Genetic sampling error of distance (delta(mu))2 and variation in mutation rate among microsatellite loci

An expression is obtained for the time-dependent variance of the microsatellite genetic distance (delta(mu))2 when the mutation rate is allowed to vary randomly among loci. An estimator is presented for the coefficient of variation, C(w), in the mutation rate. Estimated values of C(w) from genetic distances between African and non-African populations were less than 100%. Caveats to this conclusion are discussed.

Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds

We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently approximately 98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95% clustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.

Distinctive genetic signatures in the Libyan Jews

Unlinked autosomal microsatellites in six Jewish and two non-Jewish populations were genotyped, and the relationships among these populations were explored. Based on considerations of clustering, pairwise population differentiation, and genetic distance, we found that the Libyan Jewish group retains genetic signatures distinguishable from those of the other populations, in agreement with some historical records on the relative isolation of this community. Our methods also identified evidence of some similarity between Ethiopian and Yemenite Jews, reflecting possible migration in the Red Sea region. We suggest that high-resolution statistical methods that use individual multilocus genotypes may make it practical to distinguish related populations of extremely recent common ancestry.

Models of sexual selection on a quantitative genetic trait when preference is acquired by sexual imprinting

The evolution of a quantitative genetic trait under stabilizing viability selection and sexual selection is modeled for a polygynous species in which female mating preferences are acquired by sexual imprinting on the parents and by exposure to the surviving population at large. Stabilizing viability selection acts equally on both sexes in the case of a sexually monomorphic trait and on males only in the case of a dimorphic trait. A genetically fixed sensory or perceptual bias defines the origin of the scale on which the trait is measured, and the possibility is incorporated that female preferences may deviate asymmetrically from the familiar-either toward or away from this origin. When viability selection is strong relative to sexual selection, the models predict that the mean trait value will evolve to the viability optimum. With intermediate ratios of the strength of viability to sexual selection, a stable equilibrium can occur on either side of this viability optimum, depending on the direction of asymmetry in female preferences. When viability selection is relatively weak and certain other conditions are also satisfied, runaway selection is predicted.

Y chromosome sequence variation and the history of human populations

Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.

Cultural transmission in a demographic study of sex ratio at birth in China's future

A decline in fertility causes an increase in the sex ratio at birth (SRB) in countries with strong son preference. What happens to the SRB if fertility is maintained at a low level depends on the evolution of son preference. In this paper, we analyze trends in son preference and its effect on China's future SRB.

Recent common ancestry of human Y chromosomes: evidence from DNA sequence data

We consider a data set of DNA sequence variation at three Y chromosome genes (SMCY, DBY, and DFFRY) in a worldwide sample of human Y chromosomes. Between 53 and 70 chromosomes were fully screened for sequence variation at each locus by using the method of denaturing high-performance liquid chromatography. The sum of the lengths of the three genes is 64,120 bp. We have used these data to study the ancestral genealogy of human Y chromosomes. In particular, we focused on estimating the expected time to the most recent common ancestor and the expected ages of certain mutations with interesting geographic distributions. Although the geographic structure of the inferred haplotype tree is reminiscent of that obtained for other loci (the root is in Africa, and most of the oldest non-African lineages are Asian), the expected time to the most recent common ancestor is remarkably short, on the order of 50,000 years. Thus, although previous studies have noted that Y chromosome variation shows extreme geographic structure, we estimate that the spread of Y chromosomes out of Africa is much more recent than previously was thought. We also show that our data indicate substantial population growth in the effective number of human Y chromosomes.

Human population expansion and microsatellite variation

Polymorphisms at di-, tri-, and tetranucleotide microsatellite loci have been analyzed in 14 worldwide populations. A statistical index of population expansion, denoted S(k), is introduced to detect historical changes in population size using the variation at the microsatellites. The index takes the value 0 at equilibrium with constant population size and is positive or negative according to whether the population is expanding or contracting, respectively. The use of S(k) requires estimation of properties of the mutation distribution for which we use both family data of Dib et al. for dinucleotide loci and our population data on tri- and tetranucleotide loci. Statistical estimates of the expansion index, as well as their confidence intervals from bootstrap resampling, are provided. In addition, a dynamical analysis of S(k) is presented under various assumptions on population growth or decline. The studied populations are classified as having high, intermediate, or low values of S(k) and genetic variation, and we use these to interpret the data in terms of possible population dynamics. Observed values of S(k) for samples of di-, tri-, and tetranucleotide data are compatible with population expansion earlier than 60,000 years ago in Africa, Asia, and Europe if the initial population size before the expansion was on the order of 500. Larger initial population sizes force the lower bound for the time since expansion to be much earlier. We find it unlikely that bottlenecks occurred in Central African, East Asian, or European populations, and the estimated expansion times are rather similar for all of these populations. This analysis presented here suggests that modern human populations departed from Africa long before they began to expand in size. Subsequently, the major groups (the African, East Asian, and European groups) started to grow at approximately same time. Populations of South America and Oceania show almost no growth. The Mbuti population from Zaire appears to have experienced a bottleneck during its expansion.

