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PubMed2003

[Rates of molecular evolution of primates].

This review considers the history and the current state of the debatable issue of variation in accumulation rates of mutational substitutions in the phylogeny of humans and other primates. Arguments pro and contra the hypothesis on gradually decreasing tempo of molecular evolution of humans and apes are discussed. It is shown that data on proteins and (nuclear and mitochondrial) DNA confirm this hypothesis. The conclusion is drawn that the total rate of mutation accumulation is determined by a number of interacting factors. The primary of these factors in most cases (including that of hominids) is generation time, which is closely associated with the number of germ cell divisions. At the same time, fixation rates of nonsynonymous substitutions are also affected by various forms of selection.

Amino Acid Sequence↗
PubMed1996

Discord between the phylogenies inferred from molecular versus functional data: uneven rates of functional evolution or low levels of gene flow?

According to measures of molecular divergence, the three species of the Drosophila simulans clade are closely related to and essentially equidistant from each other. We introgressed 10% of the D. sechellia X chromosome into a pure D. simulans genetic background and found that males carrying this introgressed region were consistently fertile; in contrast, males carrying the same segment from D. mauritiana are sterile and suffer from incompatibilities at a minimum of four loci. Together with other recent results, these data suggest that D. simulans and D. sechellia are much more closely related to each other than either is to D. mauritiana. How can we reconcile the phylogeny inferred from the density of hybrid sterility genes with that inferred from molecular divergence? If the molecular phylogeny is correct, the discrepancy might be explained by uneven rates of functional evolution, resulting in the uneven accumulation of substitutions with corresponding negative effects in hybrids. If the functional phylogeny is correct, then low levels of gene flow across nascent species boundaries, particularly for loci not tightly linked to a hybrid sterility gene, may have erased the original pattern of lineage splitting. We propose tests that will allow us to discriminate between these hypotheses.

Animals↗
PubMed2006

Sequence diversity and rates of molecular evolution between sheep and cattle genes.

Experiments that aim to identify genes of importance in sheep are currently inhibited by a paucity of genomic resources. One approach, therefore, is to exploit the wealth of data and associated capabilities becoming available for the bovine genome. Cross-species application of microarrays and comparative sequencing to identify single nucleotide polymorphisms are two possibilities; however, both are dependant on the level of nucleotide sequence similarity between the two species. This study used 120 gene orthologues consisting of over 60 kb of aligned sequence to estimate the gene diversity between cattle and sheep. Less than 3% of protein-coding nucleotide positions were found to be different, indicating that the prospect for successfully using cross-species strategies is high. Substitution at synonymous sites ranged between 6.9 and 7.7% (+/- 0.3%), and was higher than at non-synonymous sites (1.4-1.7 +/- 0.1%). The relative rate test was used to determine whether the observed mutation rates were constant between the two lineages. While the rate at synonymous sites appeared constant, the rate at non-synonymous sites was significantly higher within the caprinae lineage (sheep) when compared with bovinae (cattle; chi2 = 10.03; d.f. = 1, P < 0.01). This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.

Animals↗
PubMed1975

Rates of protein evolution: a function of amino acid composition.

Conservation of secondary and tertiary structure in proteins suggests that rates of sequence variation reflect differences in the total number of amino acid replacements that are compatible with preservation of structure. Consequently, rates of sequence variation depend on whether the constituent amino acids of individual proteins are, over-all, more subject or less subject to evolutionary substitution than normal. Such rates correlate well with a mutability term based on amino acid composition.

Amino Acid Sequence↗
PubMed2005

Reduced rates of sequence evolution of Y-linked satellite DNA in Rumex (Polygonaceae).

One characteristic of sex chromosomes is the accumulation of a set of different types of repetitive DNA sequences in the Y chromosomes. However, little is known about how this occurs or about how the absence of recombination affects the subsequent evolutionary fate of the repetitive sequences in the Y chromosome. Here we compare the evolutionary pathways leading to the appearance of three different families of satellite-DNA sequences within the genomes of Rumex acetosa and R. papillaris, two dioecious plant species with a complex XX/XY(1)Y(2) sex-chromosome system. We have found that two of these families, one autosomic (the RAE730 family) and one Y-linked (the RAYSI family), arose independently from the ancestral duplication of the same 120-bp repeat unit. Conversely, a comparative analysis of the three satellite-DNA families reveals no evolutionary relationships between these two and the third, RAE180, also located in the Y chromosomes. However, we have demonstrated that, regardless of the mechanisms that gave rise to these families, satellite-DNA sequences have different evolutionary fates according to their location in different types of chromosomes. Specifically, those in the Y chromosomes have evolved at half the rate of those in the autosomes, our results supporting the hypothesis that satellite DNAs in nonrecombining Y chromosomes undergo lower rates of sequence evolution and homogenization than do satellite DNAs in autosomes.

