Unravelling the phylogeny of Lejeuneaceae (Jungermanniopsida): evidence for four main lineages

With about 1000 species in approximately 90 genera, Lejeuneaceae are the largest family of liverworts and make up a large and important part of cryptogamic diversity in the humid tropics. Maximum parsimony, Maximum likelihood and Bayesian analyses of a dataset including four markers (rbcL, psbA, trnL-trnF region of cp DNA, nrITS region) of 134 accessions resulted in similar topologies that support the presence of four main lineages within Lejeuneaceae. Model-based analyses support a division of Lejeuneaceae into two lineages corresponding to the subfamilies Ptychanthoideae and Lejeuneoideae. The latter lineage splits into the tribes Lejeuneeae, Brachiolejeuneeae and the genus Symbiezidium. In contrast, the Maximum parsimony analysis resolves Brachiolejeuneeae and Symbiezidium in serial sister relationships to the remainder of Lejeuneaceae. Sporophyte characters support a split into two subfamilies as seen in the model-based analyses. Some deep nodes remain unresolved, possibly indicating a series of initial diversifications which occurred over a short time period.     

A phylogenetic analysis of the genera of Lejeuneaceae (Hepaticae)

The Lejeuneaceae are the largest family of the liverworts (Hepaticae), with almost a thousand species in 91 currently accepted genera. We analysed phylogenetic relationships of 69 genera, representing all major subfamilies and tribes recognized in the family, by using 49 informative morphological characters (31 gametophytic, 18 sporophytic), one chemical character, and applying equal and successive weighting of characters and parsimony analysis. In all trees recovered, the Lejeuneaceae were monophyletic with Nipponolejeunea (subfam. Nipponolejeuneoideae) forming the basalmost lineage. The remaining genera clustered in two major groups, the monophyletic Lejeuneoideae (52 genera) and the paraphyletic Ptychanthoideae (16 genera). Within each, several multigeneric lineages corresponding in part to previously described taxa were recovered: the Acrolejeuneinae and Ptychanthinae clades in the Ptychanthoideae, and the Brachiolejeuneinae, Lejeuneeae and Tuyamaella–Cololejeunea clades in the Lejeuneoideae. Bryopteris , a genus sometimes treated as a separate family, was nested in the Ptychanthinae clade. The Tuyamaella–Cololejeunea lineage corresponded with three previously recognized subfamilies (Cololejeuneoideae, Myriocoleoideae and Tuyamaelloideae) and contained genera with neotenic features, in two subclades. These features seemed to have originated by multiple heterochronic events: single origins were detected for 'protonemal neoteny' and 'primary neoteny', whereas 'secondary neoteny' probably evolved twice. Relationships within the large Lejeuneeae clade (43 genera) remained largely unresolved, although several putative lineages were detected in majority rule trees. Additional characters such as DNA sequences may provide better phylogenetic resolution in this group.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 391–410.     

New species of Cheilolejeunea and Otolejeunea (Hepaticae; Lejeuneaceae) from Australia

Two new species belonging to Lejeuneaceae subfamily Lejeuneoideae have been found in northern Queensland, Australia: Cheilolejeunea hallingii and Otolejeunea australiensis. Both are described and illustrated, and keys to related species in the paleotropics are included.     

Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae)

In an effort to improve our knowledge of the phylogenetic relationships among species and genera of the subfamily Sarcophaginae, we analysed data from three mitochondrial gene fragments. Sequence data for portions of the genes cytochrome oxidase I (COI), cytochrome oxidase II (COII) and dehydrogenase subunit 4 (ND4) were obtained from 43 species of Sarcophagidae representing 15 genera. We used a Bayesian approach to simultaneously choose how best to partition the data and which substitution model to apply to each partition. Phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods. Our results are consistent with monophyly of the subfamily Sarcophaginae (posterior probability 1; bootstrap support 93%), as well as with monophyly of several genera within the Sarcophaginae (including Sarcophaga s.l.; posterior probability 1; bootstrap support 97%). We found support for a sister‐group relationship between Ravinia Robineau‐Desvoidy and Oxysarcodexia Townsend, which has been hypothesised by past authors on the basis of morphological similarities, although this was supported only in the Bayesian analyses (posterior probability 0. 81–0. 98), and for some novel supra‐generic clades. Contrary to a recent morphological hypothesis, we do not find Helicobia Coquillett to be nested within Sarcophaga Meigen; our data suggest, but do not strongly support, a hypothesis that Peckia Robineau‐Desvoidy is the sister group to Sarcophaga.     

