Can fast early rates reconcile molecular dates with the Cambrian explosion?

Molecular dates consistently place the divergence of major metazoan lineages in the Precambrian, leading to the suggestion that the 'Cambrian explosion' is an artefact of preservation which left earlier forms unrecorded in the fossil record. While criticisms of molecular analyses for failing to deal with variation in the rate of molecular evolution adequately have been countered by analyses which allow both site-to-site and lineage-specific rate variation, no analysis to date has allowed the rates to vary temporally. If the rates of molecular evolution were much higher early in the metazoan radiation, molecular dates could consistently overestimate the divergence times of lineages. Here, we use a new method which uses multiple calibration dates and an empirically determined range of possible substitution rates to place bounds on the basal date of divergence of lineages in order to ask whether faster rates of molecular evolution early in the metazoan radiation could possibly account for the discrepancy between molecular and palaeontological date estimates. We find that allowing basal (interphylum) lineages the fastest observed substitution rate brings the minimum possible divergence date (586 million years ago) to the Vendian period, just before the first multicellular animal fossils, but excludes divergence of the major metazoan lineages in a Cambrian explosion.     

Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?

The study of metazoan evolution has fascinated biologists for centuries, and it will certainly keep doing so. Recent interest on the origin of metazoan body plans, early metazoan evolution, genetic mechanisms generating disparity and diversity, molecular clock information, paleontology, and biogeochemistry is contributing to a better understanding of the current phyletic diversity. Unfortunately, the pattern of the metazoan tree of life still shows some important gaps in knowledge. It is the aim of this article to review some of the most important issues related to the inference of the metazoan tree, and point towards possible ways of solving certain obscure aspects in the history of animal evolution. A new hypothesis of the metazoan diversification during the Cambrian explosion is proposed by synthesizing ideas from phylogenetics, molecular evolution, paleontology, and developmental biology.     

The Cambrian "explosion" of metazoans and molecular biology: would Darwin be satisfied?

The origins of metazoan bodyplans and the extent to which they are coincident with the Cambrian "explosion" are both areas of continuing debate. The fossil record has a unique advantage in terms of historical perspective, but remains highly contentious on account of the often controversial interpretations of particular groups (e.g. halkieriids, vetulicolians) and the heavy reliance on "windows" of exceptional preservation (e.g. Chengjiang, Burgess Shale). Molecular and developmental biology offer other unique insights, but may be problematic in terms of conflicting phylogenetic signals and questions revolving around gene co-option, evolution of developmental systems and even convergence. Such topics, far from frustrating the enterprise, actually widen our understanding of the nature of the evolutionary process with the exciting promise of the discovery of more general principles.     

Butterflies of the Cambrian benthos? Shield position in bradoriid arthropods

Mode of preservation and method of recovery strongly influences our understanding of the life habits of extinct organisms. Bradoriid arthropods were abundant, and diverse members of early Cambrian ecosystems and most life reconstructions display these animals with the two shields of the carapace open in a ‘butterfly’ configuration. This favoured reconstruction is largely based on the abundance of ‘crack‐out’ specimens preserved in this position (e.g. Kunmingella from the early Cambrian of China). In contrast, large collections of acid processed bradoriids from the Arrowie Basin of South Australia (Cambrian Stage 3) are preserved with a narrow gape at the ventral margin or completely closed with the carapace folded along the dorsal midline. The relative abundance of conjoined, closed (or partially closed) specimens from the lower Cambrian Hawker Group succession suggests that at least some bradoriid taxa were capable of withdrawing appendages and tightly closing the shields, challenging the common view that the majority of bradoriids usually held their carapaces open in a ‘butterfly’ configuration during life. New data show that layers of the bradoriid carapace are continuous through the dorsal fold with no evidence for complex articulating structures as in ostracod hinges. The relatively pliable, sclerotized or lightly mineralized calcium phosphate composition of the carapace and the simple, flexible dorsal fold facilitated opening and closing of the shields. Despite not being closely related, ostracods share close biomechanical and ecological similarities with bradoriids. The evolution of more complex articulating hinge structures – together with well‐developed musculature – in ostracods during the Early Ordovician, may have provided more efficient means for shield articulation and movement, thus promoting the ecological success of ostracods throughout the Phanerozoic.     