Bayesian estimation of range for microsatellite loci

Microsatellite loci have become important in population genetics because of their high level of polymorphism in natural populations, very frequent occurrence throughout the genome, and apparently high mutation rate. Observed repeat numbers (alleles size) in natural populations and expectations based on computer simulations suggest that the range of repeat numbers at a microsatellite locus is restricted. This range is a key parameter that should be properly estimated in order to proceed with calculations of divergence times in phylogenetic studies and to better investigate the within- and between-population variability. The 'plug-in' estimate of range based on the minimum and maximum value observed in a sample is not satisfactory because of the relatively large number of alleles in comparison with typical sample sizes. In this paper, a set of data from 30 dinucleotide microsatellite loci is analysed under the assumption of independence among loci. Bayesian inference on range for one locus is obtained by assuming that constraints on range values exist as sharp bounds. Closed-form calculations and robustness revealed by our analysis suggest that the proposed Bayesian approach might be routinely used by researchers to classify microsatellite loci according to the estimated value of their allelic range.

The dynamics of repeated elements: Applications to the epidemiology of tuberculosis

We propose a stepwise mutation model to describe the dynamics of DNA fingerprint variation in Mycobacterium tuberculosis. The genome of M. tuberculosis carries insertion sequences (IS6110) that are relatively stable over time periods of months but have an observable transposition rate over longer time scales. Variability in copy number and genomic location of (IS6110) can be harnessed to generate a DNA fingerprint for each strain, by digesting the genome with a restriction enzyme and using a portion of the element as a probe for Southern blots. The number of bands found for a given genome approximates the number of copies of IS6110 it carries. A large data set of such fingerprints from tuberculosis (TB) cases in San Francisco provides an observed distribution of IS6110 copy number. Implementation of the model through deterministic and stochastic simulation indicates some general features of IS/TB dynamics. By comparing observations with outcomes of the model, we conclude that the IS/TB system is very heterogeneous and far from equilibrium. We find that the transposition parameters have a much stronger effect than the epidemic parameters on copy number distribution.

Microsatellite evolution in modern humans: a comparison of two data sets from the same populations

We genotyped 64 dinucleotide microsatellite repeats in individuals from populations that represent all inhabited continents. Microsatellite summary statistics are reported for these data, as well as for a data set that includes 28 out of 30 loci studied by Bowcock et al. (1994) in the same individuals. For both data sets, diversity statistics such as heterozygosity, number of alleles per locus, and number of private alleles per locus produced the highest values in Africans, intermediate values in Europeans and Asians, and low values in Americans. Evolutionary trees of populations based on genetic distances separated groups from different continents. Corresponding trees were topologically similar for the two data sets, with the exception that the (deltamu)2 genetic distance reliably distinguished groups from different continents for the larger data set, but not for the smaller one. Consistent with our results from diversity statistics and from evolutionary trees, population growth statistics S k and beta, which seem particularly useful for indicating recent and ancient population size changes, confirm a model of human evolution in which human populations expand in size and through space following the departure of a small group from Africa.

Niche construction, biological evolution, and cultural change

We propose a conceptual model that maps the causal pathways relating biological evolution to cultural change. It builds on conventional evolutionary theory by placing emphasis on the capacity of organisms to modify sources of natural selection in their environment (niche construction) and by broadening the evolutionary dynamic to incorporate ontogenetic and cultural processes. In this model, phenotypes have a much more active role in evolution than generally conceived. This sheds light on hominid evolution, on the evolution of culture, and on altruism and cooperation. Culture amplifies the capacity of human beings to modify sources of natural selection in their environments to the point where that capacity raises some new questions about the processes of human adaptation.

Population growth of human Y chromosomes: a study of Y chromosome microsatellites

We use variation at a set of eight human Y chromosome microsatellite loci to investigate the demographic history of the Y chromosome. Instead of assuming a population of constant size, as in most of the previous work on the Y chromosome, we consider a model which permits a period of recent population growth. We show that for most of the populations in our sample this model fits the data far better than a model with no growth. We estimate the demographic parameters of this model for each population and also the time to the most recent common ancestor. Since there is some uncertainty about the details of the microsatellite mutation process, we consider several plausible mutation schemes and estimate the variance in mutation size simultaneously with the demographic parameters of interest. Our finding of a recent common ancestor (probably in the last 120,000 years), coupled with a strong signal of demographic expansion in all populations, suggests either a recent human expansion from a small ancestral population, or natural selection acting on the Y chromosome.

