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PubMed2005

Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance.

The origin of tetraploid wheat and the divergence of diploid ancestors of wheat A and D genomes were estimated to have occurred 0.36 and 2.7 million years ago, respectively. These estimates and the evolutionary history of 3159 gene loci were used to estimate the rates with which gene loci have been deleted and duplicated during the evolution of wheat diploid ancestors and during the evolution of polyploid wheat. During diploid evolution, the deletion rate was 2.1 x 10(-3) locus(-1) MY(-1) for single-copy loci and 1.0 x 10(-2) locus(-1) MY(-1) for loci in paralogous sets. Loci were duplicated with a rate of 2.9 x 10(-3) locus(-1) MY(-1) during diploid evolution. During polyploid evolution, locus deletion and locus duplication rates were 1.8 x 10(-2) and 1.8 x 10(-3) locus(-1) MY(-1), respectively. Locus deletion and duplication rates correlated positively with the distance of the locus from the centromere and the recombination rate during diploid evolution. The functions of deleted and duplicated loci were inferred to gain insight into the surprisingly high rate of deletions of loci present apparently only once in a genome. The significance of these findings for genome evolution at the diploid and polyploid level is discussed.

Centromere↗
PubMed2006

Morphological evolution is accelerated among island mammals.

Dramatic evolutionary changes occur in species isolated on islands, but it is not known if the rate of evolution is accelerated on islands relative to the mainland. Based on an extensive review of the literature, I used the fossil record combined with data from living species to test the hypothesis of an accelerated morphological evolution among island mammals. I demonstrate that rates of morphological evolution are significantly greater--up to a factor of 3.1--for islands than for mainland mammal populations. The tendency for faster evolution on islands holds over relatively short time scales--from a few decades up to several thousands of years--but not over larger ones--up to 12 million y. These analyses form the first empirical test of the long held supposition of accelerated evolution among island mammals. Moreover, this result shows that mammal species have the intrinsic capacity to evolve faster when confronted with a rapid change in their environment. This finding is relevant to our understanding of species' responses to isolation and destruction of natural habitats within the current context of rapid climate warming.

Animals↗
PubMedDate not supplied

Pleiotropic mutation, modularity and evolvability.

The relationship between pleiotropy and the rate of evolution of a phenotypic character (evolvability) in a population is explored using computer simulations. I present results that suggest the rate of evolution of a phenotypic character may not decline when that character is pleiotropically associated to an increasing number of other characters, provided that the characters are under pure directional selection such that they are far from their optima relative to the average magnitude of a mutation. These conditions may be relevant during adaptive radiations. Adding pleiotropic associations to a set of characters in which one is under directional selection and the other is under stabilizing selection increases the rate of adaptation of the character under directional selection provided that the new characters that come to be pleiotropically associated are under directional selection. Thus, increasing the number of pleiotropic associations under these conditions increases the rate of adaptation of a character.

Adaptation, Physiological↗
PubMed2001

The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

Adaptation, Biological↗
PubMed1990

Functional analysis of the 3'-terminal part of the Balbiani ring 2.2 gene by interspecies sequence comparison.

An interspecies comparison was made between the 3' ends of Balbiani ring genes from Chironomus. The comparison was focused on the BR2.2 gene, and a part at the 3' end from Chironomus pallidivittatus (which included also a segment of the gene core) was cloned. Its sequence, and other previously published BR sequences from this species and from Chironomus tentans were used in the analysis. The 3' parts of these repetitive genes can be divided into a region belonging to the core of the genes followed by a terminal region. In the core region the repeats (each of which consists of a constant part and a subrepeated part) are highly similar and the constant parts show little interspecies differentiation. Furthermore, the two parts of the repeats are units in an evolutionary and probably also functional sense. The terminal region contains modified constant units, usually isolated between acidic so-called cys regions, the whole arrangement lying upstream of an intron toward a 3'-terminal exon. Most of the modified constant units are mosaics in rates of evolution with stable outer quarters bordering to equally stable cys regions and a central half with a very high rate of evolution. One of the terminal units, present only in the BR2.2 gene and second from the end, differs distinctly not only from corresponding core units but also from other terminal units in the three normally active BR genes. It lies upstream of all cys regions and is evolutionarily conserved over most of its length. Furthermore, two-dimensional protein structure prediction does not exclude an endoproteolytic cleavage site in this unit.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2006

Multitrait evolution in lines of Drosophila melanogaster selected for increased starvation resistance: the role of metabolic rate and implications for the evolution of longevity.

