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PubMed2006

Fisher's geometrical model of evolutionary adaptation--beyond spherical geometry.

Fisher's geometrical model of evolutionary adaptation has recently been used in a variety of contexts of interest to evolutionary biologists. The renewed interest in this model strongly motivates generalizations that make it a more realistic description of evolutionary adaptation. Previously, the distribution of mutant effects has, for analytical tractability, rather than biological realism, been taken as spherically symmetric. Here we substantially extend Fisher's model, by allowing a wider class of mutational distributions that incorporate mutational bias and more general deviations from spherical symmetry such as correlations between mutant effects. We also incorporate work on generalized fitness landscapes, thereby reducing the number of artificial assumptions underlying the model. The generalized model exhibits a substantially increased flexibility and a far richer underlying geometry. We find that the distribution characterizing selection coefficients of new mutations is expressed in terms of a number of geometrical invariants associated with mutation, selection and the parental phenotype.

Adaptation, Physiological↗

PubMed2001

Ring species as bridges between microevolution and speciation.

A demonstration of how small changes can lead to species-level differences is provided by ring species, in which two reproductively isolated forms are connected by a chain of intermediate populations. We review proposed cases of ring species and the insights they provide into speciation. Ring species have been viewed both as illustrations of the history of divergence of two species from their common ancestor and as demonstrations that speciation can occur in spite of gene flow between the diverging forms. Theoretical models predict that speciation with gene flow can occur when there is divergent ecological selection, and geographical differentiation increases the likelihood of speciation. Thus ring species are ideal systems for research into the role of both ecological and geographical differentiation in speciation, but few examples have been studied in detail. The Greenish warbler is a ring species in which two northward expansions around the Tibetan plateau have been accompanied by parallel evolution in morphology, ecology, and song length and complexity. However, songs have diverged in structure, resulting in a lack of recognition where the reproductively isolated forms come into contact in Siberia. Our analysis suggests that these differences could have arisen even with gene flow, and that parallel rather than divergent ecological changes have led to divergence in sexually selected traits and subsequent speciation.

Animals↗

PubMed2005

Common evolutionary origin and birth-and-death process in the replication-independent histone H1 isoforms from vertebrate and invertebrate genomes.

The H1 histone multigene family shows the greatest diversity of isoforms among the five histone gene families, including replication-dependent (RD) and replication-independent (RI) genes, according to their expression patterns along the cell cycle and their genomic organization. Although the molecular characterization of the RI isoforms has been well documented in vertebrates, similar information is lacking in invertebrates. In this work we provide evidence for a polyadenylation signature in the Mytilus "orphon" H1 genes similar to the polyadenylation characteristic of RI H1 genes. These mussel genes, together with the sea urchin H1delta genes, are part of a lineage of invertebrate "orphon" H1 genes that share several control elements with vertebrate RI H1 genes. These control elements include the UCE element, H1-box and H4-box. We provide evidence for a functional evolution of vertebrate and invertebrate RI H1 genes, which exhibit a clustering pattern by type instead of by species, with a marked difference from the somatic variants. In addition, these genes display an extensive silent divergence at the nucleotide level which is always significantly larger than the nonsilent. It thus appears that RI and RD H1 isoforms display similar long-term evolutionary patterns, best described by the birth-and-death model of evolution. Notably, this observation is in contrast with the theoretical belief that clustered RD H1 genes evolve in a concerted manner. The split of the RI group from the main RD group must therefore have occurred before the divergence between vertebrates and invertebrates about 815 million years ago. This was the result of the transposition of H1 genes to solitary locations in the genome.

Animals↗

PubMed1977

The evolution of dominance: Haldane v Fisher revisited.

Fisher's model for the evolution of dominance indicates that the accumulation of dominance modifiers will be accelerated by (1) an increased frequency of the mutant heterozygote, (2) increased selection for the phenotype of the normal homozygote. The model has been criticised by Haldane on the grounds that point (1) is not fulfilled, that is dominance appears to be more common in populations with a low frequency of mutant heterozygotes (populations of inbreeders). In support of Fisher's model it is argued that intense selection for the wild type phenotype is more common in inbreeders than outbreeders. This situation should promote the accumulation of dominance modifiers (point (2) above).

