The phylogeny and classification of Scaphopoda (Mollusca): an assessment of current resolution and cladistic reanalysis

The first cladistic analysis of phylogeny in the class Scaphopoda (Steiner 1992a,1996) examined relationships among family and selected sub-family taxa using morphological data. A preferred/ consensus tree of relationships illustrated monophyly of the orders Dentaliida and Gadilida, partial resolution among dentaliid families, and complete resolution among gadilid taxa. However, several alternative replications of the analysis, including use of a revised data matrix, did not produce the reported tree number or level of resolution; in all cases, monophyly of the Dentaliida was not supported by strict consensus of resultant parsimonious trees. Reanalysis, using unordered characters and outgroup rooting, only clearly resolves monophyly of the Gadilida and the sister relationship of the Entalinidae with the remaining gadilid families. These analyses emphasize the need for more comparative data and thorough parsimony analysis in scaphopod cladistic phylogenetics, as relationships in this class are still some way from resolution.     

PROTECTIVE-COMMENSAL MUTUALISM BETWEEN THE QUEEN SCALLOP CHLAMYS OPERCULARIS(LINNAEUS) AND THE ENCRUSTING SPONGE SUBERITES

The relationship between the two encrusting sponges, Suberitesrubrus (Sole-cava & Thorpe, 1986) and Sub-erites luridus(Sole-cava & Thorpe, 1986) and the pectinid bivalve molluscChlamys opercularis (Linnaeus) was shown to be a protective-commensalmutualism. The sponge protected the scallop from asteroid predation(Asterias rubens, L.) probably by reducing their tube-feet adhesionand also by excluding the settlement of other taxa likely tohinder the scallop's mobility. The sponge benefited in turnby protection from predation by the nudibranch Archidoris pseudoargus(Pallas) and more generally from transport to favourable locations. Both Asterias and Archidoris were frequently observed movingdirectly towards their prey, possibly indicating chemotaxicmechanisms. Yet, the sponges did not appear to confer any chemicalprotection to the scallop from asteroid attack. Similarly theliving scallop conferred no chemical protection to the sponge. (Received 12 December 1990; accepted 24 September 1991)     

Phylogenetics of Asphodelaceae (Asparagales): An Analysis of Plastid rbcL and trnL-F DNA Sequences

Phylogenetic relationships of Asphodelaceae were investigatedby parsimony analysis of 57 monocotrbcL nucleotide sequences,including 17 genera that have at some time been assigned tothe family. All genera of Asphodelaceae except for three (Hemiphylacus,Paradisea and Simethis) form a strongly supported monophyleticgroup with Hemerocallidaceae and Xanthorrhoeaceae as their immediatesister taxa. In a second analysis, we added 34 plastid trnL-Fsequences (an intron and a spacer between two transfer RNA genes)for the Asphodelaceae clade and nearest outgroup families (Doryanthaceae,Hemerocallidaceae, Iridaceae, Ixioliriaceae, Tecophilaeaceaeand Xanthorrhoeaceae) in an attempt to improve resolution andlevels of internal support. The results from the separate analysesproduced highly similar although not identical results. No stronglysupported incongruent groups occurred, and we combined bothsequence regions in one analysis, which demonstrated improvedresults. Strong support exists for a monophyletic subfamilyAlooideae, but this leaves a paraphyletic subfamily Asphodeloideaebecause Bulbine/Jodrellia alone are strongly supported as thesister group of Alooideae. Characters that have been used toseparate Alooideae as a distinct group (either as here a subfamilyor as a separate family by other authors), such as secondarygrowth and bimodal karyotypes, are found in at least some membersof Asphodeloideae, particularly in Bulbine and Jodrellia forthe karyotypes, making Alooideae less easily recognized. Copyright2000 Annals of Botany Company Alooideae, Asphodeloideae, Asphodelaceae, Asparagales, phylogenetic analysis, rbcL, trnL-F, molecular systematics     

The mitochondrial genome of the lizard Calotes versicolor and a novel gene inversion in South Asian draconine agamids

