Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

Vertebrates originated in the lower Cambrian. Their diversification and morphological innovations have been attributed to large-scale gene or genome duplications at the origin of the group. These duplications are predicted to have occurred in two rounds, the "2R" hypothesis, or they may have occurred in one genome duplication plus many segmental duplications, although these hypotheses are disputed. Under such models, most genes that are duplicated in all vertebrates should have originated during the same period. Previous work has shown that indeed duplications started after the speciation between vertebrates and the closest invertebrate, amphioxus, but have not set a clear ending. Consideration of chordate phylogeny immediately shows the key position of cartilaginous vertebrates (Chondrichthyes) to answer this question. Did gene duplications occur as frequently during the 45 Myr between the cartilaginous/bony vertebrate split and the fish/tetrapode split as in the previous approximately 100 Myr? Although the time interval is relatively short, it is crucial to understanding the events at the origin of vertebrates. By a systematic appraisal of gene phylogenies, we show that significantly more duplications occurred before than after the cartilaginous/bony vertebrate split. Our results support rounds of gene or genome duplications during a limited period of early vertebrate evolution and allow a better characterization of these events.     

Crustacean disparity through the Phanerozoic: comparing morphological and stratigraphic data

Crustaceans have been an important component of marine diversity and biomass since the earliest Phanerozoic. With a relatively well-documented fossil record, they provide an excellent subject for a continuous study of disparity (? bodyplan variety) from the Cambrian to the Recent. A data base of 135 morphological characters forms the basis for cladistic and morphospace studies at the ordinal and sub-ordinal level. Gross cladistic topology is: (Eumalacostraca + Hoplocarida vs Maxillopoda) vs Phyllopoda (paraphyletic). Each of these groups is of approximately equal disparity, and occupies a distinct region of the morphospace plot. A few problematical fossils (e.g. Waptia and Odaraia) fall close to the base of the tree. Comparison of the cladogram with stratigraphic range data indicates the location of probable ghost lineages, and randomization procedures provide a statistical test of the goodness of fit of a given set of stratigraphic ranges to a given tree topology. Disparity indices are calculated at series and stage intervals. Observed range data indicate that Cambrian disparity was approximately one third its present level. The Earliest Ordovician saw a marked decrease, with an increase and subsequent plateau through rest of the period. Increases through the Silurian and Devonian corresponded to the radiation of branchiopods, cephalocarids, and latterly the Eumalacostraca and Hoplocarida. By the end of the Carboniferous, observed disparity had reached over four fifths of Recent levels, and the remaining history of the group saw a gradual but slightly irregular increase up until the end of the Tertiary. Indices of disparity incorporating ghost lineages exhibit less marked peaks and troughs, with fewer perturbations overall. Cladistically-implied disparity in the Lower Cambrian is estimated at three quarters of that in the Recent. Rarefaction is used to compare actual levels of disparity at each time interval with the mean for a similar number of taxa selected randomly from the list of all realized bodyplans. Most intervals preserved a range of forms more disparate than the mean of random samples drawn from the pool of all the taxa considered. From the Triassic to the Recent this difference was intermittently significant. Once occupied, extremes of morphospace tend not to fall vacant again.     

A revision of Holm's Early and early Mid Cambrian hyoliths Of Sweden

ABSTRACT. Re-examination of type specimens of Early Cambrian and early Mid Cambrian hyoliths from Sweden confirms placement of Hyolithes teretiusculus Linnarsson in Hexitheca Syssoiev, and reassignment to the order Hyolithida rather than Orthothecida. Inclusion of Hyolithes affinis Holm within Decoritheca Syssoiev is re-confirmed, and Hyolithes socialis Linnarsson is now referred to Nevadotheca Malinky and Slapylites Marek. An operculum included under Hyolithes oelandicus Holm is transferred provisionally to Maxilites Marek, and conchs of that species are placed under Tulenicornus Val'kov with question. No other hyolith species of Holm can be definitely assigned to genus. The rarity of well preserved opercula is a major impediment to recognizing hyolith taxa confidently, and we follow Holm in attributing the comparative rarity of opercula to the fact that in some hyolith taxa the operculum may have been composed of a different, and perhaps less stable, material than the rest of the conch.     

