Transitions and transversions in evolutionary descent: An approach to understanding

Summary In this paper I lay a quantitative theoretical groundwork for understanding the proportions of the possible types of base substitutions observed between 12 genes sharing a common ancestor and isolated from extant species. The experimentally observed types of base substitution between two sequenced genes do not give a direct measure of the types of base substitutions that occur during evolutionary descent. However, by use of a statistical assemblage of these observations, we can recover, without the assumption of parsimony, the conditional base substitution probabilities that determine this descent. Three methods—direct count, regression, and informational entropy maximization—are described by which these probabilities can be estimated from experimental data. The methods are complementary in that each is most useful for somewhat different types of experimental data. These methods are used to study the ratio of transversions to transitions during gene divergence. Though this ratio is not constant during divergence, it does approach a stable limiting value that in principle can vary from zero, corresponding to 100% transition differences, to infinity, corresponding to 0% transition differences. In practice the limiting ratio tends to hover around a value of two, which is expected on a random basis. However, base substitution pathways that are very nonrandom also may lead to a limiting ratio of exactly two, so that such a value is not diagnostic for random pathways. The limiting ratio can be directly calculated from a knowledge of the twelve conditional probabilities for each type of base substitution, or from a knowledge of the equilibrium base composition of the DNAs compared. An expression is given for this calculation. Fifteen years ago Jean Derancourt, Andrew Lebor and Emile Zuckerkandl (1967), analyzing the amino acid sequence of globin chains coded by nuclear genes, made the original observation that the proportion of transition differences decreases with increasing evolutionary time. Recently Brown et al. (1982) and Brown and Simpson (1982) have reported a decrease in the observed proportion of transition differences in mitochondrial DNA with increasing evolutionary divergence. The conditions that must be satisfied for this type of behavior to occur at stable base composition and with stable base substitution probabilities are defined. Multiple substitutionsper se do not lead to a decrease in transition differences with increasing evolutionary divergence.     

Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life

Summary The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family 1) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family 11) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotesin distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree. Offprint requests to: B. Labedan     

cDNA and amino acid sequences of rainbow trout (Oncorhynchus mykiss) lysozymes and their implications for the evolution of lysozyme and lactalbumin

Summary The complete 129-amino-acid sequences of two rainbow trout lysozymes (I and II) isolated from kidney were established using protein chemistry microtechniques. The two sequences differ only at position 86, I having aspartic acid and II having alanine. A cDNA clone coding for rainbow trout lysozyme was isolated from a cDNA library made from liver mRNA. Sequencing of the cloned cDNA insert, which was 1 kb in length, revealed a 432-bp open reading frame encoding an amino-terminal peptide of 15 amino acids and a mature enzyme of 129 amino acids identical in sequence to II. Forms I and II from kidney and liver were also analyzed using enzymatic amplification via PCR and direct sequencing; both organs contain mRNA encoding the two lysozymes. Evolutionary trees relating DNA sequences coding for lysozymesc and α-lactalbumins provide evidence that the gene duplication giving rise to conventional vertebrate lysozymesc and to lactalbumin preceded the divergence of fishes and tetrapods about 400 Myr ago. Evolutionary analysis also suggests that amino acid replacements may have accumulated more slowly on the lineage leading to fish lysozyme than on those leading to mammal and bird lysozymes.     

Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences

Summary Parsimony trees relating DNA sequences coding for lysozymesc and -lactalbumins suggest that the gene duplication that allowed lactalbumin to evolve from lysozyme preceded the divergence of mammals and birds. Comparisons of the amino acid sequences of additional lysozymes and lactalbumins are consistent with this view. When all base positions are considered, the probability that the duplication leading to the lactalbumin gene occurred after the start to mammalian evolution is estimated to be 0.05–0.10. Elimination of the phylogenetic noise generated by fast evolution and compositional bias at third positions of codons reduced this probability to 0.002–0.03. Thus the gene duplication may have long preceded the acquisition of lactalbumin function.     

Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted, simulated trees. As an example we have used Monte Carlo simulation to test the constancy of evolutionary rates in a set of cytochrome-c protein sequences. Correspondence to: J. Dopazo     

Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals

The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs.     

