Cooperation: integrating evolutionary and ecological perspectives

Putting a competitive squeeze on a cooperative group has long been considered to encourage cheats. Now we learn that competition, by driving diversification among cooperators, can create groups that are both more productive and more resistant to defection.     

Chromothripsis,a credible chromosomal mechanism in evolutionary process

Chromosoma - The recent discovery of a new class of massive chromosomal rearrangements, occurring during one unique cellular event and baptized “chromothripsis,” deeply modifies our...     

Progressive improvement in the transfer of maternal antibody across the order Primates

Antibody levels were determined in adults and newborn offspring of five primate species. This cross-species comparison of intant IgG levels indicated that prosimians and New World monkeys transfer lower levels of maternal antibody via placental transmission than do Old World monkeys, apes, and humans. The evolutionary trend toward an increased reliance on prenatal antibody transfer in the higher primates appears to be most pronounced in the human infant, because our placenta has evolved an active transport process that elevates IgG in the full-term fetus over maternal levels. Higher IgG levels in the young infant ensure a more prolonged and successful period of passive immunity against pathogens previously encountered by the mother. © 1994 Wiley-Liss, Inc.     

Introduction: integrating genetic and cultural evolutionary approaches to language

The papers in this special issue of Human Biology address recent research in the field of language evolution, both the genetic evolution of the language faculty and the cultural evolution of specific languages. While both of these areas have received increasing interest in recent years, there is also a need to integrate these somewhat separate efforts and explore the relevant gene-culture coevolutionary interactions. Here we summarize the individual contributions, set them in the context of the wider literature, and identify outstanding future research questions. The first set of papers concerns the comparative study of nonhuman communication in primates and birds from both a behavioral and neurobiological perspective, revealing evidence for several common language-related traits in various nonhuman species and providing clues as to the evolutionary origin and function of the human language faculty. The second set of papers discusses the consequences of viewing language as a culturally evolving system in its own right, including claims that this removes the need for strong genetic biases for language acquisition, and that phylogenetic evolutionary methods can be used to reconstruct language histories. We conclude by highlighting outstanding areas for future research, including identifying the precise selection pressures that gave rise to the language faculty in ancestral hominin species, and determining the strength, domain specificity, and origin of the cultural transmission biases that shape languages as they pass along successive generations of language learners.     

Understanding the function of bacterial and eukaryotic thiolases II by integrating evolutionary and functional approaches

Acetoacetyl-CoA thiolase (EC 2.3.1.9), commonly named thiolase II, condenses two molecules of acetyl-CoA to give acetoacetyl-CoA and CoA. This enzyme acts in anabolic processes as the first step in the biosynthesis of isoprenoids and polyhydroxybutyrate in eukaryotes and bacteria, respectively. We have recently reported the evolutionary and functional equivalence of these enzymes, suggesting that thiolase II could be the rate limiting enzyme in these pathways and presented evidence indicating that this enzyme modulates the availability of reducing equivalents during abiotic stress adaptation in bacteria and plants. However, these results are not sufficient to clarify why thiolase II was evolutionary selected as a critical enzyme in the production of antioxidant compounds. Regarding this intriguing topic, we propose that thiolase II could sense changes in the acetyl-CoA/CoA ratio induced by the inhibition of the tricarboxylic acid cycle under abiotic stress. Thus, the high level of evolutionary and functional constraint of thiolase II may be due to the connection of this enzyme with an ancient and conserved metabolic route.     

Deciphering function and mechanism of calcium-binding proteins from their evolutionary imprints

Calcium-binding proteins regulate ion metabolism and vital signalling pathways in all living organisms. Our aim is to rationalize the molecular basis of their function by studying their evolution using computational biology techniques. Phylogenetic analysis is of primary importance for classifying cognate orthologs; profile hidden Markov models (HMM) of individual subfamilies discern functionally relevant sites by conservation probability analysis; and 3-dimensional structures display the integral protein in context. The major classifications of calcium-binding proteins, viz. EF-hand, C2 and ANX, exhibit structural diversity in their HMM fingerprints at the subfamily level, with functional consequences for protein conformation, exposure of receptor interaction sites and/or binding to membrane phospholipids. Calmodulin, S100 and annexin families were characterized in Petromyzon marinus (sea lamprey) to document genome duplication and gene creation events during the key evolutionary transition to primitive vertebrates. Novel annexins from diverse organisms revealed calcium-binding domains with accessory structural features that define their unique molecular fingerprints, protein interactivity and functional specificity. These include the first single-domain, bacterial annexin in Cytophaga hutchinsonii, the 21 tetrad annexins from the unicellular protist Giardia intestinalis, an ancestor to land plant annexins from the green alga Ostreococcus lucimarinus, invertebrate octad annexins and a critical polymorphism in human ANXA7. Receptor docking models supported the hypothesis of a potential interaction between annexin and C2 domains as a propitious mechanism for ensuring membrane translocation during signal transduction.     

