The evolution of predictive adaptive responses in human life history

Many studies in humans have shown that adverse experience in early life is associated with accelerated reproductive timing, and there is comparative evidence for similar effects in other animals. There are two different classes of adaptive explanation for associations between early-life adversity and accelerated reproduction, both based on the idea of predictive adaptive responses (PARs). According to external PAR hypotheses, early-life adversity provides a ‘weather forecast’ of the environmental conditions into which the individual will mature, and it is adaptive for the individual to develop an appropriate phenotype for this anticipated environment. In internal PAR hypotheses, early-life adversity has a lasting negative impact on the individual''s somatic state, such that her health is likely to fail more rapidly as she gets older, and there is an advantage to adjusting her reproductive schedule accordingly. We use a model of fluctuating environments to derive evolveability conditions for acceleration of reproductive timing in response to early-life adversity in a long-lived organism. For acceleration to evolve via the external PAR process, early-life cues must have a high degree of validity and the level of annual autocorrelation in the individual''s environment must be almost perfect. For acceleration to evolve via the internal PAR process requires that early-life experience must determine a significant fraction of the variance in survival prospects in adulthood. The two processes are not mutually exclusive, and mechanisms for calibrating reproductive timing on the basis of early experience could evolve through a combination of the predictive value of early-life adversity for the later environment and its negative impact on somatic state.     

Uncovering adaptive evolution in the human lineage

Background

The recent increase in human polymorphism data, together with the availability of genome sequences from several primate species, provides an unprecedented opportunity to investigate how natural selection has shaped human evolution.

Results

We compared human branch-specific substitutions with variation data in the current human population to measure the impact of adaptive evolution on human protein coding genes. The use of single nucleotide polymorphisms (SNPs) with high derived allele frequencies (DAFs) minimized the influence of segregating slightly deleterious mutations and improved the estimation of the number of adaptive sites. Using DAF ≥ 60% we showed that the proportion of adaptive substitutions is 0.2% in the complete gene set. However, the percentage rose to 40% when we focused on genes that are specifically accelerated in the human branch with respect to the chimpanzee branch, or on genes that show signatures of adaptive selection at the codon level by the maximum likelihood based branch-site test. In general, neural genes are enriched in positive selection signatures. Genes with multiple lines of evidence of positive selection include taxilin beta, which is involved in motor nerve regeneration and syntabulin, and is required for the formation of new presynaptic boutons.

Conclusions

We combined several methods to detect adaptive evolution in human coding sequences at a genome-wide level. The use of variation data, in addition to sequence divergence information, uncovered previously undetected positive selection signatures in neural genes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-599) contains supplementary material, which is available to authorized users.     

Replicated evolution of integrated plastic responses during early adaptive divergence

Colonization of a novel environment is expected to result in adaptive divergence from the ancestral population when selection favors a new phenotypic optimum. Local adaptation in the new environment occurs through the accumulation and integration of character states that positively affect fitness. The role played by plastic traits in adaptation to a novel environment has generally been ignored, except for variable environments. We propose that if conditions in a relatively stable but novel environment induce phenotypically plastic responses in many traits, and if genetic variation exists in the form of those responses, then selection may initially favor the accumulation and integration of functionally useful plastic responses. Early divergence between ancestral and colonist forms will then occur with respect to their plastic responses across the gradient bounded by ancestral and novel environmental conditions. To test this, we compared the magnitude, integration, and pattern of plastic character responses in external body form induced by shallow versus open water conditions between two sunfish ecomorphs that coexist in four postglacial lakes. The novel sunfish ecomorph is present in the deeper open water habitat, whereas the ancestral ecomorph inhabits the shallow waters along the lake margin. Plastic responses by open water ecomorphs were more correlated than those of their local shallow water ecomorph in two of the populations, whereas equal levels of correlated plastic character responses occurred between ecomorphs in the other two populations. Small but persistent differences occurred between ecomorph pairs in the pattern of their character responses, suggesting a recent divergence. Open water ecomorphs shared some similarities in the covariance among plastic responses to rearing environment. Replication in the form of correlated plastic responses among populations of open water ecomorphs suggests that plastic character states may evolve under selection. Variation between ecomorphs and among lake populations in the covariance of plastic responses suggests the presence of genetic variation in plastic character responses. In three populations, open water ecomorphs also exhibited larger plastic responses to the environmental gradient than the local shallow water ecomorph. This could account for the greater integration of plastic responses in open water ecomorphs in two of the populations. This suggests that the plastic responses of local sunfish ecomorphs can diverge through changes in the magnitude and coordination of plastic responses. Although these results require further investigation, they suggest that early adaptive evolution in a novel environment can include changes to plastic character states. The genetic assimilation of coordinated plastic responses could result in the further, and possibly rapid, divergence of such populations and could also account for the evolution of genes of major effect that contribute to suites of phenotypic differences between divergent populations.     

