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PubMed1998

Environmental hypotheses of hominin evolution.

The study of human evolution has long sought to explain major adaptations and trends that led to the origin of Homo sapiens. Environmental scenarios have played a pivotal role in this endeavor. They represent statements or, more commonly, assumptions concerning the adaptive context in which key hominin traits emerged. In many cases, however, these scenarios are based on very little if any data about the past settings in which early hominins lived. Several environmental hypotheses of human evolution are presented in this paper. Explicit test expectations are laid out, and a preliminary assessment of the hypotheses is made by examining the environmental records of Olduvai, Turkana, Olorgesailie, Zhoukoudian, Combe Grenal, and other hominin localities. Habitat-specific hypotheses have prevailed in almost all previous accounts of human adaptive history. The rise of African dry savanna is often cited as the critical event behind the development of terrestrial bipedality, stone toolmaking, and encephalized brains, among other traits. This savanna hypothesis has been countered recently by the woodland/forest hypothesis, which claims that Pliocene hominins had evolved in and were primarily attracted to closed habitats. The ideas that human evolution was fostered by cold habitats in higher latitudes or by seasonal variations in tropical and temperate zones also have their proponents. An alternative view, the variability selection hypothesis, states that large disparities in environmental conditions were responsible for important episodes of adaptive evolution. The resulting adaptations enhanced behavioral versatility and ultimately ecological diversity in the human lineage. Global environmental records for the late Cenozoic and specific records at hominin sites show the following: 1) early human habitats were subject to large-scale remodeling over time; 2) the evidence for environmental instability does not support habitat-specific explanations of key adaptive changes; 3) the range of environmental change over time was more extensive and the tempo far more prolonged than allowed by the seasonality hypothesis; and 4) the variability selection hypothesis is strongly supported by the persistence of hominins through long sequences of environmental remodeling and the origin of important adaptations in periods of wide habitat diversity. Early bipedality, stone transport, diversification of artifact contexts, encephalization, and enhanced cognitive and social functioning all may reflect adaptations to environmental novelty and highly varying selective contexts.

Adaptation, Physiological↗
PubMed2001

The rhythm of microbial adaptation.

The evolutionary biologist "studies the steps by which the miraculous adaptations so characteristic of every aspect of the organic world have evolved". But the general nature of such adaptive steps is still unclear. Evolution is often thought to be random and dependent on unpredictable events. In this light, one might expect the steps taken by adaptation to be completely random, both biologically and temporally. Here I present a mathematical derivation to show that, on the contrary, adaptive steps can have fairly strong rhythm. I find that the strength of the adaptive rhythm, that is its relative temporal regularity, is equal to a constant that is the same for all microbial populations. As a consequence, numbers of accumulated adaptations are predicted to have a universal variance/mean ratio. The theory derived here is potentially applicable to the study of molecular evolution.

Adaptation, Physiological↗
PubMed2006

Ploidy controls the success of mutators and nature of mutations during budding yeast evolution.

BACKGROUND: We used the budding yeast Saccharomyces cerevisiae to ask how elevated mutation rates affect the evolution of asexual eukaryotic populations. Mismatch repair defective and nonmutator strains were competed during adaptation to four laboratory environments (rich medium, low glucose, high salt, and a nonfermentable carbon source). RESULTS: In diploids, mutators have an advantage over nonmutators in all conditions, and mutators that win competitions are on average fitter than nonmutator winners. In contrast, haploid mutators have no advantage when competed against haploid nonmutators, and haploid mutator winners are less fit than nonmutator winners. The diploid mutator winners were all superior to their ancestors both in the condition they had adapted to, and in two of the other conditions. This phenotype was due to a mutation or class of mutations that confers a large growth advantage during the respiratory phase of yeast cultures that precedes stationary phase. This generalist mutation(s) was not selected in diploid nonmutator strains or in haploid strains, which adapt primarily by fixing specialist (condition-specific) mutations. In diploid mutators, such mutations also occur, and the majority accumulates after the fixation of the generalist mutation. CONCLUSIONS: We conclude that the advantage of mutators depends on ploidy and that diploid mutators can give rise to beneficial mutations that are inaccessible to nonmutators and haploid mutators.

Adaptation, Physiological↗
PubMed1982

Characteristics and origin of the human olfactory organ.

The structure of human ethmoid bone may be characterized not only by the labyrinthine complexity, but also by asymmetry, numerous variations and deformity. Another important specificity is the co-existence of evoluted and nonevoluted structures. These characteristics are probably the result of encephalization and insufficient adaptation due to rapid evolution since man descended to the ground from his arborial life. Kyphosis of the cranial base, displacement of the lamina lateralis anterosuperiorly and rotating of both orbits antero-medialy, restricted the space where the numerous ethmotubinates were to grow. In quadrupeds and in lower primates, the lamina lateralis serves as the site of attachment for turbinates, exists in the antero-inferior part of the nasal cavity forming a medial wall of the sinus maxillaris. However, in human and in higher class primates also this lamina enters the orbit as the lamina orbitalis or lamina papyracea participating in the medial wall of the orbita. The lamina cribrosa, the other site of attachment of turbinates, displaces to antero-superior upon the nasal cavity. Thus, the course of the basal lamellae of turbinates are forced to bend from an antero-superior to a postero-inferior direction. Then, in human, who have more turbinates (Denker u. Kahler, 1925; Miller, 1964; Negus, 1958) than simiae (Ehara, 1974; Ishii, 1955), numerous basal lamellae with scrolls, compress each other with overlapping, fusion, displacement or deformities. With further compression by a deviated septum and the space-filling effect in its concave side, the ethmoid becomes increasingly complex. The complexity of the human ethmoid bone warrants further anthropological and biostatical study with regard to the pneumatisation theory.

