Detecting the form of selection from DNA sequence data

Clues to our evolutionary history lie hidden within DNA sequence data. One of the great challenges facing population geneticists is to identify and accurately interpret these clues. This task is made especially difficult by the fact that many different evolutionary processes can lead to similar observations. For example, low levels of polymorphism within a region can be explained by a low local mutation rate, by selection having eliminated deleterious mutations, or by the recent spread to fixation of a beneficial allele. Theoretical advances improve our ability to distinguish signals left by different evolutionary processes. In particular, a new test might better detect the footprint of selection having favored the spread of a beneficial allele.     

Detecting ancient admixture in humans using sequence polymorphism data

A debate of long-standing interest in human evolution centers around whether archaic human populations (such as the Neanderthals) have contributed to the modern gene pool. A model of ancient population structure with recent mixing is introduced, and it is determined how much information (i.e., sequence data from how many unlinked nuclear loci) would be necessary to distinguish between different demographic scenarios. It is found that approximately 50-100 loci are necessary if plausible parameter estimates are used. There are not enough data available at the present to support either the "single origin" or the "multiregional" model of modern human evolution. However, this information should be available in a few years.     

Natural selection and density-dependent population growth

Natural selection was studied in the context of density-dependent population growth using a single locus, continuous time model for the rates of change of population size and allele frequency. The maximization principle of density-dependent selection was applied to a class of fitness expressions with explicit recruitment and mortality terms. Three general results were obtained: First, at low population densities, the genetic basis of selection is the difference between the mean recruitment rate and the mean mortality rate. Second, at densities much higher than the equilibrium population size, selection is expected to act to minimize the mean mortality rate. Third, as the population approaches its equilibrium density, selection is predicted to maximize the ratio of the mean recruitment rate to the mean mortality rate.     

Global dynamics of a selection model for the growth of a population with genotypic fertility differences

A population growth model is considered for a one locus two allele problem with selection based entirely on fertility differences. A local stability analysis is carried out for the critical points — which include possible polymorphic states — of the resulting nonlinear differential equations. The methods of dynamical systems theory are applied to obtain limiting genotypic proportions for every initial state. Thus the results are global and there are no periodic solutions.Research for this paper was partially supported by the National Science and Engineering Research Council of Canada Grant NSERC A-8130Research for this paper was partially supported by the National Science and Engineering Research Council of Canada Grant NSERC A-4823Research supported by NSF Grant MCS 7901069. A portion of the work was carried out while the author was a Visiting Professor at the University of Utah, Salt Lake City, Utah     

Life-history theory, fertility and reproductive success in humans

According to life-history theory, any organism that maximizes fitness will face a trade-off between female fertility and offspring survivorship. This trade-off has been demonstrated in a variety of species, but explicit tests in humans have found a positive linear relationship between fitness and fertility. The failure to demonstrate a maximum beyond which additional births cease to enhance fitness is potentially at odds with the view that human fertility behaviour is currently adaptive. Here we report, to our knowledge, the first clear evidence for the predicted nonlinear relationship between female fertility and reproductive success in a human population, the Dogon of Mali, West Africa. The predicted maximum reproductive success of 4.1+/-0.3 surviving offspring was attained at a fertility of 10.5 births. Eighty-three per cent of the women achieved a lifetime fertility level (7-13 births) for which the predicted mean reproductive success was within the confidence limits (3.4 to 4.8) for reproductive success at the optimal fertility level. Child mortality, rather than fertility, was the primary determinant of fitness. Since the Dogon people are farmers, our results do not support the assumptions that: (i) contemporary foragers behave more adaptively than agriculturalists, and (ii) that adaptive fertility behaviour ceased with the Neolithic revolution some 9000 years ago. We also present a new method that avoids common biases in measures of reproductive success.     

Detecting past population bottlenecks using temporal genetic data

Population bottlenecks wield a powerful influence on the evolution of species and populations by reducing the repertoire of responses available for stochastic environmental events. Although modern contractions of wild populations due to human-related impacts have been documented globally, discerning historic bottlenecks for all but the most recent and severe events remains a serious challenge. Genetic samples dating to different points in time may provide a solution in some cases. We conducted serial coalescent simulations to assess the extent to which temporal genetic data are informative regarding population bottlenecks. These simulations demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based solely on modern data. The difference in power between the modern and temporal DNA approaches depends significantly on effective population size and bottleneck intensity and less significantly on sample size. The temporal approach provides more power in cases of genetic recovery (via migration) from a bottleneck than in cases of demographic recovery (via population growth). Choice of genetic region is critical, as mutation rate heavily influences the extent to which temporal sampling yields novel information regarding the demographic history of populations.     

