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PubMed2006

The evolution of myiasis in humans and other animals in the Old and New Worlds (part I): phylogenetic analyses.

Myiasis, the infestation of live vertebrates with dipterous larvae, seems to take two distinct forms that, it has been suggested, evolved from two distinct phylogenetic roots: saprophagous and sanguinivorous. However, the convergent evolution of morphological and life-history traits seems to have had a major role in simplifying this overall assessment of the evolutionary routes by which myiasis arose. Moreover, this somewhat simplistic division is further complicated by the existence of both ectoparasitic and endoparasitic species of myiasis-causing Diptera, the evolutionary affinities of which remain to be resolved. To understand how different forms of parasitism arose, the evolution of the various groups of myiasis-causing flies must be separated from the evolution of the myiasis habit per se. Until recently, evolutionary studies of myiasis-causing flies were little more than discussions of morphology-based taxonomy. Since the mid-1990s, however, several formal phylogenies - based on both morphological and, increasingly, molecular data - have been published, enabling reassessment of the hypotheses concerning myiasis evolution. In part I of this review, we focus on some recent landmark studies in this often-neglected branch of parasitology and draw together phylogenetic studies based on molecular and morphological data to provide a framework for the subsequent analysis of biochemical, immunological, behavioural, biogeographical and fossil evidence relating to the evolution of myiasis.

Animals↗

PubMed2006

Evolution of transcriptional regulatory networks in microbial genomes.

Advances in sequencing and generating high-throughput expression data have created a situation in which it is possible to integrate comparative analysis with genome-wide studies of the structure and function of regulatory systems in model organisms. Recent studies have focused on topological properties and the evolution of regulatory networks. This problem can be addressed on several levels: evolution of binding sites upstream of orthologous or duplicated genes; co-evolution of transcription factors and the DNA motifs that they recognize; expansion, contraction and replacement of regulatory systems; the relationship between co-regulation and co-expression; and, finally, construction of evolutionary models that generate networks with realistic properties. This should eventually lead to the creation of a theory of regulatory evolution with a similar level of detail and understanding to the theory of molecular evolution of protein and DNA sequences.

Amino Acid Sequence↗

PubMed2005

Game-theoretical approaches to studying the evolution of biochemical systems.

Evolutionary optimization has been successfully used to increase our understanding of key properties of biochemical systems. Traditional optimization is, however, often insufficient for gaining deeper insights into the evolution of such systems because usually there is a mutual relationship between the properties optimized by evolution and the properties of the environment. Thus, by evolving towards optimal properties, organisms change their environment, which in turn alters the optimum. Evolutionary game theory provides an appropriate framework for analyzing evolution in such 'dynamic fitness landscapes'. We therefore argue that it is a promising approach to studying the evolution of biochemical systems. Indeed, recent studies have applied evolutionary game theory to key issues in the evolution of energy metabolism.

Evolution, Molecular↗

PubMed2006

The coordinated evolution of yeast proteins is constrained by functional modularity.

Functional modularity is a key attribute of cellular systems and has important roles in evolution. However, the extent to which functional modularity affects protein evolution is largely unknown. Here, we analyzed the evolution of both sequence and expression level of proteins in the yeast Saccharomyces cerevisiae and found that proteins within the same functional modules evolve at more similar rates than those between different modules. We also found stronger co-evolution of expression levels between proteins within functional modules than between them. These results suggest that a coordinated evolution of both the sequence and expression level of proteins is constrained by functional modularity.

Evolution, Molecular↗

PubMed2004

Nutrient enrichment and food chains: can evolution buffer top-down control?

