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.     

Diversity and extinction patterns of permian brachiopoda of South China

The stratigraphical and geographical distribution of 851 brachiopod species from 216 genera and 65 families in the Permian of South China are analysed. It is revealed that the brachiopod diversity underwent two sharp falls during the Permian. The first occurred at the end of Maokouan, accompaning the widely recognised, extensive regression across the Maokouan‐Wujiapingian boundary. Fifty‐seven species of 29 genera survived this first major extinction event. The second sharp reduction of brachiopod diversity took place in the later Changhsingian, with only 17 Permian‐type brachiopod species of 12 genera straggling into the earliest Triassic. Detailed stratigraphic analysis shows that more than 90% of the Changhsingian brachiopod species disappeared at different levels in the Changhsingian before the widely perceived end‐Permian ‘mass extinction’ occurred. It is also notable that each of the step‐wise diversity reduction events was apparently heterochronous. In view of the evidence from lithologies, faunal components and geochemical analyses, the two sharp falls of Permian brachiopod diversity in South China are considered to be closely related to multiple interactions of an environmental deterioration caused by large‐scale regressions.     

Mantle canals on brachiopod interareas and their significance in brachiopod classification

Wright, A.D. 1994 10 15: Mantle canals on brachiopod interareas and their significance in brachiopod classification.
Mantle canals have been located on the internal surface of the interareas in several clitambonitacean brachiopod genera. This indicates that, in contrast to the cardinal areas of Recent terebratulides and rhynchonellides, these surfaces were lined with mantle, with no fusion of the mantle lobes at the lateral ends of the hinge line, and the coelomic cavity confined to a median zone at the posterior of the shell. The discovery provides additional support for the view of Jaanusson (1971; Smiths. Contr. Paleobiol. 3 ) that the Beecher (1891) classification has considerable merit, and indicates that the calcareous brachiopods may be subdivided into the three subclasses Craniformea, Protremata and Telotremata. Brachiopoda, classification, Clitambonitacea, interareas, mantle canals, Protremata .     

广西中泥盆世腕足动物空间分布及古环境意义

统计广西中泥盆世不同沉积相区二十条剖面的腕足动物化石记录共计13目45科69属167种,其中Eifelian期47属73种,Givetian期32属100种.对不同级别分类单元的多样性分析表明,从Eifelian期到Givetian期,不仅腕足动物各个目的组成及多样性结构有明显改变,而且各个时期不同沉积环境下的腕足动物...     

Morphogenesis and evolution of Kutorgina Billings, 1861 (Brachiopoda, Kutorginida)

A comparative morphological analysis of all known members of the Lower-Middle Cambrian genus Kutorgina, one of the brachiopod genera with a carbonate shell that are oldest and richest in species. The evolution of the genus is discussed, and the borders between the Kutorgina species are emended. A new species, Kutorgina elanica sp. nov., is described.     

Brachiopod shell thickness links environment and evolution

While it is well established that the shapes and sizes of shells are strongly phylogenetically controlled, little is known about the phylogenetic constraints on shell thickness. Yet, shell thickness is likely to be sensitive to environmental fluctuations and has the potential to illuminate environmental perturbations through deep time. Here we systematically quantify the thickness of the anterior brachiopod shell which protects the filtration chamber and is thus considered functionally homologous across higher taxa of brachiopods. Our data come from 66 genera and 10 different orders and shows well-defined upper and lower boundaries of anterior shell thickness. For Ordovician and Silurian brachiopods we find significant order-level differences and a trend of increasing shell thickness with water depth. Modern (Cenozoic) brachiopods, by comparison, fall into the lower half of observed shell thicknesses. Among Ordovician–Silurian brachiopods, older stocks commonly have thicker shells, and thick-shelled taxa contributed more prominently to the Great Ordovician Biodiversification but suffered more severely during the Late Ordovician Mass Extinction. Our data highlight a significant reduction in maximum and minimum shell thickness following the Late Ordovician mass extinction. This points towards stronger selection pressure for energy-efficient shell secretion during times of crisis.     

Family Lycophoriidae (Brachiopoda) from the Ordovician of Baltoscandia

The family Lycophoriidae from the Middle Ordovician of Baltoscandia with one monotypic genus and five species is revised. New inner structures were revealed and diagnoses of the family, genera, and species were specified in the study of cross sections and microstructure of the shell. The third prismatic layer, complex dental plates, and socket ridges with short pointed lateral outgrowths were recorded. The family Lycophoriidae cannot be assigned with confidence to any known brachiopod order.     