Evidence for population growth in humans is confounded by fine-scale population structure

Although many studies have reported human polymorphism data, there has been no analysis of the effect of sampling design on the patterns of variability recovered. Here, we consider which factors affect a summary of the allele-frequency spectrum. The most important variable to emerge from our analysis is the number of ethnicities sampled: studies that sequence individuals from more ethnicities recover more rare alleles. These observations are consistent with fine-scale geographic differentiation as well as population growth. They suggest that the geographic sampling strategy should be considered carefully, especially when the aim is to infer the demographic history of humans.     

Sexual selection and fertility

Genetic models are analyzed in which sexual selection is combined with fertility selection. In these models, the sexual selection acts on males, the fertility selection on either males, females or both sexes. The phenotypes thus selected may be determined either by dominant and recessive alleles or by each homozygous and heterozygous genotype. Polymorphisms of dominant and recessive phenotypes can be maintained in equilibrium by a balance between sexual and fertility selection. Generally fertility selection has a greater effect than viability selection in determining the point of equilibrium. The dominant phenotype is maintained at a lower frequency when at a fertility disadvantage than when at a viability disadvantage. When about 20% or more of the females mate preferentially, the models show that equilibria will be established at very different frequencies depending on whether fertility selection acts on males, females or both sexes. These results, applied to data of preferential mating of melanic two-spot ladybirds, predict differences in fertility which can be use to test the models. Symmetric models of preferences for each genotype also give rise to polymorphisms if the heterozygotes obtain an overall advantage.     

Detecting population decline of birds using long-term monitoring data

Abrupt population change in birds may be caused by various factors. When such events occur, it is important to understand the population-level impact on the species. We applied a change point analysis with Markov chain Monte Carlo using long-term population count data to address this question. We first investigated the method with a simple Poisson model using synthetic data sets for different population decline scenarios and number of observations. Estimated change points were particularly accurate when a large decline in counts occurred. Accuracy and precision of posterior change magnitude tended to increase when actual change magnitude became larger. We applied the method to two cases using data from the North American Breeding Bird Survey: epidemic mortality of Florida scrub-jays (Aphelocoma coerulescens) in central Florida and population decline of American crows (Corvus brachyrhynchos) in Maryland and Virginia after West Nile virus emergence. The Florida scrub-jay case study indicated that the estimated change point was accurate compared with that reported by local monitoring. A Poisson-log model that included observer and year variability resulted in better fit to the data than a simple Poisson model. The American crow case study showed that the method detected change points towards the end of observational data, but not all change point parameters converged, which may suggest that a population decline did not occur or was small for some survey routes we analyzed. Our study demonstrates the utility of change point analysis to examine abrupt population change. Data from systematic long-term monitoring can be a basis of such an analysis.     

Demographic constraints on population growth of early humans

The human population grew at very low average rates for most of its existence. Mortality was reasonably severe and expectation of life at birth was low. The level of fertility necessary to achieve even inifinitesimal population growth under such mortality implies birth intervals sufficiently short to conflict with the ability to care for and carry children in a mobile foraging economy. Techniques for the control of mortality, especially of children before puberty and of women in childbirth, and of child care exchange, probably developed by females, may have been essential in permitting population growth under conditions of mobile foraging.     

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase

We present a statistical model for patterns of genetic variation in samples of unrelated individuals from natural populations. This model is based on the idea that, over short regions, haplotypes in a population tend to cluster into groups of similar haplotypes. To capture the fact that, because of recombination, this clustering tends to be local in nature, our model allows cluster memberships to change continuously along the chromosome according to a hidden Markov model. This approach is flexible, allowing for both "block-like" patterns of linkage disequilibrium (LD) and gradual decline in LD with distance. The resulting model is also fast and, as a result, is practicable for large data sets (e.g., thousands of individuals typed at hundreds of thousands of markers). We illustrate the utility of the model by applying it to dense single-nucleotide-polymorphism genotype data for the tasks of imputing missing genotypes and estimating haplotypic phase. For imputing missing genotypes, methods based on this model are as accurate or more accurate than existing methods. For haplotype estimation, the point estimates are slightly less accurate than those from the best existing methods (e.g., for unrelated Centre d'Etude du Polymorphisme Humain individuals from the HapMap project, switch error was 0.055 for our method vs. 0.051 for PHASE) but require a small fraction of the computational cost. In addition, we demonstrate that the model accurately reflects uncertainty in its estimates, in that probabilities computed using the model are approximately well calibrated. The methods described in this article are implemented in a software package, fastPHASE, which is available from the Stephens Lab Web site.     