Starvation resistance is a trait often associated with longevity. Animals with increased longevity frequently show elevated starvation resistance and vice versa. Consequently, both life-history traits are thought to share genetic and physiological mechanisms, such as increased fat content and lowered metabolic rate. Here, we present results from 20 generations of selection on Drosophila melanogaster for increased starvation resistance at the time of adult eclosion. We observe that starvation resistance can be the result of more than one mechanism, all associated with an increase in fat resources. In general, metabolic rate is lowered under starved conditions relative to fed conditions. Metabolic rate in the starvation resistant lines is generally higher than in control lines under starved conditions. Starvation resistant flies are able to sustain a higher metabolic rate for a longer period of time when food is unavailable. This implies depletion of the increased fat reserves. However, longevity was not consistently affected by selection for increased starvation resistance. Similarly, paraquat resistance differed between selection lines and did not associate with starvation resistance, but rather with longevity. The results are discussed in relation to previous reported results on starvation resistance and its relation with mechanisms of aging and longevity.

Animals↗
PubMed2001

Molecular evolution of Aldolase A pseudogenes in mice: multiple origins, subsequent duplications, and heterogeneity of evolutionary rates.

The Aldolase multigene family comprises three functional genes (A, B, and C) with tissue-specific expression regulated during ontogeny. DGGE analysis and nucleotide sequencing reveal a family of retropseudogenes of type A in species of MUS: Significant variation in rates of evolution of Aldolase A retropseudogenes is apparent. Our analyses demonstrate that (1) multiple events of retrotransposition are needed to account for the diversity of Aldolase A processed pseudogenes found in mice; (2) some of these sequences have undergone further duplication subsequent to the original retrotransposition event; (3) the patterns of nucleotide substitution are broadly comparable with previous estimates; and (4) estimates of rates of divergence for this array of sequences are up to four times higher than those reported in the literature.

Animals↗
PubMedDate not supplied

Taking variation of evolutionary rates between sites into account in inferring phylogenies.

As methods of molecular phylogeny have become more explicit and more biologically realistic following the pioneering work of Thomas Jukes, they have had to relax their initial assumption that rates of evolution were equal at all sites. Distance matrix and likelihood methods of inferring phylogenies make this assumption; parsimony, when valid, is less limited by it. Nucleotide sequences, including RNA sequences, can show substantial rate variation; protein sequences show rates that vary much more widely. Assuming a prior distribution of rates such as a gamma distribution or lognormal distribution has deservedly been popular, but for likelihood methods it leads to computational difficulties. These can be resolved using hidden Markov model (HMM) methods which approximate the distribution by one with a modest number of discrete rates. Generalized Laguerre quadrature can be used to improve the selection of rates and their probabilities so as to more nearly approach the desired gamma distribution. A model based on population genetics is presented predicting how the rates of evolution might vary from locus to locus. Challenges for the future include allowing rates at a given site to vary along the tree, as in the "covarion" model, and allowing them to have correlations that reflect three-dimensional structure, rather than position in the coding sequence. Markov chain Monte Carlo likelihood methods may be the only practical way to carry out computations for these models.

Algorithms↗
PubMed1998

Nonneutral evolution and differential mutation rate of gender-associated mitochondrial DNA lineages in the marine mussel Mytilus.

Mussels have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally, and the F type is transmitted maternally. To test hypotheses of the molecular evolution of both mtDNA genomes, 50 nucleotide sequences were obtained for 396 bp of the COIII gene of European populations of Mytilus edulis and the Atlantic and Mediterranean forms of M. galloprovincialis. Analysis based on the proportion of synonymous and nonsynonymous substitutions indicate that mtDNA is evolving in a non-neutral and complex fashion. Previous studies on American mussels demonstrated that the F genome experiences a higher purifying selection and that the M genome evolves faster. Here we show that these patterns also hold in European populations. However, in contrast to American populations, where an excess of replacement substitution between F and M lineages has been reported, a significant excess of replacement polymorphism within mtDNA lineages is observed in European populations of M. galloprovincialis. European populations also show an excess of replacement polymorphism within the F but not within the M genome with respect to American M. trossulus, as well as a consistent pattern of excess of rare variants in both F and M genomes. These results are consistent with a nearly neutral model of molecular evolution and a recent relaxation of selective constraints on European mtDNA. Levels of diversity are significantly higher for the M than F genome, and the M genome also accumulates synonymous and nonsynonymous substitutions at a higher rate, in contrast with earlier reports where no difference for the synonymous rate was observed. It is suggested that a subtle balance between relaxed selection and a higher mutation rate explains the faster evolutionary rate of the M lineage.

