deviations from the treatment of Schumann are the rearrangement of the genera, somewhat different stress on diagnostic characters and a much narrower concept of the genus Myrosma. A new genus, Koernickanthe is proposed for the long known species Maranta orbiculata (Koern.) Schum. The genera are arranged into informal groups and the groups and genera recognized are: Maranta group (Maranta L., Monophyllanthe Schum.), Myrosma group (Myrosma L. f., Saranthe (Regel et Koern.) Eichl., Hylaeanthe Jonker et Jonker, Ctenanthe Eichl., Stromanthe Sond.), Calathea group (Calathea G. F. W. Meyer, lschnosiphon Koern., Pleiostachya Schum.), Monotagma group (Monotagma Schum., Koernickanthe gen. nov.) and Thalia“group”(Thalia L.). It is suggested, that each group has its closest affinities with Old World genera and that this indicates that the diversification of the marantaceous stock was far–reaching already before the Old and the New World became effectively isolated. It is further suggested that the early diversification of the family took place in Africa, the flora of which, although poor in species, is morphologically very diverse. Two new combinations are made, viz. Stromanthe stromanthoides (Macbr.) Anderss. and Koernickanthe orbiculata (Koern.) Anderss.
Maranta is a neotropical genus, species of which are found in moist and shaded habitats in forests and in the cerrado. During the preparation of Maranta's monograph for the Flora Neotropica, four new species were discovered and are now described: Maranta longiflora S.Vieira & V.C.Souza, Maranta coriacea S.Vieira & V.C.Souza, Maranta pulchra S.Vieira & V.C.Souza and Maranta purpurea S.Vieira & V.C.Souza. These species are found in dry habitats, frequently near watercourses or occasionally in humid and shaded places. Two, M. pulchra and M. purpurea, seem to be endemic to the state of Mato Grosso. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 131–139.
In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100 taxa and 7,990 characters, were performed for both phylogenetic methods. The tree topology and branch-support values from each partition were compared with the tree inferred from all taxa and characters. Using this approach, we quantified the accuracy of the branch-support values assigned by the jackknife and Bayesian methods, with respect to each of 15 basal clades. In comparing the jackknife and Bayesian methods, we found that (1) both measures of support differ significantly from an ideal support index; (2) the jackknife underestimated support values; (3) the Bayesian method consistently overestimated support; (4) the magnitude by which Bayesian values overestimate support exceeds the magnitude by which the jackknife underestimates support; and (5) both methods performed poorly when taxon sampling was increased and character sampling was not increases. These results indicate that (1) the higher Bayesian support values are inappropriate (in magnitude), and (2) Bayesian support values should not be interpreted as probabilities that clades are correctly resolved. We advocate the continued use of the relatively conservative bootstrap and jackknife approaches to estimating branch support rather than the more extreme overestimates provided by the Markov Chain Monte Carlo-based Bayesian methods.
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm
include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent
restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets
of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest,
rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable
from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences
of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely
available at http://www.drive5. com/muscle.
Comparing bootstrap and posterior probability values in the four-taxon case
- Cummings
jModelTest 2: more models, new heuristics and parallel computing
- Darriba
Seed germination and genetic structure of two Salvia species in response to environmental variables among phytogeographic regions in Jordan (Part I) and Phylogeny of the pan-tropical family Marantaceae (Part II)
- Al-Gharaibeh
Al-Gharaibeh HMM. 2017. Seed germination and genetic
structure of two Salvia species in response to environmental
variables among phytogeographic regions in Jordan (Part
I) and Phylogeny of the pan-tropical family Marantaceae
(Part II). PhD Thesis. Halle: Martin Luther University
Halle-Wittenberg.