An early Ordovician patelliform gastropod, Palaelophacmaea, reinterpreted as a coelenterate

Yochelson, Ellis L. & Stanley, George D., Jr. 1981 12 15: An early Ordovician patelliform gastropod, Palaelophacmaea , reinterpreted as a coelenterate. Lethaia , Vol. 15, pp. 323–330. Oslo. ISSN W24–1164.
The fossil Palaelophacmaea criola Donaldson, from the early Ordovician Stonehenge Formation of central Pennsylvania, was described as a patelliform gastropod. A reinterpretation of the type lot and study of a few additional specimens provide the basis for an alternative placement. Palaelophacmaea is here assigned to the Hydrozoa, as a possible chondrophore. It has an exceptionally thin shell or test and concentric but irregular corrugations. Cambrian univalve genera having a more or less circular outline that are currently assigned to the Gastropoda or Monoplacophora should be reexamined to see whether they have the features of fossil chondrophore coelenterates rather than those of molluscs. The late Cambrian Palaeoacmaea Hall & Whitfield is removed from the monoplacophoran Mollusca and left unassigned as to phylum. We judge that at least some early Cambrian species of Scenella are probably coelenterate remains. * Early Ordovician , Palaelophacmaea, Gastropoda, Monoplacophora, Hydrozoa .     

Grouping in auditory temporal perception and vocal production is mutually adapted: the case of wriggling calls of mice

Auditory Gestalt perception by grouping of species-specific vocalizations to a perceptual stream with a defined meaning is typical for human speech perception but has not been studied in non-human mammals so far. Here we use synthesized models of vocalizations (series of wriggling calls) of mouse pups (Mus domesticus) and show that their mothers perceive the call series as a meaningful Gestalt for the release of instinctive maternal behavior, if the inter-call intervals have durations of 100–400 ms. Shorter or longer inter-call intervals significantly reduce the maternal responsiveness. We also show that series of natural wriggling calls have inter-call intervals mainly in the range of 100–400 ms. Thus, series of natural wriggling calls of pups match the time-domain auditory filters of their mothers in order to be optimally perceived and recognized. A similar time window exists for the production of human speech and the perception of series of sounds by humans. Neural mechanisms for setting the boundaries of the time window are discussed.     

Hybridization in the evolution of animal form and life-cycle

Examples of animal development that pose problems for Darwinian evolution by 'descent with modification' but are consistent with 'larval transfer' are discussed. Larval transfer claims that genes that prescribe larval forms originated in adults in other taxa, and have been transferred by hybridization. I now suggest that not only larvae but also components of animals have been transferred by hybridization. The ontogeny of some Cambrian metazoans without true larvae is discussed. The probable sequence of acquisition of larvae by hemichordates and echinoderms is presented. I contend (1) that there were no true larvae until after the establishment of classes in the respective phyla, (2) that early animals hybridized to produce chimeras of parts of dissimilar species, (3) that the Cambrian explosion resulted from many such hybridizations, and (4) that modern animal phyla and classes were produced by such early hybridizations, rather than by the gradual accumulation of specific differences.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 585–602.     

澄江生物群中的卵形川滇虫

近年来在云南昆明附近的海口镇和大板桥地区发现大量的节肢动物卵形川滇虫化石,这些化石隶属于澄江生物群,其所处的地层是下寒武统玉案山组。卵形川滇虫化石的不断发掘使得对该属种化石的研究和认识能在很大程度上取得新的进展。文章基于相当数量化石的信息统计,首先对化石保存的多种方式进行总结并分析其埋藏时的环境条件,其次分析卵形川滇虫一些有趣的生活习性并初步划分卵形川滇虫生长中历经3次蜕皮的发育阶段;对雌雄性个体特征（包括外部形态和内部器官的解剖）进行对照性描述。文中揭示卵形川滇虫的生活环境及运动方式,并将卵形川滇虫与中寒武世瓦普塔虾进行较为详尽的比较,列举两者不可归为一属的可靠证据。     

The peer reviewing process — A case study

A Peer Review requires a careful checking of the whole procedure of LCA/LCI, including the quality of data, the system boundaries, the assumptions made and whether or not the method used is compatible with the goal of the study. Most importantly, is has to be ex-aminded whether the results and conclusions are in accord with the quality of the data and with the assumptions made. The Peer Review of the European Life Cycle Inventory for Surfactant Production was conducted between April 1994 and March 1995 and was performed according to the SF.TAC Guidelines (A“Code of Practice” 1993). The main recommendation by the Panel was the full publication of the study. The second main recommendation is to make an update of the database in regular intervals. The third recommendation concerns the format of the international energy database, which should be harmonized. The authors recommend that the procedure proposed by SF.TAC should be considered within the framework of the ISO LCA-standardization process.     

