Evolution of Multilocus Genetic Structure in an Experimental Barley Population

Data from 311 selfed families isolated from four generations (F8, F13, F23, F45) of an experimental barley population were analyzed to determine patterns of change in character expression for seven quantitative traits, and in single-locus allelic frequencies, and multilocus genetic structure, for 16 Mendelian loci that code for discretely recognizable variants. The analyses showed that large changes in single-locus allelic frequencies and major reorganizations in multilocus genetic structure occurred in each of the generation-to-generation transitions examined. Although associations among a few traits persisted over generations, dynamic dissociations and reassociations occurred among several traits in each generation-transition period. Overall, the restructuring that occurred was characterized by gradual decreases in the number of clusters of associated traits and increases in the number of traits within each cluster. The observed changes in single-locus frequencies and in multilocus genetic structure were attributed to interplay among various evolutionary factors among which natural selection acting in a temporally heterogeneous environment was the guiding force.     

Estimation of life cycle components of selection in an experimental plant population

Viability and fertility components of selection associated with linkage blocks marked by four electrophoretically detectable loci were estimated in an experimental population of barley [Composite Cross V (CCV)]. The intensity of selection affecting the distribution of pollen types in the outcross pool was also estimated and comparisons were made between the selective values of genes in the pools of uniting ovules and pollen. The estimates show that selection was intense at various stages of the life cycle and that viability and fertility components often opposed one another. Estimates of viability and fertility components of selection were also extended to the three-locus level. The multilocus estimates reveal large differences in viability and fertility among homozygous genotypes. It is concluded that strong selection operates at all life cycle stages in CCV, although often in differing directions.     

Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.)

Molecular studies of nucleotide sequence variation have rarely attempted to test hypotheses related to geographically varying patterns of natural selection. The present study tested the role of spatially varying selection in producing significant linkage disequilibrium and large differences in the frequencies of two common alleles at the pantophysin (Pan I) locus among five populations of the Atlantic cod, Gadus morhua. Nucleotide sequences of 124 Pan I alleles showed strong evidence for an unusual mix of balancing and directional selection but no evidence of stable geographically varying selection. The alleles were highly divergent at both the nucleotide level (differing on average by 19 mutations) and at amino acid level (each having experienced three amino acid substitutions since diverging from a common ancestral allele). All six amino acid substitutions occurred in a 56-residue intravesicular loop (IV1 domain) of the vesicle protein and each involved a radical change. An analysis of molecular variation revealed significant heterogeneity in the frequencies of recently derived mutations segregating within both allelic classes, suggesting that two selective sweeps may be presently occurring among populations. The dynamic nature of the Pan I polymorphism in G. morhua and clear departure from equilibrium conditions invalidate a simple model of spatially varying selection.     

The mode of evolution of molecular markers in populations of house mice under artificial selection for locomotor behavior

A complete understanding of the mode of evolution of molecular markers is important for making inferences about different population genetic parameters, especially because a number of studies have reported patterns of allelic variation at molecular markers that are not in agreement with neutral evolutionary expectations. In the present study, house mice (Mus domesticus) from the fourteenth generation of a selection experiment for increased voluntary wheel-running activity were used to test how selection on a complex behavior affects the distribution of allelic variation by examining patterns of variation at six microsatellite and four allozyme loci. This population had a hierarchical structure that allowed for simultaneous testing of the effects of selection and genetic drift on the distribution of allelic variation by comparing observed patterns of allele frequencies and estimates of genetic divergence at multiple hierarchical levels to expectations under models of neutral evolution. The levels of genetic divergence among replicate lines and between selection groups, estimated from microsatellite data or pooled microsatellite and allozyme data, were not significantly different from expectations under neutral evolution. Furthermore, the pattern of change of allele frequencies between the base population and generation 14 was largely in agreement with expectations under neutral evolution (although the PGM locus exhibited a pattern of change within populations that was difficult to explain under neutral evolution). Overall the results generally provide support for the neutral evolution of molecular markers.     

Maximum Likelihood Analysis of Population Differences in Allelic Frequencies

Statistical techniques are presented for the analysis of geographic variation in allelic frequencies. Likelihood ratio test criteria are derived from a multinominal sampling distribution, and are used to answer three questions. (1) Are there geographic differences in allelic frequencies? (2) Are population differences in allelic frequencies associated with environmental differences? (3) Is there any residual "lack of fit" variation among populations, after accounting for that variation associated with environmental differences? The two- and three-allele cases are explicitly treated, and the extension to more alleles is indicated.     

