NONRANDOM MATING IN AN OPEN-POLLINATED MAIZE POPULATION

Variation of the adaptive substitution rate between species and within genomes

The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.

THE EFFECTS OF POPULATION SIZE AND PLANT DENSITY ON OUTCROSSING RATES IN LOCALLY ENDANGERED SALVIA PRATENSIS

Multilocus outcrossing rates were estimated in natural and experimental populations of Salvia pratensis, an entomophilous, gynodioecious, protandrous perennial. Male steriles were used to check the estimation procedure of outcrossing rates in hermaphrodites. Estimates of outcrossing rates in hermaphroditic plants ranged from 38.2% to 81.8% in natural populations and from 71.5% to 95.5% in experimental populations. No correlations were found between outcrossing rates and population size. However, outcrossing in hermaphrodites was promoted by high plant densities and low frequencies of male steriles. It is argued that effective management to preserve genetic variation in populations of S. pratensis should provide for the maintenance of high plant densities.

Genome wide analyses reveal little evidence for adaptive evolution in many plant species

The relative contribution of advantageous and neutral mutations to the evolutionary process is a central problem in evolutionary biology. Current estimates suggest that whereas Drosophila, mice, and bacteria have undergone extensive adaptive evolution, hominids show little or no evidence of adaptive evolution in protein-coding sequences. This may be a consequence of differences in effective population size. To study the matter further, we have investigated whether plants show evidence of adaptive evolution using an extension of the McDonald-Kreitman test that explicitly models slightly deleterious mutations by estimating the distribution of fitness effects of new mutations. We apply this method to data from nine pairs of species. Altogether more than 2,400 loci with an average length of approximately 280 nucleotides were analyzed. We observe very similar results in all species; we find little evidence of adaptive amino acid substitution in any comparison except sunflowers. This may be because many plant species have modest effective population sizes.

Patterns of population structure in maize landraces from the Central Valleys of Oaxaca in Mexico

Assessing the impact of farmer management of maize landraces in the Central Valleys of Oaxaca, Mexico is crucial to an understanding of maize evolution, as it was first domesticated there. In this paper, we report on the impact of traditional farmer management of maize populations in this region in structuring molecular diversity and on the population dynamics of maize landraces. These populations, from a sample of local landraces cultivated by farmers in six villages, show little among-population differentiation (Fst=0.011). Most surprisingly, there is no isolation by distance and small among-village differentiation (Fst=0.003). For an outbreeding plant such as maize, one would expect populations to fit Hardy-Weinberg equilibrium, but significant homozygote excess (Fis=0.13) was found. This homozygote excess shows remarkable interpopulation and interlocus differences. We show that this pattern is related to variation in the mean anthesis-silking interval as well as to the flowering range or heterogeneity in flowering of a given population. A short anthesis-silking interval and high level of heterogeneity in flowering precocity will favor assortative mating. This leads to a locus-dependent population substructure giving an unusual case of Wahlund effect and inbreeding while high levels of seed exchange among farmers prevent population differentiation at both village and regional levels.

Pollen pool heterogeneity in jack pine (Pinus banksiana Lamb.): a problem for estimating outcrossing rates?

Pollen pool heterogeneity, which violates an assumption of the mixed-mating model, is a major potential problem in measuring plant mating systems. In this study, isozyme markers were used to examine pollen pool heterogeneity in two natural populations of jack pine, Pinus banksiana Lamb., in northwestern Ontario, Canada. Population multilocus estimates of outcrossing rate ranged from 0.83 to 0.95 and differed significantly between populations. Single-tree multilocus outcrossing rates were found to be homogeneous among trees in both populations. Computer simulation studies indicated that a consanguineous pollen pool (pollen gametes related to the mother tree) was capable of biasing population outcrossing estimates downward. Random pollen pool heterogeneity (uncorrelated with maternal genotypes) did not appear to affect population outcrossing estimates in the simulations. Heterogeneity G-tests and Spearman rank tests showed that pollen pool heterogeneity existed in the two natural populations examined; however, it did not have a major effect on population outcrossing estimates, since the consanguineous pollen pool detected was probably a relatively minor component of the outcross pollen pool in both populations. In addition, heterogeneity G-tests were found to be not sensitive in detecting pollen pool heterogeneity caused by consanguineous pollen pool.

Genetic relatedness in open-pollinated families of two leguminous tree species, Robinia pseudoacacia L. and Gleditsia triacanthos L

When conducting tree breeding experiments, geneticists often assume that individuals from open-pollinated families are halfsibs. The reliability of this assumption was tested using data from enzyme electrophoresis to estimate the genetic relatedness among progeny within 22 open-pollinated families of Robinia pseudoacacia L. (black locust) and 34 open-pollinated families of Gleditsia triacanthos L. (honey locust) from natural stands. An algorithm employing population estimates of fixation indices, pollen allele frequencies, and selfing rates was used to calculate the mean expected number of alleles in common across loci under assumptions of either full-sib (i.e., a single pollen parent) or half-sib (i.e., random mating) relationships. For each open-pollinated family, the average coefficient of relationship among progeny was calculated by linear interpolation from the observed number of alleles in common. For most families of both species, coefficients were significantly higher than 0.25 (half-sib relation), but were significantly lower than 0.50 (full-sib relation). These results suggest that the assumption of a half-sib relationship among progeny of open-pollinated families is violated for these tree species. More critical to the estimation of heritabilities and the prediction of genetic gains was the observation that estimates of the coefficient of relationship varied widely among open-pollinated families (for R. pseudoacacia r 0=0.20-0.43, mean=0.34; for G. triacanthos r 0=0.29-0.55, mean=0.36).

Mating system in rye: variability in relation to the population and plant density

The amount of outcrossing was estimated using seven enzyme loci assayed in seven populations of rye (Secale cereale L.). Single-locus outcrossing values fluctuated widely from locus to locus in each population. The weighted mean single-locus estimates ranged from 0.716 to 0.946, and multilocus estimates ranged from 0.701 to 0.910. The analysis showed that self-pollination occurred in the rye populations, and, as a result of selfing, populations contained homozygotes in excess of random mating expectations at the seedling stage of development. Low plant density, which causes low pollen density during fertilization, seems to weaken the self-incompatibility system; at low plant density, the outcrossing estimate was significantly lower than was obtained at high plant density.

Outcrossing rates and male sterility in natural populations of Plantago coronopus

Outcrossing rates were estimated in three populations of the gynodioecious species Plantago coronopus by means of electrophoresis of adult plants and their natural progenies. A multilocus estimation procedure was used. Heterogeneity among the pollen-pool allele frequencies did not exist either in space of in time. Differences between populations in mean outcrossing rates were large (range: 0.34-0.93), probably caused by differences in densities of flowering plants. In addition, there was considerable variability between individuals, which was at least partly caused by the presence of male sterility. Population density may, via its influence on outcrossing rates, be a factor influencing the maintenance of male sterile plants in the population. The level of outcrossing in hermaphrodites was not low enough to explain the maintenance of male steriles. Outcrossing rates in two populations, established via progeny analysis, were much lower than calculated with the fixation index, possibly indicating heterozygote advantage in these natural populations.