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PubMed1993

Silk moth chorion pseudogenes: hallmarks of genomic evolution by sequence duplication and gene conversion.

The part of the genetic locus of the domesticated silk moth, Bombyx mori, in which high cysteine (Hc) chorion genes of late developmental specificity reside contains regions encompassing gene-like sequences which exhibit properties distinct from those of functional Hc genes. One of these regions has been characterized and shown to contain a chorion pseudogene, psi HcB.15, which shares pronounced similarities with a transcribed chorion pseudogene, psi HcB.12/13, which was characterized previously. Both pseudogenes are homologous to HcB chorion genes but bear multiple single nucleotide substitutions and short segmental mutations (insertions and deletions) which introduce translational frame shifts and termination codons in the coding regions. Structural characteristics unique to the two pseudogenes suggest that psi HcB.15 was generated first from a functional HcB gene and gave rise subsequently to psi HcB 12/13 as a result of a sequence duplication event. The two pseudogenes can be distinguished from each other by the presence of distinct regions of similarity to the consensus sequence of functional HcB genes which appear to have arisen from gene-conversion-mediated correctional events. These findings lend support to the hypothesis that chorion pseudogene sequences represent reservoirs of genetic information that participates in the evolution of the chorion locus rather than relics of inactivated genes passively awaiting extinction.

Animals↗

PubMed2002

A lost Neanderthal neonate found.

Fossil remains of adult Neanderthals are well documented, but juvenile specimens are rare and information about them is scant. Here we identify a beautifully preserved skeleton that has been lost to science for almost 90 years as the Neanderthal neonate known as 'Le Moustier 2', which was originally found at Le Moustier in the Dordogne, southwest France. This find will be a rich source of data for studying the evolution of human ontogeny as well as the phylogenetic relationship between these extinct hominids and anatomically modern humans.

Animals↗

PubMed1999

Linguistic diversity of the Americas can be reconciled with a recent colonization.

The Americas harbor a very great diversity of indigenous language stocks, many more than are found in any other continent. J. Nichols [(1990) Language 66, 475-521] has argued that this diversity indicates a great time depth of in situ evolution. She thus infers that the colonization of the Americas must have begun around 35,000 years ago. This estimate is much earlier than the date for which there is strong archaeological support, which does not much exceed 12,000 years. Nichols' assumption is that the diversity of linguistic stocks increases linearly with time. This paper compares the major continents of the world to show that this assumption is not correct. In fact, stock diversity is highest in the Americas, which are by consensus the youngest continents, intermediate in Australia and New Guinea, and lowest in Africa and Eurasia where the time depth is greatest. If anything, then, after an initial radiation, stock diversity decreases with time. A simple model is outlined that predicts these dynamics. It assumes that early in the peopling of continents, there are many unfilled niches for communities to live in, and so fissioning into new lineages is frequent. As the habitat is filled up, the rate of fissioning declines and lineage extinction becomes the dominant evolutionary force.

Americas↗

PubMed2004

Evolution by reticulation: European dogroses originated by multiple hybridization across the genus rosa.

The European dogroses (Rosa sect. Caninae (DC.) Ser.) are characterized by a unique meiosis system ("canina-meiosis"), which controls the heterogamous development of tetraploid egg cells and haploid pollen grains resulting in a pentaploid somatic status. This permanent anorthoploidy is supposed to have originated by a hybridization event in the postglacial period. In this study we present molecular evidence by an analysis of nuclear ribosomal DNA data that dogroses are complex allopolyploids resulting from multiple hybridization events. As previously described, the nrITS-1 region does not undergo concerted evolution in dogroses. Thus, different ITS-1 sequences persist within single individuals. Secondary structure predictions do not point to the existence of pseudogenes within these ITS-1 types. Our data suggest that the pentaploid Caninae genome originated from different members of nondogroses and the now extinct Protocaninae.

Biological Evolution↗

PubMed1998

Evolution by nearly-neutral mutations.