Animals↗
PubMed2003

Genotype, obesity and cardiovascular disease--has technical and social advancement outstripped evolution?

Teleologically, our ancestors were highly adapted hunter-gatherers. In recent history, the environment in which Homo sapiens exists has altered drastically and humans are exposed to environments for which the hunter-gatherer genotype is ill-suited. The adoption of a sedentary Western lifestyle, and the case of obtaining food of a high calorific content imposed upon a thrifty genotype, have resulted in the current global epidemic of obesity, Type 2 diabetes and the Metabolic Syndrome. The ramification of this epidemic is that cardiovascular disease is becoming a global healthcare problem, which will have its greatest impact on the developing nations. A global strategy is required to reduce the impact of the Western lifestyle on the health of developing nations and prevent obesity and Type 2 diabetes. Such an approach needs to be culturally sensitive, integrated, and multidisciplinary and involve a range of interventions that work at the individual and community levels. If lifestyle measures fail, then pharmacological intervention may be necessary. For this, novel agents such as dual PPARalpha/gamma agonists may be the therapy of the future.

Adaptation, Physiological↗
PubMed2003

Earliest evidence of cynodont burrowing.

A 251 million year old partial burrow cast containing an articulated skeleton of the mammal-like carnivore Thrinaxodon liorhinus is the oldest evidence for burrowing by a cynodont synapsid. The burrow cast comes from terrestrial flood plain sediments close to the Permian-Triassic boundary in the Karoo of South Africa. Together with those of the later cynodont Trirachodon, the Thrinaxodon burrow cast indicates that burrow-making was broadly distributed in basal synapsids and has a long history in non-mammalian synapsid evolution. A reconstruction of its appendicular skeleton in cross-section indicates that Thrinaxodon was able to adopt a facultatively mammalian stance within its burrow shaft. Burrows of cynodont design are more common in Triassic rocks than previously realized, and suggest that burrowing may represent an adaptive response by cynodonts to the environmental conditions associated with the mass extinction event that punctuated the end of the preceding Permian period. The widespread occurrence of burrowing among extant mammals implies that the ancient synapsid ability to burrow conferred a strong adaptive value in the evolution of Mammalia.

Adaptation, Biological↗
PubMed2005

The genetic theory of adaptation: a brief history.

Theoretical studies of adaptation have exploded over the past decade. This work has been inspired by recent, surprising findings in the experimental study of adaptation. For example, morphological evolution sometimes involves a modest number of genetic changes, with some individual changes having a large effect on the phenotype or fitness. Here I survey the history of adaptation theory, focusing on the rise and fall of various views over the past century and the reasons for the slow development of a mature theory of adaptation. I also discuss the challenges that face contemporary theories of adaptation.

Adaptation, Biological↗
PubMed1998

Evolution of somatic hypermutation and gene conversion in adaptive immunity.

Examples of somatic hypermutation of antigen receptor genes can be seen in most lineages of vertebrates, including the cartilaginous fish. Analysis of the phylogenetic data reveals that two distinctive features of the mechanism are shared by most species studied: the mutation hot spot sequence AGY, and a preponderance of point mutations. These data suggest that some of the components of the machinery are shared between ectotherms and mammals. However, unique characters in particular species may have occurred by independent recruitment of novel factors onto the mechanism. A spotty phylogenetic distribution of gene conversion has also been revealed and can be explained if the two mechanisms share some characteristics. Both mutation and conversion require transcription-related sequences and/or factors. We theorized that targeting to V genes can be attained by a paused replication fork that has collided with a transcription complex stalled by a defective Ig transcription activator; the paused replication fork results in recruitment of an error-prone translesion synthesis DNA polymerase (somatic hypermutation) or of DNA repair mechanisms with homologous recombination (gene conversion). In addition, the pathway recruited in different species may be directed by the degree of homology among V genes.

Animals↗
PubMed2002

Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread.

Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica-Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of recombination. The 5'-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3' terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The "basal-B" cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the "basal-BR" group of eight BR pathotype Eurasian isolates. The third and least variable group, the "Asian-BR" group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the "world-B" group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.

3' Untranslated Regions↗
PubMed2002

Mutational equilibrium model of genome size evolution.