Innocent,transit, and archipelagic sea lanes passage

Abstract

Norway is involved in two maritime boundary disputes with the Soviet Union. In relation to Svalbard, the Soviet Union argues that the archipelago has a continental shelf and an exclusive economic zone (EEZ) of its own to which all parties to the Svalbard Treaty have equal access. This is disputed by Norway, which maintains that such a view of the matter implies an expansive interpretation of the Svalbard Treaty for which there is no support in international legal practice. In the Barents Sea there is a continuing dispute between Norway and the Soviet Union over the proper location of the continental shelf and EEZ boundaries. This article sets out some of the reasons behind the different arguments on which the two base their respective cases, and the reasons why Norway in the absence of a delineated boundary has refused to accept Soviet proposals for economic cooperation in the disputed ocean area. Major emphasis is placed on the confluence of several circumstances inter alia, geopolitical and historical factors, a strongly asymmetrical power relationship, and legal ambiguity.     

The Ediacaran Period: a new addition to the geologic time scale

The International Union of Geological Sciences has approved a new addition to the geologic time scale: the Ediacaran Period. The Ediacaran is the first Proterozoic period to be recognized on the basis of chronostratigraphic criteria and the first internationally ratified, chronostratigraphically defined period of any age to be introduced in more than a century. In accordance with procedures established by the International Commission on Stratigraphy, the base of the Ediacaran Period is defined by a Global Stratotype Section and Point (GSSP) placed at the base of the Nuccaleena Formation cap carbonate directly above glacial diamictites and associated facies at Enorama Creek in the Flinders Ranges of South Australia. Its top is defined by the initial GSSP of the Cambrian Period. The new Ediacaran Period encompasses a distinctive interval of Earth history that is bounded both above and below by equally distinctive intervals. Both chemostratigraphic and biostratigraphic data indicate that the subdivision of the period into two or more series is feasible, and this should be a primary objective of continuing work by the Ediacaran Subcommission of the ICS.     

DEADLY PLURALISM? WHY DEATH‐CONCEPT,DEATH‐DEFINITION,DEATH‐CRITERION AND DEATH‐TEST PLURALISM SHOULD BE ALLOWED,EVEN THOUGH IT CREATES SOME PROBLEMS

Death concept, death definition, death criterion and death test pluralism has been described by some as a problematic approach. Others have claimed it to be a promising way forward within modern pluralistic societies. This article describes the New Jersey Death Definition Law and the Japanese Transplantation Law. Both of these laws allow for more than one death concept within a single legal system. The article discusses a philosophical basis for these laws starting from John Rawls' understanding of comprehensive doctrines, reasonable pluralism and overlapping consensus. It argues for the view that a certain legal pluralism in areas of disputed metaphysical, philosophical and/or religious questions should be allowed, as long as the disputed questions concern the individual and the resulting policy, law or acts based on the policy/law, do not harm the lives of other individuals to an intolerable extent. However, while this death concept, death definition, death criterion and death test pluralism solves some problems, it creates others.     

MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record

Both the monophyly and inter-relationships of the major annelid groups have remained uncertain, despite intensive research on both morphology and molecular sequences. Morphological cladistic analyses indicate that Annelida is monophyletic and consists of two monophyletic groups, the clitellates and polychaetes, whereas molecular phylogenetic analyses suggest that polychaetes are paraphyletic and that sipunculans are crown-group annelids. Both the monophyly of polychaetes and the placement of sipunculans within annelids are in conflict with the annelid fossil record—the former because Cambrian stem taxa are similar to modern polychaetes in possessing biramous parapodia, suggesting that clitellates are derived from polychaetes; the latter because although fossil sipunculans are known from the Early Cambrian, crown-group annelids do not appear until the latest Cambrian. Here we apply a different data source, the presence versus absence of specific microRNAs—genes that encode approximately 22 nucleotide non-coding regulatory RNAs—to the problem of annelid phylogenetics. We show that annelids are monophyletic with respect to sipunculans, and polychaetes are paraphyletic with respect to the clitellate Lumbricus, conclusions that are consistent with the fossil record. Further, sipunculans resolve as the sister group of the annelids, rooting the annelid tree, and revealing the polarity of the morphological change within this diverse lineage of animals.     

