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PubMed1999

Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system.

One of the most important aspects of mitochondrial (mt) genome evolution in Metazoa is constancy of size and gene content of mtDNA, whose plasticity is maintained through a great variety of gene rearrangements probably mediated by tRNA genes. The trend of mtDNA to maintain the same genetic structure within a phylum (e.g., Chordata) is generally accepted, although more recent reports show that a considerable number of transpositions are observed also between closely related organisms. Base composition of mtDNA is extremely variable. Genome GC content is often low and, when it increases, the two complementary bases distribute asymmetrically, creating, particularly in vertebrates, a negative GC-skew. In mammals, we have found coding strand base composition and average degree of gene conservation to be related to the asymmetric replication mechanism of mtDNA. A quantitative measurement of mtDNA evolutionary rate has revealed that each of the various components has a different evolutionary rate. Non-synonymous rates are gene specific and fall in a range comparable to that of nuclear genes, whereas synonymous rates are about 22-fold higher in mt than in nuclear genes. tRNA genes are among the most conserved but, when compared to their nuclear counterparts, they evolve 100 times faster. Finally, we describe some molecular phylogenetic reconstructions which have produced unexpected outcomes, and might change our vision of the classification of living organisms.

Animals↗
PubMedDate not supplied

Life history evolution in guppies (Poecilia reticulata): guppies as a model for studying the evolutionary biology of aging.

Natural populations of guppies can be found with different communities of predators. We have contrasted the early life history of guppies from high and low predation localities. Life history theory predicts that such differences in mortality pattern will select for evolutionary changes in the guppy's life history. Specifically, guppies in high-predation localities are predicted to mature at an earlier age and devote more of their resources to reproduction. We have demonstrated the predicted differences in life history patterns with experiments and observations on guppies from each type of locality. We have also selected for the predicted changes in the life history by manipulating mortality patterns in natural populations. Theories for the evolution of senescence predict that these same mortality patterns will also select for changes in the rate of aging. Specifically, guppies from high-predation localities should have higher rates of aging than their counterparts from low-predation localities. Experiments that select for changes in the early life history should also select for changes in the rate of aging. The existing work on guppies, therefore, presents the opportunity to use them as a new experimental system for studying the evolutionary biology of aging. Finally, I present preliminary results from a pilot study of aging in guppies. This study differs from the earlier work by Comfort because these fish have been reproductively active since they attained maturity; Comfort's fish were maintained as virgins throughout their lives. This study makes two important points. First, age-specific changes in reproductive performance represent as important an index of aging as mortality rates. Second, the rate of aging may be far more rapid in reproductively active individuals.

Aging↗
PubMed1999

Biomarkers of immunosenescence within an evolutionary perspective: the challenge of heterogeneity and the role of antigenic load.

Under an evolutionary perspective, antigens can be considered nothing else than chronic stressors that constituted the major selective pressure for immune system emergence and evolution. In this review, recent data are discussed under the hypothesis that human immunosenescence is the consequence of the continuous attrition caused by chronic antigenic overload/stress. The advantage of this theoretical approach is that a unifying hypothesis is proposed, which tries to fill in the current gap between the conceptualizations concerning the mechanisms which counteract aging and favor longevity in invertebrates and vertebrates. The hypothesis is that the immune system is, at a higher level of biological organization and complexity, the counterpart of the anti-stress response network identified in invertebrates as the major determinant of survival. We argue that some of the most important characteristics of immunosenescence, i.e. the accumulation and the clonal expansion of memory and effector T cells, the reduction/exhaustion of naive T cells, and the shrinkage of T cell repertoire, are compatible with this assumption. Thus, immunosenescence can be envisaged as a global reduction of the "immunological space." Concomitantly, immunosenescence results in the progressive generation of cellular mosaicism which is the consequence of the heterogeneous replicative histories and telomere shortening of T and B cell subsets, as well as hemopoietic stem cells. Most of the parameters affected by immunosenescence appear to be under genetic control, and future research on biomarkers should address this point. On the whole, immunosenescence can be taken as a proof that the beneficial effects of the immune system, devoted to the neutralization of dangerous/harmful agents early in life and in adulthood, turn to be detrimental late in life, in a period largely not foreseen by evolution. This perspective fits with basic assumptions of evolutionary theories of aging, such as antagonistic pleiotropy.

Aging↗
PubMed1998

A new theory on the common evolutionary origin of natural immunity, inflammation and stress response: the invertebrate phagocytic immunocyte as an eye-witness.

