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PubMed2005

Neutral mutation as the source of genetic variation in life history traits.

The mechanism underlying the maintenance of adaptive genetic variation is a long-standing question in evolutionary genetics. There are two concepts (mutation-selection balance and balancing selection) which are based on the phenotypic differences between alleles. Mutation - selection balance and balancing selection cannot properly explain the process of gene substitution, i.e. the molecular evolution of quantitative trait loci affecting fitness. I assume that such loci have non-essential functions (small effects on fitness), and that they have the potential to evolve into new functions and acquire new adaptations. Here I show that a high amount of neutral polymorphism at these loci can exist in real populations. Consistent with this, I propose a hypothesis for the maintenance of genetic variation in life history traits which can be efficient for the fixation of alleles with very small selective advantage. The hypothesis is based on neutral polymorphism at quantitative trait loci and both neutral and adaptive gene substitutions. The model of neutral - adaptive conversion (NAC) assumes that neutral alleles are not neutral indefinitely, and that in specific and very rare situations phenotypic (relative fitness) differences between them can appear. In this paper I focus on NAC due to phenotypic plasticity of neutral alleles. The important evolutionary consequence of NAC could be the increased adaptive potential of a population. Loci responsible for adaptation should be fast evolving genes with minimally discernible phenotypic effects, and the recent discovery of genes with such characteristics implicates them as suitable candidates for loci involved in adaptation.

Alleles↗

PubMed2004

Experimental evaluation of the relationship between lethal or non-lethal virulence and transmission success in malaria parasite infections.

BACKGROUND: Evolutionary theory suggests that the selection pressure on parasites to maximize their transmission determines their optimal host exploitation strategies and thus their virulence. Establishing the adaptive basis to parasite life history traits has important consequences for predicting parasite responses to public health interventions. In this study we examine the extent to which malaria parasites conform to the predicted adaptive trade-off between transmission and virulence, as defined by mortality. The majority of natural infections, however, result in sub-lethal virulent effects (e.g. anaemia) and are often composed of many strains. Both sub-lethal effects and pathogen population structure have been theoretically shown to have important consequences for virulence evolution. Thus, we additionally examine the relationship between anaemia and transmission in single and mixed clone infections. RESULTS: Whereas there was a trade-off between transmission success and virulence as defined by host mortality, contradictory clone-specific patterns occurred when defining virulence by anaemia. A negative relationship between anaemia and transmission success was found for one of the parasite clones, whereas there was no relationship for the other. Notably the two parasite clones also differed in a transmission phenotype (gametocyte sex ratio) that has previously been shown to respond adaptively to a changing blood environment. In addition, as predicted by evolutionary theory, mixed infections resulted in increased anaemia. The increased anaemia was, however, not correlated with any discernable parasite trait (e.g. parasite density) or with increased transmission. CONCLUSIONS: We found some evidence supporting the hypothesis that there is an adaptive basis correlating virulence (as defined by host mortality) and transmission success in malaria parasites. This confirms the validity of applying evolutionary virulence theory to biomedical research and adds support to the prediction that partially effective vaccines may select for increasingly virulent malaria parasite strains. By contrast, there was no consistent correlation between transmission and sub-lethal anaemia, a more common outcome of malaria infection. However, overall, the data are not inconsistent with the recent proposal that sub-lethal effects may impose an upper limit on virulence. Moreover, clone specific differences in transmission phenotypes linked to anaemia do suggest that there is considerable adaptive potential relating anaemia and transmission that may lead to uncertain consequences following intervention strategies.

Adaptation, Physiological↗

PubMed2026

Divergent trajectories of genome architecture and chromosome evolution in ferns and angiosperms.

