New data on the phylogeny of Choristitidae (Carboniferous brachiopods)

A new species and genus of Choristitinae, Adventochoristites abavus gen. et sp. nov., is described from the Upper Serpukhovian of the Donets Basin and is considered as an ancestor of the Middle-Late Carboniferous Choristites linage. The characteristic features differing Alphachoristites from Choristites and Trautscholdia are specified. New species Alphachoristites berestovensis sp. nov. and Quizhouspirifer tshaikensis sp. nov. are established.     

Pachyphragma andGagria (Brassicaceae) Revisited: Molecular data indicate close relationship toThlaspi S.Str.

The systematic position ofPachyphragma macrophyllum (Brassicaceae) is unsettled. This species was either treated as a monotypic section ofThlaspi s.l. or was treated as a distinct genus.Gagria lobata apparently closely related toPachyphragma, was also given generic rank. To unravel the phylogenetic relationships ofPachyphragma andGagria, ITS sequence studies were conducted using as a reference representatives of the main lineages ofThlaspi s.l. The molecular data indicate thatGagria lobata andPachyphragma macrophyllum are closely related to members ofThlaspi s.str., an assemblage of species well separated from the otherThlaspi s.l. lineages.     

Biogeography of the recent brachiopods

The vertical, latitudinal, and circumcontinental zonality of the distribution of the species, genera, and families of recent brachiopods is considered. The distortions of the latitudinal and meridional symmetry of the biogeographic structure of the ocean are analyzed in view of the patterns of the global circulation of the surface and intermediate waters. Thus ancient faunas may be reconstructed based on data on the structural characteristics of the taxocene of recent brachiopods. The features of the paedomorphic evolution of brachiopods from the different families in extreme habitats (interstitial, underwater caverns, submarine rises, abyssal depths, hydrothermal areas, and margins of habitats) are discussed. The biogeographic structure of bottom dwellers is shown to simplify with depth as well as with simplification of the hydrological structure of the ocean. The important role of the bathyal oceanic zone (slopes of continents, islands, submarine mountains, ridges, and rises) in the preservation of faunal relicts is shown. The historical change from brachiopods to bivalves that occurred from the Paleozoic to the Mesozoic and Cenozoic is shown to have resulted not from competitive exclusion, but from complex and global changes in the plankton composition, which were unfavorable for articulate brachiopods, which had already developed specialized feeding habits, feeding on food that led to the production of almost no metabolic waste products; they had even partly lost their alimentary canal. The development of shelly plankton and, especially, of diatoms hampered the post-Paleozoic revival of large assemblages of articulate brachiopods in shallow-water habitats. The unfilled ecological niches were colonized by bivalves, which were widely adapted to feeding on live phyto-and zooplankton. Recent articulate brachiopods, which are adapted to feeding on the products of decay of dead plankton, form a belt of densely populated settlements of the organic biofilter outside the photic zone on the seaward edge of shelves and on the upper parts of the slopes of continents, islands, and submarine rises throughout the world.     

Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data

The phylogenetic relationships of the members of the phylum Sipuncula are investigated by means of DNA sequence data from three nuclear markers, two ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), and one protein-coding gene, histone H3. Phylogenetic analysis via direct optimization of DNA sequence data using parsimony as optimality criterion is executed for 12 combinations of parameter sets accounting for different indel costs and transversion/transition cost ratios in a sensitivity analysis framework. Alternative outgroup analyses are also performed to test whether they affected rooting of the sipunculan topology. Nodal support is measured by parsimony jackknifing and Bremer support values. Results from the different partitions are highly congruent, and the combined analysis for the parameter set that minimizes overall incongruence supports monophyly of Sipuncula, but nonmonophyly of several higher taxa recognized for the phylum. Mostly responsible for this is the split of the family Sipunculidae in three main lineages, with the genus Sipunculus being the sister group to the remaining sipunculans, the genus Phascolopsis nesting within the Golfingiiformes, and the genus Siphonosoma being associated to the Phascolosomatidea. Other interesting results are the position of Phascolion within Golfingiidae and the position of Antillesoma within Aspidosiphonidae. These results are not affected by the loci selected or by the outgroup chosen. The position of Apionsoma is discussed, although more data would be needed to better ascertain its phylogenetic affinities. Monophyly of the genera with multiple representatives (Themiste, Aspidosiphon, and Phascolosoma) is well supported, but not the monophyly of the genera Nephasoma or Golfingia. Interesting phylogeographic questions arise from analysis of multiple representatives of a few species.     