Data in favor of the hypothesis of the common evolutionary origin of natural immunity inflammation and stress response are presented. These phenomena seem to be mediated by a common pool of molecules (POMC-derived peptides, cytokines, biogenic amines, glucocorticoids, and nitric oxide). Macrophages are able to release all the above mentioned molecules. They play a primary role in defence mechanisms. Thus, we argue that this cell can be considered the eye-witness of the common evolutionary origin of the immune and neuroendocrine systems.

Animals↗
PubMed2001

[Africa or Asia, which is the evolutionary origin of human schistosomes?].

The origin and the evolution of Schistosomatidae species, due to their medical importance (responsible of the second most important human parasitosis after malaria), arouse a great interest. A combination of phylogenetic studies using several molecular markers has provided support for the traditional grouping and evolutionary inferences derived from morphological and biological data. The genus Schistosoma, which comprises all species parasitizing Man, is generally split into four evolutionary lineages (mansoni, haematobium, indicum and japonicum lineages). The group of African schistosomes (including mansoni and haematobium lineages) appears very divergent from the japonicum lineage. Recent phylogenetic studies using partial 28S rDNA sequencing and including Orientobilharzia turkestanicum from Iran, an Asian parasite of livestock, found, unexpectedly, that this species nested among Schistosoma species, thus rendering the latter paraphyletic, and suggested an Asian origin for the Schistosoma genus. The present work re-examines the question of the geographical origin of human schistosomes by analysing a new genomic marker (ITS2) as well as by including the use of O. turkestanicum originating from northeastern China. Our results are in agreement with previous work using 28S, in demonstrating that Schistosoma is not monophyletic. However, O. turkestanicum, whatever the method of analysis used (distance or parsimony), was grouped with members of the japonicum group to the exclusion of African Schistosoma species. Then, our data argue strongly for the need for further phylogenetic study including new taxa and new genomic sequences before definitely concluding either an Asian or African origin for the genus Schistosoma.

Africa↗
PubMedDate not supplied

The evolutionary origins of electric signal complexity.

This study explores the evolutionary origins of waveform complexity in electric organ discharges (EODs) of weakly electric fish. I attempt to answer the basic question of what selective forces led to the transition from the simplest signal to the second simplest signal in the gymnotiform electric fishes. The simplest electric signal is a monophasic pulse and the second simplest is a biphasic pulse. I consider five adaptive hypotheses for the evolutionary transition from a monophasic to a biphasic EOD: (i) electrolocation, (ii) sexual selection, (iii) species isolation, (iv) territory defense, (v) crypsis from electroreceptive predators. Evaluating these hypotheses with data drawn largely from the literature, I find best support for predation. Predation is typically viewed as a restraining force on evolution of communication signals, but among the electric fishes, predation appears to have served as a creative catalyst. In suppressing spectral energy in the sensitivity range of predators (a spectral simplification), the EOD waveforms have become more complex in their time domain structure. Complexity in the time domain is readily discernable by the high frequency electroreceptor systems of gymnotiform and mormyrid electric fish. The addition of phases to the EOD can cloak the EOD from predators, but also provides a substrate for subsequent modification by sexual selection. But, while juveniles and females remain protected from predators, breeding males modify their EODs in ways that enhance their conspicuousness to predators.

Animals↗
PubMed2002

An evolutionary artificial neural networks approach for breast cancer diagnosis.

This paper presents an evolutionary artificial neural network (EANN) approach based on the pareto-differential evolution (PDE) algorithm augmented with local search for the prediction of breast cancer. The approach is named memetic pareto artificial neural network (MPANN). Artificial neural networks (ANNs) could be used to improve the work of medical practitioners in the diagnosis of breast cancer. Their abilities to approximate nonlinear functions and capture complex relationships in the data are instrumental abilities which could support the medical domain. We compare our results against an evolutionary programming approach and standard backpropagation (BP), and we show experimentally that MPANN has better generalization and much lower computational cost.

Algorithms↗
PubMed1998

The crystal structure of a complement-1q family protein suggests an evolutionary link to tumor necrosis factor.

ACRP30--adipocyte complement-related protein of 30 kDa or AdipoQ--is an abundant serum protein, secreted exclusively from fat cells, which is implicated in energy homeostasis and obesity [1,2]. ACRP30 is a close homologue of the complement protein C1q, which is involved in the recognition of microbial surfaces [3-5] and antibody-antigen complexes [6,7] in the classical pathway of complement. We have determined the crystal structure of a homotrimeric fragment from ACRP30 at 2.1 A resolution. The structure reveals an unexpected homology to the tumor necrosis factor (TNF) family. Identical folding topologies, key residue conservations, and similarity of trimer interfaces and intron positions firmly establish an evolutionary link between the TNF and C1q families. We suggest that TNFs--which control many aspects of inflammation, adaptive immunity, apoptosis and energy homeostasis--arose by divergence from a primordial recognition molecule of the innate immune system. The evolutionary connection between C1q-like proteins and TNFs illuminates the shared functions of these two important groups of proteins.