The ant subfamily Pseudomyrmecinae (Hymenoptera: Formicidae): phylogeny and evolution of big-eyed arboreal ants

Abstract. The ant subfamily Pseudomyrmecinae comprises three genera of hyperoptic, arboreal ants, widely distributed in tropical and subtropical regions: Pseudomyrmex (∼200 species, New World), Myrcidris (two species, South America) and Tetraponera (∼100 species, Palaeotropics). The phylogenetic relationships among these ants were investigated using DNA sequence data (∼5.2 kb from 18S rDNA, 28S rDNA, wingless, abdominal-A, and long-wavelength rhodopsin genes) and 144 morphological characters, both separately and in combination. Data were gathered from a representative set of forty-nine pseudomyrmecine species, plus eighteen species from various outgroups. There was substantial agreement among the results obtained from different datasets, and from different methods of phylogenetic inference (parsimony, Bayesian inference). The monophyly of the following groups is strongly supported (100% bootstrap support and 1.00 posterior probability in the molecular dataset): Pseudomyrmecinae, Pseudomyrmex, and Pseudomyrmex + Myrcidris. The status of the genus Tetraponera is less clear: the DNA sequence data indicate that the genus is paraphyletic, but morphological features and a unique insertion in the 28S gene support the monophyly of this taxon. Seven of nine Pseudomyrmex species groups, established previously on the basis of morphology alone, are strongly upheld, but monophyly is rejected for the P. pallens group and the P. viduus group. In the latter case, molecular evidence indicates the existence of two independent clades, associated with the ant-plants Triplaris and Tachigali, respectively, whose convergent morphological features had caused them to be placed erroneously in the same species group. The present results confirm an earlier assertion that obligate associations with domatia-bearing plants have arisen at least twelve times in the subfamily. Molecular and morphological data support the hypothesis of a sister-group relationship between Pseudomyrmecinae and Myrmeciinae (84% parsimony bootstrap, combined dataset), which implies a Cretaceous origin of the stem-group pseudomyrmecines in the southern hemisphere. Pseudomyrmecines appear to have arisen in the Palaeotropics and later dispersed from Africa to South America, where they experienced a pronounced burst of diversification.     

Evolution of Lycopodiaceae Inferred from Spacer Sequencing of Chloroplast rRNA Genes

Nucleotide sequences of a chloroplast rDNA region including 8 bp from the 3" end of 23S rDNA–ITS2–4.5S rDNA–ITS3–5S rDNA–ITS4 (approximately 800 bp) were determined in 25 species of Lycopodiaceae and two species of the genus Isoetes. The rate of molecular evolution of spacers significantly varied in different Lycopsida taxa. A phylogenetic analysis by the neighbor-joining (NJ) method revealed that the family Lycopodiaceae is monophyletic. The topology of phylogenetic trees suggests the isolation of four or probably five genera in family Lycopodiaceae. For these genera, synapomorphic indels were detected. The obtained data were compared with the results of phylogenetic analysis of Lycopsida with regard to other sequences. The relationships of taxa within the family Lycopodiaceae is discussed.     

Phylogenetic relationships in Maloideae (Rosaceae): evidence from sequences of the internal transcribed spacers of nuclear ribosomal DNA and its congruence with morphology

We used sequences from both internal transcribed spacers (ITS) and a small portion of the 5.8S gene of nuclear ribosomal DNA (nrDNA) for phylogenetic reconstruction of 19 genera of Maloideae and four potential outgroups from the Rosaceae. Parsimony analyses indicate that Maloideae are not monophyletic; Vauquelinia, which is traditionally placed in Spiraeoideae, and two genera of the Maloideae, Eriobotrya and Rhaphiolepis, form a well-supported clade that is the sister to the remainder of the subfamily. Although our ITS phylogenetic hypothesis is highly resolved, there is considerable homoplasy, and support, as indicated by bootstrap values and decay indices, is relatively weak for all groups except four: Eriobotrya-Rhaphiolepis-Vauquelinia, Crataegus-Mespilus, Amelanchier-Peraphyllum-Malacomeles, and Cydonia-Pseudocydonia. Our DNA sequence data do not support a broad interpretation of Sorbus. Intergeneric hybridization, which is prevalent in Maloideae, occurs between genera that are far removed from one another on our most-parsimonious trees. We infer an overall phylogeny from separate analyses of ITS DNA sequences and recently published morphological and wood anatomical studies of Maloideae and from analyses after pooling these data sets. The four most strongly supported clades of the ITS phylogeny appear in the phylogeny based on pooled data.     

Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia,Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA

The internal transcribed spacer (ITS) region of the 18 S–25 S nuclear ribosomal DNA repeat was sequenced from 19 populations of the tribeLactuceae, including all species of dwarf dandelion (Krigia) and five outgroup genera. The incidence of length changes and base substitutions was at least two times higher for ITS 1 than ITS 2. Interspecific sequence divergence withinKrigia averaged 9.62% (1.61%–15.19%) and 4.26% (0%–6.64%) in ITS 1 and ITS 2, respectively. Intergeneric sequence divergence ranged from 15.6% to 44.5% in ITS 1 and from 8.0% to 28.6% in ITS 2. High sequence divergence and homoplasy among genera of tribeLactuceae suggest that the phylogenetic utility of ITS sequence data is limited to interspecific studies or comparisons among closely related genera. Trees generated from ITS sequences are essentially identical to those from restriction site comparisons of the entire nuclear ribosomal (nr) DNA region. The degree of tree resolution differed depending on how gaps were treated in phylogenetic analyses. The ITS trees were congruent with the chloroplast DNA and morphological phylogenies in three major ways: 1) the sister group relationship betweenKrigia andPyrrhopappus; 2) the recognition of two monophyletic sections,Krigia andCymbia, in genusKrigia; and 3) the monophyly of theK. occidentalis-K. cespitosa clade in sect.Cymbia. However, the two nrDNA-based trees are not congruent with morphology/chloroplast DNA-based trees for the interspecific relationships in sect.Krigia. An average of 22.5% incongruence was observed among fourKrigia data sets. The relatively high degree of incongruence among data sets is due primarily to conflict between trees based on nrDNA and morphological/cpDNA data. The incongruence is probably due to the concerted evolution of nrDNA repeating units. The results fromKrigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Our combined phylogenetic analysis as a total evidence shows the least conflict to each of the individual data sets.     

Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera)

Gelechioidea are one of the most species rich and least studied superfamilies of Lepidoptera. We examine the interrelationships within the superfamily using the densest taxon sampling to date, combined with the most extensive ever morphological and molecular character data. We perform partitioned and combined analyses using maximum likelihood, Bayesian and parsimony approaches. The combined dataset consists of 155 exemplar species of Gelechioidea, representing nearly all subfamilies recognized in recent classifications. Parsimony analyses are performed with a dataset including 28 additional terminal taxa with only morphological data available. We use eight genes with a total of 6127 bp, and morphological data with 253 characters derived from larval, pupal, and adult morphology. The analyses of combined data yield more resolved trees and significantly better‐supported groupings than either dataset when analysed alone. The recurrent monophyletic groupings in all our model‐based analyses support a revision of the family classification. Deeper relationships vary between analyses and data partitions, leaving them ambiguous. The place of the root remains a challenge for future research. We propose a revised classification and suggest the division of Gelechioidea into 16 families. We redefine Depressariidae Meyrick, 1883 for a monophylum that includes Acriinae, Aeolanthinae, Cryptolechiinae, Depressariinae, Ethmiinae, Hypercalliinae, Hypertrophinae, Peleopodinae, Oditinae, Stenomatinae, Carcina, and a diversity of predominantly New World taxa previously excluded from Lypusidae (Amphisbatidae s. authors) but left without family position. A monophyletic Oecophoridae s. s., including Deuterogoniinae and Pleurotinae, is obtained for the first time with significant support. Elachistidae s. l. is found to be polyphyletic, and Elachistidae is restricted to comprise Agonoxeninae, Elachistinae, and Parametriotinae. Batrachedridae are polyphyletic, with several genera pending further study. Apart from the core Batrachedra, the taxa previously included in this family are grouped in an expanded Pterolonchidae, together with Coelopoetinae and Syringopainae. Lypusidae s. s. and Chimabachidae form a monophylum; Chimabachinae is united with Lypusidae as a subfamily, stat. n. Our results contradict the subfamily classifications of several families, notably Lecithoceridae and Autostichidae, but due to insufficient sampling of taxa we refrain from comprehensive taxonomic conclusions on the subfamily level, and encourage focused studies to resolve these groups.     