A complete mitochondrial DNA (mtDNA) sequence was determinedfor the lizard Calotes versicolor (Reptilia; Agamidae). The16,670-bp genome with notable shorter genes for some protein-codingand tRNA genes had the same gene content as that found in othervertebrates. However, a novel gene arrangement was found inwhich the proline tRNA (trnP) gene is located in the light strandinstead of its typical heavy-strand position, providing thefirst known example of gene inversion in vertebrate mtDNAs.A segment of mtDNA encompassing the trnP gene and its flankinggenes and the control region was amplified and sequenced forvarious agamid taxa to investigate timing and mechanism of thegene inversion. The inverted trnP gene organization was sharedby all South Asian draconine agamids examined but by none ofthe other Asian and African agamids. Phylogenetic analyses includingclock-free Bayesian analyses for divergence time estimationsuggested a single occurrence of the gene inversion on a lineageleading to the draconine agamids during the Paleogene period.This gene inversion could not be explained by the tandem duplication/randomloss model for mitochondrial gene rearrangements. Our availablesequence data did not provide evidence for remolding of thetrnP gene by an anticodon switch in a duplicated tRNA gene.Based on results of sequence comparisons and other circumstantialevidence, we hypothesize that inversion of the trnP gene wasoriginally mediated by a homologous DNA recombination and thatthe de novo gene organization that does not disrupt expressionof mitochondrial genes has been maintained in draconine mtDNAsfor such a long period of time.     

Taxonomic Study of Linaria depauperata and L. supina Complexes in Eastern Spain

Morphological characteristics were studied in two groups ofclosely related taxa of sectionSupinae , Linaria depauperataand L. supina, from eastern Spain. Vegetative, floral and seedcharacteristics were of little use in distinguishing betweenthese taxa as the ranges for all the taxa studied overlapped.Flower colour could be used as a diagnostic character for somebut not all of these taxa. Seed coat characters were of hightaxonomic value, both when trying to distinguish among thesetwo groups, and the taxa included within them, and also whenestablishing relationships among the taxa studied. Some differenceswere found in the indumentum distribution and density. Threetypes of trichomes were identified, two of them eglandular andcommon to all taxa. The third type of trichome was a simplegland, that varied in the number of cells in the stalk and gland.Trichome length and wall width of stalk cells allowed severalgroups of taxa to be distinguished. Similarity relationshipsamong the samples studied are shown in a UPGMA phenogram. Accordingto these results, two new species, L. cardonica and L. sulphurea,are described. L. arabiniana is conspecific with L. depauperatasubsp. hegelmaieri. A key to identify the different taxa isprovided. Copyright 2001 Annals of Botany Company Scropulariaceae, Antirrhineae, taxonomy, morphological characters, seed-coat, trichomes, Linaria depauperata,Linaria supina     

Relationships of the Ethiopian Cereal T'ef (Eragrostis tef (Zucc.) Trotter): Evidence from Morphology and Chromosome Number

The relationships of the cereal Eragrostis tef (Gramineae: Eragrostoideae)have been investigated. Nine species are closely related toT'ef on morphological grounds. Their chromosome numbers arereported. E. pilosa and some of the E. cilianensis complex areclosest to E. tef. These taxa may be useful sources of genesfor T'ef improvement. Ethiopian cereal, T'ef, Eragrostis, Gramineae: Eragrostoideae, chromosome number, poly-ploidy, improvement     

Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say

Ecological and evolutionary theories predict that parasitismand mutualism are not fixed endpoints of the symbiotic spectrum.Rather, parasitism and mutualism may be host or environmentdependent, induced by the same genetic machinery, and shifteddue to selection. These models presume the existence of geneticor environmental variation that can spur incipient changes insymbiotic lifestyle. However, for obligate intracellular bacteriawhose genomes are highly reduced, studies specify that discretesymbiotic associations can be evolutionarily stable for hundredsof millions of years. Wolbachia is an inherited obligate, intracellularinfection of invertebrates containing taxa that act broadlyas both parasites in arthropods and mutualists in certain roundworms.Here, we analyze the ancestry of mutualism and parasitism inWolbachia and the evolutionary trajectory of this variationin symbiotic lifestyle with a comprehensive, phylogenomic analysis.Contrary to previous claims, we show unequivocally that thetransition in lifestyle cannot be reconstructed with currentmethods due to long-branch attraction (LBA) artifacts of thedistant Anaplasma and Ehrlichia outgroups. Despite the use of1) site-heterogenous phylogenomic methods that can overcomesystematic error, 2) a taxonomically rich set of taxa, and 3)statistical assessments of the genes, tree topologies, and modelsof evolution, we conclude that the LBA artifact is serious enoughto afflict past and recent claims including the root lies inthe middle of the Wolbachia mutualists and parasites. We showthat different inference methods yield different results andhigh bootstrap support did not equal phylogenetic accuracy.Recombination was rare among this taxonomically diverse dataset, indicating that elevated levels of recombination in Wolbachiaare restricted to specific coinfecting groups. In conclusion,we attribute the inability to root the tree to rate heterogeneitybetween the ingroup and outgroup. Site-heterogenous models ofevolution did improve the placement of aberrant taxa in theingroup phylogeny. Finally, in the unrooted topology, the distributionof parasitism and mutualism across the tree suggests that atleast two interphylum transfers shaped the origins of nematodemutualism and arthropod parasitism. We suggest that the ancestryof mutualism and parasitism is not resolvable without more suitableoutgroups or complete genome sequences from all Wolbachia supergroups.     

