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PubMed2005

Genomic adaptation to acidic environment: evidence from Helicobacter pylori.

The origin of new functions is fundamental in understanding evolution, and three processes known as adaptation, preadaptation, and exaptation have been proposed as possible evolutionary pathways leading to the origin of new functions. Here we examine the origin of an acid resistance mechanism in the mammalian gastric pathogen Helicobacter pylori, with reference to these three evolutionary pathways. The mechanism involved is that H. pylori, when exposed to the acidic environment in mammalian stomach, restricts the acute proton entry across its membrane by its increased usage of positively charged amino acids in the inner and outer membrane proteins. The results of our comparative genomic analysis between H. pylori, the two closely related species Helicobacter hepaticus and Campylobacter jejuni, and other relevant proteobacterial species are incompatible with the hypotheses invoking preadaptation or exaptation. The acid resistance mechanism most likely arose by selection favoring an increased usage of positively charged lysine in membrane proteins.

Adaptation, Biological↗

PubMed2006

Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype.

Wrinkly spreader (WS) genotypes evolve repeatedly in model Pseudomonas populations undergoing adaptive radiation. Previous work identified genes contributing to the evolutionary success of WS. Here we scrutinize the GGDEF response regulator protein WspR and show that it is both necessary and sufficient for WS. Activation of WspR occurs by phosphorylation and different levels of activation generate phenotypic differences among WS genotypes. Five alleles of wspR, each encoding a protein with a single amino acid substitution, were generated by mutagenesis. Two alleles are constitutively active and cause the ancestral genotype to develop a WS phenotype; the phenotypic effects are allele specific and independent of phosphorylation. Three alleles contain changes in the GGDEF domain and when overexpressed in WS cause reversion to the ancestral phenotype. Ability to mimic this effect by overexpression of a liberated N-terminal domain shows that in WS, regulatory components upstream of WspR are overactive. To connect changes at the nucleotide level with fitness, the effects of variant alleles were examined in both structured and unstructured environments: alleles had adaptive and deleterious effects with trade-offs evident across environments. Despite the proclivity of mutations within wspR to generate WS, sequence analysis of wspR from 53 independently obtained WS showed no evidence of sequence change in this gene.

Alleles↗

PubMed2002

Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey.

Although the complete genome sequences of over 50 representative species have revealed the many duplicated genes in all three domains of life, the roles of gene duplication in organismal adaptation and biodiversity are poorly understood. In addition, the evolutionary forces behind the functional divergence of duplicated genes are often unknown, leading to disagreement on the relative importance of positive Darwinian selection versus relaxation of functional constraints in this process. The methodology of earlier studies relied largely on DNA sequence analysis but lacked functional assays of duplicated genes, frequently generating contentious results. Here we use both computational and experimental approaches to address these questions in a study of the pancreatic ribonuclease gene (RNASE1) and its duplicate gene (RNASE1B) in a leaf-eating colobine monkey, douc langur. We show that RNASE1B has evolved rapidly under positive selection for enhanced ribonucleolytic activity in an altered microenvironment, a response to increased demands for the enzyme for digesting bacterial RNA. At the same time, the ability to degrade double-stranded RNA, a non-digestive activity characteristic of primate RNASE1, has been lost in RNASE1B, indicating functional specialization and relaxation of purifying selection. Our findings demonstrate the contribution of gene duplication to organismal adaptation and show the power of combining sequence analysis and functional assays in delineating the molecular basis of adaptive evolution.

Amino Acid Sequence↗

PubMed1979

The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme.

An adaptationist programme has dominated evolutionary thought in England and the United States during the past 40 years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an oragnism into unitary 'traits' and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the only brake upon perfection; non-optimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental Europe) that organisms must be analysed as integrated wholes, with Baupläne so constrained by phyletic heritage, pathways of development and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of non-adaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of non-adaptive structures. We support Darwin's own pluralistic approach to identifying the agents of evolutionary change.

Adaptation, Biological↗

PubMed1989

The logic of social exchange: has natural selection shaped how humans reason? Studies with the Wason selection task.