The origin of the spiriferidine brachiopods

Wright, Anthony D. 197901 15: The origin of the spiriferidine brachiopods. Lethaia . Vol. 12. pp. 29–33. Oslo. ISSN 0024–1164.
In recent years doubts have been expressed as to whether the strophic spiriferidines should continue to be grouped with the non-strophic spiriferids in the order Spiriferida or not. The solution to this problem will only be found by establishing the origin of the spiriferidines. A characteristic feature of the spiriferidines is their well developed micro-ornament; this is shared also by the orthid Platystrophiinae, and together with the striking similarity in overall morphology (well recognized in the early nineteenth century) it suggests that here, in the Platystrophia plexus, is the ancestral stock of the strophic spirebearers.
The Platystrophünae share with the non-strophic Rhynchonellida the potential to develop a spire. It is here considered that the former gave rise to the spiriferidines and the latter to the non-strophic spire-bearers. These quite separate developments justify the separation of the spire-bearers into the two orders Spiriferida and Atrypida.     

Morphogenetic study of brachiopods

In this work we discuss the results of ontogenetic and morphobiological approaches to phylogenetic reconstructions of articulate brachiopods on the basis of morphogenetic data. These data provide the basis for generalizations concerning phylogeny and system of orders. The ontogenetic approach was the subject of criticism mainly because of arbitrary establishment of the homology of brachiopods. The constraints of the morphobiological approach are associated with the phenomena of morphological evolution without adaptive explanation so far. As an example of these phenomena, homeomorphism of brachiopods can be considered. Prospects for morphogenetic studies of brachiopods can be connected with the study of characteristic elements of their shell structure, such as porosity and mantle channels.     

Ultrastructure of the loop of terebratulide brachiopods

The folded and twisted calcareous ribbon, forming both the ascending and descending lamellae of the loop of Waltonia inconspicua (Sowerby), is a two-layered structure consisting of a wedge of regularly stacked secondary layer fibres that overlie a thin layer of non-fibrous calcite (herein termed brachiotest). On one surface, that facing into the mantle cavity, secondary fibrous mosaic predominates, but smooth, finely banded brachiotest occurs as a narrow marginal lip upon which secondary layer fibres proliferate and progressively overlap. This growing edge of the ribbon is secreted by long, folded epithelial cells with digitate extensions to their apical plasmalemmas, which are distinguishable from the cuboidal epithelium-secreting fibres and their membranous sheaths. The other surface, facing the body cavity and the brachial coelom, consists entirely of roughened brachiotest exhibiting prominent banding that is aligned parallel to the growing loop edge. This surface is overlain by microfilamentar epithelium acting as a holdfast for the connective tissue frame of the lophophore. The other edge of the ribbon consists of truncated sections of both secondary-layer fibres and brachiotest which bear signs of resorption consistent with the degenerated state of the associated epithelium. Growth of the Waltonia loop is controlled by these localized processes of secretion and resorption of the fibrous and brachiotest layers and is typical of all terebratulides so far studied. The brachiotest is not homologous with the non-fibrous primary shell secreted at the valve margin. □ Brachiopoda, Articulata, Terebratulida, ultrastructure, lophophore, loop.     

Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences

Brachiopod and phoronid phylogeny is inferred from SSU rDNA sequences of 28 articulate and nine inarticulate brachiopods, three phoronids, two ectoprocts and various outgroups, using gene trees reconstructed by weighted parsimony, distance and maximum likelihood methods. Of these sequences, 33 from brachiopods, two from phoronids and one each from an ectoproct and a priapulan are newly determined. The brachiopod sequences belong to 31 different genera and thus survey about 10% of extant genus-level diversity. Sequences determined in different laboratories and those from closely related taxa agree well, but evidence is presented suggesting that one published phoronid sequence (GenBank accession UO12648) is a brachiopod-phoronid chimaera, and this sequence is excluded from the analyses. The chiton, Acanthopleura, is identified as the phenetically proximal outgroup; other selected outgroups were chosen to allow comparison with recent, non-molecular analyses of brachiopod phylogeny. The different outgroups and methods of phylogenetic reconstruction lead to similar results, with differences mainly in the resolution of weakly supported ancient and recent nodes, including the divergence of inarticulate brachiopod sub-phyla, the position of the rhynchonellids in relation to long- and short-looped articulate brachiopod clades and the relationships of some articulate brachiopod genera and species. Attention is drawn to the problem presented by nodes that are strongly supported by non-molecular evidence but receive only low bootstrap resampling support. Overall, the gene trees agree with morphology-based brachiopod taxonomy, but novel relationships are tentatively suggested for thecideidine and megathyrid brachiopods. Articulate brachiopods are found to be monophyletic in all reconstructions, but monophyly of inarticulate brachiopods and the possible inclusion of phoronids in the inarticulate brachiopod clade are less strongly established. Phoronids are clearly excluded from a sister-group relationship with articulate brachiopods, this proposed relationship being due to the rejected, chimaeric sequence (GenBank UO12648). Lineage relative rate tests show no heterogeneity of evolutionary rate among articulate brachiopod sequences, but indicate that inarticulate brachiopod plus phoronid sequences evolve somewhat more slowly. Both brachiopods and phoronids evolve slowly by comparison with other invertebrates. A number of palaeontologically dated times of earliest appearance are used to make upper and lower estimates of the global rate of brachiopod SSU rDNA evolution, and these estimates are used to infer the likely divergence times of other nodes in the gene tree. There is reasonable agreement between most inferred molecular and palaeontological ages. The estimated rates of SSU rDNA sequence evolution suggest that the last common ancestor of brachiopods, chitons and other protostome invertebrates (Lophotrochozoa and Ecdysozoa) lived deep in Precambrian time. Results of this first DNA-based, taxonomically representative analysis of brachiopod phylogeny are in broad agreement with current morphology-based classification and systematics and are largely consistent with the hypothesis that brachiopod shell ontogeny and morphology are a good guide to phylogeny.     

