Phylogenetic Scheme Research Articles

Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin

Baikalian cyclopoids represent one of the richest endemic faunas of freshwater cyclopoid copepods. The genus Diacyclops Kiefer, 1927 is the most numerous by species number in the lake. In this work, molecular-phylogenetic analysis of 14 species and 1 sub-species from Lake Baikal and its water catchment basin is performed. The regions of mitochondrial cytochrom-oxydase I (COI) and of nuclear small-subunit 18S rRNA were used as evolution markers. In the obtained set of nucleotide sequences of COT gene, an effect of synonymous substitution saturation is revealed. Baikalian representatives of the genus Diacyclops form at phylogenetic schemes by two markers a monophyletic griup, it suggest their origin from a common ancestral form. Preliminary estimate of the age of this group is 20-25 My.

Glucosinolate biochemical diversity and innovation in the Brassicales

Glucosinolates were analysed from herbarium specimens and living tissues from representative of all families of the Brassicales, following the phylogenetic schemes of Rodman et al. (1998) and Hall et al. (2002, 2004), including specimens of Akania, Setchellanthus, Emblingia, Stixis, Forchhammeria and members of the Capparaceae for which glucosinolate content had not previously been reported. The results are reviewed along with additional published data on glucosinolate content of members of the Brassicales. In addition to providing an overview of the evolution of glucosinolate biochemical diversity within the core Brassicales, there were three main findings. Firstly, the glucosinolate content of some ‘orphan’ taxa of the Brassicales, such as Setchellanthus and Emblingia were consistent with recent phylogentic analyses based upon DNA sequence comparisons, while further analyses of Tirania and Stixis is required. Secondly, methyl glucosinolate is found within the Capparaceae and Cleomaceae, but also, unexpectedly, within Forchhammeria, with implications for the biochemical and evolutionary origin of methyl glucosinolate and the phylogenetic relationships of Forchhammeria. Thirdly, whereas Old World Capparaceae contain methyl glucosinolate, New World Capparaceae, including New World Capparis, either contain methyl glucosinolates or glucosinolates of complex and unresolved structures, indicative of continued innovation in glucosinolate biosynthesis. These taxa may be productive sources of glucosinolate biosynthetic genes and alleles that are not found in the model plant Arabidopsis thaliana.

Revision of the Permian ammonoid family Cyclolobidae

The development of views on the phylogeny of the family Cyclolobidae Zittel, 1895 is discussed. The generic composition is emended, phylogenetic links are indicated, a new version of the phylogenetic scheme is proposed, and phylogeny of the key genera is traced at species level. The sutural ontogeny of the genus Mexicoceras is examined, its placement in the family Cyclolobidae is supported, and its position in the phylogenetic reconstruction of the family is determined.

Predominance of orthal masticatory movements in the Early Miocene Eucholaeops (Mammalia, Xenarthra, Tardigrada, Megalonychidae) and other megatherioid sloths

ABSTRACT The megatherioid sloths from the Santa Cruz Formation (Santacrucian Age; early-middle Miocene, Patagonia, southernmost South America) occupy basal positions in the most recent phylogenetic schemes. The cranial morphology of Eucholaeops, particularly of the teeth, suggests interesting functional features that shed light on the type of food it was capable of processing, and thus on the diet. A detailed morphofunctional analysis of the jaw apparatus was performed, and the results briefly compared with other contemporary megatherioid sloths. Comprehensive descriptions of the teeth of Eucholaeops allow us to generate a nomenclature for describing the inferred occlusal pattern analogous to that applied to other mammals. Based on examination and mapping of occlusal wear facets, we reconstruct two distinct jaw movements during the power stroke. One corresponds to the basic therian pattern equivalent to Phase I: the working side mandibular corpus is moved dorsally, mainly orthally but also anteriorly and slightly medially; the result is puncturing, tearing and shearing of food. The second is a distinct and unrelated movement of the working side corpus dorsally, mainly orthally, but also posteriorly and slightly medially; the dominant result is to produce shearing of food. The analysis of the tooth wear facets, combined with the shape of the temporomandibular joint, the presence of a fused mandibular symphysis, and a well-developed temporalis muscle, indicates that the orthal component was predominant during mastication. Eucholaeops, and probably nearly all other Miocene megatherioids, were most likely leaf eaters and the primary method of food reduction must have been by shearing or cutting.