In order to successfully engage in social exchange--cooperation between two or more individuals for mutual benefit--humans must be able to solve a number of complex computational problems, and do so with special efficiency. Following Marr (1982), Cosmides (1985) and Cosmides and Tooby (1989) used evolutionary principles to develop a computational theory of these adaptive problems. Specific hypotheses concerning the structure of the algorithms that govern how humans reason about social exchange were derived from this computational theory. This article presents a series of experiments designed to test these hypotheses, using the Wason selection task, a test of logical reasoning. Part I reports experiments testing social exchange theory against the availability theories of reasoning; Part II reports experiments testing it against Cheng and Holyoak's (1985) permission schema theory. The experimental design included eight critical tests designed to choose between social exchange theory and these other two families of theories; the results of all eight tests support social exchange theory. The hypothesis that the human mind includes cognitive processes specialized for reasoning about social exchange predicts the content effects found in these experiments, and parsimoniously explains those that have already been reported in the literature. The implications of this line of research for a modular view of human reasoning are discussed, as well as the utility of evolutionary biology in the development of computational theories.

Adolescent↗

PubMed1998

Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci.

Among vertebrates, cichlid fishes are the paradigmatic example of adaptive radiation and ecological specialization. In turn, molecular genetic studies of cichlids have focused primarily on more recently diverged groups. Here, we present an evolutionary hypothesis of the major lineages of cichlid fishes based on DNA sequence data from two nuclear loci. One marker, Tmo-4C4, is a single-copy locus containing a region of amino acid similarity to the muscle protein TITIN. Flanking sequence from a second, microsatellite, locus Tmo-M27, shows similarity to mammalian RAS guanine nucleotide-releasing factor. We compare and combine data from these loci to evaluate phylogenetic performance. In separate and combined analyses, the sequence data support and clarify previous morphological hypotheses of cichlid major-group relationships. Indian and Malagasy cichlids form a basal, paraphyletic group. Neotropical cichlids are the sister clade to an African assemblage composed of the paraphyletic west and Pan-African lineages and a group of east African rift lake taxa. We use a consensus phylogeny of the Cichlidae to trace evolutionary changes in the microsatellite repeat motif at Tmo-M27. Analysis reveals that the repeat region was nearly lost in the ancestor to cichlids and then amplified extensively in African taxa. Results demonstrate that the two new DNA markers could be widely applied in perciform systematics. Furthermore, the comparative approach can unveil mutational dynamics of simple-sequence repeat loci over long periods of fish evolution. Simple-sequence repeat regions are increasingly being found in introns of important regulatory genes. We address issues involving their function and suggest caution in making assumptions of strict neutrality.

Animals↗

PubMed1998

Information gating: an evolutionary model of personality function and dysfunction.

Utilizing principles of evolutionary biology, a model is developed which defines the essential adaptive functions of personality as a whole, and describes how failure in those functions produces the maladaptations characteristic of personality disorders. In this model, personality is hypothesized to have evolved specifically to make human culture possible by managing the flow of information within the culture, especially by mediating teaching and learning, competition and cooperation, and leading and following. These essential culture-forming capacities of personality have at their root the more basic function of information gating, which is defined here as the continuous regulation by personality of its openness for the bidirectional flow of sensory, cognitive, emotional, and motor information between internal self and external social systems, to best meet the needs of both in various situations. The maladaptations characteristic of personality disorders are postulated to be due to their being chronically and frequently too open or too closed for expressing or assimilating social information, given their circumstances. The relationship of this model to other evolutionary models of personality is discussed, as are its clinical and research implications.

Adaptation, Psychological↗

PubMed2005

The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood.

Compensatory mutation occurs when a loss of fitness caused by a deleterious mutation is restored by its epistatic interaction with a second mutation at a different site in the genome. How many different compensatory mutations can act on a given deleterious mutation? Although this quantity is fundamentally important to understanding the evolutionary consequence of mutation and the genetic complexity of adaptation, it remains poorly understood. To determine the shape of the statistical distribution for the number of compensatory mutations per deleterious mutation, we have performed a maximum-likelihood analysis of experimental data collected from the suppressor mutation literature. Suppressor mutations are used widely to assess protein interactions and are under certain conditions equivalent to compensatory mutations. By comparing the maximum likelihood of a variety of candidate distribution functions, we established that an L-shaped gamma distribution (alpha=0.564, theta=21.01) is the most successful at explaining the collected data. This distribution predicts an average of 11.8 compensatory mutations per deleterious mutation. Furthermore, the success of the L-shaped gamma distribution is robust to variation in mutation rates among sites. We have detected significant differences among viral, prokaryotic, and eukaryotic data subsets in the number of compensatory mutations and also in the proportion of compensatory mutations that are intragenic. This is the first attempt to characterize the overall diversity of compensatory mutations, identifying a consistent and accurate prior distribution of compensatory mutation diversity for theoretical evolutionary models.