Origin and dispersal of the earliest brachiopods

Brachiopods first appeared at the very beginning of the Phanerozoic together with the first skeletal organisms. Most brachiopod taxa that arose in the first half of the Cambrian had a short temporal range and became completely extinct by the middle of the Middle Cambrian. Rigid articulation of the valves of brachiopods was provided by various structures, which also appeared in the Early Cambrian. This fact points to the importance of this feature for the formation of the whole group and at the same time testifies to the high variability of rigid articulation at the early stages of brachiopod evolution. This is a typical manifestation of archaic diversity in this animal phylum, which appeared very early in the Phanerozoic. Another important property of the archaic diversity of the early brachiopods was the large number of centers of diversification. As for the majority of groups, climatic zonality was the main factor determining the distribution of brachiopods at the beginning of the Phanerozoic. The main ecological types of brachiopods also appeared in the Early Cambrian.     

Performance data indicate summation for pictorial depth-cues in slanted surfaces

Over recent years much has been learned about the way in which depth cues are combined (e.g. Landy et al.. 1995). The majority of this work has used subjective measures, a rating scale or a point of subjective equality, to deduce the relative contributions of different cues to perception. We have adopted a very different approach by using two interval forced-choice (21FC) performance measures and a signal processing framework. We performed summation experiments for depth cue increment thresholds between pairs of pictorial depth cues in displays depicting slanted planar surfaces made from arrays of circular 'contrast' elements. Summation was found to be ideal when size-gradient was paired with contrast-gradient for a wide range of depth-gradient magnitudes in the null stimulus. For a pairing of size-gradient and linear perspective, substantial summation (> 1.5 dB) was found only when the null stimulus had intermediate depth gradients; when flat or steeply inclined surfaces were depicted, summation was diminished or abolished. Summation was also abolished when one of the target cues was (i) not a depth cue, or (ii) added in conflict. We conclude that vision has a depth mechanism for the constructive combination of pictorial depth cues and suggest two generic models of summation to describe the results. Using similar psychophysical methods. Bradshaw and Rogers (1996) revealed a mechanism for the depth cues of motion parallax and binocular disparity. Whether this is the same or a different mechanism from the one reported here awaits elaboration.     

Molecular origins of binding affinity: seeking the Archimedean point

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Phylogeny of protostome worms derived from 18S rRNA sequences

The phylogenetic relationships of protostome worms were studied by comparing new complete 18S rRNA sequences of Vestimentifera, Pogonophora, Sipuncula, Echiura, Nemertea, and Annelida with existing 18S rRNA sequences of Mollusca, Arthropoda, Chordata, and Platyhelminthes. Phylogenetic trees were inferred via neighbor-joining and maximum parsimony analyses. These suggest that (1) Sipuncula and Echiura are not sister groups; (2) Nemertea are protostomes; (3) Vestimentifera and Pogonophora are protostomes that have a common ancestor with Echiura; and (4) Vestimentifera and Pogonophora are a monophyletic clade.      

Molecular phylogenetic analyses indicate that the Ixodes ricinus complex is a paraphyletic group

The Ixodes ricinus species complex is a group of ticks distributed in almost all geographic regions of the world. Lyme borreliosis spirochetes are primarily transmitted by tick species within this complex. It has been hypothesized that the Lyme vector ticks around the world are closely related and represent a monophyletic group. This implies that vector competence in ixodid ticks for Lyme agents might have evolved only once. To test this hypothesis, we used a molecular phylogenetic approach. Two fragments of mitochondrial 16S ribosomal deoxyribonucleic acid were sequenced from 11 species in the I. ricinus complex and from 16 other species of Ixodes. Phylogenetic analysis using Bayesian methodology indicated that the I. ricinus complex is not a monophyletic group unless 3 additional Ixodes species are included in it. The known major vectors of Lyme disease agents in different areas of the world are not sister taxa. This suggests that acquisition of the ability to transmit borreliosis agents in species of Ixodes may have multiple origins.     

