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PubMed1986

The complete amino acid sequences of cytosolic and mitochondrial aspartate aminotransferases from horse heart, and inferences on evolution of the isoenzymes.

We report here the complete amino acid sequences of the cytosolic and mitochondrial aspartate aminotransferases from horse heart. The two sequences can be aligned so that 48.1% of the amino acid residues are identical. The sequences have been compared with those of the cytosolic isoenzymes from pig and chicken, the mitochondrial isoenzymes from pig, chicken, rat, and human, and the enzyme from Escherichia coli. The results suggest that the mammalian cytosolic and mitochondrial isoenzymes have evolved at equal and constant rates whereas the isoenzymes from chicken may have evolved somewhat more slowly. Based on the rate of evolution of the mammalian isoenzymes, the gene-duplication event that gave rise to cytosolic and mitochondrial aspartate aminotransferases is estimated to have occurred at least 10(9) years ago. The cytosolic and mitochondrial isoenzymes are equally related to the enzyme from E. coli; the prokaryotic and eukaryotic enzymes diverged from one another at least 1.3 X 10(9) years ago.

Amino Acid Sequence↗
PubMed1995

Molecular phylogenies and host-parasite cospeciation: gophers and lice as a model system.

Recent methodological advances permit a rigorous comparison of phylogenetic trees for hosts and their parasites to determine the extent to which these groups have cospeciated through evolutionary time. In cases where significant levels of cospeciation are indicated, comparison of amounts of evolutionary change that have accumulated along analogous branches in the host and parasite trees provides a direct assessment of relative rates of evolution in the two groups. For such a comparison to be meaningful, the features compared in the hosts and parasites should be genetically based, evolutionarily homologous, and should evolve in a roughly time-dependent fashion within each group. Nucleotide sequences encoding homologous genes in hosts and parasites are an ideal source of data for comparative studies of evolutionary rates. Recent studies of pocket gophers and their lice are used to illustrate the variety of questions that can be addressed through phylogenetic study of host-parasite systems.

Animals↗
PubMed2003

Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani.

The complete nucleotide sequence (16,650 bp) of the mitochondrial genome of the salamander Mertensiella luschani (Caudata, Amphibia) was determined. This molecule conforms to the consensus vertebrate mitochondrial gene order. However, it is characterized by a long non-coding intervening sequence with two 124-bp repeats between the tRNA(Thr) and tRNA(Pro) genes. The new sequence data were used to reconstruct a phylogeny of jawed vertebrates. Phylogenetic analyses of all mitochondrial protein-coding genes at the amino acid level recovered a robust vertebrate tree in which lungfishes are the closest living relatives of tetrapods, salamanders and frogs are grouped together to the exclusion of caecilians (the Batrachia hypothesis) in a monophyletic amphibian clade, turtles show diapsid affinities and are placed as sister group of crocodiles+birds, and the marsupials are grouped together with monotremes and basal to placental mammals. The deduced phylogeny was used to characterize the molecular evolution of vertebrate mitochondrial proteins. Amino acid frequencies were analyzed across the main lineages of jawed vertebrates, and leucine and cysteine were found to be the most and least abundant amino acids in mitochondrial proteins, respectively. Patterns of amino acid replacements were conserved among vertebrates. Overall, cartilaginous fishes showed the least variation in amino acid frequencies and replacements. Constancy of rates of evolution among the main lineages of jawed vertebrates was rejected.

Amino Acid Sequence↗
PubMed1999

Evolutionary genetics: The economics of mutation.

The presence of mutator genotypes in populations of bacteria may be favoured by selection because they produce rare beneficial mutations and thereby increase the rate of adaptive evolution. Recent work, however, shows that the relationship between mutation rates and adaptive evolution is more complicated.

Adaptation, Physiological↗
PubMed2003

Economics versus alleles: balancing integrated pest management and insect resistance management for rotation-resistant western corn rootworm (Coleoptera: Chrysomelidae).

Western corn rootworm, Diabrotica virgifera virgifera LeConte, has overcome crop rotation in several areas of the central United States. We expanded a simple model of adult behavior and population genetics to explain how rotation resistance may have developed and to study ways to manage the western corn rootworm in a landscape of corn, soybean, and winter wheat where evolution of resistance may occur. We modeled six alternative management strategies over a 15-yr time horizon, as well as a strategy involving a 2-yr rotation of corn and soybean in 85% of the landscape, to investigate their effectiveness from both a biological and economic perspective. Generally, resistance to crop rotation evolves in fewer than 15 yr, and the rate of evolution increases as the level of rotated landscape (selection pressure) increases. When resistance is recessive, all six alternative strategies were effective at preventing evolution of rotation resistance. The two most successful strategies were the use of transgenic rotated corn in a 2-yr rotation and a 3-yr rotation of corn, soybean, and wheat with unattractive wheat (for oviposition) preceding corn. Results were most sensitive to increases in the initial allele frequency and modifications of the density-dependent survival function. Economically, three alternative strategies were robust solutions to the problem, if technology fees were not too high. Repellant soybean, attractive rotated corn, and transgenic rotated corn, all in 2-yr rotations, were economically valuable approaches. However, even the currently common 2-yr rotation was economical when resistance was recessive and the actual costs of resistance would not be paid until far in the future.