Phylogenetic Signal Dissection Identifies the Root of Starfishes

Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors - Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution – have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.     

Hylid frog phylogeny and sampling strategies for speciose clades

How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed.     

CLADISTIC ANALYSIS OF THE OCTOPODS BASED ON ANATOMICAL CHARACTERS

Parsimony analysis of 29 finned and finless octopod taxa considered66 anatomical and morphological characters to discover synapomorphiesthat unite monophyletic groups. The resultant cladogram (177equally parsimonious trees at 191 steps, CI 0.429) resolvedall relationships except those among the 16 exemplars of theOctopodidae included and those among Tremoctopus, Ocythoe andArgonauta. Bootstrap values of over 90% support the monophylyof the finned and finless octopods, relationships among thefinned octopods, the bolitaenids and the monophyly of Haliphron,Tremoctopus, Ocythoe and Argonauta; bootstrap values for othernodes range from 57 to 79%. Among finned octopods, specimensrepresenting Grimpoteuthis are basal, as Voss (1988a) suggested.Specimens of Opisthoteuthis represent a distinct lineage, andare sister taxon, in this analysis, of Cirroteuthis (althoughspecimens of Stauroteuthis could not be included). New definitionsof the genera Opisthoteuthis and Grimpoteuthis are providedto reflect their separate evolutionary histories rather thantheir overt morphological similarity. Among finless octopods,bolitaenids are basal. The monophyletic Octopodidae is the sistertaxon to the clade containing the sister taxa Vitreledonellaand Amphitretus, and Haliphron, Tremoctopus, Ocythoe and Argonauta.The Ctenoglossa and Heteroglossa, families grouped by sharedradular dentition, are diphyletic and paraphyletic, respectively.The cladistic relationships demonstrate that both the Vitrele-donellidaeand Idioctopodidae are junior synonyms of the Amphitretidae;despite conspicuous morphological differences separating thesetaxa, they share a recent evolutionary history.     

Stigma-surface Esterase Activity and Stigma Receptivity in Some Taxa Characterized by Wet Stigmas

Stigma-surface esterase activity and stigma receptivity througha sequence of developmental stages of the pistil have been studiedin four taxa characterized by having wet stigmas — Petuniahybrida, Nicotiana tabacum, Crinum defixum and Amaryllis vittata.The style is solid in the first two and hollow in the lattertwo taxa. In all the taxa, stigma—surface esterase couldbe detected in a thin surface layer (pellicle) from a very earlystage of pistil development, irrespective of the presence orabsence of the exudate. However, the taxa showed variation instigma receptivity. In Petunia and Nicotiana, stigmas from pistilsof all the stages supported pollen germination and tube growth.In Amaryllis and Crinum, stigmas of only the mature pistils,when the exudate is present on the stigma, supported normalpollen germination and tube growth. It is inferred that in taxacharacterized by a wet stigma and solid style, the factors requiredfor pollen germination are present from an early stage of pistildevelopment and the exudate per se is not involved in pollengermination. In taxa characterized by a wet stigma and hollowstyle, however, the pellicle does not carry the factors requiredfor pollen germination and tube growth; they appear to be presentin the exudate. Petunia hybrida Vilm, Nicotiana tabacum L., Crinum defixum, Ker-Gawl, Amaryllis vittata Ait., tobacco, pollination, pollen germination, stigmatic exudate, stigma receptivity, stigma-surface esterase, esterase activity     