Reconsideration of systematic relationships within the order Euplotida (Protista, Ciliophora) using new sequences of the gene coding for small-subunit rRNA and testing the use of combined data sets to construct phylogenies of the Diophrys-complex

Comprehensive molecular analyses of phylogenetic relationships within euplotid ciliates are relatively rare, and the relationships among some families remain questionable. We performed phylogenetic analyses of the order Euplotida based on new sequences of the gene coding for small-subunit RNA (SSrRNA) from a variety of taxa across the entire order as well as sequences from some of these taxa of other genes (ITS1-5.8S-ITS2 region and histone H4) that have not been included in previous analyses. Phylogenetic trees based on SSrRNA gene sequences constructed with four different methods had a consistent branching pattern that included the following features: (1) the “typical” euplotids comprised a paraphyletic assemblage composed of two divergent clades (family Uronychiidae and families Euplotidae–Certesiidae–Aspidiscidae–Gastrocirrhidae), (2) in the family Uronychiidae, the genera Uronychia and Paradiophrys formed a clearly outlined, well-supported clade that seemed to be rather divergent from Diophrys and Diophryopsis, suggesting that the Diophrys-complex may have had a longer and more separate evolutionary history than previously supposed, (3) inclusion of 12 new SSrRNA sequences in analyses of Euplotidae revealed two new clades of species within the family and cast additional doubt on the present classification of genera within the family, and (4) the intraspecific divergence among five species of Aspidisca was far greater than those of closely related genera. The ITS1-5.8S-ITS2 coding regions and partial histone H4 genes of six morphospecies in the Diophrys-complex were sequenced along with their SSrRNA genes and used to compare phylogenies constructed from single data sets to those constructed from combined sets. Results indicated that combined analyses could be used to construct more reliable, less ambiguous phylogenies of complex groups like the order Euplotida, because they provide a greater amount and diversity of information.     

Phylogenetic relationships and biodiversity in Hylids (Anura: Hylidae) from French Guiana

We evaluated two biodiversity criteria, higher taxonomic diversity and phylogenetic diversity in French Guiana. For this, we used a recent assessment of the knowledge accumulated since 30 years of study on the amphibian species currently known in French Guiana. We focused on two well-represented genera, Hyla and Scinax, belonging to the subfamily Hylinae. We used partial sequences of two mitochondrial genes (16S rDNA and 12S rDNA, 813 bp) and two nuclear genes (tyrosinase and 18S rRNA, 1590 bp) covering a total of 2403 bp. According to the high bootstrap support in phylogenetic analysis of the complete dataset, the genus Scinax is a homophyletic clade formed by two species groups (rubra and rostrata) in French Guiana. The genus Hyla was confirmed to be a paraphyletic group formed by two species groups as well (30 chromosomes and the 'gladiator frogs'). We confirmed that these genera should be taxonomically reconsidered. Moreover, at the genus, subfamily and family levels, the use of only morphological characters or only molecular DNA markers would hamper estimations of biodiversity. Thus, we strongly advise the combined use of both morphology and molecular data (nuclear and mitochondrial markers).     

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid,nuclear gene and spacer sequences

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretum and Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretum is strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminalia as it forms a polytomy with Anogeissus. This clade is sister to Conocarpus. Electronic Publication     

Phylogenetic analysis of Sesuvioideae (Aizoaceae) inferred from nrDNA internal transcribed spacer (ITS) sequences and morphological data

The phylogeny of the four genera of Aizoaceae subfamily Sesuvioideae (Sesuvium, Cypselea, Trianthema and Zaleya) is elucidated employing internal transcribed spacer (ITS) sequences and 23 morphological characters. Phylogenetic analysis based on ITS sequences and a combined molecular-morphological analysis provide largely congruent results. The monophyly of Sesuvioideae and its close relationship to Aizooideae s.l. and Mesembryanthemoideae is confirmed. Zaleya is placed within Trianthema and Cypselea within Sesuvium by ITS analysis, but in the combined analysis, Zaleya forms an unresolved polytomy with the two Trianthema clades and Cypselea, as well as two Sesuvium species, remain unresolved. Sesuvium sesuvioides and S. hydaspicum, previously treated as synonyms, are closely related, but molecular data do not support conspecifity. The Trianthema triquetra complex needs further intensive study because the African T. triquetra sample is closer to the NE African-Arabian T. sheilae than to Australian samples of T. triquetra. The close relationship of four species of Trianthema (T. patellitecta, T. rhynchocalyptra, T. megasperma, and T. pilosa) from Australia based on molecular data is supported morphologically by the exclusive possession of a well-developed indumentum in these taxa.     