Base Sequence↗
PubMed2006

Evolution of vaccination rates after the implementation of a free systematic pneumococcal vaccination in Catalonian older adults: 4-years follow-up.

BACKGROUND: The systematic vaccination with 23-valent polysaccharide pneumococcal vaccine (PPV) was introduced as a strategic objective of health for all the people over 65 in Catalonia in 1999. We analysed the evolution of the pneumococcal vaccination rates from 2000 to 2003. METHODS: We conducted a retrospective population-based study including all the individuals 65 years or older assigned to 8 Primary Care Centres (PCCs) in Tarragona (Catalonia, Spain), who figured in the administrative population databases on 31 December 2003 (n = 10,410 persons). We assessed whether every person had received PPV during the last four years (2000 to 2003) or whether they had received it before January 2000. Data sources were the computerised clinical records of the 8 participating PCCs, which included adult vaccination registries and diagnoses coded of International Classification of Diseases 9th REVIEW RESULTS: The overall vaccination uptake increased to 38.6% at the end of 2000. Global accumulated coverages increased more slowly the following years: 44.4% in 2001, 50.9% in 2002, and 53.1% at the end of 2003. Vaccine uptake varied significantly according to age (46.7% in people 65-74 years-old, 60.9% in people 75 years or more; p < 0.001) and number of diseases or risk factors (DRFs) for pneumonia (47.1% vaccinated in people without DRFs, 56.8% in patients with one DRF, and 62.2% in patients with two or more DRFs; p < 0.001). The highest coverages were observed among those patients with: diabetes (65.9%), active neoplasia (64.8%), history of stroke (63.7%), and chronic lung disease (63.5%). The lowest uptake was observed among smokers (48.7%). DISCUSSION: The pneumococcal vaccination coverage increased quickly after the introduction of the recommendation for free vaccination in all the elderly people (with and without risk factors), but two years after the improvement the coverage became stable and increased slowly.

Age Factors↗
PubMed1994

Evolution of mutation rate and virulence among human retroviruses.

High mutation rates are generally considered to be detrimental to the fitness of multicellular organisms because mutations untune finely tuned biological machinery. However, high mutation rates may be favoured by a need to evade an immune system that has been strongly stimulated to recognize those variants that reproduced earlier during the infection. HIV infections conform to this situation because they are characterized by large numbers of viruses that are continually breaking latency and large numbers that are actively replicating throughout a long period of infection. To be transmitted, HIVs are thus generally exposed to an immune system that has been activated to destroy them in response to prior viral replication in the individual. Increases in sexual contact should contribute to this predicament by favouring evolution toward relatively high rates of replication early during infection. Because rapid replication and high mutation rate probably contribute to rapid progression of infections to AIDS, the interplay of sexual activity, replication rate, and mutation rate helps explain why HIV-1 has only recently caused a lethal pandemic, even though molecular data suggest that it may have been present in humans for more than a century. This interplay also offers an explanation for geographic differences in progression to cancer found among infections due to the other major group of human retroviruses, human T-cell lymphotropic viruses (HTLV). Finally, it suggests ways in which we can use natural selection as a tool to control the AIDS pandemic and prevent similar pandemics from arising in the future.

Biological Evolution↗
PubMed2000

Experimental evidence for the adaptive evolution of growth rate in the garter snake Thamnophis elegans.

The western terrestrial garter snake (Thamnophis elegans) varies significantly in individual growth rates and life-history traits (maturation, reproduction, and survival) among adjacent populations in nature. This study focuses on assessing the genetic and environmental components of the substantial among-population variation in growth rates. Litters of neonates from nine populations inhabiting either mountain meadow or lakeshore habitat were reared for one year in a common-garden experiment with two temperature treatments. Diet, frequency of feeding, light exposure, and daytime temperatures were identical for all individuals. The two different nighttime temperatures (20 degrees C and 25 degrees C) were chosen to mirror field differences in nighttime thermoregulatory constraints for mountain-meadow and lakeshore snakes, respectively. Temperature and source habitat interacted to affect first-year growth rate. Neonates from meadow dams grew fastest in the cooler treatment, whereas those from lakeshore dams grew fastest in the warmer treatment. The observation that naive neonates, which were gestated and raised under identical conditions, grew fastest in environments characteristic of their natal population is evidence both that there are genetic differences among populations for growth and that these differences reflect adaptation to local habitats at a very small geographic scale. In addition, significant directional selection for large birthweight was measured for neonates from all populations. These results are considered in the context of population colonization history, migration and selection, and competing models for growth rate variation.

Adaptation, Physiological↗
PubMed2006

Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae.