Agriculture↗
PubMed2002

Undifferentiated connective tissue disease: analysis of 83 patients with a minimum followup of 5 years.

OBJECTIVE: Undifferentiated connective tissue disease (UCTD) refers to a cluster of systemic disorders characterized by a simple clinical and autoantibody profile. Previously, we had described a series of 91 patients with UCTD who were followed at our unit for a minimum period of one year; here we report the extended followup of these patients. METHODS: Of the original 91 patients, 8 were lost to followup; the remaining 83, with a minimum followup of 5 years, were included in our analysis. RESULTS: During the followup 18 patients developed systemic lupus erythematosus (SLE) and one developed Sjögren's syndrome within a mean period of 54 months after the onset of the disease (range 17-96 mo). On analysis the 18 patients with SLE showed a clinical profile similar to cohorts reported in the literature. In one patient the evolution to SLE occurred during puerperium, but no other triggering factors were observed in our series. The presence of anticardiolipin antibodies and of multiple antibody specificities was significantly correlated with the development of SLE (p < 0.05). CONCLUSION: This analysis confirms the findings of our one year followup study that UCTD comprises a distinct group of mild diseases and that the rate of evolution to defined connective tissue diseases is higher during the first years after its onset. Patients who maintain an undifferentiated profile during the followup seem to run a decreasing risk of developing a defined CTD.

Autoantibodies↗
PubMed2001

Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes.

The order Rodentia contains half of all extant mammal species, and from an evolutionary standpoint, there are persistent controversies surrounding the monophyly of the order, divergence dates for major lineages, and relationships among families. Exons of growth hormone receptor (GHR) and breast cancer susceptibility (BRCA1) genes were sequenced for a wide diversity of rodents and other mammals and combined with sequences of the mitochondrial 12S rRNA gene and previously published sequences of von Willebrand factor (vWF). Rodents exhibit rates of amino acid replacement twice those observed for nonrodents, and this rapid rate of evolution influences estimates of divergence dates. Based on GHR sequences, monophyly is supported, with the estimated divergence between hystricognaths and most sciurognaths dating to about 75 MYA. Most estimated dates of divergence are consistent with the fossil record, including a date of 23 MYA for Mus-Rattus divergence. These dates are considerably later than those derived from some other molecular studies. Among combined and separate analyses of the various gene sequences, moderate to strong support was found for several clades. GHR appears to have greater resolving power than do 12S or vWF. Despite its complete unresponsiveness to growth hormone, Cavia (and other hystricognaths) exhibits a conservative rate of change in the intracellular domain of GHR.

Animals↗
PubMed1987

Diallelic multilocus model of neutral genes.

The evolution of a completely linked diallelic multilocus system of neutral genes in a finite population is studied. A diffusion model incorporating random genetic drift and mutation is used. We neglect the recombination. To begin with, the spectral analysis of the Kolmogorov backward equation for this model is investigated. We apply this to two extreme situations when the number of sites approaches to infinity. One is a DeMoivre-Laplace type approximation and the other is a Poisson type approximation. The former is applied to the study of the simultaneous distribution and evolution of a large number of neutral genes. It is applicable to the distribution of a polygenic character controlled by clustered loci on a chromosome, and we show that it differs from the normal distribution on account of random genetic drift and linkage disequilibrium. The latter is applied to the distribution of the number of segregating sites in DNA nucleotide sequences, and the rate of evolution is obtained.

Alleles↗
PubMed2004

Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method.

The availability of large numbers of genomic sequences has demonstrated the importance of lateral gene transfer (LGT) in prokaryotic evolution. However, considerable uncertainty remains concerning the frequency of LGT compared to other evolutionary processes. To examine LGTs in ancient lineages of prokaryotes a method was developed that utilizes the ratios of evolutionary distances (RED) to distinguish between alternative evolutionary histories. The advantages of this approach are that the variability inherent in comparing protein sequences is transparent, the direction of LGT and the relative rates of evolution are readily identified, and it is possible to detect other types of evolutionary events. This method was standardized using 35 genes encoding ribosomal proteins that were believed to share a vertical evolution. Using RED-T, an original computer program designed to implement the RED method, the evolution of the genes encoding the 20 aminoacyl-tRNA synthetases was examined. Although LGTs were common in the evolution of the aminoacyl-tRNA synthetases, they were not sufficient to obscure the organismal phylogeny. Moreover, much of the apparent complexity of the gene tree was consistent with the formation of the paralogs in the ancestors to the modern lineages followed by more recent loss of one paralog or the other.