Magnesium and sulphur in the calcite shells of two brachiopods, Terebratulina retusa and Novocrania anomala

This study determines the distribution of magnesium and sulphur in the shells of two species of brachiopod from the same environment to highlight environmental and biological influences on shell composition. In Terebratulina retusa there are differences in magnesium concentration between the primary layer and the outer and inner regions of the secondary layer. In contrast, Novocrania anomala has a shell composed of high magnesium calcite and there is no significant difference in magnesium concentration between the primary and the secondary shell layers. Sulphur provides an indication of the distribution of sulphated organic matrix within the shells of T. retusa and N. anomala . In T. retusa the distribution of magnesium and sulphur correlates across the shell; however, there is no evidence for a relationship between magnesium and sulphur distribution in N. anomala . The relationship between magnesium and sulphur in T. retusa indicates that a proportion of the magnesium content of the shell is associated with the sulphated fraction of the organic matrix. In these two species of brachiopod, from the same environment, magnesium and organic concentration and distribution are very different, emphasizing the importance of fully understanding the factors that control biomineral composition before the application of these biominerals to environmental studies.     

Brachiopod Shell Proteins: Their Functions and Taxonomic Significance

The calcareous shell of the Brachiopoda is interspersed withorganic material, chiefly protein and polysaccharide. The aminoacid compositions of these proteins reflect their geneticallycoded biosynthesis and are phylogenetically and taxonomicallyinformative. The taxonomic scheme based on protein data agreeswith the scheme based on morphological and anatomical criteria.These findings indicate Crania occupies an anomolous position. Brachiopoda exhibit two main types of calcification, carbonateand phosphate. The hydroxyproline found in phosphatic inarticulateshell protein suggests an analogy with bone collagen, but theglycine content is too low to allow triple-helix formation. The number and nature of polypeptide chains making up the shellproteins have been determined by amino and carboxy end-groupanalysis as well as disc electrophoresis with SDS. In the nativestate the shell proteins are molecular aggregates and are dissolvedby 8 M urea, suggesting that the inter-chain links are largelyH–bonds. Articulate shell protein probably serves as a resilient cushioningbetween calcite fibers to protect against mechanical shock.This would be permitted by the amorphous flexible characterof the polypeptide chain. The shell proteins of the Inarticulataare different,their chitin-protein laminated shell is more sheet-likeand its structure requires less cushioning. Study of fossil protein can shed further light on shell proteinancestry and hence on brachiopod phylogeny.     

Ecological disruption close to the Ordovician‐Silurian boundary

Following a long period of stability there was substantial ecological disruption in the late Ordovician, accompanied by widespread extinction. The ecological upheaval was spread over a period of time (1 My?) and varied in intensity between different groups.

The greatest change in brachiopod faunas occurred in the tropics, where there were widespread extinctions. In temperate regions the community structure, although disrupted, was not destroyed. The deep shelf associations (Benthic Assemblages 4–5) of the Rawtheyan persisted in an attenuated form into the Hirnantian when they were supplemented by genera of the ”Hirnantia fauna” and then became strongly re‐established in the Llandovery.

Trilobites, in contrast to brachiopods, suffered a worldwide extinction in the late Ashgill. Approximately 40% of trilobite genera became extinct at, or near, the Rawtheyan‐Hirnantian boundary.

Analysis of the distribution of Rawtheyan trilobite and brachiopod genera supports a correlation between geographical distribution and survival. Global range charts for brachiopod and trilobite genera, incorporating ecological and palaeogeographical data, have been compiled for this study.     

Study of fossil and recent brachiopods,using a skyscan 1172 X-ray microtomograph

Fossil and recent brachiopods were studied with the aid of a Skyscan 1172 microtomograph. The capabilities of this method at different stages of studying, X-ray scanning and producing slices and 3D models are described. The method enables the study of punctuation, microornamentation, and inner structures of the brachiopod shells and soft tissues. The contrast of shell structures of fossil brachiopods is discussed; it depends on differences in the mineral composition of the shell and surrounding matter. This method allows studying the inner structure of the holotypes of brachiopod species without damaging their shells. The data on the efficiency of the method are provided.     

THE PROBABLE AFFINITIES OF THE TRACE FOSSIL DIORYGMA ATRYPOPHILIA

Modifications in the ultrastructure of the exoskeleton of the atrypid brachiopod Desquamatia subzonata Biernat indicate that, for the greater part of its life, it accommodated the trace fossil Diorygma atrypophilia Biernat. When these modifications are compared with the ultrastructure of the exoskeleton of Hemothiris psittacea (Gmelin), which has been attacked by a boring clionid sponge, it is evident that the 'burrow' occupied by Diorygma was not excavated by physical or chemical digestive processes, but fashioned by simultaneous growth of brachiopod shell and occupant. Because of its morphology and inferred habits Diorygma is best placed within the Phoronida.     