We used complete sequence data from 30 complete Herpesviridae genomes to investigate phylogenetic relationships and patterns of genome evolution. The approach was to identify orthologous gene clusters among taxa and to generate a genomic matrix of gene content. We identified 17 genes with homologs in all 30 taxa and concatenated a subset of 10 of these genes for phylogenetic inference. We also constructed phylogenetic trees on the basis of gene content data. The amino acid and gene content phylogenies were largely concordant, but the amino acid data had much higher internal support. We mapped gene gain events onto the phylogenetic tree by assuming that genes were gained only once during the evolution of herpesviruses. Thirty genes were inferred to be present in the ancestor of all herpesvirus, a number smaller than previously hypothesized. Few genes of recent origin within herpesviruses could be identified as originating from transfer between virus and vertebrate hosts. Inferred rates of gene gain were heterogeneous, with both taxonomic and temporal biases. Nonetheless, the average rate of gene gain was approximately 3.5 x 10(-7) genes gained per year, which is an order of magnitude higher than the nucleotide mutation rate for these large DNA viruses.

Databases, Nucleic Acid↗
PubMed1987

Nonuniformity of nucleotide substitution rates in molecular evolution: computer simulation and analysis of 5S ribosomal RNA sequences.

The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.

Animals↗
PubMed2002

Rates of ribosomal RNA evolution are uniquely accelerated in eukaryotes.

A novel procedure for testing the relative rates of evolution is described. The procedure, the distance-matrix rate test, consists of creating a graph that displays two complete distance matrices for two different genes derived from the same group of species, an approach made practical by numerous whole genomic sequences. The results in this paper show that the molecular clock of ribosomal RNA from Eukaryotes is uniquely accelerated and highly variable while those of Archaea and Bacteria are not. This idiosyncratic eukaryotic rRNA evolution is not observed with four different protein genes. The distance matrix rate test consists of plotting the distance of one gene (from two different species) against the distance of a second gene (from the same pair of species) in the form of a simple X-Y plot. Because it is not possible to compute variances (or co-variances in this case) that can be meaningfully compared to expectations from a Poisson process, the test does not permit calculations of an index of dispersion. In place of this, equations are given for the 95% confidence limits expected for a Poisson process. The test was applied to the proteins rpsl1 and rp114, as one example, and to rps11 and ssu rRNA as a second example. In addition, the cytochrome c and cytochrome c oxidase evolution from a larger group of Eukaryotes are compared to each other and that of the ssu rRNA. This graphical test shows that the evolution of the four proteins and the archael and bacterial ssu rRNA's are consistent with a Poisson process since last common ancestor. The distance-matrix rate test that is introduced in this study needs to make no assumptions regarding evolutionary rates, divergence times, or phylogenetic relationships.

Archaea↗
PubMed2007

Chromosome painting and molecular dating indicate a low rate of chromosomal evolution in golden moles (Mammalia, Chrysochloridae).

Golden moles (Chrysochloridae) are poorly known subterranean mammals endemic to Southern Africa that are part of the superordinal clade Afrotheria. Using G-banding and chromosome painting we provide a comprehensive comparison of the karyotypes of five species representing five of the nine recognized genera: Amblysomus hottentotus, Chrysochloris asiatica, Chrysospalax trevelyani, Cryptochloris zyli and Eremitalpa granti. The species are karyotypically highly conserved. In total, only four changes were detected among them. Eremitalpa granti has the most derived karyotype with 2n = 26 and differs from the remaining species (all of whom have 2n = 30) by one centric and one telomere:telomere fusion. In addition, two intrachromosomal rearrangements were detected in A. hottentotus. The painting probes also suggest the presence of a unique satellite DNA family located on chromosomes 11 and 12 of both C. asiatica and C. zyli. This represents a synapomorphy linking these two sympatric species as sister taxa. A molecular clock was calibrated adopting a relaxed Bayesian approach for multigene data sets comprising publicly available sequences derived from five gene fragments representative of three golden moles and 39 other eutherian species. The data suggest that golden moles diverged from a common ancestor approximately 28.5 mya (95% credibility interval = 21.5-36.5 mya). Based on an inferred chrysochlorid ancestral karyotype of 2n = 30, the estimated rate of 0.7 rearrangements per 10 my (95% Credibility Interval = 0.54-0.93) differs from the 'default rate' of mammalian chromosomal evolution which has been estimated at one change per 10 million years, thus placing the Chrysochloridae among the slower-evolving chromosomal lineages thus far recorded.

Animals↗
PubMed2005

Inbreeding depression and the evolution of dispersal rates: a multilocus model.