Epistasis, Genetic↗

PubMed2005

The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions.

Trypanosoma cruzi dihydroorotate dehydrogenase (DHOD), the fourth enzyme of the de novo pyrimidine biosynthetic pathway, is localized in the cytosol and utilizes fumarate as electron acceptor (fumarate reductase activity), while the enzyme from other various eukaryotes is mitochondrial membrane-linked. Here we report that DHOD-knockout T. cruzi did not express the enzyme protein and could not survive even in the presence of pyrimidine nucleosides, substrates for the potentially active salvage pathway, suggesting a vital role of fumarate reductase activity in the regulation of cellular redox balance. Cloning and phylogenetic analysis of euglenozoan DHOD genes showed that the euglenoid Euglena gracilis had a mitochondrial DHOD and that biflagellated bodonids, a sister group of trypanosomatids within kinetoplastids, harbor the cytosolic DHOD. Further, Bodo saliens, a bodonid, had an ACT/DHOD gene fusion encoding aspartate carbamoyltransferase (ACT), the second enzyme of the de novo pyrimidine pathway, and DHOD. This is the first report of this novel gene structure. These results are consistent with suggestions that an ancient common ancestor of Euglenozoa had a mitochondrial DHOD whose descendant exists in E. gracilis and that a common ancestor of kinetoplastids (bodonids and trypanosomatids) subsequently acquired a cytosolic DHOD by horizontal gene transfer. The cytosolic DHOD gene thus acquired may have contributed to adaptation to anaerobiosis in the kinetoplastid lineage and further contributed to the subsequent establishment of parasitism in a trypanosomatid ancestor. Different molecular strategies for anaerobic adaptation in pyrimidine biosynthesis, used by kinetoplastids and by euglenoids, are discussed. Evolutionary implications of the ACT/DHOD gene fusion are also discussed.

Adaptation, Physiological↗

PubMed1998

Evolutionary neurocontrollers for autonomous mobile robots.

In this article we describe a methodology for evolving neurocontrollers of autonomous mobile robots without human intervention. The presentation, which spans from technological and methodological issues to several experimental results on evolution of physical mobile robots, covers both previous and recent work in the attempt to provide a unified picture within which the reader can compare the effects of systematic variations on the experimental settings. After describing some key principles for building mobile robots and tools suitable for experiments in adaptive robotics, we give an overview of different approaches to evolutionary robotics and present our methodology. We start reviewing two basic experiments showing that different environments can shape very different behaviours and neural mechanisms under very similar selection criteria. We then address the issue of incremental evolution in two different experiments from the perspective of changing environments and robot morphologies. Finally, we investigate the possibility of evolving plastic neurocontrollers and analyse an evolved neurocontroller that relies on fast and continuously changing synapses characterized by dynamic stability. We conclude by reviewing the implications of this methodology for engineering, biology, cognitive science and artificial life, and point at future directions of research.

Journal Article↗

PubMed1998

Pregnancy-associated adaptations to hepatic phosphatidylcholine biosynthesis in the guinea-pig.

