Molecular phylogeny of the genus Philodendron (Araceae): delimitation and infrageneric classification

The genus Philodendron (Araceae) is a large neotropical group whose classification remains unclear. Previous classifications are based on morphological characters, mainly from the inflorescence, flower and leaf shape. The classification by Krause, with few modifications, is still the most commonly used system. To examine phylogenetic relationships in the genus, two ribosomal DNA nuclear markers, internal transcribed spacer (ITS) and external transcribed spacer (ETS), and the chloroplast intron rpl 16, were sequenced and analysed for more than 80 species of Philodendron and its close relative Homalomena . According to the resulting phylogeny, the genus Homalomena may be paraphyletic to the genus Philodendron . The inclusion of the American Homalomena species within the genus Philodendron might resolve this taxonomic problem. All three subgenera of Philodendron were revealed as monophyletic. Below the subgeneric level, the groups obtained in our phylogeny globally correspond to sections recognized in previous classifications. Among the morphological characters used by previous taxonomists to build their classifications, and which we optimized onto one of the most parsimonious trees, most characters were found to be homoplasious. However, leaf shape, characteristics of the sterile zone on the spadix and venation patterns are useful for delimiting subgenera and sections within the genus.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 13–27.     

Phylogenetic relationships of woodcreepers (Aves: Dendrocolaptinae) – incongruence between molecular and morphological data

The woodcreepers is a highly specialized lineage within the New World suboscine radiation. Most systematic studies of higher level relationships of this group rely on morphological characters, and few studies utilizing molecular data exist. In this paper, we present a molecular phylogeny of the major lineages of woodcreepers (Aves: Dendrocolaptinae), based on nucleotide sequence data from a nuclear non-coding gene region (myoglobin intron II) and a protein-coding mitochondrial gene (cytochrome b ). A good topological agreement between the individual gene trees suggests that the resulting phylogeny reflects the true evolutionary history of woodcreepers well. However, the DNA-based phylogeny conflicts with the results of a parsimony analysis of morphological characters. The topological differences mainly concern the basal branches of the trees. The morphological data places the genus Drymornis in a basal position (mainly supported by characters in the hindlimb), while our data suggests it to be derived among woodcreepers. Unlike most other woodcreepers, Drymornis is ground-adapted, as are the ovenbirds. The observed morphological similarities between Drymornis and the ovenbird outgroup may thus be explained with convergence or with reversal to an ancestral state. This observation raises the question of the use of characters associated with locomotion and feeding in phylogenetic reconstruction based on parsimony.     

Small Subunit Ribosomal DNA Phylogeny of Various Microsporidia with Emphasis on AIDS Related Forms

ABSTRACT. Phylogenetic analysis of the small subunit ribosomal DNA of a broad range of representative microsporidia including five species from humans ( Enterocytozoon bieneusi, Nosema corneum, Septata intestinalis, Encephalitozoon hellem and Encephalitozoon cuniculi ), reveals that human microsporidia are polyphyletic in origin. Septata intestinalis and E. hellem are very similar to the mammalian parasite E. cuniculi . Based on the results of our phylogenetic analysis, we suggest that S. intestinalis be designated Encephalitozoon intestinalis . Furthermore, analysis of our data indicates that N. corneum is much more closely related to the insect parasite Endoreticulatus schubergi than it is to other Nosema species. This finding is supported by recent studies which have shown a similarity between E. schubergi and N. corneum based on the origin and development of the parasitophorous vacuole. Thus these opportunistic microsporidian parasites can originate from hosts closely or distantly related to humans. Finally, the phylogeny based on small subunit ribosomal DNA sequences is highly inconsistent with traditional classifications based on morphological characters. Many of the important morphological characters (diplokaryon, sporophorous vesicle, and meiosis) appear to have multiple origins.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

Phylogeny and evolution of glass sponges (porifera, hexactinellida)

Reconstructing the phylogeny of sponges (Porifera) is one of the remaining challenges to resolve the metazoan Tree of Life and is a prerequisite for understanding early animal evolution. Molecular phylogenetic analyses for two of the three extant classes of the phylum, Demospongiae and Calcarea, are largely incongruent with traditional classifications, most likely because of a paucity of informative morphological characters and high levels of homoplasy. For the third class, Hexactinellida (glass sponges)--predominantly deep-sea inhabitants with unusual morphology and biology--we present the first molecular phylogeny, along with a cladistic analysis of morphological characters. We collected 18S, 28S, and mitochondrial 16S ribosomal DNA sequences of 34 glass sponge species from 27 genera, 9 families, and 3 orders and conducted partitioned Bayesian analyses using RNA secondary structure-specific substitution models (paired-sites models) for stem regions. Bayes factor comparisons of different paired-sites models against each other and conventional (independent-sites) models revealed a significantly better fit of the former but, contrary to previous predictions, the least parameter-rich of the tested paired-sites models provided the best fit to our data. In contrast to Demospongiae and Calcarea, our rDNA phylogeny agrees well with the traditional classification and a previously proposed phylogenetic system, which we ascribe to a more informative morphology in Hexactinellida. We find high support for a close relationship of glass sponges and Demospongiae sensu stricto, though the latter may be paraphyletic with respect to Hexactinellida. Homoscleromorpha appears to be the sister group of Calcarea. Contrary to most previous findings from rDNA, we recover Porifera as monophyletic, although support for this clade is low under paired-sites models.     

A Re-assessment of Relationships within Epacridaceae

An extensive database of predominantly morphological characters has been assembled for the family Epacridaceae. Problems of homology across the family and its outgroups were encountered for several characters. A phylogenetic analysis, using only those characters for which we were fairly confident of our assessment of homology, was undertaken to establish broad relationships within the family as a basis for a re-assessment of the supra-generic classification. The resultant phylogeny is weakly resolved and lacks robustness in the basal clades. Previous classifications of the family are assessed in the light of this analysis, and an alternative arrangement of four tribes is proposed.     

Molecular phylogeny of tribe Rhipsalideae (Cactaceae) and taxonomic implications for Schlumbergera and Hatiora

Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55; 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided.     

How our view of animal phylogeny was reshaped by molecular approaches: lessons learned

In the late 1980s, researchers began applying molecular sequencing tools to questions of deep animal phylogeny. These advances in sequencing were accompanied with improvements in computation and phylogenetic methods, and served to significantly reshape our understanding of metazoan evolution. Prior to this time, researchers asserted phylogenetic hypotheses based on their experience with taxa and to some degree, their authority. Molecular phylogenetic tools provided discrete methods and objective characters for reconstructing phylogeny. Nonetheless, major changes to widely accepted views, such as animal phylogeny, take time to be accepted. Development and acceptance of our current understanding of animal evolution occurred in three main phases: initial hypotheses based on 18S data, confirmation with additional molecular markers, and continued refinement with phylogenomics. With the advent of ideas such as Lophotrochozoa and Ecdysozoa, flaws in the traditional view became apparent. We now understand that complex morphological and embryological features (e.g., segmentation, coelom formation, development of body cavities) are much more evolutionarily plastic than previously recognized. Here, I explore how the transition from the traditional to the modern phylogenetic understanding of animal phylogeny occurred and examine some implications of this change in understanding. As the field moves forward, the utility of morphological and embryological characters for reconstruction of deep animal phylogeny should be discouraged. Instead, these characters should be interpreted in the light of independent phylogeny.     

Molecular Phylogeny of Microsporidians with Particular Reference to Species that Infect the Muscles of Fish

Ribosomal DNA from eight species of microsporidians infecting fish have been sequenced. Seven of these species infect the skeletal muscle of fish ( Pleistophora spp.) and one species infects migratory mesenchyma cells ( Glugea anomala ). These sequences, in addition to other available microsporidian rDNA sequences from a broad range of host taxa, have been used in phylogenetic analysis. This analysis revealed that muscle-infecting microsporidians from fish are a polyphyletic group, indicating that characters supposed to be important in the classification of the genus Pleistophora have to be re-evaluated. One character that probably has a polyphyletic origin is the amorphous coat, which has been extensively used in the definition of this genus. Furthermore, our results showed that the insect parasitizing Pleistophora spp. are not related to the true pleistophorans parasitic in skeletal muscle of fish. Phylogenetic analysis of small subunit rDNA sequences revealed disagreements between the molecular phylogeny and classifications based upon ultrastruclure. Many of the morphological characters claimed to be important in microsporidian classifications appeared to have arisen several times during evolution: for example, the diplokaryon and sporophorous vesicles.     