Animals↗
PubMed2005

Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species.

Whole-genome duplication (WGD) produces sets of gene pairs that are all of the same age. We therefore expect that phylogenetic trees that relate these pairs to their orthologs in other species should show a single consistent topology. However, a previous study of gene pairs formed by WGD in the yeast Saccharomyces cerevisiae found conflicting topologies among neighbor-joining (NJ) trees drawn from different loci and suggested that this conflict was the result of "asynchronous functional divergence" of duplicated genes (Langkjaer, R. B., P. F. Cliften, M. Johnston, and J. Piskur. 2003. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421:848-852). Here, we test whether the conflicting topologies might instead be due to asymmetrical rates of evolution leading to long-branch attraction (LBA) artifacts in phylogenetic trees. We constructed trees for 433 pairs of WGD paralogs in S. cerevisiae with their single orthologs in Saccharomyces kluyveri and Candida albicans. We find a strong correlation between the asymmetry of evolutionary rates of a pair of S. cerevisiae paralogs and the topology of the tree inferred for that pair. Saccharomyces cerevisiae gene pairs with approximately equal rates of evolution tend to give phylogenies in which the WGD postdates the speciation between S. cerevisiae and S. kluyveri (B-trees), whereas trees drawn from gene pairs with asymmetrical rates tend to show WGD pre-dating this speciation (A-trees). Gene order data from throughout the genome indicate that the "A-trees" are artifacts, even though more than 50% of gene pairs are inferred to have this topology when the NJ method as implemented in ClustalW (i.e., with Poisson correction of distances) is used to construct the trees. This LBA artifact can be ameliorated, but not eliminated, by using gamma-corrected distances or by using maximum likelihood trees with robustness estimated by the Shimodaira-Hasegawa test. Tests for adaptive evolution indicated that positive selection might be the cause of rate asymmetry in a substantial fraction (19%) of the paralog pairs.

Evolution, Molecular↗
PubMed2002

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

MOTIVATION: A number of proteins of known three-dimensional (3D) structure exist, with yet unknown function. In light of the recent progress in structure determination methodology, this number is likely to increase rapidly. A novel method is presented here: 'Rate4Site', which maps the rate of evolution among homologous proteins onto the molecular surface of one of the homologues whose 3D-structure is known. Functionally important regions often correspond to surface patches of slowly evolving residues. RESULTS: Rate4Site estimates the rate of evolution of amino acid sites using the maximum likelihood (ML) principle. The ML estimate of the rates considers the topology and branch lengths of the phylogenetic tree, as well as the underlying stochastic process. To demonstrate its potency, we study the Src SH2 domain. Like previously established methods, Rate4Site detected the SH2 peptide-binding groove. Interestingly, it also detected inter-domain interactions between the SH2 domain and the rest of the Src protein that other methods failed to detect.

Algorithms↗
PubMed1996

The variety of human virus evolution.

There have been many wise suggestions of ways that evolution may occur but those ways seem often hard to support with good examples. Viruses have proven to be replete with some of these items. This paper reviews work that shows: (1) very fast rates of evolution; (2) positive Darwinian selection with the selective pressure specifically identified; (3) viral reassortment; (4) grossly unequal rates of evolution depending upon the host of the virus; (5) accurate dating of the cenancestor, the most recent common ancestor; (6) correspondence between the evolutionary tree and the geography of the place of isolation; (7) punctuated molecular evolution; and (8) network evolution.

Animals↗
PubMedDate not supplied

Azorhodanine derivatives as inhibitors for acidic corrosion of nickel.

Azorhodanine derivatives (HL1-HL5) were tested as corrosion inhibitors for nickel in 2M HNO3 solution using weight loss and galvanostatic polarization techniques. The results showed that these derivatives act as inhibitors for nickel in this medium. The inhibition was assumed to occur via adsorption of the inhibitor molecule on the metal surface. Polarization measurements indicated that these compounds act as mixed-type inhibitors, but the cathode is more polarized when an external current was applied. This means that these compounds retard the rate of hydrogen evolution and the rate of dissolution of the metal. Results showed that azorhodanine derivatives are adsorbed on the nickel surface following Temkin's adsorption isotherm. The activation energy and thermodynamic parameters were calculated and discussed at different temperatures (30-45 degrees C).