AN EARLY CAMBRIAN ORGANOPHOSPHATIC BRACHIOPOD WITH CALCITIC GRANULES

Abstract:  The linguliform brachiopod Eoobolus from the Early Cambrian Mural Formation (Jasper National Park, Canadian Rocky Mountains) exhibits various calcitic features in its otherwise apatitic shell. It is argued here that the decomposition of the organic matter within the shell led to a microenvironment similar to those resulting in the phosphatization of soft tissues. This diagenetic regime encouraged the initial precipitation of apatite cements followed by calcite cements. By fully coating primary structures early apatite cements separate primary structures from the later precipitation of calcite cement. Round calcareous grains, about 3  µ m in size, that occur in the centre of apatite botryoids must therefore represent original components of the shell. The equivalent pits of such calcareous granules are seen in the larval shells of many Palaeozoic linguliform brachiopods. This suggests that mixed organophosphatic-calcareous shells were relatively common at that time but that they have been overlooked owing to the obliteration of original calcareous structures by traditional acid preparation methods for the extraction of phosphatic fossils. The Eoobolus shell structure is intermediate between purely organophosphatic and calcitic shells. Although one such genus is not sufficient to reconstruct the ancestral composition of the brachiopod shell, it provides a means of recognizing other transitional forms that are needed to understand fully the shift in shell mineralogy.     

Brachiopod morphology,life mode,and crushing predation in the Ordovician Arnheim Formation,Kentucky, USA

Predation on ancient shelled prey is an often-studied topic in paleoecology, but the early Paleozoic and the brachiopods that dominated the seafloor at that time are relatively underrepresented in the predation literature. We assessed predatory repair scar frequencies among the brachiopod genera from the Early Richmondian (Late Ordovician) Oregonia Member (Arnheim Formation) near Flemingsburg, Kentucky. We found higher repair frequencies on the concavo-convex Rafinesquina and Leptaena relative to the bi-convex genera. There were no trends in repair frequency through the stratigraphic section and no relationships between repair frequency and community diversity metrics. It is possible that concavo-convex brachiopods’ flat shape, thin shell profile, and free-lying (no pedicle attachment) lifestyle made them more likely or appealing targets of Ordovician crushing predators. It is also possible that concavo-convex brachiopods were better suited to survive crushing attacks than biconvex taxa. We also found differences in shell ornament that may influence the visibility of repair scars.     

贵州安顺募役剖面晚二叠世腕足动物群落及其生态特征*

本文对贵州募役剖面长兴期腕足动物群进行了系统分类鉴定和古生态分析,发现其与前人所报道的华南同时期腕足动物群存在着显著的差别,以Spiriferellina为绝对优势属,包含少量华南长兴期的常见分子,如Fusichonetes、Araxathyris和Peltichia等。募役剖面的腕足类化石主要产自碎屑岩层位,与华南同期碎屑岩相剖面的腕足动物群落相比,该动物群中的优势分子个体较大、壳体较厚且发育较粗大的壳疹,这可能与长兴期募役剖面动物群所处的特殊栖息地环境(浅水碳酸盐岩台地与深水硅质碎屑岩盆地之间的过渡地带)有关。二叠纪末期大规模的火山作用导致水体中碎屑物质含量增加,影响腕足类的滤食效率,而募役剖面清澈、水动力弱的水体环境,为滤食性的腕足动物提供了有利的环境条件。最后,通过与华南长兴期不同沉积相区腕足动物群落(六枝剖面、稻堆山剖面、中寨剖面、新民剖面、马家山剖面和仁村坪剖面群落)的对比分析,发现募役剖面腕足动物群与毗邻的六枝剖面腕足动物群在属级组成上的相似度较高,且过渡岩相栖息地环境下的腕足动物群在生物灭绝事件前也呈现出高优势度、低均匀度的群落结构特征,指示海洋底栖生物群落已经先于二叠纪末期生物集群灭绝事件出现了早期危机信号。     

Systematic position and composition of the superfamily Notanoplioidea Gill, 1969 (Brachiopoda, Articulata)

The systematic position of several genera of articulate brachiopods grouped around Notanoplia Gill is controversial. Notanoplia was established in 1950 within the order Chonetida; this genus and several externally similar genera, which were established later, were referred by different authors to the orders Orthida, Strophomenida, Chonetida, Atrypida, Spiriferida, or considered as incertae sedis. The morphological analysis of the shell of Notanoplia and the related genera Boucotia and Costanoplia supports the placement of these genera in a separate superfamily, Notanoplioidea, within the order Strophomenida. Other genera similar in the shell outline and shape to Notanoplia and conditionally considered as related to it probably belong to other strophomenid superfamilies or other orders.     

