A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data

Drosophila melanogaster belongs to a closely related group of eight species collectively known as the melanogaster subgroup; all are native to sub-Saharan Africa and islands off the east coast of Africa. The phylogenetic relationships of most species in this subgroup have been well documented; however, the three most closely related species, D. simulans, D. sechellia, and D. mauritiana, have remained problematic from a phylogenetic standpoint as no data set has unambiguously resolved them. We present new DNA sequence data on the nullo and Serendipity-alpha genes and combine them with all available nuclear DNA sequence data; the total data encompass 12 genes and the ITS of rDNA. A methodological problem arose because nine of the genes had information on intraspecific polymorphisms in at least one species. We explored the effect of inclusion/exclusion of polymorphic sites and found that it had very little effect on phylogenetic inferences, due largely to the fact that 82% of polymorphisms are autapomorphies (unique to one species). We have also reanalyzed our previous DNA-DNA hybridization data with a bootstrap procedure. The combined sequence data set and the DNA-DNA hybridization data strongly support the sister status of the two island species, D. sechellia and D. mauritiana. This at least partially resolves what had been a paradox of parallel evolution in these two species.      

Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data.

The relative efficiencies of the maximum-parsimony (MP), UPGMA, and neighbor-joining (NJ) methods in obtaining the correct tree (topology) for restriction-site and restriction-fragment data were studied by computer simulation. In this simulation, six DNA sequences of 16,000 nucleotides were assumed to evolve following a given model tree. The recognition sequences of 20 different six-base restriction enzymes were used to identify the restriction sites of the DNA sequences generated. The restriction-site data and restriction-fragment data thus obtained were used to reconstruct a phylogenetic tree, and the tree obtained was compared with the model tree. This process was repeated 300 times. The results obtained indicate that when the rate of nucleotide substitution is constant the probability of obtaining the correct tree (Pc) is generally higher in the NJ method than in the MP method. However, if we use the average topological deviation from the model tree (dT) as the criterion of comparison, the NJ and MP methods are nearly equally efficient. When the rate of nucleotide substitution varies with evolutionary lineage, the NJ method is better than the MP method, whether Pc or dT is used as the criterion of comparison. With 500 nucleotides and when the number of nucleotide substitutions per site was very small, restriction-site data were, contrary to our expectation, more useful than sequence data. Restriction-fragment data were less useful than restriction-site data, except when the sequence divergence was very small. UPGMA seems to be useful only when the rate of nucleotide substitution is constant and sequence divergence is high.     

Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data

Scleractinian corals, which include the architects of coral reefs, are found throughout the world's oceans and have left a rich fossil record over their 240 million year history. Their classification has been marked by confusion but recently developed molecular and morphological tools are now leading to a better understanding of the evolutionary history of this important group. Although morphological characters have been the basis of traditional classification in the group, they are relatively few in number. In addition, our current understanding of skeletal growth and homology is limited, and homoplasy is rampant, limiting the usefulness of morphological phylogenetics. Molecular phylogenetic hypotheses for the order, which have been primarily focused on reef-building corals, differ significantly from traditional classification. They suggest that the group is represented by two major lineages and do not support the monophyly of traditional suborders and most traditional families. It appears that once a substantial number of azooxanthellate taxa are included in molecular phylogenetic analyses, basal relationships within the group will be clearly defined. Understanding of relationships at lower taxonomic levels will be best clarified by combined analyses of morphological and molecular characters. Molecular phylogenies are being used to inform our understanding of the evolution of morphological characters in the Scleractinia. Better understanding of the evolution of these characters will help to integrate the systematics of fossil and extant taxa. We demonstrate how the combined use of morphological and molecular tools holds great promise for ending confusion in scleractinian systematics.     

jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences

jPHYDIT is a Java application designed to furnish a visual and integrated environment for molecular phylogeny. The program can be used to visualize intra-strand base-pairing information in secondary and tertiary structures of ribosomal RNA (rRNA) sequences. A function for the semi-automated alignment was included to facilitate handling of the database containing a large number of multiple-aligned rRNA sequences. Integration of nucleotide sequence editing, pairwise alignment, multiple alignment and phylogenetic treeing functions provide an easy and efficient way of analyzing rRNA sequences for molecular evolution, systematics, epidemiology and ecology.     