Biological Evolution↗

PubMed2000

Simulated coevolution in a mutating ecology.

The bit-string Penna model is used to simulate the competition between an asexual parthenogenetic and a sexual population sharing the same environment. A newborn of either population can mutate and become a part of the other with some probability. In a stable environment the sexual population soon dies out. When an infestation by rapidly mutation genetically coupled parasites is introduced, however, sexual reproduction prevails, as predicted by the so-called Red Queen hypothesis for the evolution of sex.

Animals↗

PubMed2004

Evidence for positive selection on Mycobacterium tuberculosis within patients.

BACKGROUND: While the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of tuberculosis between individuals. This and other markers may also facilitate our understanding of the disease within patients. RESULTS: This article presents three lines of evidence supporting the action of positive selection on M. tuberculosis within patients. The arguments are based on a comparison between empirical findings from molecular epidemiology, and population genetic models of evolution. Under the hypothesis of neutrality of genotypes, 1) the mutation rate of the marker IS6110 is unusually high, 2) the time it takes for substitutions to occur within patients is too short, and 3) the amount of polymorphism within patients is too low. CONCLUSIONS: Empirical observations are explained by the action of positive selection during infection, or alternatively by very low effective population sizes. I discuss the possible roles of antibiotic treatment, the host immune system and extrapulmonary dissemination in creating opportunities for positive selection.

DNA, Bacterial↗

PubMed2002

Parsimonious basis selection in exponential spectral analysis.

Sums of decaying real exponentials (SDREs) are frequently used in models of time-varying processes. First-order compartmental models are widely employed to describe mass transit in chemical and biological systems. In these models the evolution of compartment concentration versus time is represented as the convolution of an input function with an SDRE. In exponential spectral analysis (ESA) the nonlinear problem of estimating the SDRE rate constants is replaced by the linear estimation of the coefficients of a preselected set of exponential basis functions (EBFs). This work addresses the problem of selecting the number of EBFs and the rate constant of each basis element. Basis dimension is established via model selection, in which approximation error and parameter redundancy are the criteria. The latter is estimated via simulation of the fitted model over multiple noise realizations. A constrained Cramér-Rao lower bound is derived for ESA parameters. The resulting parsimonious ESA algorithm (PESA) ameliorates the inherent problem of non-uniqueness in ESA parameters. Consequently, sets of time series may be compared in a statistically meaningfully way in terms of physically or physiologically significant parameters. PESA is applied to compare the retention of two radiotracers in the artificially perfused rabbit heart.

Algorithms↗

PubMed2004

Anion-independent iron coordination by the Campylobacter jejuni ferric binding protein.

Campylobacter jejuni, the leading cause of human gastroenteritis, expresses a ferric binding protein (cFbpA) that in many pathogenic bacteria functions to acquire iron as part of their virulence repertoire. Recombinant cFbpA is isolated with ferric iron bound from Escherichia coli. The crystal structure of cFbpA reveals unprecedented iron coordination by only five protein ligands. The histidine and one tyrosine are derived from the N-terminal domain, whereas the three remaining tyrosine ligands are from the C-terminal domain. Surprisingly, a synergistic anion present in all other characterized ferric transport proteins is not observed in the cFbpA iron-binding site, suggesting a novel role for this protein in iron uptake. Furthermore, cFbpA is shown to bind iron with high affinity similar to Neisserial FbpA and exhibits an unusual preference for ferrous iron (oxidized subsequently to the ferric form) or ferric iron chelated by oxalate. Sequence and structure analyses reveal that cFbpA is a member of a new class of ferric binding proteins that includes homologs from invasive and intracellular bacteria as well as cyanobacteria. Overall, six classes are defined based on clustering within the tree and by their putative iron coordination. The absence of a synergistic anion in the iron coordination sphere of cFbpA also suggests an alternative model of evolution for FbpA homologs involving an early iron-binding ancestor instead of a requirement for a preexisting anion-binding ancestor.

Amino Acid Sequence↗

PubMed2006

Formulation of competition between sexual and selfing forms.

