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PubMed1994

Phylogeny of the attine ant fungi based on analysis of small subunit ribosomal RNA gene sequences.

Complete 16S-like ribosomal RNA coding regions were obtained from the fungal symbiont of five genera of attine (leaf-cutting) ants and two free-living fungi. Phylogenetic analyses with distance matrix, maximum likelihood, and parsimony methods revealed that the attine fungal symbionts are homobasidiomycetes in the order Agaricales. Comparison of the topology of the attine fungal symbiont phylogenetic tree with a tree based on attine ant morphology revealed a congruent branching pattern of the more derived attine ants and their fungal symbionts. The parallel branching pattern suggests a long-term coevolution of derived leaf-cutting attine ants and their fungal symbionts.

Agaricales↗
PubMed2005

Maladaptation and natural selection.

The transformations George Williams initiated in evolutionary biology seem so blindingly obvious in retrospect that they spur the question of why he saw what no one else did. While most humans are prone to see only what theory predicts, Williams sees in bold relief whatever does not fit. Not an adaptationist or an anti-adaptationist, Williams is better described as a maladaptionist. The challenge of finding evolutionary explanations for apparent maladaptations has been overlooked with casualness akin to that once typical for group selection. Suboptimal traits tend to be dismissed as illustrations of the weakness and stochastic nature of selection compared with mutation and drift. A closer look suggests that such constraints are only one of six possible kinds of explanations for apparently suboptimal designs: mismatch, coevolution, tradeoffs, constraints, reproductive advantage at the expense of the individual, and defenses that are aversive but useful Medicine has asked proximate questions at every possible level but has only begun to ask evolutionary questions about why bodies are vulnerable to disease. Considering all six possible evolutionary reasons for apparently suboptimal traits will spur progress not only in medicine but also more generally in biology. 'Williams Vision" may not yield a net benefit to the possessor, but it is invaluable for the species.

Adaptation, Physiological↗
PubMed1984

Insect--plant adaptations.

The adaptation of insects to plants probably commenced in the early Permian period, though most current associations will be more recent. A major burst of adaptation must have followed the rise of the Angiosperms in the Cretaceous period, though some particular associations are as recent as this century. Living plants form a large proportion of the potential food in most habitats, though insects have had to overcome certain general hurdles to live and feed on them. Insects affect the reproduction and survival of plants, and thus the diversity of plant secondary chemicals may have evolved as a response. Where an insect species has a significant effect on a plant species that is its only host, coevolution may be envisaged. A spectacular example is provided by Heliconius butterflies and passion flower vines, studied by L.E. Gilbert and others. But such cases may be likened to 'vortices in the evolutionary stream': most plant species are influenced by a range of phytophagous insects so that selection will be for general defences--a situation termed diffuse coevolution. Evidence is presented on recent host-plant shifts to illustrate both the restrictions and the flexibility in current insect-plant associations.

Adaptation, Biological↗
PubMed1995

The contribution of DNA slippage to eukaryotic nuclear 18S rRNA evolution.

Six of 204 eukaryotic nuclear small-subunit ribosomal RNA sequences analyzed show a highly significant degree of clustering of short sequence motifs that indicates the fixation of products of replication slippage within them in their recent evolutionary history. A further 72 sequences show weaker indications of sequence repetition. Repetitive sequences in SSU rRNAs are preferentially located in variable regions and in particular in V4 and V7. The conserved region immediately 5' to V7 (C7) is also consistently repetitive. Whereas variable regions vary in length and appear to have evolved by the fixation of slippage products, C7 shows no indication of length variation. Repetition within C7 is therefore either not a consequence of slippage or reflects very ancient slippage events. The phylogenetic distribution of sequence simplicity in small-subunit rRNAs is patchy, being largely confined to the Mammalia, Apicomplexa, Tetrahymenidae, and Trypanosomatidae. The regions of the molecule associated with sequence simplicity vary with taxonomic grouping as do the sequence motifs undergoing slippage. Comparison of rates of insertion and substitution in a lineage within the genus Plasmodium confirms that both rates are higher in variable regions than in conserved regions. The insertion rate in variable regions is substantially lower than the substitution rate, suggesting that selection acts more strongly on slippage products than on point mutations in these regions. Patterns of coevolution between variable regions may reflect the consequences of selection acting on the incorporation of slippage-derived sequences across the gene.