Allometry, sexual dimorphism, and phylogeny: A cladistic analysis of extant African papionins using craniodental data

This study conducts a phylogenetic analysis of extant African papionin craniodental morphology, including both quantitative and qualitative characters. We use two different methods to control for allometry: the previously described narrow allometric coding method, and the general allometric coding method, introduced herein. The results of this study strongly suggest that African papionin phylogeny based on molecular systematics, and that based on morphology, are congruent and support a Cercocebus/Mandrillus clade as well as a Papio/Lophocebus/Theropithecus clade. In contrast to previous claims regarding papionin and, more broadly, primate craniodental data, this study finds that such data are a source of valuable phylogenetic information and removes the basis for considering hard tissue anatomy “unreliable” in phylogeny reconstruction. Among highly sexually dimorphic primates such as papionins, male morphologies appear to be particularly good sources of phylogenetic information. In addition, we argue that the male and female morphotypes should be analyzed separately and then added together in a concatenated matrix in future studies of sexually dimorphic taxa. Character transformation analyses identify a series of synapomorphies uniting the various papionin clades that, given a sufficient sample size, should potentially be useful in future morphological analyses, especially those involving fossil taxa.     

Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach

We present a numerical cladistic (parsimony) analysis of seed plants plus progymnosperms, using characters from all parts of the plant body, outgroup comparison, and a method of character coding that avoids biases for or against alternative morphological theories. The robustness of the results was tested by construction of alternative trees and analysis of subsets of the data. These experiments show that although some clades are strongly supported, they can often be related to each other in very different but nearly equally parsimonious ways, apparently because of extensive homoplasy. Our results support Rothwell’s idea that coniferopsids are derived fromCallistophyton- like platyspermic seed ferns with saccate pollen, but the hypothesis that they evolved fromArchaeopteris- like progymnosperms and the seed arose twice is nearly as parsimonious. Meyen’s division of seed plants into radiospermic and primarily and secondarily platyspermic lines is highly unparsimonious, but his suggestion that ginkgos are related to peltasperms deserves attention. Angiosperms belong among the platyspermic groups, as the sister group of Bennettitales,Pentoxylon, and Gnetales, and this “anthophyte” clade is best related toCaytonia and glossopterids, although relationships with other combinations of Mesozoic seed fern taxa are nearly as parsimonious. These results imply that the angiosperm carpel can be interpreted as a modified pinnate sporophyll bearing anatropous cupules (=bitegmic ovules), while gnetalian strobili are best interpreted as aggregations of highly reduced bennettitalian flowers, as anticipated by Arber and Parkin and Crane. Our most parsimonious trees imply that the angiosperm line (though not necessarily all its modern features) extended back to the Triassic, but a later derivation of angiosperms from some species ofCaytonia or Bennettitales, which would be nearly as parsimonious, should also be considered. These results raise the possibility that many features considered key adaptations in the origin and rise of angiosperms (insectpollinated flowers, rapid reproduction, drought tolerance) were actually inherited from their gymnospermous precursors. The explosive diversification of angiosperms may instead have been a consequence of carpel closure, resulting in increased speciation rates due to potential for stigmatic isolating mechanisms and/or new means of dispersal. DNA sequencing of extant plants and better information on anatomy, chemistry, sporophyll morphology, and embryology of Bennettitales and Caytoniales and the morphological diversity of Mesozoic anthophytes could provide critical tests of relationships.     