Establishment of a novel gene expression method,BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin

In this study, we describe a novel method for producing valuable chemicals from glucose and xylose in Escherichia coli. The notable features in our method are avoidance of plasmids and expensive inducers for foreign gene expression to reduce production costs; foreign genes are knocked into the chromosome, and their expression is induced with xylose that is present in most biomass feedstock. As loci for the gene knock-in, lacZYA and some pseudogenes are chosen to minimize unexpected effects of the knock-in on cell physiology. The promoter of xylF is inducible with xylose and is combined with the T7 RNA polymerase–T7 promoter system to ensure strong gene expression. This expression system was named BICES (biomass-inducible chromosome-based expression system). As examples of BICES application, 2,3-butanediol and acetoin were successfully produced from glucose and xylose, and the maximal concentrations reached 54 g L⁻¹ [99.6% in (R,S)-form] and 31 g L⁻¹, respectively. 2,3-Butanediol and acetoin are industrially important chemicals that are, at present, produced primarily through petrochemical processes. To demonstrate usability of BICES in practical situations, we produced these chemicals from a saccharified cedar solution. From these results, we can conclude that BICES is suitable for practical production of valuable chemicals from biomass.     

The need of hypothesis-driven designs and conceptual models in impact assessment studies: An example from the free-living marine nematodes

The literature on the use of marine nematodes as bioindicators of anthropogenic impact is extensive. Nevertheless, review studies have reported a high degree of variability among results and no consistent overall pattern has so far emerged. This lack of congruence might be partially because hypotheses formulation in environmental assessment studies has been largely inductive or abductive and not deductive or hypothesis-driven. In the present study, we emphasize the need of using hypothesis-driven designs and conceptual models in impact assessment studies. Hypotheses for individual and population level studies can be derived from the dynamic energy budget model (DEB). By means of differential equations, DEB model can infer whether a stressor promotes a shift in energy allocation along the life history of the individuals. For community/assemblage level studies, the predictions of the dynamic equilibrium model (DEM) for species richness is presented and extended for abundance, evenness, taxonomic distinctness, and changes in assemblage structure and sample dispersion. While it is predicted that species richness peaks at intermediate levels of disturbances and enrichment, evenness decreases with increasing disturbances and reducing enrichment/pollutant concentrations. Based on DEM,enrichment and pollutants may promote change in community structure by favoring the tolerant species, while physical disturbances may promote sample dispersion as a result of unselective mortality. Finally, we discuss the benefits of using niche-based models to select the indicator species, instead of using classical ordination methods, twinspan and similarity percentage analysis. The selection of indicator species have to be independent from the other species and must consider the set of environmental conditions. The use of conceptual models to select the best ecological indicators is highly recommended. It allows a logical way of testing for causalities and of scaling the different studies for comparisons.     

A small basic ribosomal protein in Sulfolobus solfataricus equivalent to L46 in yeast: structure of the protein and its gene

The structure of the gene for a small, very basic ribosomal protein in Sulfolobus solfataricus has been determined and the structure of the protein coded by this gene (L46e) has been confirmed by partial amino acid sequencing. The protein shows substantial sequence homology to the eukaryotic ribosomal proteins L39 in rat and L46 in yeast. There is no sequence homology to any of the eubacterial ribosomal proteins suggesting that this protein is absent in the eubacterial ribosome.     

Quantification of catch composition in fisheries: A methodology and its application to compare biodegradable and nylon gillnets

When evaluating fishing gear catches, the focus is often on a few species as opposed to the entire catch. In some fisheries this can lead to ignoring major part of catch composition. Thus, there is a need for a more holistic approach when evaluating the ecological impact of using a specific fishing gear and when comparing two or more gears. In this context, it is relevant to have a method that describes the total catch and quantifies proportions of the catch being wanted and unwanted. In this study, we outline such a method and demonstrate its applicability to catch data from a small-scale coastal gillnet fishery targeting European plaice (Pleuronectes platessa, Linnaeus, 1758) by comparing catch composition when using nylon and biodegradable gillnets. The results showed no significant differences in catch composition between gillnets made of the two materials. Therefore, the catch composition obtained using the more environmentally friendly biodegradable materials does not represent a barrier in this specific gillnet fishery. However, species selectivity of gillnets is still of concern as the primary target species constituted only half of the total catch composition in numbers while the rest was unwanted catch. The presented approach for quantifying and inferring the differences in catch composition can be further applied for assessing the performance of different fishing gears and their modifications.     

Morphological and thermal properties of mammalian insulation: the evolutionary transition to blubber in pinnipeds

Carnivora includes three independent evolutionary transitions to the marine environment: pinnipeds (seals, sea lions, and walruses), sea otters, and polar bears. Among these, only the pinnipeds have retained two forms of insulation, an external fur layer and an internal blubber layer for keeping warm in water. In this study we investigated key factors associated with the transition to the use of blubber, by comparing blubber characteristics among the pinnipeds. Characteristics included gross morphology (blubber thickness), fat composition (fatty acid profiles, percentage lipid, and water), and thermal conductivity. Sea lions, phocids, and walrus, which have lower fur densities than fur seals, have thicker blubber layers than fur seals (P < 0.001). Comparisons of lipid content, water content, and fatty acid composition indicated significant differences in the composition of the inner and outer regions of the blubber between groups (P < 0.001), consistent with the hypothesis that phocids and sea lions utilize the outer layer of their blubber primarily for thermal insulation, and the inner layer for energy storage. Fur seals, by contrast, rely more on their fur for thermal insulation, and utilize their blubber layer primarily for energy storage. Comparing across carnivore species, differences in total insulation (fur and/or blubber) are influenced substantially by body size and habitat, and to a lesser extent by latitudinal climate. Overall, these results indicate consistent evolutionary trends in the transition to blubber and evidence for convergent evolution of thermal traits across lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