Axillary bud outgrowth in herbaceous shoots: how do strigolactones fit into the picture?

Strigolactones have recently been identified as the long sought-after signal required to inhibit shoot branching (Gomez-Roldan et al. 2008; Umehara et al. 2008; reviewed in Dun et al. 2009). Here we briefly describe the evidence for strigolactone inhibition of shoot branching and, more extensively, the broader context of this action. We address the central question of why strigolactone mutants exhibit a varied branching phenotype across a wide range of experimental conditions. Where knowledge is available, we highlight the role of other hormones in dictating these phenotypes and describe those instances where our knowledge of known plant hormones and their interactions falls considerably short of explaining the phenotypes. This review will focus on bud outgrowth in herbaceous species because knowledge on the role of strigolactones in shoot branching to date barely extends beyond this group of plants.     

Contrasting patterns of disparity suggest differing constraints on the evolution of trilobite cephalic structures during the Cambrian ‘explosion’

Trilobites are an abundant group of Palaeozoic marine euarthropods that appear abruptly in the fossil record c. 521 million years ago. Quantifying the development of morphological variation (or ‘disparity’) through time in fossil groups like trilobites is critical in understanding evolutionary radiations such as the Cambrian ‘explosion’. Here, I use geometric morphometrics to quantify ‘cumulative disparity’ in functionally-important structures within the trilobite cephalon across their initial radiation during Cambrian Series 2. Overall cephalic disparity increased rapidly and attained a maximum within several million years. This pattern is dominated by the cephalic outline (in particular the genal spines), reflecting rapid, convergent expansion to the extremes of morphospace in a few early families. In contrast, removing the outline and focusing on structures such as the glabella and eye ridges (associated with feeding and vision, respectively) showed a more gradual increase in disparity, closer in line with taxonomic diversity and supporting the hypothesis of a relatively accurate trilobite fossil record. These contrasting patterns suggest that disparity in different structures was constrained in different ways, with extrinsic (ecological) factors probably having the major impact on overall disparity. It also implies that patterns of disparity in isolated substructures cannot necessarily be taken individually as representative of overall morphologies.     

How does a virus bud?

How does a virus bud from the plasma membrane of its host? Here we investigate several possible rate-limiting processes, including thermal fluctuations of the plasma membrane, hydrodynamic interactions, and diffusion of the glycoprotein spikes. We find that for bending moduli greater than 3 x 10(-13) ergs, membrane thermal fluctuations are insufficient to wrap the viral capsid, and the mechanical force driving the budding process must arise from some other process. If budding is limited by the rate at which glycoprotein spikes can diffuse to the budding site, we compute that the budding time is 10-20 min, in accord with the experimentally determined upper limit of 20 min. In light of this, we suggest some alternative mechanisms for budding and provide a rationale for the observation that budding frequently occurs in regions of high membrane curvature.     

What can DNA Tell us About the Cambrian Explosion?