Pregnancy is associated with increased phosphatidylcholine (PC) 16:0/22:6 and PC16:0/20:4 concentrations in rat liver and plasma, guinea-pig liver, and in plasma in women. These changes may be related to supply of polyunsaturated fatty acids (PUFA) to the fetus. For the rat, these adaptations to hepatic PC composition are regulated by modifications to synthesis de novo from choline. However, it is not known whether these adaptations are applicable to other species. Consequently, we have determined biochemical mechanisms for regulation of hepatic PC synthesis in the pregnant guinea pig. The PUFA content of guinea-pig liver PC synthesised de novo did not change significantly during pregnancy. [Methyl-14C]methionine incorporation into PC in vivo, however, showed increased PC16:0/22:6 and PC16:0/20:4 contents. [Methyl-14C]methionine incorporation into PC over 6 hr in vivo increased during early pregnancy, while PC synthesis de novo did not change. In contrast to the rat, modulation of PE N-methylation is a primary mechanism for regulating the PUFA content of hepatic PC in the pregnant guinea-pig. The use of distinct metabolic strategies to achieve comparable pregnancy-associated adaptations to hepatic PC composition between these animal species suggests both evolutionary convergence and a fundamental the role for PC16:0/22:6 and PC16:0/20:4 in PUFA metabolism during gestation.

Adaptation, Physiological↗

PubMed2006

African cichlid fish: a model system in adaptive radiation research.

The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and 'non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.

Adaptation, Physiological↗

PubMed2026

Flavonoid biosynthesis mediated by GmF3Hs contributes to drought tolerance in soybean.

Flavonoids are central to abiotic stress responses, yet the specific signaling roles and evolutionary dynamics of flavonoid biosynthetic intermediates in crop drought adaptation remain elusive. Here, we demonstrate that dihydrokaempferol (DHK) and dihydroquercetin (DHQ), specific intermediate products of the soybean flavanone 3-hydroxylases GmF3H1/2, function as potent signaling molecules that mitigate drought stress. Exogenous DHK/DHQ promoted abscisic acid-dependent stomatal closure and enhanced drought tolerance across diverse dicot species, including soybean and tobacco, highlighting a broadly conserved stress-mitigating signaling mechanism. CRISPR/Cas9-generated gmf3hs double mutants exhibited severe drought hypersensitivity due to compromised redox homeostasis and defective stomatal regulation, which could be specifically rescued by DHK/DHQ application. Furthermore, the loss of GmF3H triggered a distinct reproductive trade-off under stress, leading to increased pod initiation but severe filling defects. Multiomics network analysis revealed extensive rewiring of broader stress-responsive pathways and identified upstream transcription factors, among which GmPHL11 directly binds to and activates the GmF3H1 promoter; overexpression of GmPHL11 promoted DHK accumulation and enhanced drought stress tolerance in soybean hairy roots. Finally, population genomic analyses demonstrated that the GmF3H1H1 haplotype, which confers superior enzymatic activity and robust root growth under drought stress, might have undergone positive selection during soybean domestication. Collectively, our findings redefine the role of GmF3H-derived specific intermediates as potent signaling molecules, providing comprehensive mechanistic and evolutionary insights into flavonoid-mediated drought resilience, developmental trade-offs, and molecular breeding in crops.

Drought Resistance↗

PubMed1988

Recent developments in the analysis of comparative data.

Comparative methods can be used to test ideas about adaptation by identifying cases of either parallel or convergent evolutionary change across taxa. Phylogenetic relationships must be known or inferred if comparative methods are to separate the cross-taxonomic covariation among traits associated with evolutionary change from that attributable to common ancestry. Only the former can be used to test ideas linking convergent or parallel evolutionary change to some aspect of the environment. The comparative methods that are currently available differ in how they manage the effects brought about by phylogenetic relationships. One method is applicable only to discrete data, and uses cladistic techniques to identify evolutionary events that depart from phylogenetic trends. Techniques for continuous variables attempt to control for phylogenetic effects in a variety of ways. One method examines the taxonomic distribution of variance to identify the taxa within which character variation is small. The method assumes that taxa with small amounts of variation are those in which little evolutionary change has occurred, and thus variation is unlikely to be independent of ancestral trends. Analyses are then concentrated among taxa that show more variation, on the assumption that greater evolutionary change in the character has taken place. Several methods estimate directly the extent to which ancestry can predict the observed variation of a character, and subtract the ancestral effect to reveal variation of phylogeny. Yet another can remove phylogenetic effects if the true phylogeny is known. One class of comparative methods controls for phylogenetic effects by searching for comparative trends within rather than across taxa. With current knowledge of phylogenies, there is a trade-off in the choice of a comparative method: those that control phylogenetic effects with greater certainty are either less applicable to real data, or they make restrictive or untestable assumptions. Those that rely on statistical patterns to infer phylogenetic effects may not control phylogeny as efficiently but are more readily applied to existing data sets.

