DNA–DNA Hybridization Evidence for the Recent Origin of Marmots and Ground Squirrels (Rodentia: Sciuridae)

A molecular analysis, based on DNA/DNA hybridization experiments, examined seven species of the sciurid tribe Marmotini, in order to evaluate their evolutionary relationships. The branching pattern obtained from a neighbor-joining analysis and least-squares methods indicates that spermophiles and marmots are closely related. This result is in agreement with previous studies based on biochemical data which have suggested a Miospermophilus origin of Marmota (like Spermophilus), instead of the Protospermophilus origin usually proposed by paleontology. Using a molecular time scale calibrated by the fossil record of Sciurus (used here as an outgroup), we estimate the marmot/ground squirrel divergence at 6 My, at the same time as the major lineages of ground squirrels diverged from each other. Consequently, the species of Marmota appear as one of the numerous specialized forms derived from the explosive radiation of the Spermophilus lineage in the late Miocene.     

Origin of glutaminyl-tRNA synthetase: An example of palimpsest?

Sequence data and evolutionary arguments suggest that a similarity may exist between the C-terminal end of glutaminyl-tRNA synthetase (GlnRS) and the catalytic domain of glutamine amidotransferases (GATs). If true, this would seem to imply that the amidation reaction of the Glu-tRNA^GIn complex was the evolutionary precursor of the direct tRNA^GIn aminoacylation pathway. Since the C-terminal end of GlnRS does not now have an important functional role, it can be concluded that this sequence contains vestiges that lead us to believe that it represents a palimpsest. This sequence still conserves the remains of the evolutionary transition: amidation reaction aminoacylation reaction. This may be important in deciding which mechanism gave origin to the genetic code organization. These observations, together with results obtained by Gatti and Tzagoloff [J. Mol. Biol. (1991) 218: 557–568], lead to the hypothesis that the class I aminoacyl-tRNA synthetases (ARSs) may be homologous to the GATs of the trpG subfamily, while the class Il ARSs may be homologous to the GATs of the purF subfamily. Overall, this seems to point to the existence of an intimate evolutionary link between the proteins involved in the primitive metabolism and aminoacyl-tRNA synthetases.     

Transfer RNATyr of melanoma tissues and cells: relevance to melanin synthesis?

The tRNA present in swine melanoma tumor tissue and normal gray skin tissue were compared by aminoacylation of the unfractionated tRNA preparations. Of the seventeen amino acids studied, seven showed differences in rate of acceptance to tRNAs from normal and tumor tissues; the tRNAs of two amino acids, tyrosine and glycine, showed dramatic three fold increases in melanoma tumor. As melanin biosynthesis proceeds from tyrosine oxidation the investigations focused on the increase in tyrosine tRNA. Kinetic analysis of tyrosine aminoacylation to normal and melanoma tRNAs revealed no differences. Analysis of the isoaccepting species of tRNATyr from normal skin and melanoma tumor tissues identified three isoacceptors; tRNATyr, represented the predominant species in normal gray skin, while tRNA2Tyr predominated in melanoma tumor tissue. The tyrosine acceptances by tRNAs from three human melanoma cell lines were analyzed and found to be variable, but isoaccepting species analysis of the tRNATyr of these three cell lines still showed a correlation between the preponderance of tRNA2Tyr and extent of tyrosine acceptance. Additionally the enzymatic activity for the oxidation of tyrosine was found to be related to tyrosine acceptance and tRNA2Tyr predominance..     

Growth Patterns of Two Marine Isolates: Adaptations to Substrate Patchiness?