The phylogeny of rotifers: molecular,ultrastructural and behavioural data

This work discusses the nature and significance of molecular, ultrastructural, and behavioural characters that can be used in phylogenetic analyses of rotifers.Recent molecular research has demonstrated the presence of very small amounts of 4-hydroxyproline in rotifers, probably arising from acetyl-cholinesterase or glycoproteins. Thus, rotifers appear to be the first known Metazoa without collagen.Ultrastructural work also has made some interesting discoveries. (1) The myelinic cuticle of the integument and pharynx of gastrotrichs is present in the pharynx of at least two rotifers (Philodina and Brachionus) and some Annelida. (2) The intracytoplasmic lamina (IL) of the syncytial ingestive integument of Acanthocephala is similar to the IL of the syncytial stomach of Bdelloidea. (3) The fibrous terminal web of primitive epidermal ciliated cells may have evolved in the skeletal IL of the syncytial, aciliated integument of rotifers. (4) Using the ultrastructural features of the skeletal, IL of the integument, I derived two possible dendograms of rotifer evolution. (5) These models and other ultrastructural data predict that Bdelloidea should be separated from Monogononta, while Seison has several characters which suggest that it should be more closely aligned to the Monogononta than previously proposed.Molecular and ultrastructural data suggest that rotifers are primitive Metazoa, probably derived by neoteny from ancestral, ciliated larvae. Finally, I argue that information on sensory organs and the behaviour of rotifers may offer unique insights into the evolution of the phylum.     

Amino acid sequences of P1 protamines and the phylogeny of eutherian mammals: a cladistic study

Amino acid and cDNA sequences of eutherian PI protamines, known from publications of other authors, were compared by a cladistic method. Fish, toad and bird protamines were used for the pertinent “outgroup comparisons”, i.e. they provided relevant data for the comparative alignment of the sequences and for the recognition of evolutionary trends. In the sequence positions compared, each amino acid was individually assigned as a plesiomorphic or apomorphic character state (qualitative treatment). The resulting phylogenetic tree (Fig. 2) is only partially in accordance with common ideas on eutherian phylogeny. Disagreements refer to the branching points of Perissodactyla, Lagomorpha and Rodentia.     

The use of cladistic principles in the phylogeny and biogeography of the Lacerta

The methodology used in Phylogenetics remains one of the more interesting problems in comparative biology. Among the methods used, the cladistic is the most accurate. In the present case, among the Saurians, the characters chosen appeared early and cannot be referred to any adaptation bound to an evolutive progress. We have successively considered their distribution in the classification, their polarity and one phylogenetic hypothesis based on the Hennig's concepts. Such a work leads necessarily to systematical conclusions. For instance, we note the heterogeneity of some families. Among the Iguania, the Iguanidea are polyphyletics, the north-american forms breaking up from the other very early. Among the Scincomorpha, the Lacertilia result from two parts of different origins. This research verifies some systematic cuttings in the modern classification: among the Anguimorpha, the separation between Helodermatidea and the group, Varanidea-Lanthanotidea. The characters studied show a non-random distribution in the classification and show also some consistency with the geographical distribution of the extant Saurians. Therefore, it is important to search for the most parsimonious geographical hypothesis, which is in concern with the present data on the continental drift and generally on the history of the Earth, and which strengthens the cladograms posed from the selected characters.     

Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography

We investigated Viburnum phylogeny using separate and combined analyses of DNA sequence data from two chloroplast and three nuclear loci. Separate analyses of nuclear and chloroplast data sets resulted in gene trees that were generally congruent with one another and with trees from two previous analyses. Our gene trees do differ in the position of section Pseudotinus, as well as in species relationships within sections Pseudotinus and Lentago. However, tests for incongruence indicate that differences between the nuclear and chloroplast data are not significant. Furthermore, gene trees from combined analyses were highly similar to those found in separate analyses, suggesting that these localized differences do not affect other parts of the tree. Our analyses provide convincing support for numerous relationships, although there is still uncertainty at the base of the tree. To facilitate future study, we propose informal names for 12 well-supported species groups, as well as for several higher-level clades. We also discuss the biogeographic implications of our phylogeny, focusing on repeated, although apparently temporally incongruent, patterns of disjunction between the Old and New Worlds.     

TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight

TRFMA provides a Web environment for analyzing T-RFLP results based on molecular weights of the fragments, rather than the numbers of nucleotides, to increase accuracy. The 16S rRNA data are saved as an XML file containing around 650 sequences (light version) and a MySQL database containing around 50 000 sequences (full version), which are connected to Web server via PHP5 and manipulated on an Internet browser. AVAILABILITY: TRFMA is freely available at http://myamagu.dent.kyushu-u.ac.jp/bioinformatics/trfma/index.html and can be downloaded from the same site.     

