Downsized Dinosaurs: The Evolutionary Transition to Modern Birds

Living birds are the most diverse land vertebrates and the heirs of a rich chapter in the evolution of life. The origin of modern birds from animals similar to Tyrannosaurus rex is among the most remarkable examples of an evolutionary transition. A wealth of recently discovered fossils has finally settled the century-old controversy about the origin of birds and it has made the evolutionary saga toward modern birds one of the best documented transitions in the history of life. This paper reviews the evidence in support of the origin of birds from meat-eating dinosaurs, and it highlights the array of fossils that connect these fearsome animals with those that fly all around us.     

Staré Město Epipalaeolithic skull and the Palaeolithic-Neolithic Evolutionary Transition

The Epipalaeolithic find from Staré Město, Moravia was compared with upper Paleolithic Pavlovian skull Dolní Věstonice III and with four early Neolithic female skulls from Vedrovice (Moravia). The morphological changes were considered in chronological and cultural sequence.     

AstA Signaling Functions as an Evolutionary Conserved Mechanism Timing Juvenile to Adult Transition

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Fluorination of Lithium‐Excess Transition Metal Oxide Cathode Materials

Fluorination of Li‐ion cathode materials is of significant interest as it is claimed to lead to significant improvements in long‐term reversible capacity. However, the mechanism by which LiF incorporates and improves performance remains uncertain. Indeed, recent evidence suggests that fluorine is often present as a coating layer rather than incorporated into the bulk of the material. In this work, first‐principles calculations are used to investigate the thermodynamics of fluorination in transition metal oxide cathodes to determine the conditions under which bulk fluorination is possible. It is found that unlike classic well‐ordered cathodes, which cannot incorporate fluorine, disordered rock salt‐structured materials achieve significant fluorination levels due to the presence of locally metal‐poor, lithium‐rich environments that are highly preferred for fluorine. As well as explaining the fluorination process in known materials, this finding is encouraging for the development of new disordered rock salt lithium‐excess transition metal oxides, a promising new class of Li‐ion battery cathode materials that offer superior practical capacity to traditional layered oxides. In particular, it is found that bulk fluorination may serve as an alternative source of Li‐excess in these compounds that can replace the conventional substitution of a heavy redox‐inactive element on the transition metal sublattice.     

The Evolutionary Reduction of Microsporangia in Microseris (Asteraceae): Transition Genotypes and Phenotypes

Abstract: The loss of the two inner (adaxial) microsporangia (MS) on the anthers is a shared, derived character for three species of the genus Microseris (Asteraceae). In a hybrid between M. douglasii (4 MS) and M. bigelovii (2 MS), one major gene and four modifier loci are responsible for the difference in MS number. The homozygous recessive (2 MS) genotype of the major gene is necessary but not sufficient for the reduction. In addition, at least five M. bigelovii (2 MS) alleles of the three major modifiers are needed for a stable 2‐MS phenotype in all florets of a plant. One, two or three M. bigelovii alleles of the modifiers cause the random reduction or loss of some of the adaxial MS. When the major gene and two modifiers specify 2 MS and only one modifier is homozygous for the M. douglasii (4 MS) alleles, sister plants can have any phenotype from pure 2 MS to pure 4 MS. Here, we examine the phenotypic expression of these genotypes raised under the normal winter annual conditions and under long‐day conditions. In all cases, the phenotypes vary among sister plants, but the range of variation (most notably under long‐day conditions) depends on the specific modifier gene contributing the M. douglasii alleles. The phenotypic variance in one of the genotypes was decreased by a factor of ten in the depauperate heads produced in the long‐day experiment. This effect is mediated by a dependence of the MS phenotype on the position of the floret relative to the edge of the flowering head (capitulum) and directly by the size of the capitulum. Genotypes specifying phenotypes with more or less precisely two or four MS in all florets show hardly any dependence on environmental or developmental factors. The significance of these observations lies in the non‐linear, “canalized” relationship between phenotypic expression and gene dosage, which shows how a qualitative morphological change dependent on a single major gene mutation can pass through a potentially maladaptive intermediate stage.     

Evolutionary trees for the genus Bordetella

Recent data on enzyme electrophoretic mobility and DNA sequences for pertussis toxin allow the construction of evolutionary trees for various strains belonging to the genus Bordetella. In contrast to previous analyses, these data can be seen to support the separate clustering of Bordetella pertussis strains, in agreement with the traditional classification based on other phenotypic characteristics. An earlier argument placing the divergence of B. pertussis and B. parapertussis before 1912 does not follow from the evolutionary trees proposed here, which also have different implications for several other claims concerning the evolution of these strains.     

tRNA序列的进化网络研究

根据tRNA序列的反密码子,把3420 条tRNA 序列分成了21组,其中包括20 组氨基酸及1 组Stop。通过tRNA序列的相似度构建了1 组整体网络和21 组子网络,并计算了它们在不同相似度下的平均度、平均聚类系数以及平均最短路径。通过分析、比较和讨论网络中的三个重要参数,进一步说明点突变是tRNA序列进化的重要机制,并反映了它们的进化近似符合中性理论,且在同一组氨基酸和Stop 内的tRNA序列在进化历史上的同源关系更密切;同时表明了tRNA 序列在进化过程中具有自相似性。     

Interactionism and Innateness in the Evolutionary Study of Human Nature

While most researchers who use evolutionary theory to investigatehuman nature especially human sexuality describe themselves as ``interactionists', there is no clear consensus on the meaning of thisterm in this context. By interactionism most people in the fieldmean something like, both nature and nurture ``count' in thedevelopment of human psychology and behavior. Nevertheless, themultidisciplinary nature of evolutionary psychology results in a widevariety of interpretations of this general claim. Today, mostdebates within evolutionary psychology about the innateness of agiven behavioral characteristic or over its development turn as muchon which conception of ``innateness' and ``interactionism' theresearcher holds as on any empirical data they might derive.     

Evolutionary explanations for cooperation

Natural selection favours genes that increase an organism's ability to survive and reproduce. This would appear to lead to a world dominated by selfish behaviour. However, cooperation can be found at all levels of biological organisation: genes cooperate in genomes, organelles cooperate to form eukaryotic cells, cells cooperate to make multicellular organisms, bacterial parasites cooperate to overcome host defences, animals breed cooperatively, and humans and insects cooperate to build societies. Over the last 40 years, biologists have developed a theoretical framework that can explain cooperation at all these levels. Here, we summarise this theory, illustrate how it may be applied to real organisms and discuss future directions.     

细菌基因组进化的分子策略

论述了细菌基因组进化的 4个分子策略 :点突变 ,基因组内重排 ,基因水平转移 ,基因缺失。从经典的达尔文进化论角度探讨了细菌基因组进化与表型进化的关系。     

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.     

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule’s energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-transfer RNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. Although a commonly used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome.