New pigeons in old holes: Anthropology,algorithms and alpha taxonomy

Almost three-quarters of a century ago, Ernst Mayr (1950) shocked paleoanthropologists into an exceptionalist taxonomic minimalism that lingers today. As a result, a constant stream of new fossil discoveries has been shoehorned wherever possible into existing taxa, almost irrespective of morphology. This compression has been especially true at the level of the genus, where virtually all except very early hominins have over the last couple of decades been classified and named according to the unconscious algorithm, “if it isn’t Australopithecus, it is Homo” (and vice versa). This has led to a vastly overstuffed genus Homo, which has lost any phylogenetic or morphological coherence. Genera are monophyletic clusters of species; and although their boundaries in terms of species content are arbitrary, they do contain phylogenetic structure that ultimately needs to be expressed. Homininae is a large and diverse taxon; and this essay is a plea to paleoanthropologists not only to reflect the phylogenetic structure within it by employing an adequate number of generic and species names, but at the same time to acknowledge the internationally agreed rules (especially of priority) that govern the naming of zoological taxa.     

Evolution and selection of reproduction

The examination of the official records from Artas, Isère (North Dauphiné, France), provides nearly continuous information from 1540 to 1900. These allowed us to study the twinning during this period, to specify its importance, its evolution, and its links with diverse other characteristics of reproduction. The number of twins per 1000 births is on a general average very close to 11. It seems to decrease during the last four centuries. However, the variability is very high from one year to another or one decade to another, including the composition of twins (identical or different sex), with the result that no statistical argument allows us to reject the null hypothesis. Numerous data have been collected that support a partially genetic determinism in twinning. The number of children in families with twins is clearly higher that in other families. Age of death of the mother of twins is higher than that of the mother of single births. With the result that 'gemellity', fecundity and longevity are related. On the other hand, the perinatal and infant death rate is much higher for twins than for single births, so that the percentage of 'useful' children is very low for twins. There is therefore, at the same time, selection and counter-selection. The momentary importance of either could explain the extent of variation of the 'gemellity' rate. The compensations, at short or long time, between the two processes could explain the roughly constant rate of 'gemellity' during the last four centuries.     

A new look at genome size,evolutionary duration and genetic variation in salamanders

Salamanders have some of the largest genomes among vertebrates, and also some of the lowest reported levels of genetic diversity. Paedomorphs, in particular, have the largest genomes on average among urodela, and display exceptionally low levels of nucleotide and protein variation. Here, we address the question of genetic variation in relation to genome size in eight different salamander families. Using the rag1 gene as a probe for evolutionary rates, we found that rates of substitution are exceptionally low in obligate paedomorphs (neotenes) and other salamander species. Substitution rates in some cases are as low as those reported for cartilaginous fish, which have the slowest mutation rates recorded so far in vertebrates. Confirming and extending an earlier study, we also found that genome size is correlated with phylogenetic age in Plethodontidae, indicating a more general trend in genome size evolution in urodela. The Plethodontidae, furthermore, display much higher levels of genetic variance than the obligate neotene families, consistent with greater habitat heterogeneity in terrestrial salamanders. Finally, we present the first direct evidence of a gene, rag1, whose substitution rate is negatively associated with genome size. Based on these and other observations, we propose a hypothesis according to which mutation rates in nuclear genes tend to increase as genome size decreases during the course of vertebrate evolution.     

Nucleotidic cofactors and the origin of the genetic code

In this article it is suggested that the first coding system started from specific interactions between the nucleotide part of nucleotidic cofactors and enzymes. These interactions generated a first primitive code of four words of one letter each for the four primittive amino acids (phenylalanine, lysine, glycine and proline); when the triplet code (which allowed the integration of 20 amino acids into proteins) progressively appeared, it must have been modulated by the existence of this first coding system.     

Mass extinctions,biodiversity explosions and ecological niches

The logistic model proposed by Courtillot and Gaudemer to describe the growth of biodiversity during geological ages is more explored here and further developed. A new parameterisation is first proposed. Another expression of this model is obtained by introducing a new variable representing the number of ecological niches. It appears that the rates of increase of biodiversity during Jurassic and Cretaceous periods is quite different from other ones. The classical literature essentially focuses on possible extinction mechanisms, but explosions in biodiversity must be more precisely explored. For this purpose, on the basis of data analysis through different expressions of the logistic model, different ecological mechanisms can be assumed (e.g., qualitative and quantitative niches changes, possible appearance of new kinds of ecological relationships, such as 'niche-sharing', which involves coexistence or cooperation), even if genetic processes must also be involved. Finally, we emphasise the astonishing speed of biological diversification following a 'catastrophic' mass extinction. We could refer to this feature as 'catastrophic biological diversification'.     

