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Results for “Evolutionary adaptability”

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PubMed2006

Predominance of clonal reproduction, but recombinant origins of new genotypes in the free-floating aquatic bladderwort Utricularia australis f. tenuicaulis (Lentibulariaceae).

Aquatic plants are a biological group sharing several adaptations to aquatic conditions. The most striking evolutionary convergence in this group is the extensive reliance on clonal reproduction, which largely determines the patterns and process of evolution in aquatic plants. Utricularia australis f. tenuicaulis is a free-floating aquatic bladderwort that reproduces both sexually via seeds and clonally via turions and shoot fragments. Amplified fragment length polymorphism analysis was conducted on 267 ramets collected from 30 populations in Japan. The genotypic diversity within populations was extremely low, regardless of the geographical distribution range: the mean number of genotypes per population (G) was 1.4 and the mean genotypic diversity (D), including monoclonal populations, was 0.17. In contrast to the predominance of a few clones within populations, many of the populations investigated had different genotypes; a large portion of the genetic variation was explained by variation among populations. Character compatibility analysis clearly revealed that somatic mutations did not contribute to the origin of genotypic diversity in this aquatic bladderwort; instead, rare-to-sporadic sexual reproduction probably generated new genotypes. Thus, future studies should examine the role of sexual reproduction in this species from the viewpoint of long-term evolutionary benefits.

Ecosystem↗

PubMed1996

Respiratory chains of archaea and extremophiles.

Extremophilic organisms are adapted to harsh environmental conditions like high temperature, extremely acidic or alkaline pH, high salt, or a combination of those. With a few exceptions extremophilic bacteria are colonizing only moderately hot biotopes, whereas hyperthermophiles are found specifically among archaea (formerly 'archaebacteria') which can thrive at temperatures close to or even above the boiling point of water. It has been a challenging question whether the special properties of their proteins and membranes have been acquired by adaptation, or whether they might reflect early evolutionary states as suggested by their phylogenetic position at the lowest branches of the universal tree of life.

Amino Acid Sequence↗

PubMed1995

Polarization of Th-cell responses: a phylogenetic consequence of nonspecific immune defence?

CD4+ T helper (Th)-cell responses are polarized into Th1 and Th2 types. Here, Paul Garside and Allan McI. Mowat propose that this is an evolutionary consequence of the relationship between specific adaptive immunity, individual components of the nonspecific inflammatory response and different types of infection. This concept has important implications both for understanding protective immunity and for vaccine design and delivery.

Animals↗

PubMed1995

Artificial modification of the viral regulatory region improves tissue culture growth of SV40 strain 776.

We describe here changes in the regulatory region of SV40 that influence its growth potential in cultured cells. Laboratory strains of papovaviruses BK and JC differ in the sequence of their regulatory regions from archetypes that have not been passaged in cell culture. These archetypes lack sequence repeats in the regulatory region; duplications that occur upon passage in cell culture confer selective growth advantage. Changes within the enhancer-promoter region of the well-characterized 776 strain of papovavirus SV40 that might affect its growth in tissue culture cells have not been documented. We measured the effect upon the growth of SV40 (776 strain) in CV-1 cells either of adding an additional 72-basepair (bp) enhancer element or of duplicating the entire 21-bp repeat region. SV40 growth in tissue culture was improved by reiteration of enhancer elements, whereas no growth advantage was conferred by tandem duplication of the 21-bp repeats. Viral DNA infectivity in CV-1 cells was directly proportional to the number of 72-bp elements but was unaffected by tandemly repeated 21-bp repeat elements. This study suggests that the 776 strain of SV40 is an evolutionary intermediate and that tissue-culture-adapted strains of SV40 do not accurately reflect the replication potential of natural isolates from primate hosts.

Animals↗

PubMed2005

Association between antennal phenotype, wing polymorphism and sex in the genus Mepraia (Reduviidae: Triatominae).