We show how evolutionary dynamics can alter the predictions of classical models of the effects of nutrient enrichment on food webs. We compare an ecological nutrient-plant-herbivore food-chain model without evolution with the same model, including herbivore evolution, plant evolution, or both. When only herbivores are allowed to evolve, the predictions are similar to those of the ecological model without evolution, i.e., plant biomass does not change with nutrient addition. When only plants evolve, nutrient enrichment leads to an increase in the biomass of all compartments. In contrast, when plants and herbivores are allowed to coevolve, although these two classical patterns are common, a wide variety of other responses is possible. The form of the trade-offs that constrain evolution of the two protagonists is then critical. This stresses the need for experimental data on phenotypic traits, their costs and their influence on the interactions between organisms and the rest of the community.

Adaptation, Biological↗

PubMed2004

Dispersal and the evolution of specialisation in a two-habitat type metapopulation.

Metapopulation theory for the evolution of specialisation is virtually absent. In this article, therefore, we study a metapopulation model for consumers with a fitness trade-off between two habitats. We focus on effects of habitat abundance, dispersal rate and trade-off strength on the evolution of specialisation under two types of trade-off. Adaptation affects either the intrinsic growth rates r or the carrying capacities K. Depending on dispersal rate and trade-off strength, evolution can result in one generalist, one specialist or two specialist types. Higher dispersal rate and a weaker trade-off favour the evolution of a generalist, for both trade-off structures. However, we also find differences between the two trade-off structures. Our results are qualitatively similar to analyses of two-patch models, suggesting that insights from such simpler models can be extrapolated to metapopulation models. Additional effects, however, occur because in classical metapopulations patch lifetime depends on extinction rate. Counterintuitively, this favours the evolution of specialisation when the trade-off affects r.

Adaptation, Physiological↗

PubMed2005

The dawn and evolution of hormones in the adenohypophysis.

The adenohypophysial hormones have been believed to have evolved from several ancestral genes by duplication followed by evolutionary divergence. To understand the origin and evolution of the endocrine systems in vertebrates, we have characterized adenohypophysial hormones in an agnathan, the sea lamprey Petromyzon marinus. In gnathostomes, adrenocorticotropin (ACTH) and melanotropin (MSH) together with beta-endorphins (beta-END) are encoded in a single gene, designated as proopiomelanocortin (POMC), however in sea lamprey, ACTH and MSH are encoded in two distinct genes, proopoicortin (POC) gene and proopiomelanotropin (POM) gene, respectively. The POC and POM genes are expressed specifically in the rostral pars distalis (RPD) and the pars intermedia (PI), respectively. Consequently, the final products from both tissues are the same in all vertebrates, i.e., ACTH from the PD and MSH from the PI. The POMC gene might have been established in the early stages of invertebrate evolution by internal gene duplication of the MSH domains. The ancestral gene might be then inherited in lobe-finned fish and tetrapods, while internal duplication and deletion of MSH domains as well as duplication of whole POMC gene took place in lamprey and gnathostome fish. Sea lamprey growth hormone (GH) is expressed in the cells of the dorsal half of the proximal pars distalis (PPD) and stimulates the expression of an insulin-like growth factor (IGF) gene in the liver as in other vertebrates. Its gene consists of 5 exons and 4 introns spanning 13.6 kb, which is the largest gene among known GH genes. GH appears to be the only member of the GH family in the sea lamprey, which suggests that GH is the ancestral hormone of the GH family that originated first in the molecular evolution of the GH family in vertebrates and later, probably during the early evolution of gnathostomes. The other member of the gene family, PRL and SL, appeared by gene duplication. A beta-chain cDNA belonging to the gonadotropin (GTH) and thyrotropin (TSH) family was cloned. It is expressed in cells of the ventral half of PPD. Since the expression of this gene is stimulated by lamprey gonadotropin-releasing hormone, it was assigned to be a GTHbeta. This GTHbeta is far removed from beta-subunits of LH, FSH, and TSH in an unrooted tree derived from phylogenetic analysis, and takes a position as an out group, suggesting that lampreys have a single GTH gene, which duplicated after the agnathans and prior to the evolution of gnathostomes to give rise to LH and FSH.