Evolutionary consequences of niche construction and their implications for ecology

Organisms regularly modify local resource distributions, influencing both their ecosystems and the evolution of traits whose fitness depends on such alterable sources of natural selection in environments. We call these processes niche construction. We explore the evolutionary consequences of niche construction using a two-locus population genetic model, which extends earlier analyses by allowing resource distributions to be influenced both by niche construction and by independent processes of renewal and depletion. The analysis confirms that niche construction can be a potent evolutionary agent by generating selection that leads to the fixation of otherwise deleterious alleles, supporting stable polymorphisms where none are expected, eliminating what would otherwise be stable polymorphisms, and generating unusual evolutionary dynamics. Even small amounts of niche construction, or niche construction that only weakly affects resource dynamics, can significantly alter both ecological and evolutionary patterns.

Microsatellites provide evidence for Y chromosome diversity among the founders of the New World

Recently, Y chromosome markers have begun to be used to study Native American origins. Available data have been interpreted as indicating that the colonizers of the New World carried a single founder haplotype. However, these early studies have been based on a few, mostly complex polymorphisms of insufficient resolution to determine whether observed diversity stems from admixture or diversity among the colonizers. Because the interpretation of Y chromosomal variation in the New World depends on founding diversity, it is important to develop marker systems with finer resolution. Here we evaluate the hypothesis of a single-founder Y haplotype for Amerinds by using 11 Y-specific markers in five Colombian Amerind populations. Two of these markers (DYS271, DYS287) are reliable indicators of admixture and detected three non-Amerind chromosomes in our sample. Two other markers (DYS199, M19) are single-nucleotide polymorphisms mostly restricted to Native Americans. The relatedness of chromosomes defined by these two markers was evaluated by constructing haplotypes with seven microsatellite loci (DYS388 to 394). The microsatellite backgrounds found on the two haplogroups defined by marker DYS199 demonstrate the existence of at least two Amerind founder haplotypes, one of them (carrying allele DYS199 T) largely restricted to Native Americans. The estimated age and distribution of these haplogroups places them among the founders of the New World.

Theoretical considerations of cross-immunity, recombination and the evolution of new parasitic strains

We explore the dynamics of multiple strains of a parasite in order to assess the conditions under which a novel strain, perhaps a mutant or migrant, may invade a population that already carries an endemic strain. Multiple strain dynamics can be modeled through coinfection or complete cross-immunity. We examine these three modes to discuss the relationships among cross-immunity, the basic reproductive rates of each strain, and the invasion of the new strain. Superinfection is more restrictive than coinfection in the proportion of parameters that allows invasion. The coinfection model is extended to allow haploid strains to undergo recombination within the host. We investigate the effects of recombination and cross-immunity on the invasion of new strains. Interestingly, although recombination is understood to generate diversity, it is not always advantageous.

Genetic conflicts and the evolutionary origin of genomic imprinting

In mammals, both paternally and maternally inherited copies of most genes are expressed. For a small number of genes, however, only the paternal copy is active, whereas in other cases only the maternal gene is transcribed. This form of nonmendelian expression, known as genomic imprinting, amounts to functional haploidy. The most intriguing explanation for why such a system should evolve when diploidy is omnipresent invokes conflicts between genetic interests of mothers, fathers and their offspring. Recent approaches to modelling the evolutionary origin of imprinting support this hypothesis but make different predictions about its prevalence and the likelihood of polymorphism.

Migration versus mutation in the evolution of recombination under multilocus selection

We use modifier theory to compare the evolution of recombination under mutation-selection and migration-selection balance models. Recombination between loosely linked loci subject to weak multilocus selection is controlled by the genotype at a selectively neutral modifier locus. We show that the success of a new modifier depends on the sign and amount of epistasis as well as on the linkage of the modifier locus to the loci under selection. With both migration and mutation, for recombination to increase requires negative (synergistic) epistasis. When epistasis is sufficiently weak, increased recombination is always favoured under mutation-selection balance and never under migration-selection balance. With stronger negative epistasis, there exists a critical recombination value. In this case, a recombination-increasing allele invades the population under mutation-selection balance if its recombination rate with the major loci is less than the critical recombination value, whereas with weak migration it must be above this value. These results are the same for haploid and diploid populations.

Microsatellite behavior with range constraints: parameter estimation and improved distances for use in phylogenetic reconstruction

A symmetric stepwise mutation model with reflecting boundaries is employed to evaluate microsatellite evolution under range constraints. Methods of estimating range constraints and mutation rates under the assumptions of the model are developed. Least squares procedures are employed to improve molecular distance estimation for use in phylogenetic reconstruction in the case where range constraints and mutation rates vary across loci. The bias and accuracy of these methods are evaluated using computer simulations, and they are compared to previously existing methods which do not assume range constraints. Range constraints are seen to have a substantial impact on phylogenetic conclusions based on molecular distances, particularly for more divergent taxa. Results indicate that if range constraints are in effect, the methods developed here should be used in both the preliminary planning and final analysis of phylogenetic studies employing microsatellites. It is also seen that in order to make accurate phylogenetic inferences under range constraints, a larger number of loci are required than in their absence.

