Long-term evolution of an ecosystem with spontaneous periodicity of mass extinctions

Twenty years ago, after analysing palaeontological data, Raup and Sepkoski suggested that mass extinctions on Earth appear cyclically in time with a period of approximately 26 million years (My). To explain the 26 My period, a number of proposals were made involving, e.g., astronomical effects, increased volcanic acitivity, or the Earth's magnetic field reversal, none of which, however, has been confirmed. Here we study a spatially extended discrete model of an ecosystem and show that the periodicity of mass extinctions might be a natural feature of the ecosystem's dynamics and not the result of a periodic external perturbation. In our model, periodic changes of the diversity of an ecosystem and some of its other characteristics are induced by the coevolution of species. In agreement with some palaeontological data, our results show that the longevity of a species depends on the evolutionary stage at which the species is created. Possible further tests of our model are also discussed.     

Long-term evolution of an ecosystem with spontaneous periodicity of mass extinctions

Twenty years ago, after analysing palaeontological data, Raup and Sepkoski suggested that mass extinctions on Earth appear cyclically in time with a period of approximately 26 million years (My). To explain the 26 My period, a number of proposals were made involving, e.g., astronomical effects, increased volcanic activity, or the Earth's magnetic field reversal, none of which, however, has been confirmed. Here we study a spatially extended discrete model of an ecosystem and show that the periodicity of mass extinctions might be a natural feature of the ecosystem's dynamics and not the result of a periodic external perturbation. In our model, periodic changes of the diversity of an ecosystem and some of its other characteristics are induced by the coevolution of species. In agreement with some palaeontological data, our results show that the longevity of a species depends on the evolutionary stage at which the species is created. Possible further tests of our model are also discussed.     

Role of Human Sec63 in Modulating the Steady-State Levels of Multi-Spanning Membrane Proteins

The Sec61 translocon of the endoplasmic reticulum (ER) membrane forms an aqueous pore, allowing polypeptides to be transferred across or integrated into membranes. Protein translocation into the ER can occur co- and posttranslationally. In yeast, posttranslational translocation involves the heptameric translocase complex including its Sec62p and Sec63p subunits. The mammalian ER membrane contains orthologs of yeast Sec62p and Sec63p, but their function is poorly understood. Here, we analyzed the effects of excess and deficit Sec63 on various ER cargoes using human cell culture systems. The overexpression of Sec63 reduces the steady-state levels of viral and cellular multi-spanning membrane proteins in a cotranslational mode, while soluble and single-spanning ER reporters are not affected. Consistent with this, the knock-down of Sec63 increases the steady-state pools of polytopic ER proteins, suggesting a substrate-specific and regulatory function of Sec63 in ER import. Overexpressed Sec63 exerts its down-regulating activity on polytopic protein levels independent of its Sec62-interacting motif, indicating that it may not act in conjunction with Sec62 in human cells. The specific action of Sec63 is further sustained by our observations that the up-regulation of either Sec62 or two other ER proteins with lumenal J domains, like ERdj1 and ERdj4, does not compromise the steady-state level of a multi-spanning membrane reporter. A J domain-specific mutation of Sec63, proposed to weaken its interaction with the ER resident BiP chaperone, reduces the down-regulating capacity of excess Sec63, suggesting an involvement of BiP in this process. Together, these results suggest that Sec63 may perform a substrate-selective quantity control function during cotranslational ER import.     

Considering the case for biodiversity cycles: re-examining the evidence for periodicity in the fossil record

We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by, as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.     

Periodicity of the outbreaks of the carrot psyllid (<Emphasis Type="Italic">Trioza apicalis</Emphasis>) cannot be explained by sunspot activity

The periodicity of the fluctuations in the attacks of the carrot psyllid Trioza apicalis in long-term monitoring was studied by analysis of data of previous authors. The occurence of only one generation in the year shows that peaks of attack cannot arise suddenly in one year, but are prolonged over several years, as are the troughs of attack. This is the cause of the long-term fluctuation, which seems to be periodic. The statement of Ozols, that the period of the fluctuations of carrot psyllid was connected with climatic conditions via sunspot activity, was not evident statistically.     