Esterase genes in parallel composite cross barley populations

The California population of Composite Cross V of barley was used as the source of three subpopulations that were started from generations 10, 20 and 30, respectively, and were grown in parallel environmental conditions in Cambridge for eight generations. Outcrossing rates (0.2%) were even lower than in the California material, and heterozygotes were correspondingly rare, so that the populations were essentially mixtures of homozygous lines. Four esterase loci that were polymorphic in the base Composite Cross V remained so in all the derived populations, but showed considerable changes in allelic frequency over time, particularly at two of the genes. Multilocus analysis showed that strong directional changes occurred in all three populations, but they were not consistent. One particular genotype became predominant in the population derived from generation 10, whereas in the other two populations it was a genotype with different alleles at the Est1 and Est3 loci that rose to frequencies of more than 50%. Strong directional selection undoubtedly occurred in these populations, but did not cause parallel changes in esterase gene frequencies. These data do not facilitate a discrimination between the alternative explanations of hitchhiking or multilocus selection at these loci.     

Evidence of natural selection for disease resistance in Composite Cross Five (CCV) of barley

Cambridge Composite Cross Five (CCV) of barley was studied utilising hordeins, restriction fragment length polymorphisms (RFLPs) and reaction to powdery mildew with a view to understanding the genetic changes occurring in the population. Changes in the frequency of individual hordein patterns as well as pattern combinations showed directional trends in successive generations in three parallel populations maintained as discrete populations since 1977 in Cambridge. Certain hordein pattern combinations were more common in the resistance classes and there was a strong association between hordein patterns and mildew reaction. RFLP analysis revealed that 80% of a random sample taken from generation F₂₄ of Population I had the same restriction pattern as that of the cultivar Algerian, which was one of the original 30 parental lines of CCV. This cultivar is the source of the Mla1 allele in barley improvement programmes in Europe. We argue, based on supporting evidence from hordein analysis and tests of reaction to selected mildew isolates of known virulence isolates together with UK virulence surveys, that selection for Mla1 in Cambridge has been the predominant evolutionary force in CCV in Cambridge.     

Distribution of allozymic alleles and genetic diversity in the American Barley Core Collection

A survey of allozymic alleles and genetic diversity was made for 151 accessions of the American Barley Core Collection. A total of 25 alleles at ten loci were observed. Two loci were monomorphic. The average diversity index for individual loci ranged between 0.026 and 0.649. Most significant differences in allelic frequency and genetic diversity value were found between spring and winter barley. Spring barley showed a greatly higher average diversity than winter barley (t=2.124, P=0.071). The smallest differences in allelic frequencies and diversity values were observed between the two geographical regions, North and South America. Rare alleles were detected only in a few accessions. Seven rare alleles were associated with spring barley. The genetic similarities among the 151 accessions ranged from 0.20 to 1.00, which showed that a high level of genetic variability exists in this set of core accessions. Cluster analysis and principal coordinate analysis did not give clear-cut separation of different types of barley, but most of the winter barley accessions were closely associated. Received: 7 April 2000 / Accepted: 13 June 2000     

Isozyme Frequency Patterns in DROSOPHILA PAVANI Associated with Geographical and Seasonal Variables

Fourteen population samples of Drosophila pavani were obtained from a number of localities in Chile. The populations sampled were dispersed over 7 degrees of latitude and 1800 meters of elevation, and were drawn at three different times. Sixteen electrophoretic loci were assayed for each population; eight of the loci were analyzed statistically for geographic variation; the other eight were essentially monomorphic. For all eight variable loci, variation in allelic frequencies among populations was highly significant. In all cases, a significant portion of the variation among populations was associated with variation in gross environmental variables (latitude, elevation, month of collection). The implications of the evidence were discussed, and the authors concluded that there was suggestive evidence for selection.     

Balancing selection at a frog antimicrobial peptide locus: fluctuating immune effector alleles?

Balancing selection is common on many defense genes, but it has rarely been reported for immune effector proteins such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species of leopard frogs (Rana pipiens, Rana blairi, and Rana palustris). Several highly divergent allelic lineages are segregating at this locus. That this unusual pattern results from balancing selection is demonstrated by multiple lines of evidence, including a ratio of nonsynonymous/synonymous polymorphism significantly higher than 1, the ZnS test, incongruence between the number of segregating sites and haplotype diversity, and significant Tajima's D values. Our data are more consistent with a model of fluctuating selection in which alleles change frequencies over time than with a model of stable balancing selection such as overdominance. Evidence for fluctuating selection includes skewed allele frequencies, low levels of synonymous variation, nonneutral values of Tajima's D within allelic lineages, an inverse relationship between the frequency of an allelic lineage and its degree of polymorphism, and divergent allele frequencies among populations. AMP loci could be important sites of adaptive genetic diversity, with consequences for host-pathogen coevolution and the ability of species to resist disease epidemics.     