Animals↗
PubMed2006

The coevolution of genes and genetic codes: Crick's frozen accident revisited.

The standard genetic code is the nearly universal system for the translation of genes into proteins. The code exhibits two salient structural characteristics: it possesses a distinct organization that makes it extremely robust to errors in replication and translation, and it is highly redundant. The origin of these properties has intrigued researchers since the code was first discovered. One suggestion, which is the subject of this review, is that the code's organization is the outcome of the coevolution of genes and genetic codes. In 1968, Francis Crick explored the possible implications of coevolution at different stages of code evolution. Although he argues that coevolution was likely to influence the evolution of the code, he concludes that it falls short of explaining the organization of the code we see today. The recent application of mathematical modeling to study the effects of errors on the course of coevolution, suggests a different conclusion. It shows that coevolution readily generates genetic codes that are highly redundant and similar in their error-correcting organization to the standard code. We review this recent work and suggest that further affirmation of the role of coevolution can be attained by investigating the extent to which the outcome of coevolution is robust to other influences that were present during the evolution of the code.

Animals↗
PubMed2004

Multiple genotypes of influenza B virus circulated between 1979 and 2003.

The segmented genome of influenza B virus allows exchange of gene segments between cocirculating strains. Through this process of reassortment, diversity is generated by the mixing of genes between viruses that differ in one or more gene segments. Phylogenetic and evolutionary analyses of all 11 genes of 31 influenza B viruses isolated from 1979 to 2003 were used to study the evolution of whole genomes. All 11 genes diverged into two new lineages prior to 1987. All genes except the NS1 gene were undergoing linear evolution, although the rate of evolution and the degree to which nucleotide changes translated into amino acid changes varied between lineages and by gene. Frequent reassortment generated 14 different genotypes distinct from the gene constellation of viruses circulating prior to 1979. Multiple genotypes cocirculated in some locations, and a sequence of reassortment events over time could not be established. The surprising diversity of the viruses, unrestricted mixing of lineages, and lack of evidence for coevolution of gene segments do not support the hypothesis that the reassortment process is driven by selection for functional differences.

Biological Evolution↗
PubMed2004

Coevolution of gene expression among interacting proteins.

Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate that gene expression levels can coevolve, adding another dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein-protein interactions.

Amino Acid Sequence↗
PubMed1997

Phylogenetic analysis of glycolytic enzyme expression.

Although differences among species in enzyme maximal activity or concentration are often interpreted as adaptive and important for regulating metabolism, these differences may simply reflect phylogenetic divergence. Phylogenetic analysis of the expression of the glycolytic enzymes among 15 taxa of a North American fish genus (Fundulus) indicated that most variation in enzyme concentration is due to evolutionary distance and may be nonadaptive. However, three enzymes' maximal activities covary with environmental temperature and have adaptive value. Additionally, two pairs of enzymes covary, indicating coevolution. Thus, metabolic flux may be modulated by many different enzymes rather than by a single rate-limiting enzyme.

Adaptation, Physiological↗
PubMed2007

The modular nature of genetic diseases.