Cytochrome b-based phylogeny of the Praomys group (Rodentia,Murinae): a new African radiation?Phylogénie du groupe Praomys (Rodentia,Murinae) basée sur le cytochrome b : une nouvelle radiation africaine ?

Complete cytochrome b gene sequences allows, for the first time, establishing a nearly complete phylogeny among the Praomys group sensu lato. The genera Praomys, Mastomys and Stenocephalemys appear paraphyletic. Myomys is polyphyletic and this genus name probably needs to be restricted to its type species, M. verreauxii. The genera Zelotomys and Colomys appear as sister groups. Mastomys pernanus and Malacomys verschureni nest within the Praomys group, but their generic assignation must be further clarified. The genus Heimyscus appears closest to Praomys than to Hylomyscus. The different lineages probably result from an adaptive radiation at the end of the Miocene.     

A frontal lobe surface analysis in three archaic African human fossils: OH 9, Buia,and Bodo

The evolution of the frontal lobes represents a major issue in paleoneurology. In this survey, we used a surface analysis to describe the frontal morphology of three relevant East African specimens from early and middle Pleistocene: OH 9, UA 31, and Bodo. When compared with a modern human endocast, UA 31 and Bodo display a flatter dorso-lateral surface, while OH 9 shows a general flattening of the whole dorsal morphology. OH 9 is the specimen with older chronology and with orbits more separated from the prefrontal cortex than in UA 31 and Bodo. The morphology of these three specimens is in agreement with the hypothesis that increase of the frontal curvature is due to the shifting of the facial block under the anterior cranial fossa. Apart from variations in size and general proportions, surface analysis can be useful in analyzing morphological changes localized in specific cortical areas. The three fossils are used as case study to discuss and review some relevant issues concerning frontal lobe evolution and paleoneurology.     

Early steps of metabolism evolution inferred by cladistic analysis of amino acid catabolic pathways

Among abiotic molecules available in primitive environments, free amino acids are good candidates as the first source of energy and molecules for early protocells. Amino acid catabolic pathways are likely to be one of the very first metabolic pathways of life. Among them, which ones were the first to emerge? A cladistic analysis of catabolic pathways of the sixteen aliphatic amino acids and two portions of the Krebs cycle is performed using four criteria of homology. The cladogram shows that the earliest pathways to emerge are not portions of the Krebs cycle but catabolisms of aspartate, asparagine, glutamate, glutamine, proline, arginine. Earliest enzymatic catabolic functions were deaminations and transaminations. Later on appeared enzymatic decarboxylations. The consensus tree allows to propose four time spans for catabolism development and corroborates the views of Cordón in 1990 about the evolution of catabolism.     

Primary structure of the two (4 Fe-4 S) clusters ferredoxin from Desulfovibrio desulfuricans (strain Norway 4)

The primary structure of a ferredoxin isolated from D. desulfuricans Norway strain, which we called ferredoxin II (Fd II) has been elucidated. This ferredoxin is a dimer constituted of two identical subunits of molecular weight 6000. In ferredoxin II two (4 Fe-4 S) centers are present per subunit instead of one (Fe-S) center as is the case for the other ferredoxins isolated from Desulfovibrio and for Fd I from the same organism. The comparison of amino-acid sequences shows that ferredoxin II presents more homologies with clostridial type ferredoxin than with the ferredoxins from D. gigas and D. africanus.     

Birds perching on bushes: Networks to visualize conflicting phylogenetic signals during early avian radiation

Hybridization is increasingly seen as an important source of adaptive genetic variation and biotic diversity. Recent phylogenetic studies on the early evolution of birds suggest that the early diversification of neoavian orders perhaps involved a period of extensive hybridization or incomplete lineage sorting. Phylogenetic error, saturation, long-branch attraction, and convergence make it difficult to detect ancient hybridization events and differentiate them from incomplete lineage sorting using sequence data. We used recently published retroposon marker data to visualize the early radiation of Neoaves within a phylogenetic network approach, and found that the most basal neoavian taxa indeed show a complex pattern of reticulated relationships. Moreover, the reticulation levels of different parts of the network are consistent with the insertion pattern of the retroposon elements. The use of network-based analyses on homoplasy-free data shows true conflicting signals and the taxa involved that are not represented in trees.     

Adaptive branching in evolution and epigenesis

We describe one of the simplest models that exhibit an adaptive branching behaviour. It is analysed both experimentally and formally, and its successive bifurcations provide a good model of what R. Thom called 'generalized catastrophes'. Two theorems on the stochastic adaptivity of the algorithm to very general shapes of target are given. The model further displays the phenomenon of abortive branching: each macroscopic branching appears after a burst of microscopic branchings that stop growing after a very short time. The mathematical analysis of the model explains why and how this behaviour occurs. Possible applications of these models to Evolution (natural and artificial) and Epigenesis are briefly mentioned, and a higher dimensional version is applied to growing a tree in a space of shapes in the context of a database of medical images.     