Detecting evolutionary trends from molecular data

The measures of compositional nonrandomness to be discussed as to their physical significance and to their power of detecting evolutionary significant variations are (see article)(pi a priori probability for amino acid i, ni its number of occurrences in a protein of length L). As a concrete example, the pi are here supposed to represent equal frequencies of all non-stop codons. For each quantity, four levels are defined: The base level, with optimal (i.e. minimal nonrandomness) composition, admitting non-integer values of ni; the integer level with optimal integer composition; the noise level, represented by a typical random cain; and the real protein level. On all these levels, S, which is the measure with the most direct physical sense, shows the smoothest behavior with the smallest relative fluctuations and thus the highest resolution.     

Sexual selection,paternal care,and concealed ovulation in humans

Changes in the social structure of early humans greatly enhanced the potential for paternal care to contribute to offspring success. Selection therefore favored females who mated with more paternal males. Since paternal care limits mating effort, males least successful as polygynists would have the most to gain by paternal behavior, while the successful polygynists would gain least. Concealed ovulation may have evolved because it promoted the paternal tendencies of the less polygynous males who advanced female reproductive success the most. Since the offspring of indulgent males would have a competitive advantage over the offspring of more polygynous males, and females revealing the time of ovulation would become increasingly scarse, all males would eventually pursue a reproductive strategy emphasizing paternal effort over mating effort.In nonhuman primates the most polygynous males mate selectively with females who are likely to be ovulating. Such males would probably not mate with females having diminished cues to the time of ovulation. The more paternally prone males could therefore consort with these females and experience a high confidence of paternity. Another characteristic of nonhuman primates is that the most successful polygynists tend to have a high dominance rank. Thus, female hominids who mated with more paternal males may have sacrificed having offspring with some of the genetic advantages that contribute to dominance. However, subsconscious physiological and psychological correlates of ovulation in humans may have tempted females to exploit infrequent, low-risk opportunities to mate outside the pair-bond with males of superior genetic fitness. These correlates may also promote conception irrespective of mating partner, or they may have helped females avoid rape.     

Feast/famine growth environments and activated sludge population selection

The effect of feast/famine growth conditions on activated sludge cultures indicates that nonfilamentous cultures can be selected by providing proper substrate gradients and extended periods of endogenous metablism. Reactor operating strategies providing intermittently high substrate concentrations result in cultures characterized by high peak substrate and oxygen uptake activities, rapid settling rates, and high resistance to starvation. Sludge settleability can be manipulated using controlled variations in growth environment with corresponding changes noted in sludge activity. In combination with the low net growth rates associated with activated sludge systems, feast/famine environments would logically convey a selection advantage to microbes capable of readily assimilating substrate materials and maintaining viability during extended starvation periods.     

Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes

We employed a multilocus approach to examine the effects of population subdivision and natural selection on DNA polymorphism in 2 closely related wild tomato species (Solanum peruvianum and Solanum chilense), using sequence data for 8 nuclear loci from populations across much of the species' range. Both species exhibit substantial levels of nucleotide variation. The species-wide level of silent nucleotide diversity is 18% higher in S. peruvianum (pi(sil) approximately 2.50%) than in S. chilense (pi(sil) approximately 2.12%). One of the loci deviates from neutral expectations, showing a clinal pattern of nucleotide diversity and haplotype structure in S. chilense. This geographic pattern of variation is suggestive of an incomplete (ongoing) selective sweep, but neutral explanations cannot be entirely dismissed. Both wild tomato species exhibit moderate levels of population differentiation (average F(ST) approximately 0.20). Interestingly, the pooled samples (across different demes) exhibit more negative Tajima's D and Fu and Li's D values; this marked excess of low-frequency polymorphism can only be explained by population (or range) expansion and is unlikely to be due to population structure per se. We thus propose that population structure and population/range expansion are among the most important evolutionary forces shaping patterns of nucleotide diversity within and among demes in these wild tomatoes. Patterns of population differentiation may also be impacted by soil seed banks and historical associations mediated by climatic cycles. Intragenic linkage disequilibrium (LD) decays very rapidly with physical distance, suggesting high recombination rates and effective population sizes in both species. The rapid decline of LD seems very promising for future association studies with the purpose of mapping functional variation in wild tomatoes.