The brachiopod fold: a neglected body plan hypothesis

Attention is drawn to Nielsen's radical body plan concept, here named the 'brachiopod fold hypothesis', under which brachiopods and phoronids are recognized to be transversely folded across the ontogenetic anterior–posterior axis so that, to make useful comparisons with other phyla, these organisms must be conceptually unfolded. Under the hypothesis brachiopod brachial and pedicle shell valves are respectively 'anterior' and 'posterior' rather than 'dorsal' and 'ventral' as traditionally described. The hypothesis makes sense of the symmetry axes of the brachiopod shell, is consistent with various indications from fossil and Recent brachiopods, and gives rise to predicted patterns of axis–determining gene expression that differ from those obtaining under the traditional view of the body plan, whilst the variety of folding movements in different lineages implies that superficially dissimilar morphogenetic folds may be fundamentally homologous. Convergent folding patterns are noted in some other organisms. A previous conjecture that inarticulate linguloid brachiopods were derived from halkieriid–like ancestors is elaborated with proposals that recognize possible functional continuities of coelomic and marginal sclerite functions, and it is noted that an ancestrally facultative fold could have become incorporated by genetic assimilation into the brachiopod developmental program. An experimental approach is outlined to test the possibility that some members of the 'small shelly fauna' may have been members of the halkieriid–like brachiopod stem lineage and it is also suggested that buoyancy modification may have been an important function of mineralization amongst Lower Cambrian floaters and swimmers, since negative buoyancy would facilitate access to the benthic niche.     

WUCHIAPINGIAN (LOPINGIAN, LATE PERMIAN) BRACHIOPODS FROM THE EPISKOPI FORMATION OF HYDRA ISLAND, GREECE

Abstract:  Twenty-three species of silicified brachiopods are described from four samples in the middle and upper parts of the Episkopi Formation from Hydra Island, Greece. These brachiopods are newly recorded from the region and together with previously described brachiopods from the same localities constitute the most diverse Lopingian (Late Permian) brachiopod fauna reported in southern Europe. The brachiopod fauna is Wuchiapingian as indicated by the associated conodonts. The fauna from Hydra exhibits strong palaeobiogeographical links with the faunas from South China. In addition, palaeobiogeographical affinities with the faunas of Thailand and the northern peri-Gondwanan region are also present, which implies a peri-Gondwanan origin for Hydra. Palaeoecologically, the brachiopod assemblage from sample EP in the middle part of the Episkopi Formation is dominated by pedically-attached and cementing genera and reflects moderate energy conditions above storm wave base and an abundance of hard substrates provided by sponges in the biohermal habitat. By contrast, the brachiopod assemblage in the other three samples from the upper part of the Episkopi Formation is dominated by spinose genera with a free-resting life habit, suggesting soft substrates in a quiet water environment below storm wave base on the outer part of the shelf. New taxa are Petinospiriferina gen. nov., Hustedia episkopiensis sp. nov., Waterhouseiella hydraensis sp. nov. and Xenosaria tenuis sp. nov.     

Molecular Evolution of Mollusc Shell Proteins: Insights from Proteomic Analysis of the Edible Mussel Mytilus

Shell matrix proteins (SMPs) that are embedded within calcified layers of mollusc shells are believed to play an essential role in controlling the biomineral synthesis and in increasing its mechanical properties. Among the wide diversity of mollusc shell textures, nacro-prismatic shells represent a tremendous opportunity for the investigation of the SMP evolution. Indeed, nacro-prismatic texture appears early in Cambrian molluscs and is still present in the shell of some bivalves, gastropods, cephalopods and very likely also, of some monoplacophorans. One key question is to know whether these shells are constructed from similar matrix protein assemblages, i.e. whether they share a common origin. Most of the molecular data published so far are restricted to two genera, the bivalve Pinctada and the gastropod Haliotis. The shell protein content of these two genera are clearly different, suggesting independent origins or considerable genetic drift from a common ancestor. In order to describe putatively conserved mollusc shell proteins, here we have investigated the SMP set of a new bivalve model belonging to another genera, the edible mussel Mytilus, using an up-to-date proteomic approach based on the interrogation of more than 70,000 EST sequences, recently available from NCBI public databases. We describe nine novel SMPs, among which three are completely novel, four are homologues of Pinctada SMPs and two are very likely homologues of Haliotis SMPs. This latter result constitutes the first report of conserved SMPs between bivalves and gastropods. More generally, our data suggest that mollusc SMP set may follow a mosaic pattern within the different mollusc models (Mytilus, Pinctada, Haliotis). We discuss the function of such proteins in calcifying matrices, the molecular evolution of SMP genes and the origin of mollusc nacro-prismatic SMPs.