During bottle incubations of heterotrophic marine picoplankton, some bacterial groups are conspicuously favored. In an earlier investigation bacteria of the genus Pseudoalteromonas rapidly multiplied in substrate-amended North Sea water, whereas the densities of Oceanospirillum changed little (H. Eilers, J. Pernthaler, and R. Amann, Appl. Environ. Microbiol. 66:4634–4640, 2000). We therefore studied the growth patterns of two isolates affiliating with Pseudoalteromonas and Oceanospirillum in batch culture. Upon substrate resupply, Oceanospirillum lagged threefold longer than Pseudoalteromonas but reached more than fivefold-higher final cell density and biomass. A second, mobile morphotype was present in the starved Oceanospirillum populations with distinctly greater cell size, DNA and protein content, and 16S rRNA concentration. Contrasting cellular ribosome concentrations during stationary phase suggested basic differences in the growth responses of the two strains to a patchy environment. Therefore, we exposed the strains to different modes of substrate addition. During cocultivation on a single batch of substrates, the final cell densities of Oceanospirillum were reduced three times as much as those Pseudoalteromonas, compared to growth yields in pure cultures. In contrast, the gradual addition of substrates to stationary-phase cocultures was clearly disadvantageous for the Pseudoalteromonas population. Different growth responses to substrate gradients could thus be another facet affecting the competition between marine bacteria and may help to explain community shifts observed during enrichments.     

Origin of sucrose metabolism in higher plants: when,how and why?

Since the discovery of sucrose biosynthesis, considerable advances have been made in understanding its regulation and crucial role in the functional biology of plants. However, important aspects of this metabolism are still an enigma. Studies in cyanobacteria and the publication of the sequences of several complete genomes have recently significantly increased our knowledge of the structures of proteins involved in sucrose metabolism and given us new insights into their origin and further evolution.     

Hybridization and speciation in angiosperms: a role for pollinator shifts?

The majority of convincingly documented cases of hybridization in angiosperms has involved genetic introgression between the parental species or formation of a hybrid species with increased ploidy; however, homoploid (diploid) hybridization may be just as common. Recent studies, including one in BMC Evolutionary Biology, show that pollinator shifts can play a role in both mechanisms of hybrid speciation.     

Darwin,Malthus, Süssmilch,and Euler: The Ultimate Origin of the Motivation for the Theory of Natural Selection

It is fairly well known that Darwin was inspired to formulate his theory of natural selection by reading Thomas Malthus’s Essay on the Principle of Population. In fact, by reading Darwin’s notebooks, we can even locate one particular sentence which started Darwin thinking about population and selection. What has not been done before is to explain exactly where this sentence – essentially Malthus’s ideas about geometric population growth – came from. In this essay we show that eighteenth century mathematician Leonhard Euler is responsible for this sentence, and in fact forms the beginning of the logical chain which leads to the creation of the theory of natural selection. We shall examine the fascinating path taken by a mathematical calculation, the many different lenses through which it was viewed, and the path through which it eventually influenced Darwin.     

The Origin and Evolution of Metabolic Pathways: Why and How did Primordial Cells Construct Metabolic Routes?

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present on the primordial Earth imposed an important selective pressure, favoring those primordial heterotrophic cells that became able to synthesize those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria, and Eukarya reveal that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the emergence of new metabolic abilities. Among these gene elongations, gene and operon duplications played a crucial role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence, giving rise to new genes coding for new metabolic abilities. Concerning the mechanisms of pathway assembly, both the analysis of completely sequenced genomes and directed evolution experiments strongly support the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis, suggests that other different hypothesis, i.e., the retrograde hypothesis, may account for the evolution of some steps within metabolic pathways.     

Outcomes of Extensive Hybridization and Introgression in Epidendrum (Orchidaceae): Can We Rely on Species Boundaries?

Hybridization has the potential to contribute to phenotypic and genetic variation and can be a major evolutionary mechanism. However, when hybridization is extensive it can also lead to the blurring of species boundaries and the emergence of cryptic species (i.e., two or more species not distinguishable morphologically). In this study, we address this hypothesis in Epidendrum, the largest Neotropical genus of orchids where hybridization is apparently so common that it may explain the high levels of morphological diversity found. Nonetheless, this hypothesis is mostly based on the intermediacy of morphological characters and intermediacy by itself is not a proof of hybridization. Therefore, in this study, we first assessed the existence of hybrids using cpDNA and AFLP data gathered from a large-scale sampling comprising 1038 plants of three species of Epidendrum (E. calanthum, E. cochlidium and E. schistochilum). Subsequently, a Bayesian assignment of individuals into different genetic classes (pure species, F1, F2 or backcross generations) revealed that hybrid genotypes were prevalent in all sympatric populations. In most cases, parental species were not assigned as pure individuals, rather consisting in backcrossed genotypes or F₁ hybrids. We also found that reproductive barriers are apparently very weak in Epidendrum because the three species largely overlapped in their flowering periods and interspecific crosses always produced viable seeds. Further, hybridization contributed to enhance floral variability, genome size and reproductive success since we found that these traits were always higher in hybrid classes (F1, F2 and backcrosses) than in pure parental species, and offer an explanation for the blurring of species boundaries in this genus of orchids. We hypothesize that these natural hybrids possess an evolutionary advantage, which may explain the high rates of cryptic species observed in this genus.     