An Endogenous Rhythm of Spore Discharge in Sordaria fimicola

The sporulation process in Sordaria fimicola has been studiedunder controlled conditions, with particular reference to discharge.Discharge occurred with a circadian periodicity for the greaterpart of the sporulation life of the culture, with peaks at about18.00 hours in either light or darkness. The consistency ofthis phenomenon was confirmed by an analysis of previous work.Fluctuations in light intensity, temperature, relative humidity,carbon dioxide concentration, and vibration were eliminatedas far as possible, as causes of this periodicity. Minor fluctuationsin discharge rate with a period of less than 24 h were probablyrandom. The general nature of the periodicity was shown to be consistentwith some aspects of endogenous rhythms in other organisms.However, spore discharge in S. fimicola is very sensitive tolight, and it is readily entrained to discharge out of phasewith the natural period. The rate of development of two stages of spore formation (delimitationand maturation) were determined, and these were related to therate and periodicity of discharge. From the data it was impossibleto establish at which stage of sporulation the periodicity arose.     

Mass extinctions among tetrapods and the quality of the fossil record

The fossil record of tetrapods is very patchy because of the problems of preservation, in terrestrial sediments in particular, and because vertebrates are rarely very abundant. However, the fossil record of tetrapods has the advantages that it is easier to establish a phylogenetic taxonomy than for many invertebrate groups, and there is the potential for more detailed ecological analyses. The relative incompleteness of a fossil record may be assessed readily, and this can be used to test whether drops in overall diversity are related to mass extinctions or to gaps in our knowledge. Absolute incompleteness cannot be assessed directly, but a historical approach may offer clues to future improvements in our knowledge. One of the key problems facing palaeobiologists is paraphyly, the fact that many higher taxa in common use do not contain all of the descendants of the common ancestor. This may be overcome by cladistic analysis and the identification of monophyletic groups. The diversity of tetrapods increased from the Devonian to the Permian, remained roughly constant during the Mesozoic, and then began to increase in the late Cretaceous, and continued to do so during the Tertiary. The rapid radiation of 'modern' tetrapod groups--frogs, salamanders, lizards, snakes, turtles, crocodilians, birds and mammals--was hardly affected by the celebrated end-Cretaceous extinction event. Major mass extinctions among tetrapods took place in the early Permian, late Permian, early Triassic, late Triassic, late Cretaceous, early Oligocene and late Miocene. Many of these events appear to coincide with the major mass extinctions among marine invertebrates, but the tetrapod record is largely equivocal with regard to the theory of periodicity of mass extinctions.     

二月兰根系发育形态学研究

二月兰Ｏｒｙｃｈｏｐｈｒａｇｍｕｓ ｖｉｏｌａｃｅｕｓ Ｏ．Ｅ．Ｓｃｈｕｌｚ为二年生草本植物,直根系。初生结构为二原型,次生结构发达,主侧根结构相同。形成层活动随季节有明显变化,木质部可见年轮。冬季吸收根不死,无越冬根原基产生,吸收根连续不断更替,无明显季节性变化。根内淀粉含量随发育时期的变化而相应变化,其积螺高峰有两个,分别出现在第一年越冬前及第二年返青后开花前,不同播期对根系积累营养及第二年植     

Modularity and Complete Natural Homeoses in Cervical Vertebrae of Extant and Extinct Penguins (Aves: Sphenisciformes)