Ferns and angiosperms represent the two largest vascular plant lineages but exhibit striking genomic and ecological contrasts. We investigated whether differences in genome size, chromosome architecture, GC content, and stomatal traits reveal divergent evolutionary trajectories between these lineages. We assembled the most comprehensive dataset to date, integrating genome size, chromosome number and size, GC content, and stomatal traits for over 1100 fern species and compared it with an extensive angiosperm dataset. Ferns exhibited markedly lower variability and c. 16-fold slower rates of chromosome size evolution than angiosperms. A persistent positive relationship between genome size and chromosome number in ferns suggests limited cytological post-polyploid diploidization. While ferns generally possess larger stomata, this difference disappears after accounting for genome size, indicating that nucleotypic constraints, rather than lineage-specific physiology, dictate stomatal dimensions. Both groups share a unimodal GC-genome size relationship peaking at c. 14 Gbp. Larger fern chromosomes imply lower genome-wide recombination rates, potentially limiting genetic reshuffling and adaptive potential. Our results highlight fundamentally divergent evolutionary trajectories, likely shaped by meiotic symmetry in ferns and meiotic asymmetry, possibly centromere drive, and post-polyploid diploidization in angiosperms, defining the functional and genomic landscapes of these lineages across deep evolutionary timescales.

Genome, Plant↗

PubMed1983

Human behavioral development and genetics.

Behavioral development during childhood is examined in relation to recent concepts and data from evolutionary theory and developmental genetics. The epigenetic framework of Waddington is proposed as a powerful tool for analyzing the progressions in behavior, particularly for recognizing that development involves coordinated pathways of change over time. Many of these pathways appear to depend upon the activity of timed gene-action systems that switch off and on according to a predetermined plan. Behavioral development thus gives expression to the dynamics of preprogrammed change; and in this perspective, behavioral discontinuities may be as strongly rooted in the epigenetic ground plan as the continuities are. The present paper aims to pull together some common themes from different areas that bear on the central issues of behavioral development--the neural foundations, the time course followed, the interplay of maturation and experience, the extent of preorganization furnished by the genetic program, and the adaptive significance of such behaviors in an evolutionary perspective. The final section touches on some hypotheses drawn from developmental neurobiology and developmental genetics that may enrich the analyses of human behavioral development.

Biological Evolution↗

PubMed2006

Possible human impacts on adaptive radiation: beak size bimodality in Darwin's finches.

Adaptive radiation is facilitated by a rugged adaptive landscape, where fitness peaks correspond to trait values that enhance the use of distinct resources. Different species are thought to occupy the different peaks, with hybrids falling into low-fitness valleys between them. We hypothesize that human activities can smooth adaptive landscapes, increase hybrid fitness and hamper evolutionary diversification. We investigated this possibility by analysing beak size data for 1755 Geospiza fortis measured between 1964 and 2005 on the island of Santa Cruz, Galápagos. Some populations of this species can display a resource-based bimodality in beak size, which mirrors the greater beak size differences among species. We first show that an historically bimodal population at one site, Academy Bay, has lost this property in concert with a marked increase in local human population density. We next show that a nearby site with lower human impacts, El Garrapatero, currently manifests strong bimodality. This comparison suggests that bimodality can persist when human densities are low (Academy Bay in the past, El Garrapatero in the present), but not when they are high (Academy Bay in the present). Human activities may negatively impact diversification in 'young' adaptive radiations, perhaps by altering adaptive landscapes.

Adaptation, Physiological↗

PubMed2026

Comparative analyses of olfactory receptor repertoires in Schizothorax fish based on the chromosome-level genomes: Implications for regulatory roles of dietary differentiation and ploidy variation.