Amino Acid Sequence↗
PubMed2001

DNA asymmetry and the replicational mutational pressure.

The mode of replication and organisation of bacterial genomes impose asymmetry on their nucleotide composition. The asymmetry is seen in coding and non-coding sequences and is reflected in the amino acid composition of proteins. The mechanisms generating asymmetry include: unequal mutation rates connected with replication and transcription, selection forces positioning genes and signal sequences nonrandomly in the genome, and protein coding constraints on coding sequences. There are different methods of visualising and measuring the asymmetry. Some of them can assess the contribution of individual mechanisms to the observed asymmetry and those have been described in greater detail. Asymmetric mutational and selection pressures differentiate the rates of evolution of genes on leading and lagging strands. The genes relocated to the opposite strand have to adapt to a different mutational pressure or are eliminated. Translocations from leading to lagging strands are more often selected against than from lagging to leading strands. Comparison of intergenic sequences that have lost the coding function to the original genes enables finding the frequencies of the twelve substitution rates in sequences free from selection. In the absence of selection, the half-time of substitution of a given type of nucleotide is linearly correlated with the fraction of that nucleotide in the sequence.

Journal Article↗
PubMed1975

Evolution of type C viral genes: preservation of ancestral murine type C viral sequences in pig cellular DNA.

Domestic pigs (Sus scrofa) and other members of the family Suidae have multiple copies of type C viral gene sequences in the cellular DNA of all their tissues. Partially homologous viral gene sequences are also found in cellular DNA of rodents, particularly Muridae. The results lead to the conclusion that type C viral genes were introduced into the Suidae lineage as a result of trans-species infection by an ancestral xenotropic murine virus. The rate of evolution of the virogene sequences in the pig appears to be much slower than that of genes that have remained in the rodent lineage; this may be a consequence of transfer from a shorter-lived animal (the rodent) to a longer-lived one (the pig). We estimate the time of gene transmission as 5-10 million years ago and conclude that the present-day porcine type C virogenes most closely approximate the viral genes as they were several million years ago in the rodent lineage.

Animals↗
PubMed2006

Role of sexual and natural selection in evolution of body size and shape: a phylogenetic study of morphological radiation in grouse.

We use standardized independent contrasts (SICs) to elucidate the effect of ecology and mating systems on morphological radiation in grouse. The analysis of SICs for 38 skeletal measurements from 20 taxa, showed that changes in mating system had a significant effect on body size of both sexes. Sexual size dimorphism in grouse is consistent with Rensch's rule; the slope of the regression of male vs. female size SICs was 1.4, significantly >1. Changes in habitat were associated with accelerated rates of evolution of body proportions. SICs for male and female scores of size independent factors were directly proportional to each other (slope = 1), indicating extreme similarities between male and female ecology. Females, however, were better adapted to longer, more energy efficient flight than males. Size independent morphological differences among grouse are adaptive and are related to the differences in habitat and foraging behaviour among the species.

Animals↗
PubMed2006

Estimating the neutral rate of nucleotide substitution using introns.

Evolutionary biologists frequently rely on estimates of the neutral rate of evolution when characterizing the selective pressure on protein-coding genes. We introduce a new method to estimate this value based on intron nucleotide substitutions. The new method uses a metascript model that considers alternative splicing forms and an algorithm to pair orthologous introns, which we call Introndeuce. We compare the intron method with a widely used method that uses observed substitutions in synonymous coding nucleotides, by using both methods to estimate the neutral rate for human-dog and mouse-rat comparisons. The estimates of the 2 methods correlate strongly (r(S) = 0.75), but cannot be considered directly equivalent. We also investigate the effect of alignment error and G + C content on the variance in the intron method: in both cases there is an effect, and it is species-pair specific. Although the intron method may be more useful for shorter evolutionary distances, it is less useful at longer distances due to the poor alignment of less-conserved positions.

Algorithms↗
PubMed1993

Complete cDNA sequence of a rainbow trout IgM gene and evolution of vertebrate IgM constant domains.