The cervical system of extant penguins (Aves: Sphenisciformes) is organised into morphological modules, each with its biomechanical function. Indeed, for these marine pelagic birds to acquire hydrodynamic morphology, the folding of the neck is essential. Despite a common general structure, the cervical vertebrae exhibit morphological differences depending on their positioning. These characteristics are identified as apparent cases of complete natural homeotic transformations—therefore, the composition of some modules varies. Two types of complete cervical homeoses are identified between species, but the second type can also occur within some species when the post hatching development is considered. The fossil material analysed here makes it apparent that the two modular configurations characterising the anterior part of the neck—a consequence of the first homeosis—existed 36 My and 25 My ago, for one, and circa 10 My ago, for the other. These comparisons also reveal a clear differentiation in vertebral features between the fossil species of the Oligocene–Miocene ages and the more recent and extant penguins. Ultimately, these observations make the proposal of a hypothesis in relation to the ontogenetic influence of Hox genes, and their regulators, based on the changes observed in the cervical segment of Sphenisciformes.     

DNA–DNA Hybridization Evidence for the Recent Origin of Marmots and Ground Squirrels (Rodentia: Sciuridae)

A molecular analysis, based on DNA/DNA hybridization experiments, examined seven species of the sciurid tribe Marmotini, in order to evaluate their evolutionary relationships. The branching pattern obtained from a neighbor-joining analysis and least-squares methods indicates that spermophiles and marmots are closely related. This result is in agreement with previous studies based on biochemical data which have suggested a Miospermophilus origin of Marmota (like Spermophilus), instead of the Protospermophilus origin usually proposed by paleontology. Using a molecular time scale calibrated by the fossil record of Sciurus (used here as an outgroup), we estimate the marmot/ground squirrel divergence at 6 My, at the same time as the major lineages of ground squirrels diverged from each other. Consequently, the species of Marmota appear as one of the numerous specialized forms derived from the explosive radiation of the Spermophilus lineage in the late Miocene.     

Arrangement of tubulin subunits and microtubule-associated proteins in the central-pair microtubule apparatus of squid (Loligo pealei) sperm flagella

This study provides a comprehensive, high-resolution structural analysis of the central-pair microtubule apparatus of sperm flagella. It describes the arrangement of several microtubule-associated "sheath" components and suggests, contrary to previous thinking, that microtubules are structurally asymmetric. The two microtubules of the central pair are different in several respects: the C2 tubule bears a single row of 18-nm-long sheath projections with an axial periodicity of 16 nm, whereas the C1 tubule possesses rows of 9-nm globular sheath components with an axial repeat of 32 nm. The lumen of the C2 tubule always appears completely filled with electron-dense material; that of the C1 tubule is frequently hollow. The C2 tubule also possesses a series of beaded chains arranged around the microtubule; the beaded chains are composed of globular subunits 7.5-10 nm in diameter and appear to function in the pairing of the C1 and C2 tubules. These findings indicate: that the beaded chains are not helical, but assume the form of lock washers arranged with a 16-nm axial periodicity on the microtubule; and that the lattice of tubulin dimers in the C2 tubule is not helically symmetric, but that there are seams between certain pairs of protofilaments. Proposed lattice models predict that, because of these seams, central pair and perhaps all singlet microtubules may contain a ribbon of 2-5 protofilaments that are resistant to solubilization; these models are supported by the results of the accompanying paper (R. W. Linck, and G. L. Langevin. 1981. J. Cell Biol. 89: 323-337.     

Protein synthesis in epiblast versus hypoblast during the critical stages of induction and growth of the primitive streak in the chick embryo.