Complement C1q↗
PubMed2002

Phylogeny, fossils, and model systems in the study of evolutionary developmental biology.

The emerging field of evolutionary developmental biology (evo-devo) continues to operate largely under a single paradigm. In this paradigm developmental regulatory genes and processes are compared among a collection of "model organisms" selected primarily on the basis of their historical utility in the study of development. This approach has proven to be extremely informative, revealing an unexpected deep evolutionary conservation among developmental genes and genetic systems. Despite its success, concern has been expressed regarding its limitations. We discuss the "model organism" paradigm in evo-devo research. Based on our interpretation of its limitations, we propose a separate but complementary approach that is centered on "model groups." These groups are selected on the basis of their taxonomic affinity and their relevance to questions of interest to evo-devo biologists. We further discuss the Tetraodontiformes (Teleostei, Pisces) as an example of a "model group" for the evo-devo study of vertebrate skeletal elements.

Animals↗
PubMed2002

Herpetological diversity along Andean elevational gradients: links with physiological ecology and evolutionary physiology.

A well-defined macroecological pattern is the decline in biodiversity with altitude. However, this decline is taxa-specific. For example, amphibians are more diverse than squamates at extreme elevations in the tropical Andes, but this pattern is reversed at extreme elevations in the southern latitudes. Several ecophysiological and evolutionary factors may be related to this difference. At high-elevations in southern latitudes temperature differs dramatically among seasons and dry soils dominate, characteristics that appear to favor lizard physiological ecology. Tropical high altitudes, in contrast, are humid and offer abundant and diverse water resources. These characteristics allow for a richer anuran community but might complicate lizard egg development through temperature and oxygen constrains. Differences in strategies of thermal adaptation might also modulate diversity patterns. The thermal physiology of anurans is extremely labile so that behavioral and physiological performance is maintained despite an altitudinal decrease in field body temperature. Lizards, in contrast, exhibit a conservative thermal physiology and rely on behavioral thermoregulation to face cold and variable temperatures. Both, lizard behavioral strategies and anuran physiological adjustments seem equally efficient in allowing ecological success and diversification for both groups in the tropics up to approximately 3000 m. At higher elevations physiological thermal adaptation is required, and lizards are ecologically constrained, perhaps at various ontogenetic stages. Patterns of biodiversity along environmental clines can be better understood through a physiological approach, and can help to refine and propose hypotheses in evolutionary physiology.

Adaptation, Physiological↗
PubMed2005

Evolutionary relationships between Saccharomyces cerevisiae and other fungal species as determined from genome comparisons.

The increasing number of fungal genomes whose sequence has been completed permits their comparison both at the nucleotide and protein levels. The information thus obtained improves our knowledge on evolutionary relationships between fungi. Comparison of the Saccharomyces cerevisiae genome with other Hemiascomycetes genomes confirms that a whole-genome duplication occurred before the diversification between Candida glabrata and the Saccharomyces sensu stricto species and after separation from the branch leading to the other Hemiascomycetes. Duplication was followed by individual gene losses and rearrangements affecting extensive DNA regions. Although S. cerevisiae and C. glabrata are two closely related yeast species at an evolutionary scale, their different habitats and life styles correlate with specific gene differences and with more extensive gene loses having occurred in the parasitic C. glabrata. At a closer evolutive scale, diversification among the sensu stricto species began with nucleotide changes at the intergenic regions affecting sequences that are not relevant for gene regulation, together with more extensive genome rearrangements involving transposons and telomeric regions. One important characteristic of fungal genomes that is shared with other eukaryotes is the fusion of gene sequences coding for separate protein modules into a single open reading frame. This allows diversification of protein functions while saving gene information.

Evolution, Molecular↗
PubMed1999

Evolutionary genetics of Trypanosoma and Leishmania.

We review recent advances in the study of population structure and phylogenetic diversity of parasites belonging to the genera Trypanosoma and Leishmania. In all species properly analyzed, these parasites exhibit a basically clonal population structure, with occasional bouts of genetic exchange or hybridization, and a strong structuration of their populations into discrete evolutionary lineages. On an evolutionary scale, the impact of sex appears to be greater in African than in American trypanosomes. The taxonomic status of some Leishmania 'species' is questionable.