Genetic systems are complex and interact at various levels; among amino acids or nucleotide sites, among gene products, and among regulatory regions and proteins. Patterns of synonymous and nonsynonymous substitutions of mammalian genes indicate that nonsynonymous substitutions are nearly neutral, coming from interactions among amino acids. As an interactive system, the NK model of Kauffman was analysed. This model assumes that each amino acid makes a fitness contribution that depends upon the amino acid and upon K other amino acids among the N that make the protein. Through simulations, it was found that there are numerous nearly-neutral mutations in this model, and that evolution is rapid in small populations and slow in large ones. The system moves on the rugged fitness landscape by mutation, random genetic drift and selection. Small populations have more chance to attain novel genetic systems than large ones because of larger effects of random drift, but the chance of extinction becomes greater.

Animals↗

PubMed1992

Biodiversity: molecular biological domains, symbiosis and kingdom origins.

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still behave as if there were only two important kingdoms (plants and animals).

Animal Population Groups↗

PubMed2001

Modelisation of an unspecialized quadruped walking mammal.

Kinematics and structural analyses were used as basic data to elaborate a dynamic quadruped model that may represent an unspecialized mammal. Hedgehogs were filmed on a treadmill with a cinefluorographic system providing trajectories of skeletal elements during locomotion. Body parameters such as limb segments mass and length, and segments centre of mass were checked from cadavers. These biological parameters were compiled in order to build a virtual quadruped robot. The robot locomotor behaviour was compared with the actual hedgehog to improve the model and to disclose the necessary changes. Apart from use in robotics, the resulting model may be useful to simulate the locomotion of extinct mammals.

Animals↗

PubMed2006

Contributions of biogeochemistry to understanding hominin dietary ecology.

Dietary ecology is one key to understanding the biology, lifeways, and evolutionary pathways of many animals. Determining the diets of long-extinct hominins, however, is a considerable challenge. Although archaeological evidence forms a pillar of our understanding of diet and subsistence in the more recent past, for early hominins, the most direct evidence is to be found in the fossils themselves. Here we review the suite of emerging biochemical paleodietary tools based on stable isotope and trace element archives within fossil calcified tissues. We critically assess their contribution to advancing our understanding of australopith, early Homo, and Neanderthal diets within the broader context of non-biogeochemical techniques for dietary reconstruction, such as morphology and dental microwear analysis. The most significant outcomes to date are the demonstration of high trophic-level diets among Neanderthals and Late Pleistocene modern humans in Glacial Europe, and the persistent inclusion of C(4) grass-related foods in the diets of Plio-Pleistocene hominins in South Africa. Such studies clearly show the promise of biogeochemical techniques for testing hypotheses about the diets of early hominins. Nevertheless, we argue that more contextual data from modern ecosystem and experimental studies are needed if we are to fully realize their potential.

Animals↗

PubMed1992

Genetic distance and species formation in evolving populations.

We compare the behavior of the genetic distance between individuals in evolving populations for three stochastic models. In the first model reproduction is asexual and the distribution of genetic distances reflects the genealogical tree of the population. This distribution fluctuates greatly in time, even for very large populations. In the second model reproduction is sexual with random mating allowed between any pair of individuals. In this case, the population becomes homogeneous and the genetic distance between pairs of individuals has small fluctuations which vanish in the limit of an infinitely large population. In the third model reproduction is still sexual but instead of random mating, mating only occurs between individuals which are genetically similar to each other. In that case, the population splits spontaneously into species which are in reproductive isolation from one another and one observes a steady state with a continual appearance and extinction of species in the population. We discuss this model in relation to the biological theory of speciation and isolating mechanisms. We also point out similarities between these three models of evolving populations and the theory of disordered systems in physics.

Biological Evolution↗

PubMed1986

Effects of lithium and rubidium on shock-induced changes in open-field activity.

Lithium chloride and rubidium chloride were tested under conditions in which the effects of their chronic administration on aversively-controlled behavior could be assessed. Lithium attenuated shock-induced suppression of open-field activity when that suppression was under the control of mild or moderate stimulus parameters, but had no effect on the suppression produced by the presence of shock itself. Rubidium, on the other hand, increased shock-induced suppression under all conditions. When shock was removed and extinction of the activity suppression was investigated, lithium subjects failed to return to their original baseline activity levels, while subjects receiving rubidium recovered baselines in a manner indistinguishable from that observed in control animals.