Mepraia spinolai and Mepraia gajardoi (Hemiptera, Reduviidae) are only found in the arid regions of northern Chile. Mepraia is the only genus of Triatominae with marked wing polymorphism. Females of both species are micropterous, males of M. spinolai may be micropterous, brachypterous or macropterous, while males of M. gajardoi are always brachypterous. Because of this wing polymorphism, Mepraia can be used as a model to analyze morphological adaptations related to the flying activity and evolutionary relationships in the Triatominae. The study presented here analyses the antennal phenotype of the Mepraia species and carries out a comparison with the two species of Triatoma included in the spinolai complex (Triatoma eratyrusiformis and Triatoma breyeri). The analysis of the antennal phenotype of Mepraia showed a marked intraspecific phenotypic variability related with sex and wing condition. The number and length of multiporous trichoid sensilla (TH) on the pedicel are significantly higher and longer in winged males and are strongly reduced in females. The great length of the TH sensillum is an infrequent characteristic within Triatominae. The results show that phenetic distances between sexes are greater than between the two species. Similarity between the Mepraia species and T. eratyrusiformis was found as they all show long bristles (BR) and TH and two sized basiconic receptors (BA), a pattern that have not been observed in other species of Triatominae. These characters are not present in T. breyeri.

Animals↗

PubMed2006

A mixed strategy model for the emergence and intensification of social learning in a periodically changing natural environment.

Based on a population genetic model of mixed strategies determined by alleles of small effect, we derive conditions for the evolution of social learning in an infinite-state environment that changes periodically over time. Each mixed strategy is defined by the probabilities that an organism will commit itself to individual learning, social learning, or innate behavior. We identify the convergent stable strategies (CSS) by a numerical adaptive dynamics method and then check the evolutionary stability (ESS) of these strategies. A strategy that is simultaneously a CSS and an ESS is called an attractive ESS (AESS). For certain parameter sets, a bifurcation diagram shows that the pure individual learning strategy is the unique AESS for short periods of environmental change, a mixed learning strategy is the unique AESS for intermediate periods, and a mixed learning strategy (with a relatively large social learning component) and the pure innate strategy are both AESS's for long periods. This result entails that, once social learning emerges during a transient era of intermediate environmental periodicity, a subsequent elongation of the period may result in the intensification of social learning, rather than a return to innate behavior.

Genotype↗

PubMed2004

Changes along the male reproductive axis in response to social context in a gonochoristic gobiid, Zosterisessor ophiocephalus (Teleostei, Gobiidae), with alternative mating tactics.

Sexual selection has given rise, in several taxa, to intrasexual variation in male phenotype. While evolutionary studies have provided explanations of the adaptive function of this dramatic male phenotypic diversity, the proximate control of its expression has still to be completely understood. Several observations, primarily from sex-changing species, indicated a major role of social interactions in reproductive axis regulation and consequently in the expression of alternative male phenotypes. Here we documented changes along the male reproductive axis in response to social context in a gonochoristic species, the grass goby Zosterisessor ophiocephalus, where fully functional alternative male mating tactics appear to be expressed as an ontogenetic gradient. In the grass goby, larger and older males dig a nest and perform parental care, while smaller males sneak fertilization during territorial male spawning. Territorial males are characterized by a higher number of gonadotropin-releasing hormone (GnRH) neurons in forebrain preoptic area, smaller testes, larger seminal vesicles, and viscous ejaculates that last longer and contain fewer sperm than those of sneakers. To experimentally investigate the role of social factors in inducing changes along the male reproductive axis, sneakers were tested in two different situations: nesting alone or with ripe females. Sneakers that mated and performed parental care showed dramatic changes in brain, reproductive apparatus morphology, and ejaculate traits. GnRH-immunoreactive cells in forebrain preoptic area increased in number, reaching values typical of wild-caught parental males. Testes size decreased while seminal vesicle size increased and ejaculates showed lower sperm densities. These results were discussed within the framework of the social transduction hypothesis, which predicts that social experience should mediate, through a cascade of internal processes, shifts between morphs throughout life.

Animals↗

PubMed1998

Ontological measurement.