Molecular data is ideal for exploring deep evolutionary historybecause of its universality, stochasticity and abundance. Thesefeatures provide a means of exploring the evolutionary historyof all organisms (including those that do not tend to leavefossils), independently of morphological evolution, and withina statistical framework that allows testing of evolutionaryhypotheses. In particular, molecular data have an importantrole to play in examining hypotheses concerning the tempo andmode of evolution of animal body plans. Examples are given wheremolecular phylogenies have led to a re-examination of some fundamentalassumptions in metazoan evolution, such as the immutabilityof early developmental characters, and the evolvability of bauplancharacters. Molecular data is also providing a new and controversialtimescale for the evolution of animal phyla, pushing the majordivisions of the animal kingdom deep into the Precambrian. Therehave been many reasons to question the accuracy and precisionof molecular date estimates, such as the failure to accountfor lineage-specific rate variation and unreliable estimationof rates of molecular evolution. While these criticisms havebeen largely countered by recent studies, one problem has remaineda challenge: could temporal variation in the rate of molecularevolution, perhaps associated with "explosive" adaptive radiations,cause overestimation of diversification dates? Empirical evidencefor an effect of speciation rate, morphological evolution orecological diversification on rates of molecular evolution isexamined, and the potential for rate-variable methods for moleculardating are discussed.     

"Resonances" in the dielectric absorption of DNA?

An attempt was made to confirm previous reports of resonant-like dielectric absorption of plasmid DNA in aqueous solutions at 1-10 GHz. The dielectric properties of the sample were measured using an automatic network analyzer with two different techniques. One technique used an open-ended coaxial probe immersed in the sample; the other employed a coaxial transmission line. No resonances were observed that could be attributed to the sample; however, resonance-type artifacts were prominent in the probe measurements. The coaxial line technique appears to be less susceptible to such artifacts. We note two important sources of error in the calibration of the automatic network analyzer using the probe technique.     

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.     

Lithostratigraphy of the Lower Cambrian metaclastics and their age based on trace fossils in the Sand?kl? region, southwestern Turkey

In the Sand?kl? region of the Taurus Range of Turkey, greater than 3000 m in thickness metamorphosed siliciclastics and volcanics (Kocayayla Group) underlies the trilobite-and conodont-bearing Middle-Late Cambrian Hudai Quartzite and Çaltepe Formation.The Kocayayla Group, previously regarded as Infracambrian or Precambrian, is dated for the first time as Early Cambrian on the basis of trace fossils. Cruziana ?fasciculata, C. ?salomonis, ?Cruziana isp., ?Diplichnites isp., Monomorphichnus isp., Petalichnus isp., Rusophycus ?avalonensis, R. ?latus, Arenicolites isp., cf. Altichnus foeyni, Planolites isp., Skolithos isp., and ?Treptichnus isp. have been recognised. These trace fossils are considered Tommotian or younger in age but older than the overlying, trilobite and conodont bearing Middle Cambrian limestones of the Çaltepe Formation. The trace fossils were likely produced by trilobites, suspension feeding annelids and deposit feeding “worms”, probably polychaetes. Sections bearing abundant Skolithos represent the Skolithos ichnofacies, which is typical of high energy environments with loose sandy, well sorted to slightly muddy substrates in intertidal to shallow subtidal zones. The other trace fossils represent the Cruziana ichnofacies, which is typical of subtidal, poorly sorted and soft substrates, from moderate energy to low energy environments between the fairweather and storm wave base.The Kocayayla Group was deposited at an early stage in a shallow marine stable shelf condition. The shelf subsided in a later stage and was affected by normal faults along which mafic and felsic volcanic rocks erupted. The volcanic activity had ceased and a shallow marine clastic sedimentation took place in the final stage of the shelf development. The Kocayayla Group was deformed and metamorphosed before the deposition of the trilobite-bearing Middle-Upper Cambrian succession.     

Environmental and temporal patterns in bioturbation in the Cambrian–Ordovician of Western Newfoundland