Arbuscular mycorrhizal morphology in crops and associated weeds in tropical agro-ecosystems

Morphological types of arbuscular mycorrhizae (AM) in crops and associated weeds were examined in agro-ecosystems. In total, 48 plant species (8 crops and 40 weeds) belonging to 43 genera in 18 families were examined. The number of plant species with Arum-type AM was higher than those with Paris-type AM in the examined plants. AM association was absent in 6 weeds, and the average colonization rate was 62.64% in crops and 52.92% in weeds. AM morphology has been reported in 2 crops and 21 weeds for the first time. The influence of plant identity on AM morphology was also analyzed by arranging the examined plants in a current plant phylogenetic scheme. This analysis showed there was a lack of relationship between plant classification and AM morphological type. Actually, the colonization types were not distinguished at the plant family level, but were mostly distinguished at the species level.

Arbuscular mycorrhizal morphology in crops and associated weeds in tropical agro-ecosystems

Morphological types of arbuscular mycorrhizae (AM) in crops and associated weeds were examined in agro-ecosystems. In total, 48 plant species (8 crops and 40 weeds) belonging to 43 genera in 18 families were examined. The number of plant species with Arum-type AM was higher than those with Paris-type AM in the examined plants. AM association was absent in 6 weeds, and the average colonization rate was 62.64% in crops and 52.92% in weeds. AM morphology has been reported in 2 crops and 21 weeds for the first time. The influence of plant identity on AM morphology was also analyzed by arranging the examined plants in a current plant phylogenetic scheme. This analysis showed there was a lack of relationship between plant classification and AM morphological type. Actually, the colonization types were not distinguished at the plant family level, but were mostly distinguished at the species level.

MULTIMODAL PHYLOGENY FOR TAXONOMY: INTEGRATING INFORMATION FROM NUCLEOTIDE AND AMINO ACID SEQUENCES

The crucial role played by the analysis of microbial diversity in biotechnology-based innovations has increased the interest in the microbial taxonomy research area. Phylogenetic sequence analyses have contributed significantly to the advances in this field, also in the view of the large amount of sequence data collected in recent years. Phylogenetic analyses could be realized on the basis of protein-encoding nucleotide sequences or encoded amino acid molecules: these two mechanisms present different peculiarities, still starting from two alternative representations of the same information. This complementarity could be exploited to achieve a multimodal phylogenetic scheme that is able to integrate gene and protein information in order to realize a single final tree. This aspect has been poorly addressed in the literature. In this paper, we propose to integrate the two phylogenetic analyses using basic schemes derived from the multimodality fusion theory (or multiclassifier systems theory), a well-founded and rigorous branch for which its powerfulness has already been demonstrated in other pattern recognition contexts. The proposed approach could be applied to distance matrix-based phylogenetic techniques (like neighbor joining), resulting in a smart and fast method. The proposed methodology has been tested in a real case involving sequences of some species of lactic acid bacteria. With this dataset, both nucleotide sequence- and amino acid sequence-based phylogenetic analyses present some drawbacks, which are overcome with the multimodal analysis.

Are Polyphaga (Coleoptera) really a basal neopteran lineage – a reply to Kazantsev

AbstractIn a study on the mandible and mandibular articulation of larvae of the lycid genus Platerodrilus Kazantsev proposes a phylogenetic scheme with Polyphaga as a basal group of Neoptera and Lycidae as a basal group within Polyphaga. Here we point out different problems with his interpretation. The taxon sampling was not sufficient. The characters of endopterygote larvae cannot be compared to characters of adults in a phylogenetic context. The neotenic characters of female and adult male Lycidae are not sufficiently taken into account. A phylogenetic hypothesis should be based on multiple character systems and all available data must be considered. Kazantsev based his conclusions on a single isolated character complex. His hypothesis is in deep conflict with a phylogeny based on the molecular data, which clearly show that Lycidae are nested within Elateroidea. The molecular and morphological evidence also implies that females are aberrant neotenic forms and by no means ‘primitive’. Kazantsev's hypothesis is problematic because the presented data are insufficient and the character evaluation is not based on a numerical analysis.