The adaptive evolution of plasticity: phytochrome-mediated shade avoidance responses

Many plants display a characteristic suite of developmental"shade avoidance" responses, such as stem elongation and acceleratedreproduction, to the low ratio of red to far-red wavelengths(R:FR) reflected or transmitted from green vegetation. ThisR:FR cue of crowding and vegetation shade is perceived by thephytochrome family of photoreceptors. Phytochrome-mediated responsesprovide an ideal system for investigating the adaptive evolutionof phenotypic plasticity in natural environments. The molecularand developmental mechanisms underlying shade avoidance responsesare well studied, and testable ecological hypotheses exist fortheir adaptive significance. Experimental manipulation of phenotypesdemonstrates that shade avoidance responses may be adaptive,resulting in phenotypes with high relative fitness in the environmentsthat induce those phenotypes. The adaptive value of shade avoidancedepends upon the competitive environment, resource availability,and the reliability of the R:FR cue for predicting the selectiveenvironment experienced by an induced phenotype. Comparativestudies and a reciprocal transplant experiment with Impatienscapensis provide evidence of adaptive divergence in shade avoidanceresponses between woodland and clearing habitats, which mayresult from population differences in the frequency of selectionon shade avoidance traits, as well as differences in the reliabilityof the R:FR cue. Recent rapid progress in elucidating phytochromesignaling pathways in the genetic model Arabidopsis thalianaand other species now provides the opportunity for studyinghow selection on shade avoidance traits in natural environmentsacts upon the molecular mechanisms underlying natural phenotypicvariation.     

Localizing recent adaptive evolution in the human genome

Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and single-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome with very strong evidence (p < 10⁻⁵) of a recent selective sweep and where our estimate of the position of the selective sweep falls within 100 kb of a known gene. Within these regions, genes of biological interest include genes in pigmentation pathways, components of the dystrophin protein complex, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general, we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.     

Microbial adaptive evolution

Bacterial species can adapt to significant changes in their environment by mutation followed by selection, a phenomenon known as “adaptive evolution.” With the development of bioinformatics and genetic engineering, research on adaptive evolution has progressed rapidly, as have applications of the process. In this review, we summarize various mechanisms of bacterial adaptive evolution, the technologies used for studying it, and successful applications of the method in research and industry. We particularly highlight the contributions of Dr. L. O. Ingram. Microbial adaptive evolution has significant impact on our society not only from its industrial applications, but also in the evolution, emergence, and control of various pathogens.     

Predicting adaptive evolution

Phylogenetic trees reconstruct past evolution and can provide evidence of past evolutionary pressure on genes and on individual codons. In addition to tracing past evolutionary events, molecular phylogenetics might also be used to predict future evolution. Our ability to verify adaptive hypotheses using phylogenetics has broad implications for vaccine design, genomics and structural biology.     