In the chick the inducing power of the hypoblast for primitive streak was assumed to reach its maximum at the beginning of the primitive streak stage and to last until its completion. It was therefore of interest to trace the protein synthetic activity of the epiblast and hypoblast during five successive developmental stages and to correlate them with the known morphogenetic events.The investigation was done along two lines: 1) A quantitative survey was made of the uptake of tritiated phenylalanine into epiblasts versus hypoblasts and their incorporation into trichloroacetic acid-precipitable protein. 2) Incorporation of label into protein was followed by a comparative investigation of the electropherograms of epiblast versus hypoblast at the different stages.The quantitative survey has shown an almost uniform and rather low incorporation of label into protein in the hypoblast layer with a very short period of doubled activity between full hypoblast and initial primitive streak (p.s.). During this period the inductive capacity of the hypoblast for primitive streak was supposed to reach its maximal value.The qualitative survey indicated different patterns of incorporation in the two layers studied. Of special interest are two peaks (III and IV) which appear in the hypoblast previous to p.s. formation at the time of its augmented synthetic activity which also coincides with the onset of its inductive capacity. At later stages two similar peaks appear in the epiblast. It is suggested that a protein included in the above peaks might represent the inductor of the primitive streak.     

Longevity of orders is related to the longevity of their constituent genera rather than genus richness

Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime (Van Valen in Evol Theory 1:1–30, 1973). Using the fossil marine animal genera database (Sepkoski in Bull Am Paleontol 363, pp 563, 2002) we here examine the relationship between longevity of a higher taxonomic group (orders) and the longevity of its lower taxonomic groups (genera). We find insignificant correlation between the size of an order and its longevity, whereas we observe large correlation between the lifetime of an order and the lifetime of its constituent genera. These observations suggest that longevity of taxonomic groups is heritable intrinsically or on the grounds of environmental preferences.     

Health and Welfare in Animals and Humans

This paper contains a brief comparative analysis of some philosophical and scientific discourses on human and animal health and welfare, focusing mainly on the welfare of sentient animals. The paper sets forth two kinds of proposals for the analysis of animal welfare which do not appear in the contemporary philosophical discussion of human welfare, viz. the coping theory of welfare and the theory of welfare in terms of natural behaviour. These proposals are scrutinized in the light of some similar theories dealing with human health and quality of life. My conclusion is that the coping theory and the natural behaviour theory are not in themselves adequate for the characterization of welfare, either for humans or for sentient animals. I contend, finally, that, in the light of the previous discussion, there are good arguments for a particular set of analyses of both animal and human welfare, viz. the ones that are based on the notions of preference satisfaction and positive subjective experiences.     

CLADISTIC REAPPRAISAL OF NEOTROPICAL STENODERMATINE BAT PHYLOGENY

Abstract— Several phylogenies have been proposed for neotropical stenodermatine fruit-eating bats (Phyllostomidae), based on detention, external morphology, osteology and chromosomes. However, these previous analyses did not incorporate fully the idea that relationships should be identified based solely on shared derived characteristics. A critique of past methodology and results, and an alternative phylogeny using a morphological data set supplemented with karyotypic information, is presented. In my analysis, there appear two main lineages. The eight genera of white-shouldered bats form a monophyletic clade based on three synapomorphies (white patch of fur on shoulders, lack of a palatial extension with varying degrees of emargination and modified upper incisors); previous work suggested a paraphyletic relationship for this group. Furthermore, the monophyly of the four genera endemic to the Antilles is supported by two synapomorphies, suggesting a common origin as opposed to a multiple invasion for these genera. The appearance of the derived 2n = 30 and FN = 56 standard karyotype suggests that the morphologically distinct Sturnira forms the sister taxon to the remaining genera which are united by the synapomorphy of white facial stripes. This supports the inclusion of Sturnira within the stendodermatines and not in its own monotypic higher-level taxon. My results do not refute the traditional systematic view of Artibeus (including Dermanura, Koopmania and Enchisthenes ) being monophyletic, and supports Mesophylla and Vampyressa being distinct non-sister genera.     