Ontogenèse,variabilité et évolution morphofonctionnelle du pédoncule et du calice chez les millericrinida (Échinodermes,Crinoïdes)

Stalked Crinoids are generaly rheophilic. The shape of the skeleton parts depends on morphofunctional connections. The various fossil and recent species of Millericrinida permit a discussion of the morphology of the calyx and the stem, their variability and their ontogeny. Several examples are investigate with details: Apiocrinus. Millericrinus, Conocrinus, Democrinus and Bourgueticrinus. The stem characteristics are the most constant and significant for systematics. The architecture of the calyx and its morphology are strongly variable in a taxon. Their evolution rate is often hight, but to disclose it an analysis and a comparison between some populations with numerous specimens is necessary.     

Stabilité de l'espèce et évolution: La théorie de l'équilibre intermittent («Punctuated equilibrium)

Paleontologists' traditional conceptions on evolution do not seem to be in perfect accord with these of biologists. The gradual phyletism is compatible neither with E. Mayr's model of the Founder, nor with the actual stability of most of the paleontological species. The punctuated equilibrium model proposed by N. Eldredge & S.J. Gould offers a solution which integrates both paleontological observations and the data of modern biology.     

The first known fossil record of pipehorses (Teleostei: Syngnathidae: Haliichthyinae) from the Miocene Coprolitic Horizon from the Tunjice Hills,Slovenia

The first known fossil specimens of pipehorses (Haliichthyinae) were unearthed from the Middle Miocene (Sarmatian) beds of the Coprolitic Horizon in the Tunjice Hills, Slovenia. These fossil pipehorses belong to a new genus and species Hippohaliichthys edis, which was similar to the extant species Haliichthys taeniophorus. The body morphology indicates that the described fossil pipehorses were also closely related to the pygmy pipehorse Hippotropiscis frenki and the seahorse Hippocampus sarmaticus, two taxa which were also found in the Coprolitic Horizon. The described fossil material of pipehorses indicates that seahorses evolved from a group of pipehorses that were similar in size and shape to extant and fossil pipehorses of the Haliichthyinae subfamily.     

Brain size and the human cranial base: a prenatal perspective

Pivotally positioned as the interface between the neurocranium and the face, the cranial base has long been recognized as a key area to our understanding of the origins of modern human skull form. Compared with other primates, modern humans have more coronally orientated petrous bones and a higher degree of basicranial flexion, resulting in a deeper and wider posterior cranial fossa. It has been argued that this derived condition results from a phylogenetic increase in the size of the brain and its subcomponents (infra- and supratentorial volumes) relative to corresponding lengths of the cranial base (posterior and anterior, respectively). The purpose of this study was to test such evolutionary hypotheses in a prenatal ontogenetic context. We measured the degree of basicranial flexion, petrous reorientation, base lengths, and endocranial volumes from high-resolution magnetic resonance images (hrMRI) of 46 human fetuses ranging from 10-29 weeks of gestation. Bivariate comparisons with age revealed a number of temporal trends during the period investigated, most notable of which were coronal rotation of the petrous bones and basicranial retroflexion (flattening). Importantly, the results reveal significant increases of relative endocranial sizes across the sample, and the hypotheses therefore predict correlated variations of cranial base flexion and petrous orientation in accordance with these increases. Statistical analyses did not yield results as predicted by the hypotheses. Thus, the propositions that base flexion and petrous reorientation are due to increases of relative endocranial sizes were not corroborated by the findings of this study, at least for the period investigated.     

Degeneracy in the genetic code and its symmetries by base substitutions

Degeneracy in the genetic code is known to minimise the deleterious effects of the most frequent base substitutions: transitions at the third base of codons are generally synonymous substitutions. Transversions that alter degeneracy were reported by Rumer. Here the other transversions are shown to leave invariant degeneracy when applied to the first base of codons. As a summary, degeneracy is considered with respect to all three types of base substitutions, the transitions and the two types of transversions. The symmetries of degeneracy by base substitutions are independent of the representation of the genetic code and discussed with respect to the quasi-universality of the genetic code.     

Electron microprobe analysis into interactions of a resin-modified glass-ionomer cement and a modified composite with human dentin in vitro

When materials used in restorative dentistry, such as a glass-ionomer cement or a compomer, were applied to dentin, ion exchanges occur between the material and the dentin. This work is based on an assessment in vitro of the ion exchanges occurring over time between (i) a glass-ionomer cement and dentin and (ii) a compomer and dentin. An electron microprobe analysis, technique not previously used for such a study, permitted qualitative and quantitative analysis of the interface and of the peripheral dentin. Analysis of the distribution of the elements in the interface and nearby showed continuous, progressive exchanges between the glass-ionomer cement and the dentin and absence of diffusion between the compomer and the dentin.