Animals↗

PubMed2003

Baseline criteria and the evolution of hosts and parasites: D0, R0 and competition for resources between strains.

Our understanding of the evolution of diseases has been greatly aided by the use of baseline criteria. Here we examine the theoretical and biological relationships of the well known baseline criteria for the evolution of disease (R0) and the recently introduced corresponding criterion for the evolution of resistance in hosts (D0). We show that there is a formal theoretical equivalence between the two criteria and discuss the characteristics of seperability that determine whether the criteria define the course of evolution. These theoretical determinants correspond biologically to whether strains compete for resources or not. We discuss the biological application of the criteria and argue that D0 may be less widely applicable than R0, but does determine the evolution of resistance in populations with fixed carrying capacities.

Animals↗

PubMed2002

Cell-selfish modes of evolution and mutations directed after transcriptional bypass.

During transcription, prokaryotic and eukaryotic RNA polymerases bypass and misread (transcriptional mutagenesis) several classes of DNA lesions. For example, misreading of 8-OH-dG generates mRNAs containing G to T transversions. After translation, if the mutant protein briefly allowed the cell a growth-DNA replication advantage, then precocious DNA replication would bypass that unrepaired 8-OH-dG and misinsert dA opposite the directing DNA lesion with a higher probability than would be experienced for 8-OH-G lesions at other positions in otherwise identical neighboring cells. Such retromutations would have been tested for their imparted growth advantage as mRNA before they became heritable DNA mutations. The logical properties of a mode of evolution that utilizes directed-retromutagenesis were compared one by one with those of the standard neo-Darwinian mode. The retromutagenesis mode, while minimizing mutational load, is cell-selfish; fitness is for an immediate growth advantage rather than future reproductive potential. In prokaryotes, an evolutionary mode that involves standard Darwinian fitness testing of novel alleles in the genetic background of origin followed by clonal expansion also favors cell-selfish allele combinations when linkage disequilibrium is practiced. For metazoa and plants to have evolved organized tissues, cell-selfish modes of evolution represent systems-poisons that must be totally suppressed. The feedback loops that allow evolution to be cell-serving in prokaryotes are actively blocked in eukaryotes by traits that restrict fitness to future reproductive potential. These traits include (i) delay of fitness testing until after the mutation is made permanently heritable, (ii) diploidy to further delay fitness testing, (iii) segregation of somatic lines from germ lines, (iv) testing of novel alleles against randomized allele combinations constructed by obligate sex, and (v) obligate genetic death to insure that that the most basic systems unit of selfish allele combinatorial uniqueness is the species instead of the cell. The analyses indicate that modes of evolution in addition to our neo-Darwinian one could have existed utilizing known molecular mechanisms. The evolution of multicellularity was as much the discarding of old cell-selfish habits as the acquisition of new altruistic ones.

Alleles↗

PubMed2001

The molecular evolution of Trypanosomatidae.

In the absence of a fossil record, theories relating to the evolution of protozoa have, for most of the twentieth century, been based on morphological and life cycle data despite their known limitations. However, recent advances in molecular methodology, notably the wide availability of accurate, automated DNA sequencing, have made it possible to deduce the evolutionary relationships of extant species from their genes. This paper focuses on new findings concerning the evolution of the Trypanosomatidae, based on the ever-expanding body of molecular data now available. Classically, the evolution of digenetic parasitism in kinetoplastids has centred around two opposing theories--invertebrate first or vertebrate first--depending on which was the original host of the monogenetic parasite. However, data supporting a close phylogenetic relationship between genera of monogenetic insect parasites and digenetic vertebrate parasites challenge the simplicity of these hypotheses and suggest that the transition may not have been a major evolutionary barrier. The implications of these observations for the evolution of parasitism within the group are discussed. Phylogenetic analysis of a diverse selection of trypanosomatid species suggests that the genus Trypanosoma is monophyletic and that the human parasites, T. brucei, T. cruzi and Leishmania spp., have fundamentally different patterns of evolution. T. brucei clusters with mammalian trypanosomes of African origin, suggesting an evolutionary history confined to Africa. T. cruzi shows association with trypanosomes from bats, T. rangeli, and trypanosomes from a range of South American mammals and an Australian kangaroo. The origins of most parasites within this clade lie in South America and Australia, suggesting an ancient southern super-continent origin for T. cruzi, possibly in marsupials. The divergence between the Leishmania and Trypanosoma lineages is also ancient. The topology of Leishmania phylogenies suggests an independent transition to digenetic parasitism, a neotropical origin and an early tertiary radiation of the parasite.

Animals↗

PubMed2005

Molecular evolution and population genetics of circadian clock genes.

This article discusses a number of common methodologies used in the field of population genetics and evolution and reviews their application within circadian rhythm research. We examine the basic principles behind phylogenetic analysis and how these can be used to illuminate clock gene evolution. We then discuss genetic variation between and within species and show how neutrality tests can reveal the signatures of selection or drift on clock genes. These tests are particularly important for moving beyond "just so" stories when discussing the evolution of clock phenotypes, and we provide relevant circadian examples. We also focus on methods that can be used to study genetic variation, such as quantitative trait loci analysis. We discuss the various bootstrapping or resampling techniques that can be applied to generate confidence intervals in the various methodologies and then examine the use of interspecific transformation studies, which can, and have, provide some useful insights, not only into clock gene evolution in particular, but "behavioral" gene evolution in general. Finally, we assess gene/protein alignments and protein structure predictions and their implicit evolutionary bases.

Animals↗

PubMed2001

Molecular evolution of proglucagon.

The vertebrate proglucagon gene encodes glucagon, and the two glucagon-like peptides GLP-1 and GLP-2. To better understand the origin and diversification of the distinct hormonal roles of the three glucagon-like sequences encoded by the proglucagon gene, we have examined the evolution of this gene. The structure of proglucagon has been largely maintained within vertebrates. Duplication of the proglucagon gene or duplications of sequences within the proglucagon gene are rare. All proglucagon gene duplications are likely to be the result of genome duplication events. Examination of the rates of amino acid sequence evolution of each hormone reveals that they have not evolved in a uniform manner. Each hormone has evolved in an episodic fashion, suggesting that the selective constraints acting upon the sequence vary between, and within, vertebrate classes. Changes in selection on a sequence often reflect changes in the function of the sequence, such as the change in function of GLP-1 from a glucagon-like hormone in fish to an incretin in mammals. We found that the GLP-2 sequence underwent rapid sequence evolution in the early mammal lineage, therefore we have concluded that mammalian GLP-2 has acquired a new biological function that is not found in other vertebrates. Comparisons of the hormone sequences show that many amino acid residues that are functionally important in mammalian hormones are not conserved through vertebrate evolution. This observation suggests that the sequences involved in hormone action change through evolution.

Animals↗

PubMed2003

Cooperation and conflict in the evolution of individuality. IV. Conflict mediation and evolvability in Volvox carteri.