Endophysics ultimately deduces an indefinite interface between an object and an observer. Objects, given such an interface, cannot be distinguished from the measurement process used to identify them. Evolutionary processes comprising of emergent properties and adaptability are seen in a new light. The concept of indefiniteness and/or paradox appears on the surface to be based on the epistemological framework of the Cartesian cut. However, perpetual processes consisting of generation and resolution of paradoxes are beyond the epistemological framework of measurement. They lead to the notion of progression, which one can refer to as ontological (or inherent) measurement.

Biological Evolution↗

PubMed2003

Ageing purpose: another thrifty genotype.

For evolutionary biology, ageing is a non-adaptive process. The 'disposable soma' theory proposes that senescence is the consequence of a reduction in the energy invested in the processes of cell maintenance and repair due to the fact that it is more beneficial to invest it in reproduction. Recently, various genes have been identified whose mutations modify the life span of certain animals. Most of these genes are related to energy metabolism, especially insulin, IGF-1 and their receptors. Furthermore, it has also been demonstrated that there is a modification in metabolic pathways during ageing. As a result, the energy-storing pathways are strengthened and there is a reduction in the pathways that use energy. All these findings suggest that ageing is a strategy designed by natural selection to save energy, in accordance with other saving strategies. This way the energy that is not used can be dedicated to offspring to improve their pre-reproductive survival.

Aging↗

PubMed2003

Phylogeography of the Chionodraco genus (Perciformes, Channichthydae) in the Southern Ocean.

Antarctic fish of the suborder Notothenioidei represent one of the most notable examples of adaptive radiation in the marine environment. The evolutionary relationships between and within the eight families of this suborder have been well established by numerous studies, whereas the microevolutionary processes of notothenioid species remain largely unexplored. In the present paper we investigated the evolutionary relationships between three closely related species of the genus Chionodraco (family Channichthyidae), namely Chionodraco hamatus, Chionodraco rastrospinosus, and Chionodraco myersi by analysing portions of the mitochondrial genome (D-loop and 16S rRNA). The taxonomic status of C. hamatus and C. rastrospinosus as separate species has been questioned because of the limited number of key morphological characters that distinguish these two taxa. Our results, based on the analysis of several specimens belonging to both morphological groups revealed a small genetic differentiation among haplotypes, however, a clear separation between the two nominal species emerged since all individuals of each of the two taxa clustered together in distinct monophyletic groups. C. myersi appeared more distantly related in the phylogenetic analysis. For one species, C. hamatus, sampling was carried out at three different geographic locations in the area of the Ross Sea and Weddell Sea. The results showed that the partition of the genetic variation within this species is not compatible with the hypothesis of panmixia as gene flow between populations was significantly reduced.

Animals↗

PubMed2001

Transmission bottlenecks and the evolution of fitness in rapidly evolving RNA viruses.

We explored the evolutionary importance of two factors in the adaptation of RNA viruses to their cellular hosts, size of viral inoculum used to initiate a new infection, and mode of transmission (horizontal versus vertical). Transmission bottlenecks should occur in natural populations of viruses and their profound effects on viral adaptation have been previously documented. However, the role of transmission mode has not received the same attention. Here we used a factorial experimental design to test the combined effects of inoculum (bottleneck) size and mode of transmission in evolution of vesicular stomatitis virus (VSV) in tissue culture, and compared our results to the predictions of a recent theoretical model. Our data were in accord with basic genetic principles concerning the balance between mutation, selection and genetic drift. In particular, attenuation of vertically transmitted viruses was a consequence of the random accumulation of deleterious mutations, whereas horizontally transmitted viruses experiencing similar bottlenecks did not suffer the same fitness losses because effective bottleneck size was actually determined by the number of host individuals. In addition, high levels of viral fitness in horizontally transmitted populations were explained by competition among viral variants.

Animals↗

PubMed2003

A 'fair go' for coral hybridization.