Phylogenetic reconstruction ofAegilopssectionSitopsisand the evolution of tandem repeats in the diploids and derived wheat polyploids

The evolution of 2 tandemly repeated sequences Spelt1 and Spelt52 was studied in Triticum species representing 2 evolutionary lineages of wheat and in Aegilops sect. Sitopsis, putative donors of their B/G genomes. Using fluorescence in situ hybridization we observed considerable polymorphisms in the hybridization patterns of Spelt1 and Spelt52 repeats between and within Triticum and Aegilops species. Between 2 and 28 subtelomeric sites of Spelt1 probe were detected in Ae. speltoidies, depending on accession. From 8 to 12 Spelt1 subtelomeric sites were observed in species of Timopheevi group (GAt genome), whereas the number of signals in emmer/aestivum accessions was significantly less (from 0 to 6). Hybridization patterns of Spelt52 in Ae. speltoides, Ae. longissima, and Ae. sharonensis were species specific. Subtelomeric sites of Spelt52 repeat were detected only in T. araraticum (T. timopheevii), and their number and chromosomal location varied between accessions. Superimposing copy number data onto our phylogenetic scheme constructed from RAPD data suggests 2 major independent amplifications of Spelt52 and 1 of Spelt1 repeats in Aegilops divergence. It is likely that the Spelt1 amplification took place in the ancient Ae. speltoides before the divergence of polyploid wheats. The Spelt52 repeat was probably amplified in the lineage of Ae. speltoides prior to divergence of the allopolyploid T. timopheevii but after the divergence of T. durum. In a separate amplification event, Spelt52 copy number expanded in the common ancestor of Ae. longissima and Ae. sharonensis.

Catálogo bibliográfico dos taxa superiores da ordem Lepidoptera

A list with the names of the superior categories of the Lepidoptera order is presented occasioning the establishment of some synonymies. The first part contains the sequence of names in chronological order of publication as well as relevant subsequent citations; the second part contains the phylogenetic scheme of Lepidoptera proposed by HEPPNER (2003); the third part contains the synonymies in accordance with HEPPNER’s system; the fourth part contains the phylogenetic scheme of HEPPNER based on the synonymies established and the fifth part contains an index with the names of the authors and date of publication. The following names are revalidated and the respective synonyms are established: Lepidopteroidea Heymons, 1915, syn. syn.: Amphiesmenoptera Kiriakoff, 1948; Micropterygina Herrich-Schaffer, 1856, syn. syn.: Zeugloptera Chapman, 1916; Paleolepidoptera Packard, 1895, syn. syn.: Dacnonypha Hinton, 1946; Archifrenata Kuppers & Speidel, V-1980, syn. syn.: Neopseustina Davis & Nielsen, XI-1980; Hepialites Latreille, 1809, syn. syn.: Exoporia Common, 1975; Anisoneuria Karsch, 1898, syn. syn.: Heteroneura Tillyard, 1918; Nepticulae Chapman, 1898, syn. syn.: Nepticulina Meyrick, 1928; Adeliformes Lameere, 1936, syn. syn.: Incurvariina Borner, 1939; Tineae Scopoli, 1763, syn. syn.: Tineina Stainton, 1857; Zygaenides Leach, 1815, syn. syn.: Sesiina Heppner, 1995; Bombyces Scopoli, 1763, syn. syn.: Bombycina Stainton, 1857.

Tunicates and not cephalochordates are the closest living relatives of vertebrates

Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.

Genus-specific host range of Phomopsis amaranthicola (Sphaeropsidales), a bioherbicide agent for Amaranthus spp.

Phomopsis amaranthicola, a newly described species discovered in Florida, is under development as a biological control agent for weeds belonging to the genus Amaranthus. Host-range testing was performed on the fungus, using the centrifugal phylogenetic scheme, with Amaranthus hybridus as the focal plant. Forty-five accessions of 21 species in the genus Amaranthus were tested for susceptibility to infection by this fungus. Fifty-six plant species outside the genus Amaranthus were also tested. The latter included crops in which the fungus might be used as a bioherbicide, members of genera that are closely related to Amaranthus, and selections of species that have been reported as hosts of other species of the genera Phomopsis or Diaporthe. Phomopsis amaranthicola did not infect any of the plants from outside the genus Amaranthus but was highly pathogenic to several species in the genus Amaranthus. All Amaranthus species tested were infected to varying degrees by P. amaranthicola; the resulting mortality levels were also variable. Thus, P. amaranthicola appears to be host-specific to the members of the genus Amaranthus. The generic level of specificity of this pathogen renders it not only a safe bioherbicide agent but also one that could be used against several weedy Amaranthus species.