Causation and the Origin of Life. Metabolism or Replication First?

The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. In conjunction with existing empirical evidence and theoretical reasoning, our analysis concludes that there is no substantive evidence for a 'metabolism first' mechanism for life's emergence, while a coherent case can be made for the 'replication first' group of mechanisms. The analysis reaffirms our conviction that life is an extreme expression of kinetic control, and that the emergence of metabolic pathways can be understood by considering life as a manifestation of 'replicative chemistry'.     

Sex and Status Effects on Primate Volubility: Clues to the Origin of Vocal Languages?

Natural human languages are predominantly vocal. This suggests that, during evolution, speech may have enhanced the efficiency, utility, or flexibility of previous vocal behaviors. If so, there may be parallels between certain aspects of the vocalization patterns of human and nonhuman primates. The literature on humans contains evidence for greater frequency of vocalization, or volubility, between female–female than male–male dyads, and greater volubility among individuals of higher than lower social rank or status. We analyzed two classes of vocalization in free-ranging vervet monkey infants. In both classes, females vocalized significantly more often than males, and high-ranking animals were more voluble than mid- and low-ranking animals. If these findings are confirmed in primates other than vervets, it is conceivable that the voice contributes to the solution of some pan-primate problems, offering clues to the vocal bias in human languages.     

Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change?

Understanding the degree of genetic exchange between subspecies and populations is vital for the appropriate management of endangered species. Blue whales (Balaenoptera musculus) have two recognized Southern Hemisphere subspecies that show differences in geographic distribution, morphology, vocalizations and genetics. During the austral summer feeding season, the Antarctic blue whale (B. m. intermedia) is found in polar waters and the pygmy blue whale (B. m. brevicauda) in temperate waters. Here, we genetically analyzed samples collected during the feeding season to report on several cases of hybridization between the two recognized blue whale Southern Hemisphere subspecies in a previously unconfirmed sympatric area off Antarctica. This means the pygmy blue whales using waters off Antarctica may migrate and then breed during the austral winter with the Antarctic subspecies. Alternatively, the subspecies may interbreed off Antarctica outside the expected austral winter breeding season. The genetically estimated recent migration rates from the pygmy to Antarctic subspecies were greater than estimates of evolutionary migration rates and previous estimates based on morphology of whaling catches. This discrepancy may be due to differences in the methods or an increase in the proportion of pygmy blue whales off Antarctica within the last four decades. Potential causes for the latter are whaling, anthropogenic climate change or a combination of these and may have led to hybridization between the subspecies. Our findings challenge the current knowledge about the breeding behaviour of the world's largest animal and provide key information that can be incorporated into management and conservation practices for this endangered species.     

How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations

Cholesteryl ester transfer protein (CETP) mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides) and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL)-cholesterol and decrease low density lipoprotein (LDL)-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases.     

The Creativity of Natural Selection? Part I: Darwin,Darwinism, and the Mutationists

This is the first of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. Here I focus on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled “mutationists.” The second part focuses on the evolutionary synthesis and some of its critics, especially the “neutralists” and “neo-mutationists.” Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as “Darwinism.” I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection being responsible for the presence of the variation it acts upon, for example by directing the course of variation. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.     

Origin and Evolution of GALA-LRR,a New Member of the CC-LRR Subfamily: From Plants to Bacteria?

The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.