A small basic ribosomal protein in Sulfolobus solfataricus equivalent to L46 in yeast: Structure of the protein and its gene

The structure of the gene for a small, very basic ribosomal protein in Sulfolobus solfataricus has been determined and the structure of the protein coded by this gene (L46e) has been confirmed by partial amino acid sequencing. The protein shows substantial sequence homology to the eukaryotic ribosomal proteins L39 in rat and L46 in yeast. There is no sequence homology to any of the eubacterial ribosomal proteins suggesting that this protein is absent in the eubacterial ribosome.     

Evolution and instability in ring species complexes: An in silico approach to the study of speciation

Ring species are a biological complex that theoretically forms when an ancestral population extends its range around a geographic barrier and, despite low-level gene flow, differentiates until reproductive isolation exists when terminal populations come into secondary contact. Due to their rarity in nature, little is known about the biological factors that promote the formation of ring species. We use evolutionary algorithms operating on two simple computational problems (SAW and K-max) to study the process of speciation under the conditions which may yield ring species. We vary evolutionary parameters to measure their influence on ring species’ development and stability over evolutionary time. Using the SAW problem, ring species consistently form, i.e. fertility is negatively correlated with distance (R-values between −0.097 and −0.821, p<0.001), and terminal populations show substantial infertility. However, all SAW simulations demonstrate instability in the complex after sympatric zones are established between terminal populations. Higher mutation rates and larger dispersal/breeding radii promote ring species’ formation and stability. Using a problem with a simple fitness landscape, the K-max problem, ring species do not form. Instead, speciation around the ring occurs before ring closure as good genotypes become locally dominant.     

Developmental change in RNA: DNA ratios of fed and starved laboratory-reared Japanese flounder larvae and juveniles, and its application to assessment of nutritional condition for wild fish

Starved Japanese flounder Paralichthys olivaceus larvae were characterized by relatively lower levels of RNA content throughout their early life stages. Significant differences in the RNA: DNA ratios were found between fed and starved fish, and appeared to increase as starvation proceeded. Ontogenetic changes in RNA: DNA ratios were clearly observed during metamorphosis, especially decreasing during the period from the late-metamorphic to postmetamorphic stages. The criteria established from these laboratory experiments, were applied to the nutritional condition of wild larvae and juveniles collected in Wakasa Bay, Sea of Japan in 1994 and 1995 by measuring RNA and DNA content. Starved fish were mainly found in stage I (settling stage) fish during the late season of settlement in 1995. This suggests that starvation could be associated with settlement in Japanese flounder.     

Hydrogen-isotope composition of leaf water in C3 and C4 plants: its relationship to the hydrogen-isotope composition of dry matter

The natural abundance hydrogen-isotope composition of leaf water ( ) and leaf organic matter ( _D ^org ) was measured in leaves of C₃ and C₄ dicotyledons and monocotyledons. The value of leaf water showed a marked diurnal variation, greatest enrichment being observed about midday. However, this variation was greater in the more slowly transpiring C₄ plants than in C₃ plants under comparable environmental conditions. A model based on analogies with a constant feed pan of evaporating water was developed and the difference between C₃ and C₄ plants expressed in terms of either differences in kinetic enrichment or different leaf morphology. Microclimatic and morphological features of the leaves which may be associated with this factor are discussed. There was no daily excursion in the _D ^org value in leaves of either C₃ or C₄ plants. When _D ^org values were referenced to the mean values during the period of active photosynthesis, the discrimination against deuterium during photosynthetic metabolism (D) was greater in C₃ plants (-117 to -121) than in C₄ plants (-86 to -109).These results show that the different water use strategies of C₃ and C₄ plants are responsible for the measured difference in deuterium-isotope composition of leaf water. However, it is unlikely that these physical processes account fully for the differences in hydrogen-isotope composition of the products of C₃ and C₄ photosynthetic metabolism.Symbols Hydrogen-isotope composition of leaf water - _D ^org hydrogen-isotope composition of leaf organic matter     

An analysis of genetic stock identification on a small geographical scale using microsatellite markers,and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed‐stock fishery to an almost exclusively single‐stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.