In a recent issue, Rausch and Morgan (2005) analyzed the role of selfing in the autopolyploidization process theoretically based on the formulation of Felber (1991), although they did not explicitly model a pollen pool. This paper reformulates the male contribution to outcrossing in terms of gamete frequencies within a pollen pool. This is a general issue when considering competition between sexual and selfing or asexual forms in a single population, which must be considered in theoretical treatments.

Biological Evolution↗

PubMed2006

Testing for spatial clustering of amino acid replacements within protein tertiary structure.

Widely used models of protein evolution ignore protein structure. Therefore, these models do not predict spatial clustering of amino acid replacements with respect to tertiary structure. One formal and biologically implausible possibility is that there is no tendency for amino acid replacements to be spatially clustered during evolution. An alternative to this is that amino acid replacements are spatially clustered and this spatial clustering can be fully explained by a tendency for similar rates of amino acid replacement at sites that are nearby in protein tertiary structure. A third possibility is that the amount of clustering exceeds that which can be explained solely on the basis of independently evolving protein sites with spatially clustered replacement rates. We introduce two simple and not very parametric hypothesis tests that help distinguish these three possibilities. We then apply these tests to 273 homologous protein families. The null hypothesis of no spatial clustering is rejected for 102 of 273 families. The explanation of spatially clustered rates but independent change among sites is rejected for 43 families. These findings need to be reconciled with the common practice of basing evolutionary inferences on models that assume independent change among sites.

Amino Acid Substitution↗

PubMed2004

The current status of the small subunit rRNA phylogeny of the coccidia (Sporozoa).

There is no current comprehensive assessment of the molecular phylogeny of the coccidia, as all recently published papers either deal with subsets of the taxa or sequence data, or provide non-robust analyses. Here, we present a comprehensive and consistent phylogenetic analysis of the available data for the small-subunit ribosomal RNA gene sequence, including a number of taxa not previously studied, based on a Bayesian tree-building analysis and the covariotide model of evolution. The assumptions of the analysis have been rigorously tested, and the benefits and limitations highlighted. Our results provide support for a number of prior conclusions, including the monophyly of the families Sarcocystidae (cyst-forming coccidia) and Eimeriidae (oocyst-forming coccidia), but with bird-host Isospora species in the Eimeriidae and mammal-host species in the Sarcocystidae. However, it is clear that a number of previously reported relationships are dependent on the evolutionary model chosen, such as the placements of Goussia janae, Lankesterella minimia and Caryospora bigenetica. Our results also confirm the monophyly of the subfamilies Toxoplasmatinae and Sarcocystinae, but only some of the previously reported groups within these subfamilies are supported by our analysis. Similarly, only some of the previously reported groups within the Eimeriidae are supported by our analysis, and the genus Eimeria is clearly paraphyletic. There are unambiguous patterns of host-parasite relationship within the coccidia, as most of the well-supported groups have a consistent and restricted range of hosts, with the exception of the Toxoplasmatinae. Furthermore, the previously reported groups for which we found no support all have a diverse range of unrelated hosts, confirming that these are unlikely to be natural groups. The most interesting unaddressed questions may relate to Isospora, which has the fewest available sequences and host-parasite relationships apparently not as straightforward as elsewhere within the suborder.

Animals↗

PubMed2007

Ascertainment bias and the pattern of nucleotide diversity at the human ALDH2 locus in a Japanese population.

Many East Asian human populations harbor a high-frequency deficiency allele for the aldehyde dehydrogenase 2 (ALDH2) enzyme, a critical protein involved in the metabolism of ethanol. Here we use resequencing and long-range SNP haplotype data from a Japanese sample to test whether patterns of nucleotide diversity and linkage disequilibrium at this locus are compatible with a standard neutral model of evolution. Examination of the pattern of polymorphism at a locus such as this, where the frequency of a common allele is known a priori, introduces an ascertainment bias that must be corrected for in analyses of the frequency spectrum of polymorphisms. We apply a flexible and generally applicable simulation approach to correct for this bias in our ALDH2 data and, also, to explore the effect of bias on the commonly used summary statistics Tajima's D, Fu and Li's D, and Fay and Wu's H. Our study finds no evidence that the pattern of genetic variation at ALDH2 differs from that expected under a standard neutral model. However, our general examination of ascertainment bias indicates that a priori knowledge of segregating alleles greatly affects the expected distributions of summary statistics. Under many parameter combinations we find that ascertainment bias introduces an elevated rate of false positives when summary statistics are used to test for deviations from a standard neutral model. However, we also show that over a wide range of conditions the power of all summary statistics can be greatly increased by incorporating prior knowledge of segregating alleles.