The olfactory receptor (OR) genes constitute the molecular basis of fish olfaction, mediating survival behaviors and environmental adaptation while coevolving with habitat-driven evolution. Schizothorax, a cyprinid genus endemic to the Qinghai-Tibetan Plateau, exhibits remarkable dietary divergence and ploidy variation in response to plateau environmental changes, which presumably facilitates the adaptive evolution of OR genes. However, the evolutionary patterns of OR genes associated with trophic divergence and ploidy variation in this genus remain unclear. In this study, three species were selected: the herbivorous diploid S. macropogon, the carnivorous diploid S. lantsangensis, and the herbivorous tetraploid S. curvilabiatus. S. macropogon possessed 142 OR genes (92.25% functional), primarily located on chromosomes 14 and 24, with the fewest sequence clusters. Such compact gene repertoire and highly overlapping chromosomal clusters indicated specialization for a herbivorous olfactory niche. S. lantsangensis contained 127 OR genes (93.70% functional), concentrated on chromosomes 4 and 5, with fewer sequence clusters and a scattered distribution, reflecting evolution of OR genes under carnivorous feeding habits. The herbivorous tetraploid S. curvilabiatus exhibited striking features: 316 OR genes (94.30% functional), the most subfamilies, unique ε and κ OR subfamilies, and species-specific motifs. These characteristics revealed that ploidy, rather than herbivory, dominated OR gene evolution. In conclusion, dietary differentiation and ploidy variation together drove olfactory adaptive evolution in Schizothorax, providing new insights into vertebrate OR gene ecological adaptation.

Animals↗

PubMed2005

An evolutionary framework for common diseases: the ancestral-susceptibility model.

Unlike rare mendelian diseases, which are due to new mutations (i.e. derived alleles), several alleles that increase the risk to common diseases are ancestral. Moreover, population genetics studies suggest that some derived alleles that protect against common diseases became advantageous recently. These observations can be explained within an evolutionary framework in which ancestral alleles reflect ancient adaptations to the lifestyle of ancient human populations, whereas the derived alleles were deleterious. However, with the shift in environment and lifestyle, the ancestral alleles now increase the risk of common diseases in modern populations. In this article, we develop an explicit evolutionary model and use population genetics simulations to investigate the expected haplotype structure and type of disease-association signals of ancestral risk alleles.

Alleles↗

PubMed1998

Contingency and determinism in replicated adaptive radiations of island lizards

The vagaries of history lead to the prediction that repeated instances of evolutionary diversification will lead to disparate outcomes even if starting conditions are similar. We tested this proposition by examining the evolutionary radiation of Anolis lizards on the four islands of the Greater Antilles. Morphometric analyses indicate that the same set of habitat specialists, termed ecomorphs, occurs on all four islands. Although these similar assemblages could result from a single evolutionary origin of each ecomorph, followed by dispersal or vicariance, phylogenetic analysis indicates that the ecomorphs originated independently on each island. Thus, adaptive radiation in similar environments can overcome historical contingencies to produce strikingly similar evolutionary outcomes.

Journal Article↗

PubMed2001

Diverse virulence traits underlying different clinical outcomes of Salmonella infection.

Salmonella strains have evolved to infect a wide variety of reptiles, birds, and mammals resulting in many different syndromes ranging from colonization and chronic carriage to acute fatal disease. Adaptation to a large number of different evolutionary niches has undoubtedly driven the high degree of phenotypic and genotypic diversity in Salmonella strains. Differences in LPS and flagellar structure generate the antigenic variation that is reflected in the more than 2,000 known serotypes. Moreover, variations of LPS structure affect the virulence of the strain. The differential expression of various fimbriae by Salmonella is likely to be due to the wide variety of mucosal surfaces that are encountered by various strains, and the host immune response may select for a different expression pattern. As with these surface structures, a variety of other important virulence determinants show a variable distribution in Salmonella strains and also serve to delineate the divergence of the Salmonella lineage from E. coli. The acquisition of the SPI-1 region may have represented the defining genetic event in the separation of the Salmonella and E. coli lineages. The SPI-1 cell invasion function allowed Salmonella to establish a separate niche in epithelial cells. The mgtC locus on SPI-3 is also present in all lineages and facilitates the adaptation of the bacteria to the low Mg2+, low pH environment of the endosome that results from SPI-1-mediated invasion. Subsequent acquisition of SPI-2 allowed Salmonella to manipulate the sorting of the endosome or phagosome, altering the intracellular environment and facilitating bacterial growth within infected cells. The ability to disseminate from the bowel and establish extraintestinal niches is promoted by the spv locus. Since Salmonella proliferates within macrophages and must avoid phagocytosis by neutrophils to establish a systemic infection, the spv genes appear to promote the macrophage phase of the disease process. Here the polymorphism of the spv locus is clearly demonstrated, since the serovars that cause most cases of nontyphoid bacteremia contain the spv genes. The absence of the spv genes from S. typhi is particularly puzzling and is a strong indication that the pathogenesis of typhoid fever is fundamentally different from that of bacteremia due to nontyphoid Salmonella. There is currently no genetic explanation for the phenotype of host adaptation or for the finding that only a few serovars cause the majority of human infections. Based on recent findings that multiple individual virulence genes have a variable distribution in Salmonella, it is unlikely that a single locus will be found to be responsible for these complex biological traits. Instead, a complicated combination of genes are likely to contribute to the overall virulence phenotype.