Molecular systematics of the order anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI)

Fragments from three mitochondrial genes (12S, 16S, and COI) were sequenced to reconstruct a molecular phylogeny of the opisthobranch order Anaspidea. The molecular phylogeny supports the placement of the genus Akera, a taxon previously regarded by some authors as a cephalaspidean, within the Anaspidea. Incongruence between the molecular data and the classifications based on morphology suggests that some of the taxonomic characters (i.e., shell, parapodia fusion) traditionally used for the classification of sea hares must be reevaluated, since they may be homoplastic. The ancestral nature of Notarchus based on the molecular evidence suggests that homoplasy may be an explanation for the morphological resemblance of this species to the more derived sea hares with highly fused parapodia and concentrated nerve ganglia. Finally, examples are given of how comparative studies of the evolution of learning mechanisms in the anaspidean clade will benefit from the phylogenetic hypothesis presented in this paper.     

Vegetative anatomy and systematics of subtribe Dendrobiinae (Orchidaceae)

Anatomy of leaf, stem, and root of more than 100 species in subtribe Dendrobiinae (Orchidaceae) was studied with the light microscope to provide a comparative anatomical treatment of these organs, to serve as an independent source of evidence that might be taxonomically important, and to recommend such reinterpretations of existing classifications as are suggested by a phylogenetic assessment of data. We based our classification on that of Rudolf Schlechter as the most complete and widely accepted today. We found that the anatomy of plants in subtribe Dendrobiinae reflects a high degree of morphological diversity, and many of the anatomical characters appear to be homoplasous. When these anatomical data are used to interpret the systematic relationships among the genera, they indicate that Dendrobium is not monophyletic and that Cadetia and Pseuderia are apparently nested within the structure of Dendrobium when section Grastidium is chosen as a functional outgroup. Lack of resolution in the strict consensus tree illustrates the difficulty of determining the phylogenetic relationships of many of Schlechter's sections using anatomical characters. Nevertheless, we recommend that his sectional classification, with appropriate modifications based on available data, be retained for the present, pending a more detailed understanding of the phylogeny of Dendrobiinae based on morphology, micromorphology, anatomy, and DNA studies.     

Phylogeny and classification of the Catantopidae at the tribal level (Orthoptera, Acridoidea)

The grasshopper family Catantopidae is a well-known group, whose members include some of the most notorious agricultural pests. The existing classifications of the family are mostly utilitarian rather than being based on phylogenetic analysis and therefore unable to provide the stability desired for such an economically important group. In the present study, we present the first comprehensive phylogenetic analysis of the family based on morphology. By extensively sampling from the Chinese fauna, we included in the present analysis multiple representatives of each of the previously recognized tribes in the family. In total, we examined 94 genera represented by 240 species and evaluated 116 characters, including 84 for external morphology and 32 for male genitalia. The final matrix consists of 86 ingroup taxa and 88 characters. Our phylogenetic analyses resulted in a high resolution of the basal relationships of the family while showed considerable uncertainty about the relationships among some crown taxa. We further evaluated the usefulness of morphological characters in phylogeny reconstruction of the catantopids by examining character fit to the shortest trees found, and contrary to previous suggestions, our results suggest that genitalia characters are not as informative as external morphology in inferring higher-level relationship. We further suggest that earlier classification systems of grasshoppers in general and Catantopidae in particular most probably consist of many groups that are not natural due the heavy reliance on genitalia features and need to be revised in the light of future phylogenetic studies. Finally, we outlined a tentative classification scheme based on the results of our phylogenetic analysis.     

Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes

With the increase of laboratory facilities, molecular phylogenies are playing a predominant role in evolutionary analyses. However, understanding the evolution of morphological traits remains essential for a comprehensive view of the evolution of a group. Here we present a new approach based on co-inertia analysis for identifying characters which variations are dependent to the phylogeny, a prerequisite for analyzing the evolution of characters. Our approach has the advantage of treating the full data set at once, including qualitative and quantitative variables. It provides a graphical output giving the contribution of each variable to the co-structure, allowing a direct discrimination among phylogenetically dependent and independent variables. We have implemented this approach in deciphering the evolution of morphological traits in a highly specialized group of Neotropical catfishes: the Loricariinae. We have first inferred a molecular phylogeny of this group based on the 12S and 16S mitochondrial genes. The resulting phylogeny indicated that the subtribe Harttiini was restricted to the single genus Harttia, and within the subtribe Loricariini, two sister subtribes were distinguished, Sturisomina (new subtribe), and Loricariina. Among Loricariina, the morphological groups Loricariichthys and Loricaria+Pseudohemiodon were confirmed. The co-inertia analysis highlighted a strong relationship between the morphological and the genetic data sets, and identified three quantitative and eight qualitative variables linked to the phylogeny. The evolution of quantitative variables was assessed using the orthogram method and showed a major punctual event in the evolution of the number of caudal-fin rays, and a more gradual pattern of evolution of the number of teeth along the phylogeny. The evolution of qualitative variables was inferred using ancestral states reconstructions and highlighted parallel patterns of evolution in characters linked to the mouth, suggesting co-evolution of the traits for adapting to divergent substrates.     