Aldehyde Dehydrogenase↗

PubMed2001

Predicting natural attenuation of xylene in groundwater using a numerical model.

The aquifer beneath an abandoned refinery in the Lower Rhine area, Germany, was contaminated with a number of different mineral oil products. Groundwater sampling in the area around the former xylene plant revealed that a xylene plume had developed in the underlying groundwater, and moreover, that there is strong evidence for in situ microbial xylene degradation with oxygen, nitrate, sulfate and ferric iron as electron acceptors. In order to prevent further xylene spreading, three pumping wells extracting contaminated water were installed downgradient of the spill zone. The numerical reactive transport code Transport Biochemisty Chemistry (TBC) was applied to this situation to quantify the relation of microbial degradation to xylene removal by the pumping wells. It could be shown that the unamended in situ degradation was an appreciable xylene removal process that contributed to about one-third to the total xylene removal (degradation plus extraction). A further objective of the model application was to predict xylene spreading under regional flow conditions, i.e. without operation of the three pumping wells, to consider the possible effects of natural xylene attenuation. To accomplish this, the model calibrated for the situation with operating wells was transferred to the hydraulic situation of regional flow while retaining the parameters of the biochemical model. It turned out that the xylene plume that is expected to develop downgradient of the source area will be limited to an extension of not more than 1000 m. An interesting feature of the simulations results was that xylene degradation under iron-reducing conditions, which was of minor importance for the situation with operating pumping wells, becomes the dominant degradation mechanism under regional flow conditions. Moreover, iron reduction will be the key process in controlling plume evolution. The model application illustrates that multi-species reactive transport models are needed to adequately transfer reactive processes from one hydraulic situation to another, while single species models are not suited for this predictive task.

Forecasting↗

PubMed2001

The evolution of dispersal rates in a heterogeneous time-periodic environment.

A reaction-diffusion model for the evolution of dispersal rates is considered in which there is both spatial heterogeneity and temporal periodicity. The model is restricted to two phenotypes because of technical difficulties, but a wide range of mathematical techniques and computational effort are needed to obtain useful answers. We find that the question of selection is a great deal richer than in the autonomous case, where the phenotype with the lowest diffusion is selected for. In the current model either the lower or higher diffuser rate may be selected, or there may be coexistence of phenotypes. The paper raises several open questions and suggests in particular that a mutation-selection multi-phenotypic model would repay study.

Animals↗

PubMed2005

The evolution of immune-related genes from disease carrying mosquitoes: diversity in a peptidoglycan- and a thioester-recognizing protein.

Adaptive polymorphism may be common in immune system genes as co-evolutionary interactions foster diversity; either through ongoing positive selection (arms races), or balancing selection. DNA sequence diversity in two putative immune system genes was examined in species of the genus Anopheles and from Aedes aegypti. For one gene, encoding the peptidoglycan recognizing protein PGRPLB, there was evidence of purifying selection, suggesting that selection acts to eliminate sequence variation. For another gene, encoding the thioester-containing protein TEP3, higher levels of amino acid replacement were found than would be expected under neutral models of evolution - an indication that this gene has been subject to repeated bouts of positive selection.

Aedes↗

PubMed2005

Molecular evolution of enolase.