Phylogeny of the Archiborborinae (Diptera: Sphaeroceridae) Based on Combined Morphological and Molecular Analysis

The Archiborborinae is a diverse Neotropical subfamily of Sphaeroceridae, with many undescribed species. The existing generic classification includes three genera consisting of brachypterous species, with all other species placed in the genus Archiborborus. We present the first phylogenetic hypothesis for the subfamily based on morphological, molecular, and combined datasets. Morphological data include 53 characters and cover all valid described taxa (33 species in 4 genera) in the subfamily, as well as 83 undescribed species. Molecular data for five genes (mitochondrial 12S rDNA, cytochrome c oxidase subunit I, and cytochrome B, and nuclear alanyl-tRNA synthetase and 28S rDNA) were obtained for 21 ingroup taxa. Data support the separation of the Archiborborinae from the Copromyzinae, with which they were formerly combined. Analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. The validity of the brachypterous genera Penola Richards and Frutillaria Richards is supported. The former genus Archiborborus Duda is paraphyletic, and will be divided into monophyletic genera on the basis of this work. Aptery and brachyptery have evolved multiple times in the subfamily. Antrops Enderlein, previously including a single brachypterous species, is a senior synonym of Archiborborus.     

Phylogenetic position of the house dust mite subfamily Guatemalichinae (Acariformes: Pyroglyphidae) based on integrated molecular and morphological analyses and different measures of support

Based on multilocus phylogenetic analyses (18S, 28S, EF1‐α, SRP54, HSP70, CO1, 10 860 nt aligned), we show that the house dust mite subfamily Guatemalichinae is nested within non‐onychalgine pyroglyphid mites and forms the sister group to the genus Sturnophagoides (bootstrap support 100, posterior probability 1.0). Because high bootstrap support values may be misleading in the presence of incongruence, we evaluate robustness of the Guatemalichinae+Sturnophagoides clade using: (1) internode certainty indices to estimate the frequency of conflicting bipartitions in maximum‐likelihood bootstrap trees, (ii) consensus networks to investigate conflict among different loci; and (iii) statistical hypothesis testing based on information theory, both multi‐scale and regular bootstrap. Results suggest that this grouping is very well supported given the data. The molecular analyses were integrated with detailed morphological study using scanning electron and light microscopy. We suggest that the subfamilial status of Guatemalichinae should be reconsidered, and this lineage should be placed within the subfamily Dermatophagoidinae. The latter subfamily is currently accepted in the literature as a monophyletic group but was here inferred as paraphyletic and was not supported by any morphological synapomorphy. The paraphyly involved the most species‐rich and medically important genus, Dermatophagoides. Our findings suggest the need for a comprehensive revision of the higher‐level relationships of pyroglyphid house dust mites using both DNA sequences and morphology coupled with a broad taxonomic sampling.     

On the systematics of the fungus gnat subfamily Mycetophilinae (Diptera): a combined morphological and molecular approach

The phylogenetic relationships within the fungus gnat subfamily Mycetophilinae (Diptera) are addressed using a combined morphological and molecular approach. Twenty-four species, representing nine genera of the tribe Mycetophilini and 15 genera of the tribe Exechiini, were included in the study. Analyses include nucleotide sequences of mitochondrial (cytochrome oxidase I and 16S), and nuclear (18S and 28S rDNA) genes, in addition to 65 morphological characters. A combined parsimony analysis, including all characters, supports the monophyly of the subfamily Mycetophilinae and two of its tribes, Exechiini and Mycetophilini. There is also statistical support for a Mycetophila- group and a Phronia- group within the tribe Mycetophilini. The Phronia- group includes the genera Phronia , Macrobrachius and Trichonta . The Mycetophila- group includes the genera Mycetophila , Epicypta , Platurocypta , Sceptonia and Zygomyia . A Bayesian analysis based on the nucleotide sequences alone also support these clades within Mycetophilini except for the position of Dynatosoma which is recovered as the sister taxon to the Phronia- group. A somewhat different pattern, however, is observed for the tribe Exechiini – neither molecular data nor the combined data set support unambiguously any intergeneric relationships within Exechiini.     