A complete cDNA clone encoding secreted IgM molecules was isolated from a spleen cDNA library of rainbow trout (Oncorhynchus mykiss). It encodes the leader peptide, VH, DH, JH, and the whole constant region of the secreted IgM molecule. We also studied the copy number of the IgM gene and an unusual RNA splicing mechanism which generates membrane IgM lacking the CH4 domain in rainbow trout. Amino acid sequence comparison of IgM protein sequences from this fish and other vertebrates indicates that some domains of IgM have evolved at a relatively constant rate. The evolution of salmonid fish including divergence time is discussed.

Amino Acid Sequence↗
PubMed2004

The ultrastructure of the spermatozoon of the lizard Iguana iguana (Reptilia, Squamata, Iguanidae) and the variability of sperm morphology among iguanian lizards.

The spermatozoon of Iguana iguana is filiform and resembles that of other iguanian lizards, being most similar to Tropidurus. All sperm synapomorphies of Tetrapoda, Amniota and Squamata are present in the sperm of Iguana iguana. By reconstructing the evolution of 30 sperm characters we identified a novel synapomorphy of Iguania: the presence of a well-developed acrosomal ridge at the level of the epinuclear lucent zone. Because of the poor topological resolution among iguanian clades we could not discount the possibility of convergence or neutral selection as determinant of the variability in characteristics of the sperm cell. In agreement with previous studies, we identified heterogeneous rates of evolution among the three main regions of the sperm cell, namely the head, midpiece and tail.

Acrosome↗
PubMed1976

Molecular evolution of the polypeptide hormones.

Any biological function is at least bimolecular and its evolution therefore is at least dual, with variations in two lines of molecules. The hormone specificity results from a particular fit between the three-dimensional structure of the agent and that of the receptor but, because receptors are not known at the structural level, a discussion on the evolution of the polypeptide hormones is mainly limited to the possible progressive changes of the latter. As for other proteins (enzymes, oxygen carriers etc.) two degrees of complexity can be distinguished according to whether the hormone comprises one or several polypeptide chains. Protein assembly can bring new biological properties, each subunit playing a particular role. In this case, the 'internal' evolution (chain-chain interactions) overlaps the 'external' evolution (hormone-receptor contacts). The 'monomeric' hormones present the following problems: evolution of the prohormone and of the converting enzyme (for insulin), duplication and differentiation of two lines of hormones either by amino acid substitutions (neurohypophysial hormones and neurophysins) or by substitutions and size modifications (corticotropin and lipotropin), duplication and fusion leading to internal homology in the single polypeptide chain (somatotropin, prolactin, placental lactogen). The 'dimeric' hormones lead to several problems: successive duplications giving different subunits, selective associations between subunits, unequal rates of evolution of the subunits, the function of each subunit (lutropin, follitropin, thyrotropin, choriogonadotropin). An attempt is made to integrate the evolution of polypeptide hormones in the frame of the evolution of proteins.

Amino Acid Sequence↗
PubMed2000

Undermining the Baldwin expediting effect: does phenotypic plasticity accelerate evolution?

The claim that phenotypic plasticity speeds up evolution towards a target phenotype is a recent incarnation of the Baldwin effect. To differentiate this theory from earlier interpretations of Baldwin's ideas, we name it the Baldwin expediting effect. Models that demonstrate this effect assume an extreme fitness scenario which bestows high fitness upon a single optimal phenotype and treats all other phenotypes as equal. In two modeling frameworks, we demonstrate that the effects of plasticity on the rate of evolution are highly dependent on the fitness function and population starting conditions. We argue that phenotypic plasticity does not universally facilitate evolution. Furthermore, in cases where the Baldwin expediting effect occurs, it is not necessarily correlated with increased fitness and therefore is not sufficient to explain the evolutionary success of plasticity.

Biological Evolution↗
PubMed1998

Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe: Anatini).

Rates of sequence evolution were estimated for the cytochrome b (cyt b) and NADH dehydrogenase sub-unit 2 (ND2) genes using a phylogeny of the dabbling ducks (Tribe: Anatini) and outgroups. This speciose group was densely sampled, reducing the impact of undetected homoplasy on rate comparisons. Phylogenies based on sequences of the two gene regions and various weighting schemes differed, but most of the differences involved weakly supported nodes. In addition, partition homogeneity tests show that these differences were not due to statistically significant conflict between the data sets. Cyt b and ND2 also showed similar rates and types of both nucleotide and amino acid substitutions. For both genes, substitutions between isoleucine and valine and between alanine and threonine were most common; both of these substitution types are the result of A-G transitions at first positions of codons. Rates of sequence evolution varied substantially and significantly among nucleotide positions, and even within a given codon position (first, second, or third), rates were significantly heterogeneous among sites. Within Anatini, cyt b and ND2 show similar levels of variation and homoplasy, and are equally useful for reconstructing the species level phylogeny of this group.

Amino Acid Substitution↗