Dependence of thick filament structure in relaxed mammalian skeletal muscle on temperature and interfilament spacing

Contraction of skeletal muscle is regulated by structural changes in both actin-containing thin filaments and myosin-containing thick filaments, but myosin-based regulation is unlikely to be preserved after thick filament isolation, and its structural basis remains poorly characterized. Here, we describe the periodic features of the thick filament structure in situ by high-resolution small-angle x-ray diffraction and interference. We used both relaxed demembranated fibers and resting intact muscle preparations to assess whether thick filament regulation is preserved in demembranated fibers, which have been widely used for previous studies. We show that the thick filaments in both preparations exhibit two closely spaced axial periodicities, 43.1 nm and 45.5 nm, at near-physiological temperature. The shorter periodicity matches that of the myosin helix, and x-ray interference between the two arrays of myosin in the bipolar filament shows that all zones of the filament follow this periodicity. The 45.5-nm repeat has no helical component and originates from myosin layers closer to the filament midpoint associated with the titin super-repeat in that region. Cooling relaxed or resting muscle, which partially mimics the effects of calcium activation on thick filament structure, disrupts the helical order of the myosin motors, and they move out from the filament backbone. Compression of the filament lattice of demembranated fibers by 5% Dextran, which restores interfilament spacing to that in intact muscle, stabilizes the higher-temperature structure. The axial periodicity of the filament backbone increases on cooling, but in lattice-compressed fibers the periodicity of the myosin heads does not follow the extension of the backbone. Thick filament structure in lattice-compressed demembranated fibers at near-physiological temperature is similar to that in intact resting muscle, suggesting that the native structure of the thick filament is largely preserved after demembranation in these conditions, although not in the conditions used for most previous studies with this preparation.     

The effects of taxonomic standardization on sampling-standardized estimates of historical diversity

Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodating the heterogeneities of the fossil record when evaluating historical diversity patterns. Although palaeontologists have given ample attention to the effects of taxonomic practice on diversity patterns derived from synoptic databases (those using first and last appearances of taxa), workers have not examined the effects of taxonomic error on occurrence-based diversity studies. Here, we contrast diversity patterns and diversity dynamics between raw data and taxonomically vetted data in the PBDB to evaluate the effects of taxonomic errors. We examine three groups: Palaeozoic gastropods, Jurassic bivalves and Cenozoic bivalves. We contrast genus-level diversity patterns based on: (i) all occurrences assigned to a genus (i.e. both species records and records identifying only the genus), (ii) only occurrences for which a species is identified, and (iii) only occurrences for which a species is identified, but after vetting the genus to which the species is assigned.Extensive generic reassignments elevate origination and extinction rates within Palaeozoic gastropods and origination rates within Cenozoic bivalves. However, vetting increases generic richness markedly only for Cenozoic bivalves, and even then the increase is less than 10%. Moreover, the patterns of standing generic richness are highly similar under all three data treatments. Unless our results are unusual, taxonomic standardization can elevate diversity dynamics in some cases, but it will not greatly change inferred richness over time.     

The shape of pterosaur evolution: evidence from the fossil record

Abstract Although pterosaurs are a well‐known lineage of Mesozoic flying reptiles, their fossil record and evolutionary dynamics have never been adequately quantified. On the basis of a comprehensive data set of fossil occurrences correlated with taxon‐specific limb measurements, we show that the geological ages of pterosaur specimens closely approximate hypothesized patterns of phylogenetic divergence. Although the fossil record has expanded greatly in recent years, collectorship still approximates a sigmoid curve over time as many more specimens (and thus taxa) still remain undiscovered, yet our data suggest that the pterosaur fossil record is unbiased by sites of exceptional preservation (lagerstätte). This is because as new species are discovered the number of known formations and sites yielding pterosaur fossils has also increased – this would not be expected if the bulk of the record came from just a few exceptional faunas. Pterosaur morphological diversification is, however, strongly age biased: rarefaction analysis shows that peaks of diversity occur in the Late Jurassic and Early Cretaceous correlated with periods of increased limb disparity. In this respect, pterosaurs appear unique amongst flying vertebrates in that their disparity seems to have peaked relatively late in clade history. Comparative analyses also show that there is little evidence that the evolutionary diversification of pterosaurs was in any way constrained by the appearance and radiation of birds.