Animals↗

PubMed2026

Evolutionary diversification of invertase paralogs couples carbon metabolism and sexual reproduction in fission yeasts.

Dynamic patterns of gene gain and loss play a major role in the diversification of eukaryotes, reflecting adaptation to a broad range of ecological contexts. Reconstructing the evolutionary history of genes provides a powerful framework for understanding how functional innovation shapes life-history traits. Here we report a comprehensive analysis of gene gain and loss across the fission yeast clade, whose evolutionary trajectory remains elusive. Reductive evolution of metabolic genes is a major contributor to species diversification, as observed in other fungal taxa. Notably, we uncovered an evolutionary scenario in which an ancestral gene duplication was followed by lineage-specific loss of one or the other paralog, except in S. pombe, which retained both. We demonstrate that these paralogs encode catalytically-active invertases, named Inv1 and Inv2, with distinct enzymatic properties, localization, regulation, and physiological roles. Inv1 is a secreted enzyme subject to glucose catabolite repression and is the sole invertase required for sucrose assimilation, resembling canonical yeast invertases. In contrast, Inv2 is intracellular, constitutively expressed, and required for inducing sexual differentiation in response to nutrient availability. Overall, these findings reveal an unexpected role for carbon metabolism in modulating the haploid-diploid cycle of fission yeasts, suggesting that diversification of core metabolic functions may contribute to adaptation to environments with distinct sugar compositions.

Evolution↗

PubMed2004

Molecular adaptation in plant hemoglobin, a duplicated gene involved in plant-bacteria symbiosis.

The evolutionary history of the hemoglobin gene family in angiosperms is unusual in that it involves two mechanisms known for potentially generating molecular adaptation: gene duplication and among-species interaction. In plants able to achieve symbiosis with nitrogen-fixing bacteria, class 2 hemoglobin is expressed at high concentrations in nodules and appears to be a key factor for the achievement and regulation of the symbiotic exchange. In this study, we make use of codon models of DNA sequence evolution with the goal of determining the nature of the selective forces which have driven the evolution of this gene. Our results suggest that adaptive evolution occurred during the period of time following the duplication event (functional divergence) and that a change in the selective pressures arose in class 2 hemoglobin in relation to the acquisition of a symbiotic function.

Adaptation, Biological↗

PubMedDate not supplied

The evolutionary basis of some clinical disorders of the human foot: a comparative survey of the living primates.

The living primates are a highly diverse group of essentially arboreal animals whose feet are variously adapted for grasping, climbing, and leaping in trees. One of the most remarkable aspects of the anatomical variation in the feet of the extant primates is that this diversity can be arranged in a graduated sequence ranging from the primitive transtarsal-opposition type of grasping foot found in the lemurs, through the specialized transmetarsal-adduction type that characterizes the higher primates, to the unique nongrasping foot of humans. The comparative study of this graded series makes it possible, without recourse to the fossil record, to appreciate the adaptive and functional stages through which the human foot passed in its evolution. It is hypothesized that the initial stage of human erect posture was characterized by a foot which was adapted to both hallucial grasping and short distance bipedal walking. In many respects, the structure of the foot of this primitive human was probably similar to that of the living highland gorilla. When compared with the feet of our closest living relatives, the African apes, the human foot is characterized by two major evolutionary specializations: the longitudinal and transverse arches, and the parallel first and second metatarsals. These two morphological adaptations, together with several associated specializations, are the structural basis of the bipedal human foot. Reconstructing the evolutionary and adaptive history of these specializations creates a better understanding of some of the more common clinical podiatric disorders. The modern human foot is structurally so well adapted to prolonged bipedal walking and standing that even slight deviations from its evolutionarily established pattern will produce debilitating clinical manifestations. In most cases, successful treatment of such disorders involves restoration of the foot's basic adaptive configuration.