Predictive adaptive responses: Condition-dependent impact of adult nutrition and flight in the tropical butterfly Bicyclus anynana

The experience of environmental stress during development can substantially affect an organism's life history. These effects are often mainly negative, but a growing number of studies suggest that under certain environmental conditions early experience of such stress may yield individuals that are less sensitive to environmental stress later on in life. We used the butterfly Bicyclus anynana to study the effects of limited larval and adult food and forced flight on individual performance measured as reproduction and adult life span. Larvae exposed to food stress showed longer development and produced smaller adults. Thus, they were not able to fully compensate for the food deprivation during development. Females that experienced food stress during development did not increase tolerance for adult food limitation. However, females exposed to food stress during development coped better with forced flight compared with the control group. The apparent absence of costs of flight in poor-quality females may be a by-product of an altered body allocation, as females experiencing both food stress treatments had increased thorax ratios, compared with controls, and increased flight performances. The results reveal an important plasticity component to variation in flight performance and suggest that the cost of flight depends on an individual's internal condition.     

Cytogenetic and survival adaptive responses in G1 phase human lymphocytes.

Human lymphocytes from six donors were treated with 5 cGy of X-rays followed by 200 or 400 cGy in the first G1 phase after PHA stimulation, and assayed for cytogenetic aberrations and cell survival. Four donors showed cytogenetic adaptive responses with 400 cGy, and one with both 200 cGy and 400 cGy. Both exchanges and deletions were reduced, indicating that the cytogenetic adaptive response acts by restitution of chromosome breaks. Good correlations were found between nonaberrant cells and survival, although the former were often higher than the later, especially with the 400 cGy dose. In four of six donors, 5 cGy alone had significant effects on cell survival; however, this was independent of the 5 cGy effect on high-dose-induced responses. Two donors had survival adaptive responses with 5 + 200 cGy, while none were found with the 5 + 400 cGy treatment. The comparisons between the cytogenetic and survival responses suggests that a survival adaptive response will only be seen with a sufficient increase in nonaberrant cells. To date, adaptive responses to ionizing radiation have been reported to occur in G0, G1 and late S/early G2 human lymphocytes.     

Protein evolution in dynamically managed populations of wheat: adaptive responses to macro-environmental conditions

 Dynamic management of genetic resources aims to conserve genetic variability between different populations evolving in contrasting environments. It is thus of importance to determine whether differences appearing between populations are stochastic or if they come about from adaptation. Two-dimensional electrophoresis (2DE) was used to study genetic differentiation of 11 wheat populations evolving since 1984 in a multi-site network covering the major cultivation area of wheat in France. Gels were scanned and protein-spot intensities were measured through image analysis. As it was not possible to assay each individual, populations were characterized using pooled extracts from several plants. In the first step, two parents among the 16 parental lines involved in the initial wheat composite-cross population were exhaustively studied to identify a set of polymorphic spots against which the entire set of evolved populations could be compared. This analysis confirmed the efficiency of gel image-processing to determine the composition of pooled extracts. Of the 48 spots used to investigate population differentiation, 15 showed significant differences at the P<0.05 level. Populations that evolved independently at the same location showed similar differentiation, even when their cultivation methods were different. These results suggest that natural selection acted strongly on the evolution of the populations, and that responses to selection were determined primarily by macro-environmental conditions. Received: 10 February 1997 / Accepted: 18 April 1997     

Development and evolution of adaptive polyphenisms

Phenotypic plasticity is the primitive character state for most if not all traits. Insofar as developmental and physiological processes obey the laws of chemistry and physics, they will be sensitive to such environmental variables as temperature, nutrient supply, ionic environment, and the availability of various macro- and micronutrients. Depending on the effect this phenotypic plasticity has on fitness, evolution may proceed to select either for mechanisms that buffer or canalize the phenotype against relevant environmental variation or for a modified plastic response in which some ranges of the phenotypic variation are adaptive to particular environments. Phenotypic plasticity can be continuous, in which case it is called a reaction norm, or discontinuous, in which case it is called a polyphenism. Although the morphological discontinuity of some polyphenisms is produced by discrete developmental switches, most polyphenisms are due to discontinuities in the environment that induce only portions of what is in reality a continuous reaction norm. In insect polyphenisms, the environmental variable that induces the alternative phenotype is a token stimulus that serves as a predictor of, but is not itself, the environment to which the polyphenism is an adaptation. In all cases studied so far, the environmental stimulus alters the endocrine mechanism of metamorphosis by altering either the pattern of hormone secretion or the pattern of hormone sensitivity in different tissues. Such changes in the patterns of endocrine interactions result in the execution of alternative developmental pathways. The spatial and temporal compartmentalization of endocrine interactions has produced a developmental mechanism that enables substantial localized changes in morphology that remain well integrated into the structure and function of the organism.     