Azo Compounds↗
PubMed2003

Capacity of model biobeds to retain and degrade mecoprop and isoproturon.

Biobeds are used to increase the adsorption and degradation of pesticide spillage on sites used for mixing and loading and for cleaning of sprayers. The adsorption and the rate of degradation of 14C-labelled isoproturon and mecoprop (MCPP) at concentrations from 0.0005 to 25 000 mgkg(-1) were determined in biobed soil. Further leaching of the two herbicides was determined in a model biobed with a surface area of 2 m2. The biobed material showed enhanced ability to adsorb the two herbicides. Kd was 5.2 litre kg(-1) for isoproturon and 1.6 litre kg(-1) for MCPP in biobed material, which is higher than in natural soil. In different experiments with natural soil, Kd ranges from 0.07 to 0.6 litrekg(-1) for MCPP and from 1.5 to 4.6 litre kg(-1) for isoproturon in soils with varying organic carbon content. Degradation of MCPP was rapid at concentrations from 0.0005 to 500 mg kg(-1), delayed at 5000 mg kg(-1), and very slow at 25 000 mg kg(-1). For isoproturon, the relative degradation was most rapid at the lowest concentration and decreasing with increasing concentrations. After 120 days, between 55% and 8% 14C was evolved as 14CO2 at concentrations between 0.0005 and 25 000 mg kg(-1). The rate of evolution of 14CO2 indicated that degradation rates at low concentrations were of first-order and at higher concentrations of zero-order. Leaching of MCPP and isoproturon was determined in a newly established model biobed during a 2-year period. About 13% of applied MCPP and 1.4% of applied isoproturon leached out during the winter following the first autumn application (worst-case scenario). Leaching was completely prevented when the biobed had a well-developed grass cover and was covered during the winter.

2-Methyl-4-chlorophenoxyacetic Acid↗
PubMed2006

Evidence that protein length expansion and contraction is partly due to mutational events in premeiotic cells.

Studies on the rate of evolution of proteins typically concentrate on rates of change of orthologous amino acids rather than on changes in size (i.e., generation of nonorthologous domains). Recent work has focused attention on Ser/Thr-rich regions in yeast as these tend to undergo size changes rapidly, with size polymorphisms commonly being found, especially in proteins with cell-surface localization. The underlying mechanism generating the indels is presently unclear though, due to a lack of correlation with the location of meiotic double-strand breaks, it has, by exclusion, been conjectured to be replication slippage. Here we provide new evidence to support this possibility. Notably, we show that Ser/Thr-rich repeat regions are more generally associated with the location of Mre11p in premeiotic cells. This is to be expected if the repeats were produced by mutational events in mitotic cells possibly through replication slippage.

Cell Cycle↗
PubMed2002

Essential genes are more evolutionarily conserved than are nonessential genes in bacteria.

The "knockout-rate" prediction holds that essential genes should be more evolutionarily conserved than are nonessential genes. This is because negative (purifying) selection acting on essential genes is expected to be more stringent than that for nonessential genes, which are more functionally dispensable and/or redundant. However, a recent survey of evolutionary distances between Saccharomyces cerevisiae and Caenorhabditis elegans proteins did not reveal any difference between the rates of evolution for essential and nonessential genes. An analysis of mouse and rat orthologous genes also found that essential and nonessential genes evolved at similar rates when genes thought to evolve under directional selection were excluded from the analysis. In the present study, we combine genomic sequence data with experimental knockout data to compare the rates of evolution and the levels of selection for essential versus nonessential bacterial genes. In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales.

Conserved Sequence↗
PubMed1986

Primary structure of adult hemoglobin of white-throated capuchin, Cebus capucinus.

The alpha and beta chains of White-Throated Capuchin (Cebus capucinus) hemoglobin were separated and digested by trypsin. The tryptic peptides were isolated and sequenced by conventional methods. The peptides in each chain were aligned by the homology of their sequences with those of human adult hemoglobin. The primary structures thus deduced are compared with those of other primate hemoglobins, and we discuss the molecular evolution of hemoglobins, in particular the rate of evolution in New World monkey hemoglobins.

Amino Acid Sequence↗