Do new reconstructions clarify the relationships between the Phanerozoic diversity dynamics of marine invertebrates and long-term eustatic trends?

A relationship between global sea levels and the diversity of marine invertebrates throughout the Phanerozoic remains an urgent matter for debates. Its recognition depends on a proper selection of diversity and eustatic curves. A comparison of changes in the revised sample-standardized generic diversity and long-term global sea-level changes provides a weaker evidence for a direct covarying relationship than established earlier, although the eustatic control on diversity dynamics of marine invertebrates was important during ∼74% of the Phanerozoic. Multiple causation of biodiversity changes, data bias, erroneous reconstructions, and conceptual misinterpretations are likely explanations of observed difference between the new biodiversity and eustatic curves.     

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood

Most phylogenetic models of protein evolution assume that sites are independent and identically distributed. Interactions between sites are ignored, and the likelihood can be conveniently calculated as the product of the individual site likelihoods. The calculation considers all possible transition paths (also called substitution histories or mappings) that are consistent with the observed states at the terminals, and the probability density of any particular reconstruction depends on the substitution model. The likelihood is the integral of the probability density of each substitution history taken over all possible histories that are consistent with the observed data. We investigated the extent to which transition paths that are incompatible with a protein's three-dimensional structure contribute to the likelihood. Several empirical amino acid models were tested for sequence pairs of different degrees of divergence. When simulating substitutional histories starting from a real sequence, the structural integrity of the simulated sequences quickly disintegrated. This result indicates that simple models are clearly unable to capture the constraints on sequence evolution. However, when we sampled transition paths between real sequences from the posterior probability distribution according to these same models, we found that the sampled histories were largely consistent with the tertiary structure. This suggests that simple empirical substitution models may be adequate for interpolating changes between observed sequences during phylogenetic inference despite the fact that the models cannot predict the effects of structural constraints from first principles. This study is significant because it provides a quantitative assessment of the biological realism of substitution models from the perspective of protein structure, and it provides insight on the prospects for improving models of protein sequence evolution.     

Analysis of forces of ACL reconstructions at the tunnel entrance: is tunnel enlargement a biomechanical problem?

Bone tunnel enlargement is a common phenomenon following reconstruction of the anterior cruciate ligament (ACL). Biomechanical and biological factors have been reported as potential causes of this problem. However, there is no analysis of forces between the graft and bone, as the graft changes direction at the bone tunnel entrance. The purpose of this study was to study these 'redirecting forces'. Magnetic resonance images of 10 patients with an ACL reconstruction (age: 26+/-6.8 years) were used to determine the angle between graft and drill holes. Vector analysis was used to calculate the direction and magnitude of the perpendicular component of the force between the bone tunnel and the graft at the entrance of the bone tunnel. Force components were projected into the radiographically important sagittal and coronal planes. Tension of ACL reconstructions was recorded during passive knee motion in 10 cadaveric knee experiments (age: 28.9+/-10.6 years) and the tension multiplied with the force component for each plane. Results are reported for the coronal and sagittal planes, respectively: For -10 degrees of extension, the percentages of graft tension were determined to be 17+/-7 (max: 26; min: 7%) and 26+/-9 (max: 39; min: 16%) for the tibia. They were 59+/-6 (max: 66; min: 48%) and 99+/-1 (max: 1.00; min: 99%) for the femur. Force components were 14.68+/-6.54 and 25.73+/-12.96 N for the tibial tunnel. For the femoral tunnel, they were 52.48+/-19.03 and 90.77+/-32.06 N. Percentages of graft tension and force components were significantly higher for the femoral tunnel compared with the tibial tunnel. Moreover, in the sagittal direction, force components for the femoral tunnel were significantly higher compared with the coronal plane (Wilcoxon test, p < 0.01). The differences in force components calculated in this study corresponds with the amount of tunnel enlargement in the radiographic planes in the literature providing evidence that biomechanical forces play a key role in postoperative tunnel expansion.     