Adaptation, Biological↗

PubMed2004

Phylogenetic and evolutionary relationships between Elymus humidus and other Elymus species based on sequencing of non-coding regions of cpDNA and AFLP of nuclear DNA.

Species of the genus Elymus are closely related to some important cereal crops and may thus serve as potential alien genetic resources for the improvement of these crops. E. humidus is indigenous to Japan and is well adapted to a humid climate. However, the phylogenetic and evolutionary relationships between E. humidus and other Elymus species are unclear. To elucidate these relationships, we examined the sequences of three non-coding regions of chloroplast DNA (cpDNA) and the amplified fragment length polymorphism (AFLP) variation of nuclear DNA in E. humidus and other related species. A total of 15 sequence mutations from the three non-coding regions, trnL-trnF, trnF- ndhJ(C), and atpB-rbcL, covering approximately 1,800 bp, were detected in the Elymus species. A phylogenic tree resulting from the cpDNA sequence data revealed that all the species containing the St nuclear genome (St, StH, StY, and StHY) formed a well-supported clade that is remote from the Hordeum species (H). This result strongly supports the finding that Pseudoroegneria is the maternal genome donor to the genus Elymus. In addition, E. humidus showed the closest relationship with the cpDNA genome of the Pseudoroegneria species. The AFLP analysis detected 281 polymorphic bands with 11 AFLP primer combinations. The AFLP result showed that E. humidus is relatively closer to E. tsukushiensis. However, the cpDNA sequencing results indicated that E. humidus and E. tsukushiensis have different cytoplasmic origins. Our results suggest that the evolutionary process between E. humidus and E. tsukushiensis is not monophyletic, although the two species have similar morphological characters and adaptability.

Cell Nucleus↗

PubMed2000

Adaptive dynamics in diploid, sexual populations and the evolution of reproductive isolation.

Evolutionary branching is the process whereby an initially monomorphic population evolves to a point where it undergoes disruptive selection and splits up into two phenotypically diverging lineages. We studied evolutionary branching in three models that are ecologically identical but that have different genetic systems. The first model is clonal, the second is sexual diploid with additive genetics on a single locus and the third is like the second but with an additional locus for mate choice. Evolutionary branching occurred under exactly the same ecological circumstances in all three models. After branching the evolutionary dynamics may be qualitatively different. In particular, in the diploid, sexual models there can be multiple evolutionary outcomes whereas in the corresponding clonal model there is only one. We showed that evolutionary branching favours the evolution of (partial) assortative mating and that this in turn effectively restores the results from the clonal model by rendering the alternative outcomes unreachable except for the one that also occurs in the clonal model. The evolution of assortative mating during evolutionary branching can be interpreted as the initial phase of sympatric speciation with phenotypic divergence and partial reproductive isolation.

Adaptation, Physiological↗

PubMed1995

[The adaptive-compensatory reactions in adjusting to space flights].

In this paper an evolutionary approach is used to substantiate the steps of life evolution on Earth towards overcoming the gravitational forces with the formation of metabolic cycles controlling the energetic of anti-G processes. The step of an adaptation to hypogravity was similar to return of surface animals to an aquatic environment. The impossibility of coming back to land was the "price" of adaptation to the aquatic environment. This phenomenon was used by the author as a logical model of human adaptation to a weightless environment. The concept of adaptation is examined from two points of view: adaptation and compensation. The scheme contains 4 steps of adaptation to space mission environments: Step I-preadaptation (phase of primary reactions); Step II-compensation of body structures not being in line with the conditions of a novel environment; Step III-the formation of parameters of an organism corresponding to the norm of adaptation to weightlessness; Step IV-the return of cosmonauts to Earth under hypergravity conditions. In compliance with these steps we consider the tasks of supporting space missions to facilitate body readaptation after return to Earth, i.e., to decrease the "price" of adaptation.