Adaptation, Physiological↗

PubMedDate not supplied

[Schizophrenia in the light of the evolutionary theories].

The aim of the article was to review the hypotheses of schizophrenia in the light of the evolutionary theory. The authors distinguished adaptationist and non-adaptationist hypotheses concerning the evolutionary underpinnings of schizophrenia. The adaptationist hypotheses are firmly based on notions of adaptation, natural selection and proximate and ultimate causes. The standard hypotheses of this sort proposed by Steven and Price as well as by Pollimeni and Reiss were discussed. Also, the other similar conceptions originated from McGuire and Troisi and proposed by David Horrobin were presented of which the latter is especially promising and worth further investigating. The non-adaptationistic authors criticised many assumptions of the adapationist program i.e. too broad use of term "adaptation" in the area of human behaviour or the very idea of proximate and ultimate causes. Unlike the adaptionists, they focus their attention on other aspects of the evolutionary processes i.e. the role of the mutation and also they are searching in a much intensive way than their opponents for verification of the hypotheses based on the empirical evidence. The theories developed by Crow and by Yeo were listed among the non-adaptationistic ones and presented.

Adaptation, Physiological↗

PubMed2006

Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon).

Adaptive radiations have served as model systems for quantifying the build-up of species richness. Few studies have quantified the tempo of diversification in species-rich clades that contain negligible adaptive disparity, making the macroevolutionary consequences of different modes of evolutionary radiation difficult to assess. We use mitochondrial-DNA sequence data and recently developed phylogenetic methodologies to explore the tempo of diversification of eastern North American Plethodon, a species-rich clade of woodland salamanders exhibiting only limited phenotypic disparity. Lineage-through-time analysis reveals a high rate of lineage accumulation, 0.8 species per million years, occurring 11-8 million years ago in the P. glutinosus species group, followed by decreasing rates. This high rate of lineage accumulation is exceptional, comparable to the most rapid of adaptive radiations. In contrast to classic models of adaptive radiation where ecological niche divergence is linked to the origin of species, we propose that phylogenetic niche conservatism contributes to the rapid accumulation of P. glutinosus-group lineages by promoting vicariant isolation and multiplication of species across a spatially and temporally fluctuating environment. These closely related and ecologically similar lineages persist through long-periods of evolutionary time and form strong barriers to the geographic spread of their neighbours, producing a subsequent decline in lineage accumulation. Rapid diversification among lineages exhibiting long-term maintenance of their bioclimatic niche requirements is an under-appreciated phenomenon driving the build-up of species richness.

Animals↗

PubMed1989

The problem of adaptations: an holistic approach.

On the basis of recent advances in molecular genetics and embryology the role of phenotypic plasticity in the origin of adaptations has been reviewed and emphasized. Carrying on Waddington's experimental research on genetic assimilation, the epigenetic landscape, where genotype, phenotype and environment meet, should be investigated as the place in which environmental information may be embodied in the organism and evolutionary novelties could arise. An holistic, multilevel approach, with the organism as the basic level for the genesis of adaptations and the population as upper level as improving and/or altering, through selective and random factors, the evolutionary pattern, is then envisaged.

Adaptation, Biological↗

PubMed2006

Direct demonstration of an adaptive constraint.

The role of constraint in adaptive evolution is an open question. Directed evolution of an engineered beta-isopropylmalate dehydrogenase (IMDH), with coenzyme specificity switched from nicotinamide adenine dinucleotide (NAD) to nicotinamide adenine dinucleotide phosphate (NADP), always produces mutants with lower affinities for NADP. This result is the correlated response to selection for relief from inhibition by NADPH (the reduced form of NADP) expected of an adaptive landscape subject to three enzymatic constraints: an upper limit to the rate of maximum turnover (kcat), a correlation in NADP and NADPH affinities, and a trade-off between NAD and NADP usage. Two additional constraints, high intracellular NADPH abundance and the cost of compensatory protein synthesis, have ensured the conserved use of NAD by IMDH throughout evolution. Our results show that selective mechanisms and evolutionary constraints are to be understood in terms of underlying adaptive landscapes.

3-Isopropylmalate Dehydrogenase↗