Genome evolution: recombination speeds up adaptive evolution

Mutual interference among linked genetic sites subject to selection may reduce the level of adaptation. A recent study detected this effect using data on protein sequence evolution and codon usage in Drosophila.     

Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes

Molecular adaptation, as characterized by the detection of positive selection, was quantified in a number of genes from different human immunodeficiency virus type 1 (HIV-1) group M subtypes, group O, and an HIV-2 subtype using the codon-based maximum-likelihood method of Yang and coworkers (Z. H. Yang, R. Nielsen, N. Goldman, and A. M. K. Pedersen, Genetics 155:431-449, 2000). The env gene was investigated further since it exhibited the strongest signal for positive selection compared to those of the other two major HIV genes (gag and pol). In order to investigate the pattern of adaptive evolution across env, the location and strength of positive selection in different HIV-1 sequence alignments was compared. The number of sites having a significant probability of being positively selected varied among these different alignment data sets, ranging from 25 in HIV-1 group M subtype A to 40 in HIV-1 group O. Strikingly, there was a significant tendency for positively selected sites to be located at the same position in different HIV-1 alignments, ranging from 10 to 16 shared sites for the group M intersubtype comparisons and from 6 to 8 for the group O to M comparisons, suggesting that all HIV-1 variants are subject to similar selective forces. As the host immune response is believed to be the dominant driving force of adaptive evolution in HIV, this result would suggest that the same sites are contributing to viral persistence in diverse HIV infections. Thus, the positions of the positively selected sites were investigated in reference to the inferred locations of different epitope types (antibody, T helper, and cytotoxic T lymphocytes) and the positions of N and O glycosylation sites. We found a significant tendency for positively selected sites to fall outside T-helper epitopes and for positively selected sites to be strongly associated with N glycosylation sites.     

Fluctuation domains in adaptive evolution

We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains-parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.     

The evolution and adaptive significance of heterostyly

The origin and adaptive significance of heterostylous breeding systems have fascinated evolutionary biologists since Darwin's early work on the subject. Models of the evolution of heterostyly differ in the emphasis given to different selective forces and in the sequence in which the physiological and morphological components of the polymorphism are thought to arise. Recent field studies of the population biology of heterostylous plants provide support for Darwin's hypothesis that the style-stamen polymorphism promotes disassortative pollination among the floral morphs.     

Parasitism shaping host life-history evolution: adaptive responses in a marine gastropod to infection by trematodes

1. Variation in life-history strategies among conspecific populations indicates the action of local selective pressures; recently, parasitism has been suggested as one of these local forces. 2. Effects of trematode infections on reproductive effort, juvenile growth, size at maturity and susceptibility were investigated among different natural populations of the marine gastropod Zeacumantus subcarinatus, Sowerby 1855. 3. Reproductive effort was not higher in uninfected snails from populations experiencing a high trematode prevalence, but females from high prevalence populations produced significantly larger offspring compared with their conspecifics from other populations. 4. Juvenile growth rate was significantly higher in laboratory-raised snails originating from females in a high prevalence population compared with other populations. 5. Size at maturity, determined by the appearance of functional gonads, was significantly and negatively related to trematode prevalence, and positively related to mean snail size, across 10 populations in the study area. 6. There was no evidence of different host resistance against trematodes in sentinel snails from high and low prevalence populations exposed to the same infection pressure in the field. 7. Our results strongly indicate that Z. subcarinatus adapt to trematodes by reaching maturity early, thereby maximizing their chance of reproducing in populations experiencing a high prevalence of infection by castrating trematodes.