Allometric studies of fossil brachiopods

In different groups of fossil brachiopods new adaptations were formed by changes in size, shape, and proportions of morphological structures in ontogenetic and phylogenetic development.     

Euryhalinity of Palaeozoic articulate brachiopods

OMonotypic and very low diversity virgianid shell beds from the Upper Ordovician to Lower Silurian dolomites of North Greenland were formed in marginal marine quiet-water hypersaline environments. In the light of this evidence the salinity tolerances of other Palaeozoic articulate brachiopods is evaluated. There are only a small number of species apparently invading hypersaline or brackish environments, but it is significant considering that previously all articulate brachiopods were thought to be fully marine. Two types of occurrence are noted, those species specifically related to marginally marine environments, disappearing with the introduction of fully marine faunas, and the majority of species which extend their normal marine range into marginal conditions. No brachiopod species appears to have invaded very hypersaline or truly brackish conditions. No single group of articulate brachiopods specifically specialised in colonising marginal marine environments, apart from possibly the virgianid pentamerids. Palaeozoic, Upper Ordovician, Lower Silurian, Brachiopoda. Pentamerida, Virgianidae, Greenland, palaeoecology. hypersaline environments, brackish environments .     

Ecophenotypic strategies of dalmanellid brachiopods

General ecophenotypic patterns, of particular interest when they apply to all, or most, taxa of the group concerned, can never be demonstrated until after monophyletic taxa have been recognized, that is, until after the initial stages of phylogeny construction have been carried out. In criticizing certain dalmanellid phylogenies, and based in large part on a study of five 'species subgroups'. Hurst & Watkins (1978; Geologica et Palaeontologica 12 ) postulate ecophenotypic patterns for Isorthis , and Hurst (1978; Palaeontology 21 ) postulates general patterns of ecophenotypic variation for dalmanellid brachiopods. These patterns may be invalid for four reasons: (1) Univariate and 'bivariate' statistical analysis of the samples used to define the five subgroups reveals no significant differences between subgroups, or vertical trends, for the very morphological characters claimed to exhibit the ecophenotypic patterns; (2) Hurst & Watkins' discriminant function analysis contains procedural errors and its results are ambiguous; (3) several of the five subgroups represent mixtures of unrelated taxa; (4) in recognizing the alleged patterns, Hurst & Watkins ignored contrary evidence from many taxa (and from many dalmanellid studies). □ Brachiopoda, Dalmanellidae, Silurian, ecology, evolution, systematics.     

Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity

A conserved domain, called GGDEF (referring to a conserved central sequence pattern), is detected in many procaryotic proteins, often in various combinations with putative sensory-regulatory components. Most sequenced bacterial genomes contain several different GGDEF proteins. The function of this domain has so far not been experimentally shown. Through genetic complementation using genes from three different bacteria encoding proteins with GGDEF domains as the only element in common, we present genetic data indicating (a) that the GGDEF domain is responsible for the diguanylate cyclase activity of these proteins, and (b) that the activity of cellulose synthase in Rhizobium leguminosarum bv. trifolii and Agrobacterium tumefaciens is regulated by cyclic di-GMP as in Acetobacter xylinum.     

Chemico-structure of the organophosphatic shells of siphonotretide brachiopods

The organophosphatic shell of siphonotretide brachiopods is stratiform with orthodoxly secreted primary and secondary layers. The dominant apatitic constituents of the secondary layer are prismatic laths and rods arranged in monolayers (occasionally in cross-bladed successions), normally recrystallized as platy laminae. Sporadically distributed, interlaminar, lenticular chambers, containing apatitic meshes of laths and aggregates of plates and spherulites, probably represent degraded, localized exudations of glycosaminoglycans (GAGs) with dispersed apatite.
The shells of Helmersenia and Gorchakovia are perforated by canals with external depressions (antechambers) that possibly contained chitinous tubercles in vivo . The immature shell of Siphonotreta and most other siphonotretids is similarly perforated and pitted; but the mature part bears recumbent, rheomorphic, hollow spines that grew forward out of pits. Internally, spines pierce the shell as independent structures to terminate as pillars in GAGs chambers. Spines and pillars were probably secreted by collectives of specialized cells (acanthoblasts) within the mantle.
The shell of the oldest siphonotretide, Schizambon , is imperforate but the ventral valve has a pedicle foramen that lies forward of the posterior margin of the juvenile valve. This relationship characterizes all siphonotretides, suggesting that the pedicle, in vivo , originated within the ventral outer epithelium and not from the posterior body wall as in lingulides.