Electron microscopy in cell biology: integrating structure and function

Electron microscopy (EM) is at the highest-resolution limit of a spectrum of complementary morphological techniques. When combined with molecular detection methods, EM is the only technique with sufficient resolution to localize proteins to small membrane subdomains in the context of the cell. Recent procedural and technical developments have increasingly improved the power of EM as a cell-biological tool.     

Elder knowledge and sustainable livelihoods in post-Soviet Russia: finding dialogue across the generations

Russia's indigenous peoples have been struggling with economic, environmental, and socio-cultural dislocation since the fall of the Soviet Union in 1991. In northern rural areas, the end of the Soviet Union most often meant the end of agro-industrial state farm operations that employed and fed surrounding rural populations. Most communities adapted to this loss by reinstating some form of pre-Soviet household-level food production based on hunting, fishing, and/or herding. However, mass media, globalization, and modernity challenge the intergenerational knowledge exchange that grounds subsistence practices. Parts of the circumpolar north have been relatively successful in valuing and integrating elder knowledge within their communities. This has not been the case in Russia. This article presents results of an elder knowledge project in northeast Siberia, Russia that shows how rural communities can both document and use elder knowledge to bolster local definitions of sustainability and, at the same time, initiate new modes of communication between village youth and elders.     

DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning

Background  

Accurate identification of protein domain boundaries is useful for protein structure determination and prediction. However, predicting protein domain boundaries from a sequence is still very challenging and largely unsolved.     

Genetic mapping in maize with hybrid progeny across testers and generations: plant height and flowering

DNA markers were used to identify quantitative trait loci (QTLs) for plant height, ear height, and three flowering traits in hybrid progeny of two generations (F_2:3, F_6:8) of lines from a Mo17×H99 maize population. For both generations, testcross (TC) progeny were developed by crossing the lines to three inbred testers (B91, A632, B73). The hybrid progeny from the two generations were evaluated at the same locations but in different years as per an early generation testing program. QTLs were identified within each TC population and for mean testcross (MTC) performance. Overall, more QTLs were detected in the F_6:8 than the F_2:3 generation. Totalled over all five traits, 41 (B91) to 69% (B73) of the QTLs for tester effects and 67% of the QTLs for MTC detected in the F_2:3 generation were verified in the F_6:8 generation. Although differences in relative rank of the QTL effects across generations were observed, especially for the flowering traits, parental contributions were nearly always consistent. Several (8–11) QTLs were identified with effects for all three tester populations and for all traits except the anthesis-silk interval, which had only two such regions. Over all five traits, previous evaluations in this population identified 26 QTLs with consistent effects for two (F_2:3, F_6:8) inbred-progeny evaluations, and 20 (77%) were also associated with MTC in at least one of the generations evaluated herein. In all instances of common inbred and TC QTLs, parental contributions were the same. Received: 26 November 1999 / Accepted: 18 April 2000     

Light transmission in the human cornea as a function of position across the ocular surface: theoretical and experimental aspects

This article investigates the theoretical basis for differences in visible light transmission through the human cornea as a function of distance from the center. Experimentally, transmission decreases approximately linearly up to 3 mm from the central axis, then quadratically beyond this. It is known that collagen fibril number density and collagen fibril radii change from the central region to the corneal periphery. We modeled, using the direct-summation-of-scattered-fields method, the effects these ultrastructural changes would be expected to have on light transmission, accounting for the increase in corneal thickness from center to edge. Fibril positions for the modeling were obtained from electron micrographs of human cornea. Theoretically, transmission remains fairly constant across the central cornea; then, as the fibril diameter increases, the predicted scattering increases. Interfibrillar spacing changes alter the refractive index ratio between matrix and fibril; this was modeled in our theoretical deductions. Fibril number density had a minimal effect on light propagation. Our theoretical deductions were in broad agreement with our experimental data. It is concluded that the reduced transparency in the peripheral stroma is primarily caused by changes in fibril radius and an increase in refractive index ratio between the fibril and the interfibrillar substance.     

Quinolones inhibit DNA religation mediated by Staphylococcus aureus topoisomerase IV. Changes in drug mechanism across evolutionary boundaries

Quinolones are the most active oral antibacterials in clinical use and act by increasing DNA cleavage mediated by prokaryotic type II topoisomerases. Although topoisomerase IV appears to be the primary cytotoxic target for most quinolones in Gram-positive bacteria, interactions between the enzyme and these drugs are poorly understood. Therefore, the effects of ciprofloxacin on the DNA cleavage and religation reactions of Staphylococcus aureus topoisomerase IV were characterized. Ciprofloxacin doubled DNA scission at 150 nM drug and increased cleavage approximately 9-fold at 5 microM. Furthermore, it dramatically inhibited rates of DNA religation mediated by S. aureus topoisomerase IV. This inhibition of religation is in marked contrast to the effects of antineoplastic quinolones on eukaryotic topoisomerase II, and suggests that the mechanistic basis for quinolone action against type II topoisomerases has not been maintained across evolutionary boundaries. The apparent change in quinolone mechanism was not caused by an overt difference in the drug interaction domain on topoisomerase IV. Therefore, we propose that the mechanistic basis for quinolone action is regulated by subtle changes in drug orientation within the enzyme.drug.DNA ternary complex rather than gross differences in the site of drug binding.     