Waiting with and without recombination: the time to production of a double mutant

R.A. Fisher and H.J. Muller argued in the 1930s that a major evolutionary advantage of recombination is that it allows favorable mutations to be combined within an individual even when they first appear in different individuals. This effect is evaluated in a two-locus, two-allele model by calculating the average waiting time until a new genotypic combination first appears in a haploid population. Three approximations are developed and compared with Monte Carlo simulations of the Wright-Fisher process of random genetic drift in a finite population. First, a crude method, based on the deterministic accumulation of single mutants, produces a waiting time of 1/square root of N mu(2) with no recombination and [formula: see text] with recombination between the two loci, where mu is the mutation rate, N is the haploid population size, and R is the recombination rate. Second, the waiting time is calculated as the expected value of a heterogeneous geometric distribution obtained from a branching process approximation. This gives accurate estimates for small values of N mu large. The estimates for small values of N mu are considerably lower than the simulated values. Finally, diffusion analysis of the Wright-Fisher process provides accurate estimates for N mu small, and the time scales of the diffusion process show a difference between R = 0 and for R >> 0 of the same order of magnitude as seen in the deterministic analysis. In the absence of recombination, accurate approximations to the waiting time are obtained by using the branching process for high N mu and the diffusion approximation for low N mu. For low N mu the waiting time is well approximated by 1/the square root of 8N2 mu(3). With R >> 0, the following dependence on N mu is observed: For N mu > 1 the waiting time is virtually independent of recombination and is well described by the branching process approximation. For N mu approximately equal to 1 the waiting time is well described by a simplified diffusion approximation that assumes symmetry in the frequencies of single mutants. For N mu << 1 the waiting time is well described by the diffusion approximation allowing asymmetry in the frequencies of single mutants. Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small compared to that of the mutation rate and population size. For large N mu, recombination has a negligible effect, and its effect is strongest for small N mu, in which case the waiting time approaches a fixed fraction of the waiting time for R = 0. Free recombination lowers the waiting time to about 45% of the waiting time for absolute linkage for small N mu. Selection has little effect on the importance of recombination in general.

Genetic conflicts, multiple paternity and the evolution of genomic imprinting

We present nine diallelic models of genetic conflict in which one allele is imprintable and the other is not to examine how genomic imprinting may have evolved. Imprinting is presumed to be either maternal (i.e., the maternally derived gene is inactivated) or paternal. Females are assumed to be either completely monogamous or always bigamous, so that we may see any effect of multiple paternity. In contrast to previous verbal and quantitative genetic models, we find that genetic conflicts need not lead to paternal imprinting of growth inhibitors and maternal imprinting of growth enhancers. Indeed, in some of our models--those with strict monogamy--the dynamics of maternal and paternal imprinting are identical. Multiple paternity is not necessary for the evolution of imprinting, and in our models of maternal imprinting, multiple paternity has no effect at all. Nevertheless, multiple paternity favors the evolution of paternal imprinting of growth inhibitors and hinders that of growth enhancers. Hence, any degree of multiple paternity means that growth inhibitors are more likely to be paternally imprinted, and growth enhancers maternally so. In all of our models, stable polymorphism of imprinting status is possible and mean fitness can decrease over time. Neither of these behaviors have been predicted by previous models.

A gene-culture coevolutionary model for brother-sister mating

We present a gene-culture coevolutionary model for brother-sister mating in the human. It is shown that cultural--as opposed to innate--determination of mate preference may evolve, provided the inbreeding depression is sufficiently high. At this coevolutionary equilibrium, sib mating is avoided because of cultural pressures.

Biased mutations and microsatellite variation

Mutation bias is one of the forces that may constrain the variation at microsatellite loci. Here, we study the dynamics of population statistics and the genetic distance between two populations under multiple stepwise mutations with linear bias and random drift. Expressions are derived for these statistics as functions of time, as well as at mutation-drift equilibrium. Applying these expressions to published data on humans and chimpanzees, the regression coefficient of mutation bias on allele size was estimated to be at least between -0.0064 and -0.013. The assumption of mutational bias produces larger estimates of divergence times than are obtained in its absence; in particular, the time of split between African and non-African human populations is estimated to be between 183,000 and 222,000 years, assuming one-step mutations and no selection. With multistep mutations, the divergence time is estimated to be lower.