Early hominid femora: The inside story

Paleontology allows exploration of evolutionary novelty in the deep past. But paleontological taxa are at risk of being inaccurately characterized by modern humans who are over-reliant on models taken from the comparatively rich but relatively evolved neontological world. The recent discovery of the earliest hominid femora from Kenya provides an opportunity to explore earliest hominid locomotion beyond the usual constraints of phylogenetic and functional models based rigidly on contemporary species. The full measure of this opportunity remains unrealized because the internal structure of the crucial fossil femora recovered has been inadequately explored and documented. One result is that phylogenetic schemes purporting to exclude all hominids except Orrorin from human ancestry are unsupported. Another result may be that earliest hominid locomotion has been inaccurately portrayed. To cite this article: T.D. White, C. R. Palevol 5 (2006) .

The histology and affinities of sinacanthid fishes: primitive gnathostomes from the Silurian of China

Craniofacial Development, Dental Institute, Guy’s Tower, London, SE1 9RT, UKReceived October 2003; accepted for publication March 2005On the basis of well preserved specimens from the Lower Silurian of the Tarim Basin, Xinjiang Uygur AutonomousRegion and Shiqian County, Guizhou Province, People’s Republic of China we describe in detail the histologicalstructure of sinacanthid spines, the only known remains of a group of fishes common in Silurian strata from China.The sinacanthids have previously been assigned either to the acanthodians or to the chondrichthyans. The spinestructure is composed of an outer layer of atubular dentine and an inner layer of globular calcified cartilage, and thenature and distribution of these tissues indicates that the spines were formed as a result of interaction between theendoskeleton and dermoskeleton. The tissue distribution and style of growth described herein places the sina-canthids crownwards of the placoderms, and possibly within the total group Chondrichthyes. However, before theycan be firmly placed within a phylogenetic scheme, further evidence is required both on the general anatomy ofsinacanthids and on the nature of chondrichthyan apomorphies. © 2005 The Linnean Society of London, ZoologicalJournal of the Linnean Society, 2005, 144, 379–386.

A starfish with three-dimensionally preserved soft parts from the Silurian of England

Palaeozoic asteroids represent a stem-group to the monophyletic post-Palaeozoic Neoasteroidea, but many aspects of their anatomy are poorly known. Using serial grinding and computer reconstruction, we describe fully articulated Silurian (ca 425 Myr) specimens from the Herefordshire Lagerstätte, preserved in three dimensions complete with soft tissues. The material belongs to a species of Bdellacoma, a genus previously assigned to the ophiuroids, but has characters that suggest an asteroid affinity. These include a pyloric system in the gut, and the presence of large bivalved pedicellariae, the latter originally described under the name Bursulella from isolated valves. Ampullae are external and occur within podial basins; the radial canal is also external. Podia are elongate and lack terminal suckers. The peristome is large relative to the mouth. Aspects of the morphology are comparable to that of the extant Paxillosida, supporting phylogenetic schemes that place this order at the base of the asteroid crown group.

EVALUATION OF 7SL RNA GENE SEQUENCES FOR THE IDENTIFICATION OF LEISHMANIA SPP.

We evaluated the use of 7SL RNA gene sequences for the identification of Leishmania spp. A fragment (approximately 137 basepairs) of the 7SL RNA gene from 13 reference strains and 18 clinical isolates of 11 different Leishmania species was amplified and sequenced using conserved primers. Reference strains from each Leishmania spp. complex showed unique sequences. The nucleotide sequences were compared pairwise and a range of 81.0-99.3% intercomplex similarity was observed. Clinical isolates of the same species had sequences identical to the corresponding reference strains; thus, the intraspecies similarity was 100%. A phylogenetic tree derived from the 7SL RNA gene partial sequences was constructed and is in agreement with accepted phylogenetic schemes.

Gelechioidea (Insecta: Lepidoptera) systematics: A reexamination using combined morphology and mitochondrial DNA data

Phylogenies of Gelechioidea (Insecta: Lepidoptera) historically have been in disagreement and definitions vary at the family and subfamily levels. Addition of new taxa or new characters drastically changes relationships indicating that current phylogenetic schemes require more investigation. This study is the first phylogenetic analysis of Gelechioidea to include molecular data. Here we present a combined analysis using Maximum Parsimony to investigate sister-group relationships within Gelechioidea. The addition of Cytochrome oxidase I and II to revised published morphological matrices gives 453 parsimony informative characters for the 42 taxa for which we have sequence data. The combined analysis resulted in two trees with mostly novel sister-group relationships. These results challenge current concepts of Gelechioidea, suggesting that traditional morphological characters that have united taxa may not be homologous structures and are in need of further investigation. A combination of morphological data with new molecular data will be the most robust method of study for Gelechioidea phylogenetics.