The continued well being of evolutionary individuals (units of selection and evolution) depends upon their evolvability, that is their capacity to generate and evolve adaptations at their level of organization, as well as their longer term capacity for diversifying into more complex evolutionary forms. During a transition from a lower- to higher-level individual, such as the transition between unicellular and multicellular organisms, the evolvability of the lower-level (cells) must be restricted, while the evolvability of the new higher-level unit (multicellular organism) must be enhanced. For these reasons, understanding the factors leading to an evolutionary transition should help us to understand the factors underlying the emergence of evolvability of a new evolutionary unit. Cooperation among lower-level units is fundamental to the origin of new functions in the higher-level unit. Cooperation can produce a new more complex evolutionary unit, with the requisite properties of heritable fitness variations, because cooperation trades fitness from a lower-level (the costs of cooperation) to the higher-level (the benefits for the group). For this reason, the evolution of cooperative interactions helps us to understand the origin of new and higher-levels of fitness and organization. As cooperation creates a new level of fitness, it also creates the opportunity for conflict between levels of selection, as deleterious mutants with differing effects at the two levels arise and spread. This conflict can interfere with the evolvability of the higher-level unit, since the lower and higher-levels of selection will often "disagree" on what adaptations are most beneficial to their respective interests. Mediation of this conflict is essential to the emergence of the new evolutionary unit and to its continued evolvability. As an example, we consider the transition from unicellular to multicellular organisms and study the evolution of an early-sequestered germ-line in terms of its role in mediating conflict between the two levels of selection, the cell and the cell group. We apply our theoretical framework to the evolution of germ/soma differentiation in the green algal group Volvocales. In the most complex member of the group, Volvox carteri, the potential conflicts among lower-level cells as to the "right" to reproduce the higher-level individual (i.e. the colony) have been mediated by restricting immortality and totipotency to the germ-line. However, this mediation, and the evolution of an early segregated germ-line, was achieved by suppressing mitotic and differentiation capabilities in all post-embryonic cells. By handicapping the soma in this way, individuality is ensured, but the solution has affected the long-term evolvability of this lineage. We think that although conflict mediation is pivotal to the emergence of individuality at the higher-level, the way in which the mediation is achieved can greatly affect the longer-term evolvability of the lineage.

Adaptation, Physiological↗

PubMed2003

Evolution of evolvability via adaptation of mutation rates.

We examine a simple form of the evolution of evolvability-the evolution of mutation rates-in a simple model system. The system is composed of many agents moving, reproducing, and dying in a two-dimensional resource-limited world. We first examine various macroscopic quantities (three types of genetic diversity, a measure of population fitness, and a measure of evolutionary activity) as a function of fixed mutation rates. The results suggest that (i) mutation rate is a control parameter that governs a transition between two qualitatively different phases of evolution, an ordered phase characterized by punctuated equilibria of diversity, and a disordered phase of characterized by noisy fluctuations around an equilibrium diversity, and (ii) the ability of evolution to create adaptive structure is maximized when the mutation rate is just below the transition between these two phases of evolution. We hypothesize that this transition occurs when the demands for evolutionary memory and evolutionary novelty are typically balanced. We next allow the mutation rate itself to evolve, and we observe that evolving mutation rates adapt to values at this transition. Furthermore, the mutation rates adapt up (or down) as the evolutionary demands for novelty (or memory) increase, thus supporting the balance hypothesis.

Adaptation, Physiological↗

PubMed1999

Evolution of the genetic code: the nonsense, antisense, and antinonsense codes make no sense.

According to the molecular recognition theory, the complementarity of the sense and nonsense DNA strands is reflected in a complementarity of polypeptides and the corresponding nonsense polypeptides. A comparison of the sense and nonsense code matrices, and of the antisense and antinonsense code matrices, either by visual inspection or by comparing the corresponding hydrophobicity matrices (e.g. by simply adding them together), revealed no complementarity of these pairs of matrices in terms of possible attractive physical forces. Instead, it was evident that the codes divide the amino acids into two major groups: hydrophilic and hydrophobic, a division which is directly correlated with the folding property of proteins. A simple primordial genetic code distinguishing between these two types of amino acids would have been capable of generating three-dimensionally folded peptides, which could stabilize coding RNAs by forming ribonucleoprotein complexes. This evolutionary scheme is reflected in the present organisation of information processing and storage in essentially all organisms. RNAs are processed and translated into proteins by ribonucleoproteins, while other steps in information retrieval and processing, such as DNA replication, transcription, protein folding and posttranslational processing, are catalyzed by proteins. This shows that the evolution of DNA as an information storage medium was a secondary event, unrelated to the evolution of the genetic code. From the primordial hydrophilic/hydrophobic (f.ex. Leu/Arg) code, evolution proceeded by introduction of a catalytic amino acid (Ser). The further evolution of the code has mainly served to increase the number of functional hydrophilic amino acids, since there has not been a great advantage in increasing the number of structural, hydrophobic amino acids. At some stage during the evolution of the genetic code, double-stranded DNA was introduced as a maximally safe genetic copy of RNA. This required the action of highly specific enzymes, and was therefore preceded by the refinement of the genetic code. As a conclusion of this evolutionary scheme, it can be inferred that, in general only the sense strand encodes proteins.