COMBINED AND SEPARATE ANALYSES OF MORPHOLOGICAL AND MOLECULAR DATA IN THE PLANT FAMILY RUBIACEAE

Abstract— The Rubiaceae are one of the largest of the families of angiosperms, with over 10000 species. The tribal and subfamilial classification is provisional due to the lack of phylogenetic hypotheses. The present study of the Rubiaceae is based on 33 genera and three data sets, one morphological and two molecular from chloroplast DNA, restriction sites andrbcL sequences. There is much congruence between the morphological and the molecular data sets, but also conflict. For parsimony reasons, the best phylogenetic hypothesis is a tree based on an analysis of the combined data sets. The so-called “total evidence” criterion for the combined analysis is simply a reiteration of the principle of parsimony. In this particular study, the classification would be almost the same even if based on the separate analyses instead of the combined. Despite the inapplicability of consensus trees or trees from separate analyses for phylogenetic hypotheses and classification, separate analyses may provide important information. It is the best way to reveal conflicts between different data sets. Knowledge of the conflicts can promote further detailed investigation in order to improve understanding of characters and phylogenetic hypotheses. In this study, the tribe Vanguerieae provides such an example; morphological data support a position in the subfamily Cinchonoideae, but DNA and a tree based on the combined data support a position in subfamily Ixoroideae. The tribe's position in the morphological tree is probably due to missing information concerning the correct pollen presentation system. Bootstrap fractions and K. Bremer's branch support values are used to evaluate the stability of particular nodes in the trees. Interestingly these values are not always correlated, e.g. in the morphological tree, the node with the highest branch support value has very low bootstrap fraction. The reasons for these differences are unclear, but large differences are presumably more likely to occur on short branches.     

Molecular phylogenetic analysis of Violaceae (Malpighiales) based on plastid and nuclear DNA sequences

A phylogenetic analysis of Violaceae is presented using sequences from rbcL, atpB, matK and 18S rDNA from 39 species and 19 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree, and 33 of all 38 nodes within Violaceae are supported by a bootstrap proportion of more than 50%. Fusispermum is in a basal-most position and Rinorea, Decorsella, Rinoreocarpus and the other Violaceae are successively diverged. The monogeneric subfamily Fusispermoideae is supported, and it shares a number of plesiomorphies with Passifloraceae (a convolute petal aestivation, actinomorphic flowers and connate filaments). The other monogeneric subfamily Leonioideae is sunken within the subfamily Violoideae and is sister to Gloeospermum, sharing some seed morphological characteristics. The present molecular phylogenetic analysis suggests that the convolute, apotact and quincuncial petal aestivation is successively derived within the family. The evolutionary trends of the other morphological characteristics, such as a filament connation, the number of carpels and floral symmetry, are discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogenic Diversity and Taxonomic Problems of the Dictyosphaerium Morphotype within the Parachlorella Clade (Chlorellaceae,Trebouxiophyceae)

The Parachlorella clade was put forward as a group within the family Chlorellaceae in 2004. Recent molecular analyses have revealed that Dictyosphaerium morphotype algae form several independent lineages within the Parachlorella clade, and new genera and species have been established. In this study, we focus on the diversity of Dictyosphaerium morphotype algae within the Parachlorella clade, based on 42 strains from China. We used combined analyses of morphology and molecular data based on SSU and internal transcribed spacer region (ITS) rDNA sequences to characterize these algae. In addition, the secondary structure of ITS2 was compared to delineate new lineages. Our results revealed high phylogenic diversity of Dictyosphaerium morphotype algae, and we describe five distinct lineages. We examined the morphological features of these five lineages, and morphological differences are difficult to find compared with other Dictyosphaerium morphotype algae. The five distinct lineages were not described as new genera currently. We lastly discuss the taxonomic problems regarding the Dictyosphaerium morphotype within the Parachlorella clade, and possible solutions are considered.