Evidence from many sources suggests that similar phenotypes are begotten by functionally related genes. This is most obvious in the case of genetically heterogeneous diseases such as Fanconi anemia, Bardet-Biedl or Usher syndrome, where the various genes work together in a single biological module. Such modules can be a multiprotein complex, a pathway, or a single cellular or subcellular organelle. This observation suggests a number of hypotheses about the human phenome that are now beginning to be explored. First, there is now good evidence from bioinformatic analyses that human genetic diseases can be clustered on the basis of their phenotypic similarities and that such a clustering represents true biological relationships of the genes involved. Second, one may use such phenotypic similarity to predict and then test for the contribution of apparently unrelated genes to the same functional module. This concept is now being systematically tested for several diseases. Most recently, a systematic yeast two-hybrid screen of all known genes for inherited ataxias indicated that they all form part of a single extended protein-protein interaction network. Third, one can use bioinformatics to make predictions about new genes for diseases that form part of the same phenotype cluster. This is done by starting from the known disease genes and then searching for genes that share one or more functional attributes such as gene expression pattern, coevolution, or gene ontology. Ultimately, one may expect that a modular view of disease genes should help the rapid identification of additional disease genes for multifactorial diseases once the first few contributing genes (or environmental factors) have been reliably identified.

Computational Biology↗
PubMed2005

Maternal inheritance, sexual conflict and the maladapted male.

Females differ from males in transmitting not only nuclear genes but also cytoplasmic genetic elements (CGEs), including DNA in mitochondria, chloroplasts and microorganisms that are present in the cell. Until recently, evolutionary research has adopted a nucleocentric approach in which organelles have been viewed as subservient energy suppliers. In this article, we propose that a more equitable view of nuclear genes and organelle genomes will lead to a better understanding of the dynamics of sexual selection and the constraints on male adaptation. Maternal inheritance of CGEs intensifies sexually-antagonistic coevolution and provides a parsimonious explanation for the relatively high frequency in males of such apparently maladaptive traits as infertility, homosexuality and baldness.

Adaptation, Biological↗
PubMed1999

Phylogenetic analysis of Sarcocystis spp. of mammals and reptiles supports the coevolution of Sarcocystis spp. with their final hosts.

Sequences of the small subunit rRNA genes were obtained for two coccidians, Sarcocystis dispersa and an unnamed Sarcocystis sp. which parasitise the European barn owl and an African viperid snake as their final host, respectively, and share mouse as their intermediate host. Phylogenetic analysis of the sequence data showed that Sarcocystis sp. from the viperid snake is most closely related to another Sarcocystis sp. isolated from an American crotalid snake, while S. dispersa grouped with other bird-transmitted species. The available dataset failed to resolve the evolutionary relationships among four major branches into which all Sarcocystidae and Isospora spp. were split. However, within these branches, the phylogenetic relationships of the majority of analysed members of the genus Sarcocystis reflected coevolution with their final, rather than intermediate hosts.

Animals↗
PubMed2002

Host range and local parasite adaptation.

Parasites may be expected to become locally adapted to their hosts. However, while many empirical studies have demonstrated local parasite adaptation, others have failed to demonstrate it, or have shown local parasite maladaptation. Researchers have suggested that gene flow can swamp local parasite-host dynamics and produce local adaptation only at certain geographical scales; others have argued that evolutionary lags can account for both null and maladaptive results. In this paper, we use item response theory (IRT) to test whether host range influences the likelihood of parasites locally adapting to their hosts. We collated 32 independent experiments testing for local adaptation, where parasites could be assigned as having either broad or narrow host ranges (BHR and NHR, respectively). Twenty-five tests based on BHR parasites had a significantly lower average effect size than seven NHR tests, indicating that studies based on BHR parasites are less likely to demonstrate local parasite adaptation. We argue that this may relate to evolutionary lags during diffuse coevolution of BHR parasites with their hosts, rather than differences in experimental approaches or other confounds between BHR and NHR studies.

Adaptation, Physiological↗
PubMed2005

Experimentally enforced monogamy: inadvertent selection, inbreeding, or evidence for sexually antagonistic coevolution?