Animals↗

PubMed2004

[Hallux valgus--an atavism?].

In biology, atavism is generally understood as a biological phenomenon which brings to sight a recurrent phenotypic character which was lost for extinct generations. Phylogenic evolution of homo sapiens demonstrates today that the first plantar ray in tetrapods has always been a very stable ray and the lateral foot experienced a progressive adduction to the talo-metatarsal axis, together with a remodeling of the lateral column of the foot and a progressive valgus of the calcaneus beneath the talus. The foot appears as a strongly modified extremity, starting at a prehensile foot organ, common to our ancestors. In homo sapiens, the hand became a very mobile, less loaded organ, while the foot became a rather less mobile, but more loaded organ. The first ray, distal to Lisfranc's ligament, has no ligamentous structure holding it to the second ray. Stability is thus precarious and controlled by extrinsic and intrinsic muscles. Passive mobility of the tarso-metatarsal joints has been studied in vitro and in vivo. A relationship between unstable or hypermobile first ray and relevant Hallux valgus deformity has been demonstrated. Factors which facilitate the deformity are a long hallux and a functional equinus of the foot. Clinical pathology includes metatarsalgia, hammer toes, together with metatarsus primus varus and shortened gastrocnemii. Logical treatment of relevant and painful deformity includes tarso-metatarsal fusion with or without fusion to the second metatarsus. Osteotomies seem less secure in severe cases on the long run. In conclusion, Hallux valgus cannot be considered as an atavism because clinical history and findings do not correspond to the archaic prehensile foot and its evolution, but rather do correspond to a weak spot on a (still) fragile, often overloaded, phylogenetically young organ.

Child↗

PubMed1999

Phosphorescent platinum/palladium coproporphyrins for time-resolved luminescence microscopy.

Streptavidin and antibodies were labeled with phosphorescent platinum and palladium coproporphyrin. The optimal conjugates were selected on the basis of spectroscopic analysis (molar extinction coefficient, quantum yield, lifetime) and using ELISA assays to determine the retention of biological activity and immunospecificity. They were subsequently tested for the detection of prostate-specific antigen, glucagon, human androgen receptor, p53, and glutathione transferase in strongly autofluorescent tissues. Furthermore, platinum and palladium coproporphyrin-labeled dUTPs were synthesized for the enzymatic labeling of DNA probes. Porphyrin-labeled DNA probes and porphyrin-labeled streptavidin conjugates were evaluated for DNA in situ hybridization on metaphase spreads, using direct and indirect methods, respectively. The developed in situ detection technology is shown to be applicable not only in mammals but also in plants. A modular- based time-resolved microscope was constructed and used for the evaluation of porphyrin-stained samples. The time-resolved module was found suitable for detection of antigens and DNA targets in an autofluorescent environment. Higher image contrasts were generally obtained in comparison with conventional detection systems (e.g., fourfold improvement in detection of glutathione transferase).

Acyltransferases↗

PubMed2001

Amygdala lesions block conditioned enhancement of the early component of the rat eyeblink reflex.

A tone conditioned stimulus (CS) previously paired with a grid shock unconditioned stimulus (US) can greatly enhance the early electromyographic (EMG) component (R1) of the rat eyeblink reflex. The hypothesis that the central nucleus of the amygdala (ACe) is an essential part of the circuitry mediating conditioned R1 enhancement was tested. After bilateral ACe lesions (L) or a sham operation (S), rats received paired presentations of the CS and US (P) or explicitly unpaired CS and US presentations (U), resulting in 4 groups: P/S, P/L, U/S, and U/L. ACe lesions completely prevented conditioned R1 enhancement, which was only exhibited in Group P/S. In the latter group, the "preextinction" conditioned enhancement effect was roughly a 2-fold increase in the R1 magnitude. Circuit-level mechanisms are discussed, and some advantages of the eyeblink EMG response in this general conditioning paradigm are considered.