The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data

The pantropical Zingiberaceae is the largest family in the order Zingiberales with 53 genera and over 1200 species. Classifications of the family first proposed in 1889 and refined by others since that time recognize four tribes (Globbeae, Hedychieae, Alpinieae, and Zingibereae) based on morphological features, such as number of locules and placentation in the ovary, development of staminodia, modifications of the fertile anther, and rhizome-shoot-leaf orientation. New phylogenetic analyses based on DNA sequences of the nuclear internal transcribed spacer (ITS) and plastid matK regions suggest that at least some of these morphological traits are homoplasious and three of the tribes are paraphyletic. The African genus Siphonochilus and Bornean genus Tamijia are basal clades. The former Alpinieae and Hedychieae for the most part are monophyletic taxa with the Globbeae and Zingibereae included within the latter. The results of these phylogenetic investigations are used to propose a new classification of the Zingiberaceae that recognizes four subfamilies and four tribes: Siphonochiloideae (Siphonochileae), Tamijioideae (Tamijieae), Alpinioideae (Alpinieae, Riedelieae), and Zingiberoideae (Zingibereae, Globbeae). Morphological features congruent with this classification and the taxonomic status of various monotypic genera are discussed.     

Taxonomy and phylogeny of European Monochamus species: first molecular and karyological data

The worldwide distributed genus Monochamus Megerle, 1821 (Coleoptera Cerambicydae) comprises beetles that may become pests of economic importance in conifer stands in the Nearctic and Palearctic Regions. Besides direct damage due to the larval tunnelling habits, they have also been recognized as main vectors of the phytoparasitic nematode Bursaphelenchus xylophilus (Steiner & Buhrer, 1934) (Nematoda Aphelenchoididae). We analysed the complete mitochondrial cytochrome oxidase I gene and a fragment of the small subunit RNA gene sequences (1536 base pairs) in the five European species. These are: Monochamus galloprovincialis (Olivier, 1795), morphologically distinguished in two subspecies M. galloprovincialis galloprovincialis (Olivier, 1795) and M. galloprovincialis pistor (Germar, 1818); Monochamus sutor (Linneus 1758); Monochamus saltuarius (Gebler 1830); Monochamus sartor (Fabricius, 1787) and Monochamus urussovi (Fischer, 1806). For appropriate comparisons, also the Asiatic Monochamus alternatus Hope, 1842 and a Japanese M. saltuarius sample have been analysed. Both genes show an absolute identity between the two subspecies of M. galloprovincialis and a strong affinity between M. sartor and M. urussovi: the morphological subdivisions of the former taxon in two subspecies and of the latter in two entities of specific level are therefore not supported genetically. On the other hand, the Italian and the Japanese samples of M. saltuarius always cluster together in all trees, and for the remaining taxa, no doubt about their rank of specific differentiation emerges from present analyses. From a phyletic point of view, tree topology indicates the Japanese M. alternatus as the most differentiated taxon and the Euroasiatic M. saltuarius as basal to all other strictly European entities. Chromosome analyses show that the diploid autosomal complement ranges from 18 in M. saltuarius to 20 in M. galloprovincialis, and 22 in M. sartor, but a XX–Xy_p sex determining system is shared by all analysed taxa. The M. saltuarius karyotype appears as the most primitive from which the others may be derived through Robertsonian fissions. Karyological data therefore agree with molecular analyses in indicating a basal position of Euroasiatic M. saltuarius with respect to the group of European Monochamus taxa; among these, M. galloprovincialis and M. sartor represent two clearly diverging evolutionary units. Furthermore, karyotype analyses substantiate molecular conclusions about the identity between M. galloprovincialis galloprovincialis and M. galloprovincialis pistor.     