Comparative vegetative anatomy and systematics of the Oncidiinae (Maxillarieae, Orchidaceae)

Subtribe Oncidiinae comprises a vegetatively heterogeneous assemblage of species that has persistently been incapable of organization. Anatomy was considered to be a possible means to resolve the perplexity of relationships amongst the constituent taxa. The consistent occurrence of a foliar hypodermis, homogeneous mesophyll, conical silica bodies in stegmata, and ubiquitous fibre bundles in leaves provides a matrix for linking the taxa, as do the parenchymatous pith and O-thickened endodermal cell walls in roots. However, the strict consensus of the 40 genera studied was completely unresolved, suggesting that vegetative characters alone are insufficient to assess the relationships amongst these taxa, a conclusion also reached for the remainder of Maxillarieae.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 91–107.     

The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization

A recent total evidence analysis of the position of cetaceans(whales, dolphins and porpoises and extinct relatives) amongmammals indicated that the phylogeny of these taxa remains poorlyresolved. Molecular data show that 1) the order Artiodactyla(even-toed ungulates) is paraphyletic unless whales are includedwithin it and 2) that the traditional relationships of cladeswithin Artiodactyla are not supported. This controversy alsoaffects the position of a wholly extinct clade, Mesonychia,which has been argued to be the group of terrestrial mammalsmost closely related to whales. Here I update a previous totalevidence analysis by adding several hundred new informativemolecular characters from the literature. Even with the additionof these characters the phylogeny remains unresolved. All mostparsimonious trees, however, indicate a paraphyletic Artiodactylawith conflict existing over the exact sister taxon of Cetacea.Congruence between different equally parsimonious cladogramsand the stratigraphic record as measured using the modifiedManhattan Stratigraphic Measure shows that all of the competingtopologies, including those with a paraphyletic Artiodactyla,are significantly congruent with the stratigraphic record. Infossil taxa cladistic optimization can be used as an alternativeto "argument from design" (Lauder, 1996) to reconstruct behaviorand soft tissues that do not fossilize or osteological charactersthat have not preserved. In certain scenarios of cetacean phylogeny,optimization indicates that taxa such as the archaic whalesAmbulocetus and Pakicetus, and possibly mesonychians, are morecorrectly reconstructed without hair.     

Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran

Background and Aims: The diploid goat grass Aegilops tauschii (2n = 2x = 14) is nativeto the Middle East and is the D-genome donor to hexaploid breadwheat. The aim of this study was to measure the diversity ofdifferent subspecies and varieties of wild Ae. tauschii collectedacross the major areas where it grows in Iran and to examinepatterns of diversity related to the taxa and geography. Methods: Inter-retroelement amplified polymorphism (IRAP) markers wereused to analyse the biodiversity of DNA from 57 accessions ofAe. tauschii from northern and central Iran, and two hexaploidwheats. Key Results: Eight IRAP primer combinations amplified a total of 171 distinctDNA fragments between 180 and 3200 bp long from the accessions,of which 169 were polymorphic. On average, about eight fragmentswere amplified with each primer combination, with more bandsbeing amplified from accessions from the north-west of the countrythan from other accessions. Conclusions: The IRAP markers showed high levels of genetic diversity. Analysisof all accessions together did not allow the allocation of individualsto taxa based on morphology, but showed a tendency to put accessionsfrom the north-west apart from others regions. It is speculatedthat this could be due to different activity of retroelementsin the different regions. Within the two taxa with most accessions,there was a range of IRAP genotypes that could be correlatedclosely with geographical origin. This supports suggestionsthat the centre of origin of the species is towards the south-eastof the Caspian Sea. IRAP is an appropriate marker system toevaluate genetic diversity and evolutionary relationships withinthe taxa, but it is too variable to define the taxa themselves,where more slowly evolving morphological, DNA sequence or chromosomalmakers may be more appropriate.     

Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes

Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.     