Hybridisation between coral species clearly occurs in vitro, but the evolutionary significance of this cross-fertility is still the subject of much debate. Compelling genetic and reproductive evidence support introgressive hybridization amongst Indo-Pacific members of the scleractinian genus Acropora. Although population genetic analyses indicate that interspecific hybridization events are relatively rare, they are likely be important on evolutionary time scales, creating the capacity for adaptive evolution by increasing genomic diversity and heterozygosity. However, in a recent paper based exclusively on the three endemic Caribbean Acropora species, Vollmer and Palumbi (2002) dispute the occurrence of reticulation in corals. Here we use data from both the Vollmer and Palumbi study and our earlier paper on the same species (van Oppen et al., 2000) to show that reticulation has occurred amongst the Caribbean Acropora species. Furthermore, conclusions based on the limited Caribbean Acropora fauna cannot simply be extrapolated to Indo-Pacific corals, and it is inappropriate to view some coral species as 'immortal mules'.

Animals↗

PubMed2005

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.

By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.

Biological Evolution↗

PubMed2005

Characterization of two avian MHC-like genes reveals an ancient origin of the CD1 family.

Many of the genes that comprise the vertebrate adaptive immune system are conserved across wide evolutionary time scales. Most notably, homologs of the mammalian MHC gene family have been found in virtually all jawed vertebrates, including sharks, bony fishes, reptiles, and birds. The CD1 family of antigen-presenting molecules are related to the MHC class I family but have evolved to bind and present lipid antigens to T cells. Here, we describe two highly divergent nonclassical MHC class I genes found in the chicken (Gallus gallus) that have sequence homology to the mammalian CD1 family of proteins. One of the chicken CD1 genes expresses a full-length transcript, whereas the other has multiple splice variants. Both Southern blot and single nucleotide polymorphism analysis indicates that chicken CD1 is relatively nonpolymorphic. Moreover, cross-hybridizing bands are present in other bird species, suggesting broad conservation in the avian class. Northern analysis of chicken tissue shows a high level of CD1 expression in the bursa and spleen. In addition, molecular modeling predicts that the potential antigen-binding pocket is probably hydrophobic, a universal characteristic of CD1 molecules. Genomic analysis indicates that the CD1 genes are located on chicken chromosome 16 and maps to within 200 kb of the chicken MHC B locus, suggesting that CD1 genes diverged from classical MHC genes while still linked to the major histocompatibility complex locus. The existence of CD1 genes in an avian species suggests that the origin of CD1 extends deep into the evolutionary history of terrestrial vertebrates.

Amino Acid Sequence↗

PubMed2002

Antioxidant gene expression in active and sedentary house mice (Mus domesticus) selected for high voluntary wheel-running behavior.

We present liver mRNA levels of the two antioxidant enzymes catalase (CAT) and Mn-superoxide dismutase (SOD2) in four treatment groups of house mice assayed by RNase protection at 20 months of age. These groups were mice from four replicate selection and four replicate control lines from the sixteenth generation of selective breeding for high voluntary wheel running, housed with or without running wheels from age 3 weeks through 20 months. Exercising control females had induced CAT expression; SOD2 exhibited a similar pattern in females from two of the four control lines. Exercising male mice had induced CAT expression, but not SOD2 expression, irrespective of genetic background. We discuss these results with respect to both evolutionary (genetic) and training (exercise-induced) adaptations and explore predictions of these results in relation to the oxidative-damage theory of senescence.

Aging↗

PubMed1996

The evolution of the antiaging action of dietary restriction: a hypothesis.

Reducing the intake of dietary energy by laboratory rodents to well below that of animals allowed to eat ad libitum slows the rate of aging. This phenomenon, which is robust and reproducible, is known as the antiaging action of dietary restriction (DR). We hypothesize that this DR response arose because of its evolutionary advantage with respect to survival during periods of unpredictable, short-term food shortage. In our evolutionary scenario, food shortage led to an adaptive redirection of resources away from reproduction toward somatic maintenance via an enhanced heat shock protein response in invertebrates. In vertebrates, an additional involvement of the hypothalamic-adenohypophyseal-adrenal glucocorticoid system was necessitated to protect against excessive systemic defense responses. We suggest several general implications of our hypothesis.

Aging↗

PubMed1997

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.

Algorithms↗

PubMed2000

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.

Animals↗