What can genome-scale metabolic network reconstructions do for prokaryotic systematics?

It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1–5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.     

Where did Mikrotia magna originate? Drawing ecogeographical inferences from body mass reconstructions

Terre Rosse deposits (upper Miocene; Gargano, Italy) have provided fossil remains of an insular fauna among which the genus Mikrotia (Rodentia) stands out. Several paleobiological studies have already been conducted on this genus, but its body mass has not yet been calculated accurately. The aim of the present work is to reconstruct Mikrotia magna's weight, a paramount aspect of organismal biology, especially on islands where mammals modify their size, becoming giants or dwarfs (‘island rule’). Our analysis using postcranial elements (femora and humeri) predicts weights ranging from 1300 g to 1900 g (old and young populations, respectively). The presence of a large number of micromammals on the Gargano paleo-island suggests a high interspecific competition for species of the same ecological guild (Prolagus or cricetids were direct competitors of Mikrotia), which may lead to only moderate gigantism, or even body mass reductions in small mammals, following Palkovacs's model. This contrasts with the huge weight of M. magna inferred in this study. In this regard, stratigraphic and taxonomic studies suggest that M. magna was an immigrant from a neighboring island, indicating that this species originated and achieved its enormous size under other selective pressures. A native island with a lower number of competitors, and therefore with less resource limitation than Terre Rosse, might be the principal explanation for such a degree of gigantism.     

Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions?

Our curiosity about biodiversity compels us to reconstruct the evolutionary past of species. Molecular evolutionary theory now allows parameterization of mathematically sophisticated and detailed models of DNA evolution, which have resulted in a wealth of phylogenetic histories. But reconstructing how species and population histories have played out is critically dependent on the assumptions we make, such as the clock-like accumulation of genetic differences over time and the rate of accumulation of such differences. An important stumbling block in the reconstruction of evolutionary history has been the discordance in estimates of substitution rate between phylogenetic and pedigree-based studies. Ancient genetic data recovered directly from the past are intermediate in time scale between phylogenetics-based and pedigree-based calibrations of substitution rate. Recent analyses of such ancient genetic data suggest that substitution rates are closer to the higher, pedigree-based estimates. In this issue, Navascués & Emerson (2009) model genetic data from contemporary and ancient populations that deviate from a simple demographic history (including changes in population size and structure) using serial coalescent simulations. Furthermore, they show that when these data are used for calibration, we are likely to arrive at upwardly biased estimates of mutation rate.     

Response of a shallow boreal lake to recent nutrient enrichment – implications for diatom-based phosphorus reconstructions

Water quality of the shallow, mesotrophic, and macrophyte-dominated Lake Kaljasjärvi has been monitored at three to four year intervals since 1978. During the monitoring period, surface-water total phosphorus (TP) concentrations have typically varied between 20 and 25 g P l^–1. However, elevated total phosphorus concentrations were measured in 1987, 1991, and 1999. Diatom-based reconstruction of the historical lake-water TP concentrations was therefore employed to study the recent development of the lake. However, the diatom-TP model did not predict the high measured phosphorus concentrations despite the changes observable in diatom assemblages. In addition, the ratio of sedimentary diatom remains to chrysophycean stomatocysts declined towards the top of the sediment core, indicating decreasing trophy rather than eutrophication. Analysis of sedimentary pigments and phosphorus fractions, used to examine further the changes, also produced results that contradicted the simple eutrophication hypothesis. In particular, the proportion of chlorophyll derivatives instead of carotenoids increased and there was a rise in the concentration of refractory instead of NaOH-extracted phosphorus. These features appear to be related to the extensive littoral areas of the lake since enhanced littoral production can explain both the observed changes in sediment chemistry and the low diatom-inferred TP (DI-TP). Littoral primary producers are suggested to have benefited from the increased phosphorus inputs to the lake, transferring some of the phosphorus to the detrital pool and contributing to the increased pigment concentrations of sedimentary organic matter. High proportions of non-planktonic diatoms in the samples lower DI-TP because periphytic taxa are assigned low TP optima in the inference models used. Abundant aquatic macrophytes may also have made the lake resistant to eutrophication by assimilating nutrients, providing refuge for zooplankton, and having an allelopathic effect on phytoplankton. Since 1980, however, the sedimentary diatom assemblages also indicate increasingly eutrophic conditions. Additional loading from numerous cottages during the last 20 years seems to have caused observable changes in the phytoplankton communities.     