Enolase (EC 4.2.1.11) is an enzyme of the glycolytic pathway catalyzing the dehydratation reaction of 2-phosphoglycerate. In vertebrates the enzyme exists in three isoforms: alpha, beta and gamma. The amino-acid and nucleotide sequences deposited in the GenBank and SwissProt databases were subjected to analysis using the following bioinformatic programs: ClustalX, GeneDoc, MEGA2 and S.I.F.T. (sort intolerant from tolerant). Phylogenetic trees of enolases created with the use of the MEGA2 program show evolutionary relationships and functional diversity of the three isoforms of enolase in vertebrates. On the basis of calculations and the phylogenetic trees it can be concluded that vertebrate enolase has evolved according to the "birth and death" model of evolution. An analysis of amino acid sequences of enolases: non-neuronal (NNE), neuron specific (NSE) and muscle specific (MSE) using the S.I.F.T. program indicated non-uniform number of possible substitutions. Tolerated substitutions occur most frequently in alpha-enolase, while the lowest number of substitutions has accumulated in gamma-enolase, which may suggest that it is the most recently evolved isoenzyme of enolase in vertebrates.

Animals↗

PubMed1994

The kinetic aspects of intracellular fluorescence labeling with TMA-DPH support the maturation model for endocytosis in L929 cells.

TMA-DPH (1-(4-trimethylammonium)-6-phenyl-1,3,5-hexatriene), a hydrophobic fluorescent membrane probe, interacts with living cells by instantaneous incorporation into the plasma membrane, where it becomes fluorescent. It then follows the intracellular constitutive membrane traffic and acts as a bulk membrane marker of the endocytic pathway (Illinger, D., P. Poindron, P. Fonteneau, M. Modolell, and J. G. Kuhry. 1990. Biochim. Biophys. Acta. 1030:73-81; Illinger, D., P. Poindron, and J. G. Kuhry. 1991. Biol. Cell. 73:131-138). As such, TMA-DPH displays particular properties mainly due to partition between membranes and aqueous media. From these properties, original arguments can be inferred in favor of the maturation model for the endocytic pathway, against that of pre-existing compartments, in L929 cultured mouse fibroblasts. (a) TMA-DPH labeling is seen to progress from the cell periphery to perinuclear regions during endocytosis without any noticeable loss in fluorescence intensity; with a vesicle shuttle model this evolution would be accompanied by probe dilution with a decrease in the overall intracellular fluorescence intensity, and the labeling of the inner (late) compartments could in no way become more intense than that of the peripheral (early) ones. (b) From TMA-DPH fluorescence anisotropy assays, it is concluded that membrane fluidity is the same in the successive endocytic compartments as in the plasma membrane, which probably denotes a similar phospholipidic membrane composition, as might be expected in the maturation model. (c) TMA-DPH internalization and release kinetics are more easily described with the maturation model.

Animals↗

PubMed2006

Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids.

Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic inferences. About half of the dinoflagellate protists species are photosynthetic and unique in harboring a diversity of plastids acquired from a wide range of eukaryotic algae. They are therefore ideal for studying evolutionary processes of plastids gained through secondary and tertiary endosymbioses. In the light of these processes, we have evaluated the origin of 2 types of dinoflagellate plastids, containing the peridinin or 19'-hexanoyloxyfucoxanthin (19'-HNOF) pigments, by inferring the phylogeny using "covarion" evolutionary models allowing the pattern of among-site rate variation to change over time. Our investigations of genes from secondary and tertiary plastids derived from the rhodophyte plastid lineage clearly reveal "heterotachy" processes characterized as stationary covarion substitution patterns and changes in proportion of variable sites across sequences. Failure to accommodate covarion-like substitution patterns can have strong effects on the plastid tree topology. Importantly, multigene analyses performed with probabilistic methods using among-site rate and covarion models of evolution conflict with proposed single origin of the peridinin- and 19'-HNOF-containing plastids, suggesting that analysis of secondhand plastids can be hampered by convergence in the evolutionary signature of the plastid DNA sequences. Another type of sequence convergence was detected at protein level involving the psaA gene. Excluding the psaA sequence from a concatenated protein alignment grouped the peridinin plastid with haptophytes, congruent with all DNA trees. Altogether, taking account of complex processes involved in the evolution of dinoflagellate plastid sequences (both at the DNA and amino acid level), we demonstrate the difficulty of excluding independent, tertiary origin for both the peridinin and 19'-HNOF plastids involving engulfment of haptophyte-like algae. In addition, the refined topologies suggest the red algal order, Porphyridales, as the endosymbiont ancestor of the secondary plastids in cryptophytes, haptophytes, and heterokonts.

Animals↗