A PHYLOGENETIC ANALYSIS OF THE SYNUROPHYCEAE USING MOLECULAR DATA AND SCALE CASE MORPHOLOGY

The phylogeny of the Synurophyceae was investigated by parsimony analysis of scale case characters and small-sub unit (18S) ribosomal RNA (rRNA) sequence data. Analysis of 1 eustigmatophycean (outgroup), 3 chrysophycean, and 10 synurophycean 18S rRNA sequences corroborated the inference from ultrastructural information that the Synurophyceae is a monophyletic assemblage . Tessellaria vol-vocina, which had been tentatively proposed as a member of the Synurophyceae, was confirmed as the earliest lineage within the Synurophyceae by both the molecular analysis and an evaluation of published ultrastructural data. A second set of analyses investigated the relationships among Tessellaria volvocina, 6 Synura species, and 10 Mallomonas species/varieties, with particular reference to the validity of current classifications of the Synurophyceae and the characters upon which they are based. The molecular and scale case phylogenies were not totally resolved but were largely congruent. The data sets were combined to produce another phylogeny, which showed greater resolution. The combined phylogeny weakly supported our representatives of Synura and Mallomonas as monophyletic groupings and also upheld several of the sections within these genera that are recognized by current classifications. However, some changes to the classification and delineation of these genera are recommended and predicted. Both our 18S rRNA sequence and scale case data sets were more appropriate for examining the branching order among the more closely related text rather than resolving the deeper branching points of the synurophycean phylogeny .     

Critical Reexamination of Palynological Characters Used to Delimit Asclepiadaceae in Comparison to the Molecular Phylogeny Obtained from PlastidmatK Sequences

The family Asclepiadaceae (Dicotyledones) was created by Brown in 1810 by splitting in two the family Apocynaceae of Jussieu established in 1789. The morphological characters used to make this distinction were mainly palynological, such as presence of tetrads or pollinia and number and orientation of pollinia. Those characters, still used in higher taxonomic delimitation (families, subfamilies, and tribes), are here critically reexamined and compared to a molecular phylogeny obtained with one of the more variable plastid genes (matK) of 46 species in the order Gentianales. In this molecular phylogeny, Asclepiadaceae form a monophyletic group derived from within Apocynaceae. Each of the subfamilies of Asclepiadaceae is monophyletic and based on reliable palynological characters, but palynological characters are not useful to delimit tribes of the subfamily Asclepiadoideae. Based on the molecular data, these tribes have undergone parallelisms in several reproductive traits.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Preliminary comments on a phylogenetic study of the order Diphyllidea van Beneden in Carus, 1863

The basis for a preliminary analysis of the relationships within the monophyletic Diphyllidea is outlined. Information on morphological characters and their interpretation within a phylogenetic context are presented. A cladistic analysis at the species level was conducted based on a matrix of 21 morphological characters. Character polarity was determined by taxonomic outgroup analysis relative to the basal orders, Pseudophyllidea and Haplobothriidea. The phylogeny for the diphyllideans was found to be poorly resolved based on characters currently available for evaluation. Computer assisted cladistic analysis found three equally parsimonious trees with a consistency index of 0.54. The topology of these trees shows that Ditrachybothridium macrocephalum is the basal taxon and the putative sister group for species of Echinobothrium; Macrobothridium rhynchobati is grouped among species of Echinobothrium. If the classification is to be consistent with this tree, M. rhynchobati should be included in the genus Echinobothrium. This observation should be carefully examined, considering the relative paucity of useful morphological characters currently available for this group.     

Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)

Background and Aims

Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented.

Methods

A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications.

Key Results

The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions.

Conclusions

This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.     

Molecular insights into Cumacean family relationships (Crustacea, Cumacea)

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.