The early Paleozoic emergence of bioturbating (sediment-dwelling and -mixing) animals has long been assumed to have led to substantial changes in marine biogeochemistry, seafloor ecology, and the preservation potential of both sedimentary and fossil archives. However, the timing of the rise of bioturbation and environmental patterns in its expansion have long been subjects of debate—resolution of which has been hampered, in part, by a paucity of high-resolution bioturbation data or of systematic investigations of facies trends in lower Paleozoic bioturbation. To address these issues, we conducted an integrated sedimentological and ichnological characterization of the Cambrian–Ordovician Port au Port succession and Cow Head Group of western Newfoundland, encompassing over 350 meters of stratigraphy logged at the centimeter to decimeter scale. We find that, across a wide range of marine facies, bioturbation does not on average exceed moderate intensities—corroborating observations from other lower Paleozoic successions indicating that the early Paleozoic development of bioturbation was a protracted process. Moreover, bioturbation intensities in the Port au Port succession and Cow Head Group are commonly characterized by considerable variability at even fine scales of stratigraphic resolution and changes in bioturbation intensity correlate strongly with variability in sedimentary facies. We observe that facies recording nearshore depositional environments and carbonate-rich lithologies are each characterized by the highest intensities of both burrowing and sediment mixing. These data highlight the need for a high-resolution and facies-specific approach to reconstructing the evolutionary history of bioturbation and suggest that average levels of bioturbation, although relatively low throughout this interval, increased notably earlier in nearshore marine settings.     

Is there anything "autonomous" in the nervous system?

The terms "autonomous" or "vegetative" are currently used to identify one part of the nervous system composed of sympathetic, parasympathetic, and gastrointestinal divisions. However, the concepts that are under the literal meaning of these words can lead to misconceptions about the actual nervous organization. Some clear-cut examples indicate that no element shows "autonomy" in an integrated body. Nor are they solely "passive" or generated "without mental elaboration." In addition, to be "not consciously controlled" is not a unique attribute of these components. Another term that could be proposed is "homeostatic nervous system" for providing conditions to the execution of behaviors and maintenance of the internal milieu within normal ranges. But, not all homeostatic conditions are under the direct influence of these groups of neurons, and some situations clearly impose different ranges for some variables that are adaptative (or hazardous) in the tentative of successfully coping with challenging situations. Finally, the name "nervous system for visceral control" emerges as another possibility. Unfortunately, it is not only "viscera" that represent end targets for this specific innervation. Therefore, it is commented that no quite adequate term for the sympathetic, parasympathetic, and gastrointestinal divisions has already been coined. The basic condition for a new term is that it should clearly imply the whole integrated and collaborative functions that the components have in an indivisible organism, including the neuroendocrine, immunological, and respiratory systems. Until that, we can call these parts simply by their own names and avoid terms that are more "convenient" than appropriate.     

Is there "Metabolic" DNA in the Mouse Seminal Vesicle?

This study was designed to answer the question: Is H³-thymidine uptake by nuclei of the mouse seminal vesicle evidence for DNA synthesis and mitosis, or does it signify some "metabolic" function of DNA unrelated to chromosome duplication? Mice were given an intraperitoneal injection of H³-thymidine. Six hours later Feulgen squashes of the seminal vesicle epithelium were made and covered with autoradiographic stripping film. The silver grains above labeled nuclei were counted, and the Feulgen dye contents of these same nuclei were determined photometrically after removal of the grains from the emulsion. Unlabeled nuclei were also measured. The dye contents of non-radioactive nuclei form a unimodal distribution, indicating that polyploidy is absent from this tissue. The radioactive nuclei fall into two groups. In the first, the average dye content is the same as that of the cold nuclei (2C). In the second, the values range from 2C to 4C. In the 2C to 4C group the grain count is proportional to the dye content, showing that incorporation is correlated with synthesis. The radioactive 2C nuclei arose by mitosis during the course of the experiment. This is shown by the following facts: (1) They frequently occur in pairs. (2) They average smaller than unlabeled 2C nuclei. (3) Their average grain count is approximately half that of the 4C nuclei. (4) Labeled division figures are found. (5) A mitotic rate estimated from the number of labeled 2C nuclei accords reasonably well with one based on the number of observed mitoses. Since the incorporation of thymidine accompanies DNA synthesis and precedes mitosis, there is no reason to postulate a special "metabolic" DNA in this tissue.