Molecular markers to study genetic drift and selection in wheat populations

Studying the heterogeneity in variation of gene frequency among populations or between generations may be a possible way to detect genomic regions experiencing selection. In order to evaluate this approach, RFLP markers were used to compare the allelic frequencies in wheat populations that had been submitted to natural selection. In 1984, samples of two composite cross populations were distributed in the French network for dynamic management of genetic resources. Since then, all the sub-populations have been cultivated in the same sites with no human selection. The strong differentiation between populations found for agro-morphological traits (earliness, resistance to pathogens, ...) provided evidence of their adaptation to local conditions. The two initial populations and six derived sub-populations cultivated for 10 years in four contrasted sites were studied with RFLP markers. Differentiation between sub-populations based on RFLP diversity was highly significant. Variations on allelic frequencies of the 30 loci scored were found to be much greater than expected under genetic drift only. This led us to conclude that selection greatly influenced the evolution of the populations. Some of the loci clearly presented a higher differentiation than the others. This might indicate that they were genetically linked to other loci polymorphic in the populations and involved in adaptation. However, the effect of one selected gene on a marker, even located very close to the gene, could not be predicted with certainty. Hence, though the populations were predominantly selfing, it seems that initial linkage disequilibriums between markers and selected genes were not strong enough to control closely the evolution of allelic frequencies at the markers.     

Genetic variation associated with chronic water and nutrient stress in pinyon pine

We examined how genotypic variation at the glycerate dehydrogenase (GLY) locus in pinyon pine might be affected by environmental stress and herbivory. We compared GLY allelic and genotypic frequencies among mature and juvenile trees growing in stressful cinder soil and adjacent sandy-loam soil. While no association was found with herbivory, three lines of evidence support the hypothesis that GLY slow homozygotes (SS) are selected for under conditions of environmental stress. 1) We found no differences at the GLY locus between juvenile and mature trees growing in sandy-loam soil. 2) However, in the stressful cinder soil we found a lower frequency of SS homozygotes in juvenile trees than in mature trees, suggesting that selection has occurred in one generation. 3) Using biomass as a measure of fitness, SS homozygotes were superior to other GLY genotypes in cinder soil. Two lines of evidence were inconsistent with the hypothesis of selection for SS homozygotes in stressful environments. 1) SS homozygote frequency between habitats was not significantly different, suggesting that too few generations have passed for differentiation to occur, and/or insufficient selection pressure. 2) The low frequency of SS homozygote juvenile trees growing in cinder soil suggests that counterbalancing selection may prevent SS homozygotes from increasing in the population.     

Hordoindolines are associated with a major endosperm-texture QTL in barley (Hordeum vulgare).

Endosperm texture has a tremendous impact on the end-use quality of wheat (Triticum aestivum L.). Cultivars of barley (Hordeum vulgare L.), a close relative of wheat, also vary measurably in grain hardness. However, in contrast to wheat, little is known about the genetic control of barley grain hardness. Puroindolines are endosperm-specific proteins found in wheat and its relatives. In wheat, puroindoline sequence variation controls the majority of wheat grain texture variation. Hordoindolines, the puroindoline homologs of barley, have been identified and mapped. Recently, substantial allelic variation was found for hordoindolines among commercial barley cultivars. Our objective was to determine the influence of hordoindoline allelic variation upon grain hardness and dry matter digestibility in the 'Steptoe' x 'Morex' mapping population. This population is segregating for hordoindoline allele type, which was measured by a HinA/HinB/Gsp composite marker. One-hundred and fifty lines of the 'Steptoe' x 'Morex' population were grown in a replicated field trial. Grain hardness was estimated by near-infrared reflectance (NIR) and measured using the single kernel characterization system (SKCS). Variation attributable to the HinA/HinB/Gsp locus averaged 5.7 SKCS hardness units (SKCS U). QTL analysis revealed the presence of several areas of the genome associated with grain hardness. The largest QTL mapped to the HinA/HinB/Gsp region on the short arm of chomosome 7 (5H). This QTL explains 22% of the SKCS hardness difference observed in this study. The results indicate that the Hardness locus is present in barley and implicates the hordoindolines in endosperm texture control.     