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?

In recent years, several studies have reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even in the absence of macrofossils) in order to obtain genetic "profiles" from past environments. One of the hazards associated with this approach, particularly in nonfrozen environments, is the potential for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal for this purpose as the presence or absence of DNA from nonindigenous fauna (such as sheep) in sediments deposited prior to European settlement can serve as an indicator of DNA movement. Additionally, these strata are well defined and dated. DNA from sheep was found in strata that also contained moa DNA, indicating that genetic material had migrated downwards. Quantitative polymerase chain reaction analyses demonstrated that the amount of sheep DNA decreased as the age of sediments increased. Our results suggest that sedimentary aDNA is unlikely to be deposited from wind-borne DNA and that physical remains of organisms or their ejecta need to have been incorporated in the sediments for their DNA to be detected. Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for.     

Are pollen records from small sites appropriate for REVEALS model-based quantitative reconstructions of past regional vegetation? An empirical test in southern Sweden

In this paper we test the performance of the Regional Estimates of VEgetation Abundance from Large Sites (REVEALS) model using pollen records from multiple small sites. We use Holocene pollen records from large and small sites in southern Sweden to identify what is/are the most significant variable(s) affecting the REVEALS-based reconstructions, i.e. type of site (lakes and/or bogs), number of sites, site size, site location in relation to vegetation zones, and/or distance between small sites and large sites. To achieve this objective we grouped the small sites according to (i) the two major modern vegetation zones of the study region, and (ii) the distance between the small sites and large lakes, i.e. small sites within 50, 100, 150, or 200 km of the large lakes. The REVEALS-based reconstructions were performed using 24 pollen taxa. Redundancy analysis was performed on the results from all REVEALS-model runs using the groups within (i) and (ii) separately, and on the results from all runs using the groups within (ii) together. The explanatory power and significance of the variables were identified using forward selection and Monte Carlo permutation tests. The results show that (a) although the REVEALS model was designed for pollen data from large lakes, it also performs well with pollen data from multiple small sites in reconstructing the percentage cover of groups of plant taxa (e.g. open land taxa, summer-green trees, evergreen trees) or individual plant taxa; however, in the case of this study area, the reconstruction of the percentage cover of Calluna vulgaris, Cyperaceae, and Betula may be problematic when using small bogs; (b) standard errors of multiple small-site REVEALS estimates will generally be larger than those obtained using pollen records from large lakes, and they will decrease with increasing size of pollen counts and increasing number of small sites; (c) small lakes are better to use than small bogs if the total number of small sites is low; and (d) the size of small sites and the distance between them do not play a major role, but the distance between the small sites and landscape/vegetation boundaries is a determinant factor for the accuracy of the vegetation reconstructions.     

Did the evolution of the phytoplankton fuel the diversification of the marine biosphere?