Wood and bark anatomy of Muntingiaceae: A phylogenetic comparison within Malvales s. l.

Quantitative and qualitative data on wood and bark anatomy are given for Muntingia calabura L. and Dicraspidia donnell-smithii Standley. These data are compared with phylogenetic schemes, based on DNA analysis, in which Muntingiaceae belong to the “dipterocarp clade” within Malvales. The data are consistent with this hypothesis, although Muntingiaceae lack pit vestures in vessels, which are seen in the other malvalean families (Cistaceae, Dipterocarpaceae, Neuradaceae, Sarcolaenaceae, Thymeleaceae), and this may represent a loss of pit vestures. All families of the dipterocarp clade agree with both genera of Muntingiaceae in having tracheids as the imperforate tracheary element type (at least ancestrally), although fiber-tracheids also occur in some Dipterocarpaceae and Thymeleaceae. The large size of some malvalean families (with attendant greater diversity in character states) and a paucity of wood studies in those families make for difficulty in comparison of features such as axial parenchyma and ray types with those of Muntingiaceae; character states of these features are consistent with placement of Muntingiaceae in the dipterocarp clade of Malvales. Banded phloem fibers in bark of Muntingiaceae are much like those of other Malvales. Wood of Muntingiaceae is highly mesomorphic according to quantitative vessel features.

Phylogeny of the Nymphalidae (Lepidoptera)

A generic-level phylogeny for the butterfly family Nymphalidae was produced by cladistic analysis of 234 characters from all life stages. The 95 species in the matrix (selected from the 213 studied) represent all important recognized lineages within this family. The analysis showed the taxa grouping into six main lineages. The basal branch is the Libytheinae, with the Danainae and Ithomiinae on the next branch. The remaining lineages are grouped into two main branches: the Heliconiinae-Nymphalinae, primarily flower-visitors (but including the fruit-attracted Coeini); and the Limenitidinae (sensu strictu), Biblidinae, and the satyroid lineage (Apaturinae, Charaxinae, Biinae, Calinaginae, Morphinae, Brassolinae, and Satyrinae), primarily fruit-attracted. Data partitions showed that the two data sets (immatures and adults) are very different, and a partitioned Bremer support analysis showed that the adult characters are the main source of conflict in the nodes of the combined analysis tree. This phylogeny includes the widest taxon coverage of any morphological study on Nymphalid butterflies to date, and supports the monophyly and relationships of most presently recognized subgroups, providing strong evidence for the presently accepted phylogenetic scheme.

The evolution of arthropod limbs

Limb morphology across the arthropods is reviewed using external morphological and internal anatomical data from both recent and fossil arthropods. Evolutionary trends in limb structure are identified primarily by reference to the more rigorous of the many existing phylogenetic schemes, but no major new phylogenetic inferences are presented. Tagmosis patterns are not considered, although the origins and patterns of heteronomy within the postantennulary limb series are analysed. The phenomenon of annulation is examined and two basic types of annuli are recognised: terminal and intercalary. The annulation of the apical segment of a limb results in the formation of terminal flagella, and is typical of primarily sensory appendages such as insect and malacostracan antennules and maxillary palps of some hexapods. Intercalary annulation, arising by subdivision of existing subterminal segments, is common, particularly in the tarsal region of arthropodan walking limbs. Differentiating between segments and annuli is discussed and is recognised as a limiting factor in the interpretation of fossils, which usually lack information on intrinsic musculature, and in the construction of groundplans. Rare examples of secondary segmentation, where the criteria for distinguishing between segments and annuli fail, are also highlighted. The basic crown-group arthropodan limb is identified as tripartite, comprising protopodite, telopodite and exopodite, and the basic segmentation patterns of each of these parts are hypothesised. Possible criteria are discussed that can be used for establishing the boundary between protopodite and telopodite in limbs that are uniramous through loss of the exopodite. The subdivision of the protopodite, which is typical of the postantennulary limbs of mandibulates, is examined. The difficulties resulting from the partial or complete failure of expression of articulations within the mandibulate protopodite and subsequent incorporation of partial protopodal segments into the body wall, are also discussed. The development and homology between the various exites, including gills, on the postantennulary limbs of arthropods are considered in some detail, and the question of the possible homology between crustacean gills and insect wings is critically addressed. The hypothesis that there are only two basic limb types in arthropods, antennules and postantennulary limbs, is proposed and its apparent contradiction by the transformation of antennules into walking limbs by homeotic mutation is discussed with respect to the appropriate level of serial homology between these limbs.