Electrophoretic Variation in Esterases, Peroxidases and Acid Phosphatases in Some Native Greek Taxa of the Genera Hordeum and Taeniatherum

Horizontal starch gel electrophoresis has been applied to thestudy of esterase, peroxidase and acid phosphatase patternsin seven taxa, namely Hordeum diploids (2n=14) (H. marinum,H. marinum I and H. hystrix), tetraploids (2n=28) (H. bulbosumand H. murinum subsp. leporinum) and Taeniatherum (2n=14) (T.caput-medusae and T. caput-medusae I) in order to elucidatetheir phylogenetic relationships. On the basis of our experimentalresults the seven taxa may be placed in the following threegroups; (1) diploid Hordeum (H. marinum, H. marinum I, H. hystrix);(2) tetraploid Hordeum (H. bulbosum, H. murinum subsp. leporinum);(3) Taeniatherum (T. caput-medusae, T. caput-medusae I). Esterase, peroxidase and acid phosphatase patterns of the twoHordeum diploid taxa (H. marinum and H. marinum I) are verysimilar suggesting their close phylogenetic relationship; thesame is true for both the taxa of the genus Taeniatherum (T.caput-medusae and T. caput-medusae I). The taxa of the Taeniatherumgroup compared with the diploid Hordeum (H. marinum, H. marinumI, H. hystrix) and the tetraploid Hordeum (H. bulbosum, H. murinumsubsp. leporinum) show a lower degree of phylogenetic relationshipand seem to be equally distant from them. The tetraploid Hordeumgroup shows a higher phylogenetic relationship with diploidHordeum group than with the Taeniatherum group. These results confirm that the genus Taeniatherum, previouslyconsidered as part of the genus Hordeum, should be regardedas a separate genus. Gramineae (Poaceae), Hordeum L., Taeniatherum Nevski., esterase, peroxidase and acid phosphatase patterns, phylogenetic relationships     

Reorganising the order Bacillales through phylogenomics

Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae “family” clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.     

The Phylogenetic Relationships of Eucynodontia (Amniota: Synapsida)

The phylogeny of Eucynodontia is an important topic in vertebrate paleontology and is the foundation for understanding the origin of mammals. However, consensus on the phylogeny of Eucynodontia remains elusive. To clarify their interrelationships, a cladistic analysis, based on 145 characters and 31 species, and intergrating most prior works, was performed. The monophyly of Eucynodontia is confirmed, although the results slightly differ from those of previous analyses with respect to the composition of both Cynognathia and Probainognathia. This is also the first numerical cladistic analysis to recover a monophyletic Traversodontidae. Brasilodon is the plesiomorphic sister taxon of Mammalia, although it is younger than the oldest mammals and is specialized in some characters. A monophyletic Prozostrodontia, including tritheledontids, tritylodontids, and mammals, is well supported by many characters. Pruning highly incomplete taxa generally has little effect on the inferred pattern of relationships among the more complete taxa, although exceptions sometimes occur when basal fragmentary taxa are removed. Taxon sampling of the current data matrix shows that taxon sampling was poor in some previous studies, implying that their results are not reliable. Two major unresolved questions in cynodont phylogenetics are whether tritylodontids are more closely related to mammals or to traversodontids, and whether tritylodontids or tritheledontids are closer to mammals. Analyses of possible synapomorphies support a relatively close relationship between mammals and tritylodontids, to the exclusion of traversodontids, but do not clearly indicate whether or not tritheledontids are closer to mammals than are tritylodontids.     

Molecular and evolutionary relationships among enteric bacteria

Classification of bacterial species into genera has traditionally relied upon variation in phenotypic characteristics. However, these phenotypes often have a multifactorial genetic basis, making unambiguous taxonomic placement of new species difficult. By designing evolutionarily conserved oligonucleotide primers, it is possible to amplify homologous regions of genes in diverse taxa using the polymerase chain reaction and determine their nucleotide sequences. We have constructed a phylogeny of some enteric bacteria, including five species classified as members of the genus Escherichia, based on nucleotide sequence variation at the loci encoding glyceraldehyde-3-phosphate dehydrogenase and outer membrane protein 3A, and compared this genealogy with the relationships inferred by biotyping. The DNA sequences of these genes defined congruent and robust phylogenetic trees indicating that they are an accurate reflection of the evolutionary history of the bacterial species. The five species of Escherichia were found to be distantly related and, contrary to their placement in the same genus, do not form a monophyletic group. These data provide a framework which allows the relationships of additional species of enteric bacteria to be inferred. These procedures have general applicability for analysis of the classification, evolution, and epidemiology of bacterial taxa.     

Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.