Induction of congenital malformation in mice by parental irradiation: transmission to later generations

In order to investigate the genetic basis of the increased incidence of congenital malformations in the offspring of irradiated mice, the frequency of malformations among the offspring of individual F1 sons of irradiated females was studied in detail. Among 90 fully tested F1 sons of females which had been mated 15-21 days after receiving 360 cGy X-rays 4 were definite or probable carriers of dominant genes giving a low penetrance of malformations. This confirms that the malformations seen in the first generation are of genetic origin and can be transmitted to later generations. However, the incidence and penetrance of the mutant genes detected were too low to account for all the anomalies found in the first generation. It was concluded that the genetic basis of the original anomalies was heterogeneous, with some due to genetic changes of high penetrance and rapidly eliminated, and others due to genes of low penetrance like those found in this work. Other malformations, in both the irradiated and control series, were probably of non-genetic origin.     

Plant physiological ecology: An essential link for integrating across disciplines and scales in plant ecology

A sizeable number of scientists and funding organisations are of the opinion that the relevance of plant physiological ecology as an important discipline has declined to the point that it is no longer considered as one of the important topics of ecological research. Plant physiological ecology is typically associated with the autecological plant research conducted during the latter portion of the 20th century or, even worse, simply with gas exchange measurements. However, taking a closer look, it becomes obvious that, by focusing on the intermediate integration levels (individuals, populations), this discipline represents an essential link between the high integration levels (communities, ecosystems, biosphere) and the disciplines at the bottom of the complexity hierarchy (physiology, molecular biology). In this paper we show that the principal question of all ongoing community and ecosystem level research – What is the mechanistic background of vegetation composition, biodiversity structure and dynamics and how is this linked to fluxes of matter at the community and higher levels of organisation? – can only be answered if the mechanism of interactions between the relevant organisms are understood. In consequence, the classical discipline of plant physiological ecology will continuously develop into a truly interdisciplinary experimental ecology of interactions and its importance will rather increase than diminish. Promising activities of this kind are already underway. Scientists needed for this new direction should have a rather broad scientific perspective, including knowledge and experience in fields outside of typical ecological research, instead of being specialists for single ecophysiological aspects.     

Bacterial mechanosensitive channels: integrating physiology, structure and function.

When confronted with hypo-osmotic stress, many bacterial species are able rapidly to adapt to the increase in cell turgor pressure by jettisoning cytoplasmic solutes into the medium through membrane-tension-gated channels. Physiological studies have confirmed the importance of these channels in osmoregulation. Mutagenesis of one of these channels, combined with structural information derived from X-ray crystallography, has given the first clues of how a mechanosensitive channel senses and responds to membrane tension.     

Hemoglobin function in the vertebrates: An evolutionary model

Comparative data on quaternary structure, cooperativity, Bohr effect and regulation by organic phosphates are reviewed for vertebrate hemoglobins. A phylogeny of hemoglobin function in the vertebrates is deduced. It is proposed that from the monomeric hemoglobin of the common ancestor of vertebrates, a deoxy dimer, as seen in the lamprey, could have originated with a single amino acid substitution. The deoxy dimer has a Bohr effect, cooperativity and a reduced oxygen affinity compared to the monomer. One, or two, additional amino acid substitutions could have resulted in the origin of a tetrameric deoxy hemoglobin which dissociated to dimers on oxygenation. Gene duplication, giving incipient alpha and beta genes, probably preceded the origin of a tetrameric oxyhemoglobin. The origin of an organic phosphate binding site on the tetrameric hemoglobin of an early fish required only one, or two, amino acid substitutions. ATP was the first organic phosphate regulator of hemoglobin function. The binding of ATP by hemoglobin may have caused the original elevation in the concentration of ATP in the red blood cells by relieving end product inhibition of ATP synthesis. The switch from regulation of hemoglobin function by ATP to regulation by DPG may have been a consequence of the curtailment of oxidative phosphorylation in the red blood cell. The basic mechanisms by which ATP and DPG concentrations can respond to strss on the oxygen transport system were present before the origin of an organic phosphate binding site on hemoglobin. A switch from ATP regulation to IP5 regulation occurred in the common ancestor of birds.