Codon, Nonsense↗

PubMed2001

Changing views of brain evolution.

Although brain studies began in ancient Egypt, speculations on vertebrate brain evolution occurred only much later, after the publication of Darwin's Origin of Species in 1859. Subsequently, views of brain evolution have been shaped by a complex interplay of theory and technique. Darwin's theory allowed the variation in brain size and complexity to be re-interpreted within an evolutionary context, albeit an erroneous pre-Darwinian context based on scala naturae. With the development of histological techniques, research shifted to descriptions of cellular structure, cellular aggregates and their putative interconnections. In spite of these technical advances, brain evolution continued to be viewed within the context of scala naturae. Following the publication of The Comparative Anatomy of the Nervous System of Vertebrates by Ariëns Kappers, Huber, and Crosby in 1936, there followed a period of stasis, after which biological views of evolution were radically altered by the confluence of genetics, paleontology, and systematics, termed the Evolutionary Synthesis. Against this background, the development of new experimental techniques for establishing neural connections resulted in a new flowering of comparative neuroanatomy. While comparative descriptive and experimental studies of brain organization continue, the rapprochement of embryology and genetics is fueling a new renaissance that promises to increase our understanding of brain evolution and its genetic basis.

Animals↗

PubMed2000

Adaptive evolution of animal toxin multigene families.

Animal toxins comprise a diverse array of proteins that have a variety of biochemical and pharmacological functions. A large number of animal toxins are encoded by multigene families. From studies of several toxin multigene families at the gene level the picture is emerging that most have been functionally diversified by gene duplication and adaptive evolution. The number of pharmacological activities in most toxin multigene families results from their adaptive evolution. The molecular evolution of animal toxins has been analysed in some multigene families, at both the intraspecies and interspecies levels. In most toxin multigene families, the rate of non-synonymous to synonymous substitutions (dN/dS) is higher than one. Thus natural selection has acted to diversify coding sequences and consequently the toxin functions. The selection pressure for the rapid adaptive evolution of animal toxins is the need for quick immobilization of the prey in classical predator and prey interactions. Currently available evidence for adaptive evolution in animal toxin multigene families will be considered in this review.

Adaptation, Biological↗

PubMed2001

Mathematical model of the evolution of statoconia.

A mathematical model of the evolution of statoconia in statocysts of freshwater snails based on the analysis of experimental data [Wiederhold et al., 1990; Pedrozo et al., 1996; Gao et al., 1997; Gao and Wiederhold, 1997; Wiederhold et al., 1999] is proposed. The growth of statoconia is considered as the process of solution crystallization. The model proposed assumes that two main processes determine the evolution of statoconia in developing snails: the generation of new statoconia and the linear growth of statoconia sizes. The analytical solution of the model and qualitative comparison of theoretical results with the experimental data show: (1) there are at least three periods of statoconia evolution; (2) the generation of new statoconia mainly determines the first period of evolution when the shell diameter of snails D < 4 mm; (3) when D > 6 mm the size distribution of statoconia is determined by the growth of their sizes with a constant rate; (4) on the interval deltaD = 4-6 mm the transformation of size distribution with selective dissolution of statoconia takes place. The model agrees well with the experimental data and makes it possible to estimate some parameters of the statoconia kinetics. Additional experiments, which are necessary for further development of the model, and quantitative estimates of the mechanisms of statoconia evolution are formulated.

Animals↗