Acoustic Stimulation↗

PubMed1992

Planetary protection issues and the future exploration of Mars.

A primary scientific theme for the Space Exploration Initiative (SEI) is the search for life, extant or extinct, on Mars. Because of this, concerns about Planetary Protection (PP), the prevention of biological cross-contamination between Earth and other planets during solar system exploration missions, have arisen. A recent workshop assessed the necessity for, and impact of, PP requirements on the unmanned and human missions to Mars comprising the SEI. The following ground-rules were adopted: 1) information needed for assessing PP issues must be obtained during the unmanned precursor mission phase prior to human landings; 2) returned Mars samples will be considered biologically hazardous until proven otherwise; 3) deposition of microbes on Mars and exposure of the crew to Martian materials are inevitable when humans land; and, 4) human landings are unlikely until it is demonstrated that there is no harmful effect of Martian materials on terrestrial life forms. These ground-rules dictated the development of a conservative PP strategy for precursor missions. Key features of the proposed strategy include: 1) for prevention of forward contamination, all orbiters will follow Mars Observer PP procedures for assembly, trajectory, and lifetime. All landers will follow Viking PP procedures for assembly, microbial load reduction, and bioshield; and, 2) for prevention of back contamination, all sample return missions will have PP requirements which include fail-safe sample sealing, breaking contact chain with the Martian surface, and containment and quarantine analysis in an Earth-based lab. In addition to deliberating on scientific and technical issues, the workshop made several recommendations for dealing with forward and back contamination concerns from non-scientific perspectives.

Containment of Biohazards↗

PubMed1985

Effect of classical conditioning on an internal clock.

Six experiments with rats used a psychophysical choice procedure to study the internal clock used to discriminate duration. They investigated if the clock is sensitive to the signal value (associative strength) of a stimulus. The experiments involved two types of trials. On choice trials, a stimulus lasted a short (e.g., 3 s) or long (e.g., 12 s) duration; then the rats chose between two levers. The rewarded choice depended on the duration of the stimulus. On conditioning trials, the stimulus used on choice trials was presented, but it ended without food (extinction trials) or with food (pairing trials) regardless of what the rat did. The main stimulus minus accuracy with the long stimulus. Experiment 1 showed that extinction trials increased short bias relative to training without conditioning trials or to training with pairing trials. The rest of the experiments tested explanations of these results. The same results were found when extinction trials were the same duration as the short stimulus (Experiment 2), when extinction trials were a random duration (Experiment 5), and when the signal value of the conditioned stimulus was changed in another way (Experiment 6). The effect of conditioning trials was modality specific (Experiments 3 and 4). Of the explanations considered, the best one--the only one not contradicted at least once--is that changing the signal value of a stimulus changes how the clock times the stimulus. Reducing signal value reduces the measured duration.

Animals↗

PubMed1991

Self-similarity in biological classifications.

Size distributions of supraspecific taxa, e.g. genera, measured as the number of included subtaxa, e.g. species, are found to follow a power law. This behaviour has been verified for a number of taxa of different size and taxonomic rank, thus suggesting a fractal structure of biological classifications. This is regarded as probably dependent on evolutionary processes shaping the phylogenetic tree, especially speciation and extinction, as well as on the topological properties of developmental constraints and/or of the ecospace(s) with which the group has been confronted during its history. The role of taxonomic bias is deemphasized.

Animals↗

PubMed2005

Ancient DNA.

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

DNA↗

PubMed2007

Molecular paleoscience: systems biology from the past.

Experimental paleomolecular biology, paleobiochemistry, and paleogenetics are closely related emerging fields that infer the sequences of ancient genes and proteins from now-extinct organisms, and then resurrect them for study in the laboratory. The goal of paleogenetics is to use information from natural history to solve the conundrum of modern genomics: How can we understand deeply the function of biomolecular structures uncovered and described by modern chemical biology? Reviewed here are the first 20 cases where biomolecular resurrections have been achieved. These show how paleogenetics can lead to an understanding of the function of biomolecules, analyze changing function, and put meaning to genomic sequences, all in ways that are not possible with traditional molecular biological studies.

Animals↗