Inbreeding depression is one of the possible reasons organisms disperse. In this article, we present a two-locus model for the evolution of dispersal in the presence of inbreeding depression. The first locus codes for a modifier of the migration rate, while the second locus is a selected locus generating inbreeding depression. We express the change in frequency of the migration modifier as a function of allele frequencies and genetic associations and then use a quasi-equilibrium assumption to express genetic associations as functions of allele frequencies. Our model disentangles two effects of inbreeding depression: it gives an advantage to migrant individuals because their offspring are on average less homozygous, but it also decreases the degree of population structure, thus decreasing the strength of kin selection for dispersal. We then extend our model to include an infinite number of selected loci. When the cost of dispersal is not too high, the model predictions are confirmed by multilocus simulation results and show that inbreeding depression can have a substantial effect on the dispersal rate. For high costs of dispersal, we observe discrepancies between the model and the simulations, probably caused by associations among selected loci, which are neglected in the analysis.

Animal Migration↗
PubMed2005

Selection for high gamete encounter rates explains the evolution of anisogamy using plausible assumptions about size relationships of swimming speed and duration.

A previous general model describing physical constraints on gamete encounter rates was modified to incorporate assumptions that increased size causes decreased swimming speed and increased fertile period (or other proportional enhancement to gamete fertility). The analysis indicates that with moderately strong size dependence of fertile period and a range of speed dependencies, selection for high encounter rates pressures mating systems that develop any heritable difference in size between the gametes of different mating types to exaggerate the difference and evolve from isogamy to anisogamy. The smaller gamete has an optimal size, but the larger faces continuing selection for increased size. This continues to a size that is estimated to be sufficient to make pheromone production of sperm attractants practical. This mechanism then bridges the missing link between isogametes and oogamy in a previous analysis of the effectiveness of pheromones in explaining the success of male-female mating systems. The evolution and success of anisogamy and oogamy can be explained solely on the basis of physical effects on the encounter process.

Animals↗
PubMed2004

Rates of molecular evolution in nuclear genes of east Mediterranean scorpions.

Scorpions of the genus Mesobuthus represent a useful terrestrial model system for studying molecular evolution. They are distributed on several Aegean islands and the adjacent mainland, they are believed to have low rates of dispersal, and evolutionary divergence dates of taxa are available based on biogeographic events that separated islands from each other and the mainland. Here, we present data on polymorphism and synonymous (Ks) and non-synonymous (Ka) substitution rates for nine nuclear protein-coding genes of two east Mediterranean scorpion species, Mesobuthus gibbosus and M. cyprius (Buthidae). Levels of polymorphism tend to be lower in populations from islands (mean nucleotide diversity pi = 0.0071 +/- 0.0028) than in mainland populations (mean pi = 0.0201 +/- 0.0085). By using linear regression of genetic divergence versus isolation time, we estimate Ks to be 3.17 +/- 1.54 per (site x 10(9) years), and Ka to be 0.39 +/- 0.94 per (site x 10(9) years). These estimates for both Ks and Ka are considerably lower than for many other invertebrates, such as Drosophila, and may be attributed to scorpions' mammal-like generation times (approximately 2 years) and low metabolic rates. Phylogenetic analysis using maximum likelihood revealed a phylogeny that is congruent with that expected based on biogeographic events and in which divergences at synonymous sites are proportional to the dates that the taxa are believed to have split. Tests of equality of branch lengths for the Cyprus and Crete lineages revealed that Ks-estimates are about the same in both lineages, as expected from the biogeographic events that separated the islands, but Ka was increased in the Cyprus lineage compared to the Cretan lineage.

Animals↗
PubMed1979

Antepartum fetal heart rate testing. I. Evolution of the nonstress test.

On May 1, 1975, at Women's Hospital, Los Angeles County--University of Southern California Medical Center, a new antepartum fetal heart rate (AFHRT) protocol was put into clinical use. This included the widely used contraction stress test (CST) and a new concept of nonstress testing (NST). The NST was based on FHR response associated with fetal movements and was categorized as reactive (normal) or nonreactive (abnormal). The nonreactive fetus was then evaluated with a CST if not contraindicated. During the 24 months, May 1, 1975 to April 30, 1977, a total of 2,422 NST's were done in 1,169 patients with 1,547 (64 per cent) reactive and 829 (35 per cent) nonreactive. CST was done 939 times, with 851 (90.6 per cent) negative, 29 (3 per cent) positive, 13 (1.4 per cent) equivocal, and 46 (5.0 per cent) unsatisfactory. There were ten (3.3 per cent) perinatal deaths within one week of a negative CST, five (1.0 per cent) within one week of a reactive NST, and two (8.7 per cent) with a positive CST. A reactive NST was as predictive of good outcome as was a negative CST. Analysis of the nonreactive NST showed that two or more accelerations were not associated with abnormal CST's. Also, some nonreactive fetuses became reactive with oxytocin and had good outcome. These observations were utilized in the development of a newer, shorter NST which allows for fetal stimulation in an attempt to further define fetal well-being.

California↗