A new red alga preserved with possible reproductive bodies from the 518-million-year-old Qingjiang biota

Macroalgae have been a key ecological component of marine ecosystems since the Proterozoic period and are common fossil forms in Cambrian Burgess Shale-type Lagerstätten. However, in most cases, it is difficult to place these early fossil algae into modern groups because little distinctive morphology is preserved. Here, we describe a new form of macroalgae, Qingjiangthallus cystocarpium gen. & sp. nov., from the Qingjiang biota of South China. The new taxon is represented by 546 specimens remarkably preserved with characteristics that allow a phylogenetic placement into crown groups of red algae. Centimeter-sized thalli resemble members of the extant Rhodymeniophycidae (a subclass of the class Florideophyceae), and hence suggest a florideophycean affinity, which indicates that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518 Ma, accordant with estimations of molecular studies. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovation of a triphasic life cycle in red algae may have occurred no later than the Early Cambrian. The branching patterns and branch width of Qingjiangthallus are consistent with the coarsely dichotomously branched morphogroup, which was previously present in the Ediacaran, Ordovician, and afterward, but absent in the Cambrian.     

Cambrian agnostid communities in Tasmania

Jago, J. B.: Cambrian agnostid communities in Tasmania.
Two or possibly three different agnostid trilobite assemblages can be distinguished in the late Middle and early Upper Cambrian sequences of northern and western Tasmania. This is significant because in recent years agnostid trilobites have been widely used in local and international correlations of Middle and Upper Cambrian rocks. The three assemblages recognized are (1) an agnostid assemblage in which polymerid trilobites are abscnt, rare or present as thanatocoenotic fossils, (2) a ptychagnostid-non-nepeid assemblage, and (3) a nepeid-clavagnostid-peronopsid assemblage in which non-agnostid trilobites are abundant but ptychag-nostids are absent. It is proposed that assemblage (1) represents an open sea fauna, with assemblages (2) and (3) occurring in progressively shallower water.     

关山生物群中始海百合化石的再研究*

关山生物群是继澄江生物群之后云南寒武纪早期地层中发现的又一个特异埋藏的化石宝库。现已报道10多个门类的化石动物,对研究寒武纪生命大爆发、后生动物起源及演化、寒武纪早期生态系统的复原等重大学术问题具有特殊的意义。始海百合属于棘皮动物门海蕾亚门,于寒武纪早期出现,志留纪灭绝。笔者将荧光显微镜等先进成像方式与传统的研究手段相结合,对新采集到的关山生物群始海百合化石标本进行深入细致的系统古生物学研究,对其精细形态学构造和生活习性获得更深入的了解。这对于认识寒武纪早期的生物多样性和棘皮动物的演化都具有重要的意义。     

寒武纪早期疑难生物类群阿纳巴管(Anabarites)亲缘性的探讨

阿纳巴管为生活于寒武纪早期、具三射对称管栖疑难生物。文中通过对采自陕西南部宁强下寒武统宽川铺组阿纳巴管壳体SEM和岩石薄片的观察,并以对称性和矿物组成作为线索对阿纳巴管的系统学位置和生物属性开展了探索。通过对称性对比研究和骨骼矿物组成的研究,将阿纳巴管解释为珊瑚虫纲古老干支类群的化石代表,为现生六射珊瑚的祖先类群。根据阿纳巴管个体发育过程对称性的演变所提供的线索进一步认为以六射及其倍数对称为特征的现代六射珊瑚可能经过三射对称中间阶段,起源于圆形辐射对称的祖先。阿纳巴管为由圆形经三射向六射转变这一中间阶段的化石代表。此外,还对阿纳巴管的成岩模式以及生活方式开展了探索性研究。     

The Ordovician Radiation: A Follow-up to the Cambrian Explosion?

There was a major diversification known as the Ordovician Radiation,in the period immediately following the Cambrian. This eventis unique in taxonomic, ecologic and biogeographic aspects. While all of the phyla but one were established during the Cambrianexplosion, taxonomic increases during the Ordovician were manifestat lower taxonomic levels although ordinal level diversity doubled.Marine family diversity tripled and within clade diversity increasesoccurred at the genus and species levels. The Ordovician radiationestablished the Paleozoic Evolutionary Fauna; those taxa whichdominated the marine realm for the next 250 million years. Communitystructure dramatically increased in complexity. New communitieswere established and there were fundamental shifts in dominanceand abundance. Over the past ten years, there has been an effort to examinethis radiation at different scales. In comparison with the Cambrianexplosion which appears to be more globally mediated, localand regional studies of Ordovician faunas reveal sharp transitionswith timing and magnitudes that vary geographically. These transitionssuggest a more episodic and complex history than that revealedthrough synoptic global studies alone. Despite its apparent uniqueness, we cannot exclude the possibilitythat the Ordovician radiation was an extension of Cambrian diversitydynamics. That is, the Ordovician radiation may have been anevent independent of the Cambrian radiation and thus requiringa different set of explanations, or it may have been the inevitablefollow-up to the Cambrian radiation. Future studies should focuson resolving this issue.     

Preservational folds simulating tergite junctions in tegopeltid and naraoiid arthropods

The exoskeleton in the Middle Cambrian Burgess Shale arthropod Tegopelte has previously been described as divided into tergites. Evidence from its sister taxon Saperion and from a Naraoia specimen from the Lower Cambrian Chengjiang fauna enables a reinterpretation of the suggested tergite boundaries in Tegopelte as preservational artefacts. They are considered here as folds that were formed during flattening of the undivided dorsal shield. As in the Naraoia specimen, the folds were initiated in the axial region between appendage pairs and then continue laterally. In Tegopelte and Saperion , segmentally arranged furrows in the axial region facilitated fold formation. Characters other than presence of thoracic tergites and pygidium must be used to assess the affinities of Tegopelte, Arthropoda, Tegopeltidae, tagmosis, segmentation, Chengjiang fauna, Burgess Shale.     

The Early Cambrian colonization of pelagic niches exemplified by Isoxys (Arthropoda)

The anatomy of the bivalved arthropod Isoxys (Early and Middle Cambrian) is reconstructed, based on new evidence from soft parts and exoskeletal design and on a critical review of previous work. Isoxys had a long segmented body flanked with a pair of short antennules, followed by a series of 14 biramous appendages provided with long paddle-like exopods concealed under a widely open bivalved carapace folded dorsally and bearing long cardinal spines. The close resemblance between Isoxys and Recent pelagic crustaceans (halocyprid ostracods, larval stages of malacostracans) indicates that Isoxys was probably an active epipelagic swimmer (evidence from soft parts, carapace design and distributional pattern). Some species (e.g. I. auritus and I. paradoxus from the Maotianshan Shale biota; Early Cambrian) may have lived in the vicinity of the bottom either permanently or temporarily, whereas others may have had ecological preferences for more open-marine settings. The spinosity of Isoxys had a possible role in predatorial deterrence rather than in buoyancy control or in retarding sinking within the water column. The presence of Isoxys in the Maotianshan Shale of S. China indicates that arthropods had already colonized midwater niches by the Early Cambrian. The midwater communities of the Maotianshan Shale comprised numerous other invertebrates, such as abundant medusiform eldonids, vetulicolids, chordates and possibly early vertebrates. This contradicts the opinion that pelagic communities remained poorly developed until late Cambrian/Ordovician times and that the occupation of the midwater niches largely post-dates the initial diversification of the benthic faunas.     

Giving the early fossil record of sponges a squeeze

Twenty candidate fossils with claim to be the oldest representative of the Phylum Porifera have been re‐analysed. Three criteria are used to assess each candidate: (i) the diagnostic criteria needed to categorize sponges in the fossil record; (ii) the presence, or absence, of such diagnostic features in the putative poriferan fossils; and (iii) the age constraints for the candidate fossils. All three criteria are critical to the correct interpretation of any fossil and its placement within an evolutionary context. Our analysis shows that no Precambrian fossil candidate yet satisfies all three of these criteria to be a reliable sponge fossil. The oldest widely accepted candidate, Mongolian silica hexacts from c. 545 million years ago (Ma), are here shown to be cruciform arsenopyrite crystals. The oldest reliable sponge remains are siliceous spicules from the basal Cambrian (Protohertzina anabarica Zone) Soltanieh Formation, Iran, which are described and analysed here in detail for the first time. Extensive archaeocyathan sponge reefs emerge and radiate as late as the middle of the Fortunian Stage of the Cambrian and demonstrate a gradual assembly of their skeletal structure through this time coincident with the evolution of other metazoan groups. Since the Porifera are basal in the Metazoa, their presence within the late Proterozoic has been widely anticipated. Molecular clock calibration for the earliest Porifera and Metazoa should now be based on the Iranian hexactinellid material dated to c. 535 Ma. The earliest convincing fossil sponge remains appeared at around the time of the Precambrian‐Cambrian boundary, associated with the great radiation events of that interval.