Evidence for positive selection at the pantophysin (Pan I) locus in walleye pollock, Theragra chalcogramma

Nucleotide polymorphism at the pantophysin (Pan I) locus in walleye pollock, Theragra chalcogramma, was examined using DNA sequence data. Two distinct allelic lineages were detected in pollock, resulting from three amino acid replacement mutations in the first intravesicular domain of the protein. The common Pan I allelic group, comprising 94% of the samples, was less polymorphic (pi = 0.005) than the uncommon group (pi = 0.008), and nucleotide diversity in both was higher than for two allelic lineages in the related Atlantic cod, Gadus morhua. Phylogenetic analyses of Pan I sequences from these two species did not clearly resolve orthology among allelic groups, in part because of recombination that has occurred between the two pollock lineages. Conventional tests of neutrality comparing polymorphisms within and between homologous regions of the Pan I locus in walleye pollock and Atlantic cod did not detect the effects of selection. This result is likely attributed to low levels of synonymous divergence among allelic lineages and a lack of mutation-drift equilibrium inferred from nucleotide mismatch frequency distributions. However, the ratio of nonsynonymous to synonymous substitutions per site (dN/dS) exceeded unity in two intravesicular domains of the protein and the influence of positive selection at multiple codon sites was strongly inferred through the use of maximum-likelihood analyses. In addition, the frequency spectrum of linked neutral variation showed indirect effects of adaptive hitchhiking in pollock resulting from a selective sweep of the common allelic lineage. Recombination between the two allelic classes may have prevented complete loss of the older, more polymorphic lineage. The results suggest that recurrent sweeps driven by positive selection is the principle mode of evolution at the Pan I locus in gadid fishes.     

An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.)

Exploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar ‘Harrington’ as the recurrent parent, and a wild barley accession from the Fertile Crescent ‘Caesarea 26–24’, as the donor parent (Matus et al. Genome 46:1010–23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool. Twenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388–92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach. We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. This study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.     

Effects of genetic background on response to selection in experimental populations of Arabidopsis thaliana

The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population genetic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection in one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci.     

Sexual selection and the evolutionary dynamics of the major histocompatibility complex

The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host–pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host–parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern.     

Behavior and Genetic Variation in Natural Populations

An analysis of allelic variation at genetic loci controllingseveral esterases and hemoglobin, as demonstrated by electrophoresis,indicates that wild populations of the house mouse (Mus musculus)are characterized by fine-scale genetic subdivision, which,through the territorial behavior of family groups (tribes),is achieved even in the absence of physical or ecological barriersto migration. Heterogeneity in allele frequencies among samples from farmsin the same region and from barns on the same farm was demonstrated.Spatial variation in allele frequencies within single barns,involving a clustering of like genotypes, was shown by grid-trapping,thus providing direct evidence of tribal subdivision in continuouslydistributed populations. For two loci, Es-3 and Hbb, an excess of heterozygotes appearedin samples from small populations, while a deficit characterizedsamples from large populations. The evolutionary significance of subdivision and consequentdrift in house mouse populations cannot properly be evaluatedat this time. Although stochastic processes may play the dominantrole in determining, at a given locus, the genotypes of individualsand frequencies of alleles in small populations, geographicpatterns of variation, as studied in Texas, are characterizedby uniformity of allelic frequency in major physiographic orclimatic regions, as would be expected if selection is determiningthe frequencies.     

BIOCHEMICAL GENETICS OF FUNDULUS HETEROCLITUS (L.). VI. GEOGRAPHICAL VARIATION IN THE GENE FREQUENCIES OF 15 LOCI

Geographic variation in the gene frequencies corresponding to 15 polymorphic enzymes were studied in the common killifish Fundulus heteroclitus. Aat-A, Est-B, Fum-A, H6pdh-A, Mpi-A and Pgm-B showed clinal variation in allelic frequencies along the Atlantic coast of North America, while Aat-B, Ap-A, and the EST-C phenotypes did not. The clinal allelic variation of six previously examined loci (Ldh-B, Mdh-A, Gpi-B, Idh-A, Pgm-A, and 6-Pgdh-A) was extended to locations farther north. Gene diversity was lowest in the cold waters of northern latitudes and highest in the warmer waters of southern latitudes. The variety of clinal shapes and widths suggests that selection has affected the allelic distributions for at least some of these loci. This hypothesis is discussed with regard to the range contractions and extensions caused by the glacial advances and retreats during the Pleistocene.     

Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon (Salmo salar) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.