Adaptation, Physiological↗

PubMed1997

Temporal filtering properties of ampullary electrosensory neurons in the torus semicircularis of Eigenmannia: evolutionary and computational implications.

Weakly electric fish have parallel electrosensory systems, the phylogenetically older ampullary system and the novel tuberous system. The tuberous system is an adaptation related to the evolution of active electrolocation. To examine the evolutionary relationship of the ampullary and tuberous systems, the temporal filtering properties of ampullary neurons in the dorsal torus semicircularis of Eigenmannia were studied. 'Whole-cell' recordings were made in vivo using patch-type pipettes. The responses of 19 neurons to sinusoidal electric signals (< 40 Hz) were recorded and the anatomy of these neurons demonstrated by injection of biocytin. All eight low-pass ampullary neurons had broad, relatively smooth post-synaptic potentials (psps) that at low frequencies nicely reflected the sinusoidal stimuli. These neurons had somata of 10-14 microns diameter and thick, spiny dendrites. Eight high-pass neurons were recorded, representing three physiological classes. The first class (3 neurons) had psps that roughly followed the sinusoidal time course of the stimulus; the psp morphology was similar to low-pass neurons. The second class had many small, fast, individual psps; their rate of occurrence varied with the stimulus. Finally, four neurons showed psps that were of constant width across stimulus frequencies. All three classes of high-pass neurons had small somata (8-10 microns diameter) with thin dendrites and either few or no spines. Some of these neurons had large varicosities on the dendrites. Three neurons had band-pass filtering properties: neurons that showed strong band-pass properties were morphologically similar to low-pass neurons. Comparisons of the temporal filtering, shapes of post-synaptic potentials, and anatomy of ampullary and tuberous neurons in the torus suggest that the circuitry for tuberous processing in the torus may have evolved as an elaboration or duplication of the ampullary system. The mechanisms underlying the low-pass filtering characteristics of tuberous neurons therefore appear to have predated the evolution of the tuberous system and to have served as a pre-adaptation for the evolution of the jamming avoidance response. In addition, these data support the hypothesis that spine density influences the temporal filtering properties of neurons.

Animals↗

PubMed2006

A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model.

BACKGROUND: Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources. Here, we describe an Expression Sequence Tag (EST) project for Bicyclus anynana that has identified the largest available collection to date of expressed genes for any butterfly. RESULTS: By targeting cDNAs from developing wings at the stages when pattern is specified, we biased gene discovery towards genes potentially involved in pattern formation. Assembly of 9,903 ESTs from a subtracted library allowed us to identify 4,251 genes of which 2,461 were annotated based on BLAST analyses against relevant gene collections. Gene prediction software identified 2,202 peptides, of which 215 longer than 100 amino acids had no homology to any known proteins and, thus, potentially represent novel or highly diverged butterfly genes. We combined gene and Single Nucleotide Polymorphism (SNP) identification by constructing cDNA libraries from pools of outbred individuals, and by sequencing clones from the 3' end to maximize alignment depth. Alignments of multi-member contigs allowed us to identify over 14,000 putative SNPs, with 316 genes having at least one high confidence double-hit SNP. We furthermore identified 320 microsatellites in transcribed genes that can potentially be used as genetic markers. CONCLUSION: Our project was designed to combine gene and sequence polymorphism discovery and has generated the largest gene collection available for any butterfly and many potential markers in expressed genes. These resources will be invaluable for exploring the potential of B. anynana in particular, and butterflies in general, as models in ecological, evolutionary, and developmental genetics.

Animals↗

PubMed2007

Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata.

The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.

Adaptation, Biological↗