Plasmid profiles and restriction fragment length polymorphism of Rhizobium leguminosarum bv. viciae in field populations

Abstract 56 isolates of Rhizobium leguminosarum biovar viciae from one field were characterized by analysis of plasmid profile, total DNA restriction pattern and restriction fragment length polymorphism (RFLP) of 2 chromosomal regions and of symbiotic (Sym) plasmid. Different levels of similarity exist in patterns generated by the different techniques. At the level of partial similarity these techniques give comparable results for more than 80% of the isolates, with the exception of RFLP profiling with the Sym probe. Analysis at this level allows the grouping of the isolates that have most of their non-Sym genome similarly organized. At the level of total similarity, the techniques are no more equivalent and provide complementary information on possible evolution of the different elements of the genome identified by each specific technique. The non-Sym plasmids defining classes were strongly associated with specific chromosomal backgrounds. In contrast, variations in Sym plasmids were not related with variations in the remaining genome. Host range towards chromosomes was variable among the Sym plasmids, which may reflect plasmid transfer between strains.     

Relationships of Droseraceae: a cladistic analysis of rbcL sequence and morphological data

Molecular support for the monophyly of Droseraceae and its phylogenetic relationships to other dicot families was investigated using parsimony analysis of nucleotide sequences of the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL). Analysis of 100 species of plants including families of subclasses Rosidae, Hamamelidae, Dilleniidae, and Caryophyllidae (sensu Cronquist) placed monophyletic Droseraceae in the same clade as Caryophyllidae and Nepenthaceae (Dilleniidae). In a second analysis of 14 species of Droseraceae, 15 caryophyllids, one Nepenthaceae, and three Santalales, a single most-parsimonious tree was found in which Droseraceae are monophyletic, although the position of Drosophyllum as a member of Droseraceae is only weakly supported. The rbcL tree identified four major lineages within genus Drosera: 1) Dionaea; 2) the regia-clade that contains only Drosera regia; 3) the capensis-clade that contains the South African and temperate species outside of Australia; and 4) the peltata-clade that consists of principally Australian endemics. A separate analysis of 14 morphological and phytochemical characters is in general agreement with the rbcL tree except for the placement of Nepenthes, Drosophyllum, and Drosera burmanni. A combined analysis of both data sets places Drosophyllum in a clade with Triphyophyllum (Dioncophyllaceae).     

Comments on the cladistic approach to the phylogeny of the “bryophytes” by Mishler and Churchill

Brittonia - Basic errors are seen in failure to recognize problems of large phyletic gaps, failure to include fossil evidence which might help bridge phyletic gaps, inconsistency on transferability...     

Phylogenetic relationships of bolitoglossine salamanders: a demonstration of the effects of combining morphological and molecular data sets

We analyzed sequence data for 555 bp of the mitochondrial gene cytochrome bin plethodontid salamanders, taken from 18 ingroup (tribe Bolitoglossini)and 4 outgroup (tribe Plethodontini) taxa. There were 257 variable sites,of which 219 were phylogenetically informative. Sequence differences amongtaxa exceeded 20%, and there were up to 15% amino acid differences amongthe sequences. We also analyzed 37 morphological (including karyological)characters, taken from the literature. Data were analyzed separately andthen combined using parsimony and likelihood approaches. There is littleconflict between the morphological and DNA data, and that which occurs isat nodes that are weakly supported by one or both of the data sets. Treatedseparately, the morphological and DNA data provide strong support for somenodes but not for others. The combined data act synergistically so thatgood support is obtained for nearly all of the nodes in the tree. Recentdivergences are supported by silent transitions, and older divergences aresupported by a combination of morphological, karyological, DNAtransversion, and amino acid changes. Eliminating silent changes from theDNA data improves the consistency index and improves some bootstrap anddecay index values for several deeper branches in the tree. However, thecombined data set with all characters included provides a better supportedtree overall. Maximum likelihood and parsimony with all of the data givenot only the same topology but also remarkably similar branch lengths.Results of this analysis support the monopoly of the supergeneraHydromantes and Batrachoseps, and of a sister group relationship ofBatrachoseps and the supergenus Bolitoglossa (represented in this study onespecies of the genus Bolitoglossa).