We discuss the possible links between the fossil record of marine biodiversity, nutrient availability and primary productivity. The parallelism of the fossil records of marine phytoplankton and faunal biodiversity implicates the quantity (primary productivity) and quality (stoichiometry) of phytoplankton as being critical to the diversification of the marine biosphere through the Phanerozoic. The relatively subdued marine biodiversity of the Palaeozoic corresponds to a time of relatively low macronutrient availability and poor food quality of the phytoplankton as opposed to the diversification of the Modern Fauna through the Mesozoic–Cenozoic. Increasing nutrient runoff to the oceans through the Phanerozoic resulted from orogeny, the emplacement of Large Igneous Provinces (LIPs), the evolution of deep-rooting forests and the appearance of more easily decomposable terrestrial organic matter that enhanced weathering. Positive feedback by bioturbation of an expanding benthos played a critical role in evolving biogeochemical cycles by linking the oxidation of dead organic matter and the recycling of nutrients back to the water column where they could be re-utilized. We assess our conclusions against a recently published biogeochemical model for geological time-scales. Major peaks of marine diversity often occur near rising or peak fluxes of silica, phosphorus and dissolved reactive oceanic phosphorus; either major or minor ⁸⁷Sr/⁸⁶Sr peaks; and frequently in the vicinity of major (Circum-Atlantic Magmatic Province) and minor volcanic events, some of which are associated with Oceanic Anoxic Events. These processes appear to be scale-dependent in that they lie on a continuum between biodiversification on macroevolutionary scales of geological time and mass extinction.     

Is the Octomacridae the sister family of the Diplozodae?

Diplozoidae and Octomacridae are usually considered as sister families. Essentially this is because they are the only polyopisthocotyleans parasitising primary freshwater teleosts. Because of the lack of phylogenetically informative morphological characters to explore the pattern of colonisation of the primary continental freshwater teleosts and in order to understand the appearance of the "natural parabiosis" of Diplozoidae, a molecular phylogeny was inferred by comparing newly obtained partial 28S and 18S rDNA gene sequences of Eudiplozoon nipponicum and Diplozoon homoion with other already available sequences. The phylogenetic analysis seems to show that Diplozoidae and Octomacridae are not sister groups. Thus, the colonisation of primary freshwater teleosts by these two families could be independent.     

Imperfect Batesian mimicry—the effects of the frequency and the distastefulness of the model

Batesian mimicry is the resemblance between unpalatable models and palatable mimics. The widely accepted idea is that the frequency and the unprofitability of the model are crucial for the introduction of a Batesian mimic into the prey population. However, experimental evidence is limited and furthermore, previous studies have considered mainly perfect mimicry (automimicry). We investigated imperfect Batesian mimicry by varying the frequency of an aposematic model at two levels of distastefulness. The predator encountered prey in a random order, one prey item at a time. The prey were thus presented realistically in a sequential way. Great tits (Parus major) were used as predators. This experiment, with a novel signal, supports the idea that Batesian mimics gain most when the models outnumber them. The mortalities of the mimics as well as the models were significantly dependent on the frequency of the model. Both prey types survived better the fewer mimics there were confusing the predator. There were also indications that the degree of distastefulness of the model had an effect on the survival of the Batesian mimic: the models survived significantly better the more distasteful they were. The experiment supports the most classical predictions in the theories of the origin and maintenance of Batesian mimicry.     

Phytochemicals: the good, the bad and the ugly?

Phytochemicals are constitutive metabolites that enable plants to overcome temporary or continuous threats integral to their environment, while also controlling essential functions of growth and reproduction. All of these roles are generally advantageous to the producing organisms but the inherent biological activity of such constituents often causes dramatic adverse consequences in other organisms that may be exposed to them. Nevertheless, such effects may be the essential indicator of desirable properties, such as therapeutic potential, especially when the mechanism of bioactivity can be delineated. Careful observation of cause and effect, followed by a coordinated approach to identify the responsible entities, has proved extremely fruitful in discovering roles for phytochemical constituents. The process is illustrated by selected examples of plants poisonous to animals and include the steroidal alkaloid toxin of Veratrum californicum (Western false hellebore), piperidine alkaloids of Lupinus species (lupines), and polyhydroxy indolizidine, pyrrolizidine and nortropane alkaloids of Astragalus and Oxytropis species (locoweeds), Castanospermum australe (Moreton Bay chestnut) and Ipomoea species (morning glories).