There has been recent criticism of experiments that applied enforced monogamous mating to species with a long history of promiscuity. These experiments indicated that the newly introduced monogamy reversed sexually antagonistic coevolution and caused males to evolve to be less harmful to their mates and females to evolve reduced resistance to harm from males. Several authors have proposed alternative interpretations of these experimental results based on qualitative analysis. If well-founded, these criticisms would invalidate an important part of the empirical foundation for sexually antagonistic coevolution between the sexes. Although these criticisms have a reasonable basis in principle, we find that after quantitative evaluation that they are not supported.

Animals↗
PubMed1979

[Immunological reactivity of the host as an environmental factor and its significance for the development of parasitism].

Concepts--mainly of SPRENT (1959, 1963), DINEEN (1963) and DAMIAN (1964)--concerning the immunological aspects of the phylogeny of host-parasite associations and the function of immune processes in the host-parasite relationship are discussed. In the light of some recent findings an integrating interpretation of the available body of evidence is attempted. The significance of the immuno-selection pressure during the course of host-parasite coevolution is stressed and some of the consequences of this pressure seen in the existing host-parasite systems are pointed out.

Adaptation, Physiological↗
PubMed2002

The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations.

BACKGROUND: Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles. RESULT: Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains. CONCLUSIONS: Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.

Amino Acid Motifs↗
PubMed1994

Diversity within diversity: molecular approaches to studying microbial interactions with insects.

DNA sequence information has greatly augmented the number of characters available for analysis in phylogenetic research. Nowhere is this more evident than in studies of microbial evolution. Ribosomal DNA sequence data has simultaneously permitted the distinction between individual species and the inference of their phylogenetic relationships in many cases where both were formerly impossible. These have contributed to our understanding of the ecology of particular microbe-host interactions and the history of these relationships over evolutionary time. We describe examples from two ends of the ecological spectrum in insect/bacterial associations: one in which bacteria mediate host cytoplasmic incompatibility and parthenogenesis, and the other in which mycetocyte bacteria augment host nutrition. In the former, the pattern of bacterial interaction is general, with the same or closely related strains of the genus Wolbachia associating with a wide range of insect taxa. In the latter, concordance between host and microbe phylogenies suggests cospeciation between bacteria and host, although it is as yet unclear whether this process has involved step-wise, reciprocal coevolution. We conclude with a discussion of how developments in molecular techniques may aid in analyzing more complex interactions between insects and microbes.

Animals↗
PubMed1989

Exon-intron-like pattern of the first propagating molecule?

A biogeochemical scenario is proposed, according to which prebiotic self-replication of RNA-like molecules evolved gradually from domain propagation to entire strand replication. The hypothetical replicating entities that formed an evolutionary continuity in time, the prebioectons, were characterized by self-structuring, and started their evolution from strands possessing one or more templatable domains. The inherent self-structuring implies a very early coevolution of the replicating molecules with prebiotic peptides, in line with the cassette model of Cedergren and Grosjean (1987). The proposed approach can be partially tested in the laboratory.

Biological Evolution↗
PubMed2004

Fitness of indirectly transmitted pathogens: restraint and constraint.

Many pathogens of medical and veterinary importance have obligatory multihost life cycles. Yet, theoretical models aiming to predict patterns of pathogen reproductive success and the limited empirical data available with which to evaluate them, focus on directly transmitted microparasites. Patterns of host exploitation and the relative fitness of individual pathogen genotypes throughout the different host stages of multihost life cycles have thus remained ignored. We examined correlated responses to artificial selection of Schistosoma mansoni lines selected for high or low infection intensity in the intermediate host. Pathogen fitness in the intermediate host was strongly inversely correlated with pathogen fitness in the definitive host. Moreover, high pathogen infection intensity was associated with decreased, rather than increased, virulence to its intermediate host. These results raise important implications regarding the impact of genetic constraints on the maintenance of genetic and phenotypic polymorphisms in natural populations, the evolution and coevolution of parasite virulence and host specialization, as well as the success of host-directed control programs.

Animals↗