Animals↗
PubMed2003

Extraction of short-latency evoked potentials using a combination of wavelets and evolutionary algorithms.

Somatosensory evoked potentials, recorded at the spine or scalp of a patient, are contaminated by noise. It is common practice to use ensemble averaging to remove the noise, which usually requires a large number of responses to produce one averaged signal. In this paper a post-processing technique is shown which uses a combination of wavelets and evolutionary algorithms to produce a representative waveform with fewer responses. The most suitable wavelets and a set of weights are selected by an evolutionary algorithm to form a filter bank, which enhances the extraction of evoked potentials from noisy recordings.

Algorithms↗
PubMed2002

Plant evolutionary genomics.

Evolutionary genomics combines functional and evolutionary analyses of genome conservation and differentiation. Gene duplication and polyploidy have fundamentally shaped the genomes of Arabidopsis and all angiosperms. Recent comparative studies have focussed on gene regulation, the function of untranscribed genomic regions, and the effects of natural selection on protein function. A large fraction of interspecific protein divergence is probably adaptive, and may be useful for experimental studies of genes and proteins.

Animals↗
PubMed2000

Comparison of papillomavirus and immunodeficiency virus evolutionary patterns in the context of a papillomavirus vaccine.

In contemplating a vaccine for human papillomaviruses (HPVs), it is important to consider the evolutionary context in which such a vaccine would be deployed. The human immunodeficiency virus, having been the subject of even more extensive study than HPV, shares certain salient features with regards to phylogenetic structure, and may serve as a model for contemplation of possible difficulties with HPV vaccination. However, there are also striking differences in the evolutionary potentials and histories of the viruses that permit an optimistic outlook for HPV. These similarities and differences, as well as their implications for vaccination studies, are reviewed.

Animals↗
PubMed2002

Autoimmunity on alert: naturally occurring regulatory CD4(+)CD25(+) T cells as part of the evolutionary compromise between a 'need' and a 'risk'.

Autoimmunity, at least in the central nervous system (CNS), is not only an outcome of immune system malfunction, but is the body's own protective mechanism against destructive self-compounds. Likewise, the naturally occurring regulatory CD4(+)CD25(+) T cells have a physiological function, and are not merely an evolutionary adaptation to suppress self-reactive T-cell clones that escaped deletion in the thymus. We postulate that the regulatory T (Tr) cells are the product of an evolutionary compromise between the need for autoimmunity on alert for tissue maintenance and the need to control autoimmunity to avoid autoimmune disease. In the event of an insult to the CNS, the balance between self-reactive (effector) T cells and Tr cells determines the time of onset, the intensity and the duration of the autoimmune response. This response might thus represent an adaptive mechanism, which is optimal for day-to-day maintenance, but insufficient in extreme cases of CNS damage or failure of regulation. Downregulation or upregulation of CD4(+)CD25(+) Tr cells might be a way to achieve better protection from neurodegenerative conditions induced by self-destruction or avoid autoimmune inflammatory disease development, respectively.

Animals↗
PubMed2003

The origin, emergence and evolutionary genetics of dengue virus.

Dengue is one of the most important emerging viruses, posing a threat to one-third of the global human population. Herein we show how the comparative analysis of gene sequence data has shed light on the origin and spread of dengue virus, as well as on the evolutionary processes that structure its genetic diversity. This reveals that dengue virus has a relatively recent evolutionary history, with the four serotypes originating approximately 1000 years ago and only establishing endemic transmission in humans in the last few hundred years. However, its place of origin remains uncertain as does the extent of genetic and phenotypic diversity present in the sylvatic (primate) transmission cycle. Although there is some evidence that viral strains differ in key phenotypic features such as virulence, and for positive selection at immunologically important sites, it seems likely that stochastic processes also play a major role in shaping viral genetic diversity, with lineage extinction a common occurrence. A more complete understanding of the evolution and epidemiology of dengue virus, particularly with respect to the aetiology of severe disease, will require large-scale prospective studies and the comparative analysis of complete genome sequences.

Animals↗
PubMed2000

Analysis of birth intervals in a non-contracepting Indian population: an evolutionary ecological approach.

Reproductive strategies are related to ecological constraints. This paper examines data on early birth spacing in a scheduled caste, Bengali-speaking, non-contracepting population of the Karimganj district of southern Assam, India, taking an evolutionary ecological perspective. It is found that on average birth intervals closed by boy-boy are longer than those closed by girl-girl. Birth spacing tends to be longer among upper-income and Craftsman sub-caste mothers. The presence of a 'grandmother' in the household shortens spacing. These findings are compatible with an evolutionary-based reproductive decision-making process.

Analysis of Variance↗