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories). Instead the genome size is suggested to evolve until the loss of DNA through more frequent small deletions is equal to the rate of DNA gain through more frequent long insertions. The empirical basis for this theory is the finding of a strong correlation and of a clear power-function relationship between the rate of mutational DNA loss (per bp) through small deletions and genome size in animals. Genome size scales as a negative 1.3 power function of the deletion rate per nucleotide. Such a relationship is not predicted by either adaptive or junk DNA theories. However, if genome size is maintained at equilibrium by the balance of mutational forces, this empirilical relationship can be readily accommodated. Within this framework, this finding would imply that the rate of DNA gain through large insertions scales up a quarter-power function of genome size. On this view, as genome size grows, the rate of growth through large insertions is increasing as a quarter power function of genome size and the rate of DNA loss through small deletions increases linearly, until eventually, at the stable equilibrium genome size value, rates of growth and loss equal each other. The current data also suggest that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions. Both the origin of mutational biases and the adaptive consequences of such a mode of evolution of genome size are discussed.

Base Sequence↗
PubMed2025

Constraints in temperature adaptation reinforce differences in thermal niche between mesophilic and psychrotolerant Bacillus cereus group species.

Experimental evolution has demonstrated that mesophilic microbes readily adapt to increases in temperature. However, many microbes are psychrotolerant and resistant to cold, which is associated with physiological specializations, suggesting constraints in thermal adaptation. We hypothesized that constraints would limit adaption differently in a mesophilic species (Bacillus thuringiensis) compared with its psychrotolerant relative B. mycoides-with adaptation at cooler temperatures and adaptation at higher temperatures being constrained in each species, respectively. To test this hypothesis, we imposed 140 generations of selection at temperatures at and below the optimum for productivity for both species. The fitness and thermal performance of evolved bacteria showed ancestral thermal niche plays a role in thermal adaptation over this time scale, in support of our hypothesis of adaptive constraints. Temperature-dependent trade-offs appeared common in B. mycoides, with fitness gains associated with decreases in operational niche width; fitness gains at one temperature caused a decrease in the range of temperatures that the bacterium showed appreciable growth. Genome resequencing showed that variation in mutation supply and selection strength could not explain temperature-dependent responses to selection. Importantly, metabolic theory only held true for mesophilic B. thuringiensis, showing abundant but less studied psychrotolerant species could follow different adaptive trajectories.

Bacillus thuringiensis↗
PubMed1994

[Evolution of hepatitis C virus (HCV) viremia and adaptation of HCV in persistent infection in patients with acute hepatitis].

HCV viremia had ceased in majority of patients with acute resolving hepatitis C, and it continued for at least 1 year in all patients with chronicity. The HCV RNA titer in serum decreased markedly after the onset of acute hepatitis and then re-elevated in patients with chronicity. During this period, amino acid substitution rate in the E2/NS1 region (especially in HVR) was significantly higher in patients with acute hepatitis than in patients with chronic hepatitis. When patients with acute hepatitis C became persistent HCV carriers, the substitution rate decreased to the level seen in patients with chronic hepatitis. These observations suggest that rapid substitution of the amino acid sequence in the HVR of the E2/NS1 region may be one of the mechanisms of persistent HCV infection.

Acute Disease↗
PubMed2001

Chromosomal effects of rapid gene evolution in Drosophila melanogaster.

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.

Alleles↗
PubMed1980

Experiments in microbial evolution: new enzymes, new metabolic activities.

Biological evolution has resulted in a richness and diversity of species. Among microorganisms this is most evident in the wealth and diversity of biochemical transformations. Evidence for evolutionary relationships may be obtained from comparative studies, but with microorganisms it is also possible to follow evolution in action. Microbial populations adapt rapidly to changes in the environment and the evolution of new metabolic activities can be observed in laboratory experiments. The enzymes of many catabolic pathways are synthesized in response to the presence of inducing substrates. New catabolic activities may be acquired by mutations in regulatory genes resulting in alterations in the specificity of induction, or in enzyme synthesis in the absence of inducer. Mutations in structural genes may given rise to enzymes with altered substrate specificities. In bacteria, catabolic genes may be carried on plasmids and the exchange of plasmids among bacterial populations increases the evolutionary potential. Experiments in microbial evolution have produced strains with novel catabolic activities involving regulatory or structural gene mutations, gene duplications and plasmid exchange. Enzymes studied in this way include amidase, ribitol dehydrogenase, evolved beta-galactosidase, and enzymes of the catabolic pathways for pentoses and pentitols and haloaromatic compounds.

Amidohydrolases↗
PubMed2007

Reinforcement of mate preference among hybridizing Heliconius butterflies.

Recent models of mate preference evolution suggest that direct selection on alleles at preference loci and correlated evolution of preference with locally adapted mating cues are more likely to drive the evolution of assortative mate preference than reinforcement. Mate preference evolution in mimetic Heliconius butterflies has been attributed to all three forms of selection, but here we show that reinforcement has been critical. By examining geographical variation in assortative mating and male mate preference among seven populations of three hybridizing Heliconius species from Costa Rica, we found pronounced character displacement of preference such that sexual isolation was enhanced in areas of interspecific contact. Of the different explanations for the evolution of assortative mate preference, only reinforcement is dependent on interspecific contact in this system. Thus, the observed pattern of reproductive character displacement of mate preference is best explained as a product of indirect selection generated by natural selection against nonmimetic hybrids.

Animals↗