Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis

Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover

The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness ("flattest"). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers. We also identify an inverse relationship between CMR and the number of genes, confirming that, for a similar number of genes to that for the plant Arabidopsis thaliana (25,000), the CMR is close to its known wild-type mutation rate; mutation rates for additional organisms were also found to be within one order of magnitude of the CMR. This is the first time such a simulation model has been assigned input and produced output within range for a given biological organism. The decrease in CMR with population size previously observed is maintained; there is potential for the model to influence understanding of populations undergoing bottleneck, stress, and conservation strategy for populations near extinction.

The pattern and distribution of deleterious mutations in maize

Most nonsynonymous mutations are thought to be deleterious because of their effect on protein sequence and are expected to be removed or kept at low frequency by the action of natural selection. Nonetheless, the effect of positive selection on linked sites or drift in small or inbred populations may also impact the evolution of deleterious alleles. Despite their potential to affect complex trait phenotypes, deleterious alleles are difficult to study precisely because they are often at low frequency. Here, we made use of genome-wide genotyping data to characterize deleterious variants in a large panel of maize inbred lines. We show that, despite small effective population sizes and inbreeding, most putatively deleterious SNPs are indeed at low frequencies within individual genetic groups. We find that genes associated with a number of complex traits are enriched for deleterious variants. Together, these data are consistent with the dominance model of heterosis, in which complementation of numerous low-frequency, weak deleterious variants contribute to hybrid vigor.

Sublingual nucleotides prolong run time to exhaustion in young physically active men

Although dietary nucleotides have been determined to be required for normal immune function, there is limited direct interventional evidence confirming performance-enhancing effects of sublingual nucleotides in humans. A double-blind, placebo-controlled, randomized trial was conducted to evaluate the effect of sublingual nucleotides (50 mg/day) administered for 14 days in thirty young healthy physically active males, on endurance performance and immune responses. Fasting white blood cell count, natural killer cells (NKC) number, NKC cytotoxic activity, and serum immunoglobulin (IgA, IgM, IgG), and time to exhaustion, peak rate of perceived exertion, peak heart rate, and peak running speed during the exercise test were measured at baseline (day 0) and post-intervention (day 14). Time to exhaustion, as well as serum immunoglobulin A and NKC cytotoxic activity, were significantly higher at day 14 (p < 0.05) in participants supplemented with nucleotides compared with those who consumed placebo. No significant differences in other parameters were observed between groups at post-intervention. No volunteers withdrew before the end of the study nor reported any vexatious side effects of supplementation. The results of the present study suggest that sublingual nucleotides may provide pertinent benefit as both an ergogenic and immunostimulatory additive in active males.

Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives

Xa27 is one of the important R-genes, effective against bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Using natural population of Oryza, we analyzed the sequence variation in the functionally important domains of Xa27 across the Oryza species. DNA sequences of Xa27 alleles from 27 rice accessions revealed higher nucleotide diversity among the reported R-genes of rice. Sequence polymorphism analysis revealed synonymous and non-synonymous mutations in addition to a number of InDels in non-coding regions of the gene. High sequence variation was observed in the promoter region including the 5'UTR with 'π' value 0.00916 and 'θ w ' = 0.01785. Comparative analysis of the identified Xa27 alleles with that of IRBB27 and IR24 indicated the operation of both positive selection (Ka/Ks > 1) and neutral selection (Ka/Ks ≈ 0). The genetic distances of alleles of the gene from Oryza nivara were nearer to IRBB27 as compared to IR24. We also found the presence of conserved and null UPT (upregulated by transcriptional activator) box in the isolated alleles. Considerable amino acid polymorphism was localized in the trans-membrane domain for which the functional significance is yet to be elucidated. However, the absence of functional UPT box in all the alleles except IRBB27 suggests the maintenance of single resistant allele throughout the natural population.

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

Thanks to genome-scale diversity data, present-day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up-to-date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self-fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype-environment correlations and five designed to detect adaptive differentiation (based on F(ST) or similar measures). We show that genotype-environment correlation methods have substantially more power to detect selection than differentiation-based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype-environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations.

Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution

The common morning glory (Ipomoea purpurea) is an annual vine native to Central and Southern Mexico. The genetics of flower color polymorphisms and interactions with the biotic environment have been extensively studied in I. purpurea and in its sister species I. nil. In this study, we examine nucleotide sequence polymorphism in 11 loci, 9 of which are known to participate in a pathway that produces floral pigments. A sample of 30 I. purpurea accessions from the native range of Central and Southern Mexico comprise the data, along with one accession from each of the two sister species I. alba and I. nil. We observe moderate levels of nucleotide sequence polymorphism of ~1%. The ratio of recombination to mutation parameter estimates (ρ/θ) of ~2.5 appears consistent with a mixed-mating system. Ipomoea resequencing data from these genic regions are noteworthy in providing a good fit to the standard neutral model of molecular evolution. The derived silent site frequency spectrum is very close to that predicted by coalescent simulations of a drift-mutation process, and Tajima's D values are not significantly different from expectations under neutrality.

An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.)

With the aim to study variability in genes involved in ecological adaptations, we have analysed sequence polymorphisms of eight unique genes putatively involved in drought response by isolation and analysis of allelic sequences in eight inbred lines of sunflower of different origin and phenotypic characters and showing different drought response in terms of leaf relative water content (RWC). First, gene sequences were amplified by PCR on genomic DNA from a highly inbred line and their products were directly sequenced. In the absence of single nucleotide polymorphisms, the gene was considered as unique. Then, the same PCR reaction was performed on genomic DNAs of eight inbred lines to isolate allelic variants to be compared. The eight selected genes encode a dehydrin, a heat shock protein, a non-specific lipid transfer protein, a z-carotene desaturase, a drought-responsive-element-binding protein, a NAC-domain transcription regulator, an auxin-binding protein, and an ABA responsive-C5 protein. Nucleotide diversity per synonymous and non-synonymous sites was calculated for each gene sequence. The π (a)/π (s) ratio range was usually very low, indicating strong purifying selection, though with locus-to-locus differences. As far as non-coding regions, the intron showed a larger variability than the other regions only in the case of the dehydrin gene. In the other genes tested, in which one or more introns occur, variability in the introns was similar or even lower than in the other regions. On the contrary, 3'-UTRs were usually more variable than the coding regions. Linkage disequilibrium in the selected genes decayed on average within 1,000 bp, with large variation among genes. A pairwise comparison between genetic distances calculated on the eight genes and the difference in RWC showed a significant correlation in the first phases of drought stress. The results are discussed in relation to the function of analysed genes, i.e. involved in gene regulation and signal transduction, or encoding enzymes and defence proteins.

Strong population structure characterizes weediness gene evolution in the invasive grass species Brachypodium distachyon

Mediterranean annual grasses have invaded California and have replaced vast areas of native grassland. One of these invasive grasses is Brachypodium distachyon, a new model species for the grasses with extensive genomic resources and a nearly completed genome sequence. This study shows that the level of genetic variation in invaded California grasslands is lower compared to the native range in Eurasia. The invaded regions are characterized by highly differentiated populations of B. distachyon isolated by distance, most likely as a result of founder effects and a dearth of outcrossing events. EXP6 and EXP10 encoding alpha-expansins responsible for rapid growth, and AGL11 and AGL13 encoding proteins involved in vegetative phase regulation, appear to be under purifying selection with no evidence for local adaptation. Our data show that B. distachyon has diverged only recently from related Brachypodium species and that tetraploidization might have been as recent as a few thousand years ago. Observed low genetic variation in EXP10 and AGL13 appears to have been present in Eurasia before tetraploidization, potentially as a result of strong selective pressures on advantageous mutations, which are most likely responsible for its fast growth and rapid completion of its life cycle.

Nucleotide sequence variability of the Adh gene of the coastal plant Calystegia soldanella (Convolvulaceae) in Japan

Calystegia soldanella (Convolvulaceae) is a self-incompatible perennial herb distributed on sandy seashores throughout the temperate zone of the world. In Japan, the species occasionally grows on the sandy shores of Lake Biwa. To clarify the genetic differentiation among local populations, we investigated the nucleotide sequence variability of the Adh gene. In a 1625-bp sequence between exon 2 and the 3' noncoding region of the Adh gene, a total of 44 polymorphic sites were found among 91 individuals from 19 populations. The nucleotide diversity for the entire sample was 0.00212. Similar values were determined for geographical groups of populations. No genetic differentiation among the groups of populations was found. The complete lack of genetic differentiation between the sea coastal populations and the inland populations could not be attributed to gene flow. Although the inland populations are geographically isolated from the sea coastal populations, the time since separation might be insufficient to establish significant genetic differentiation.

Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent

Cereal agriculture originated with the domestication of barley and early forms of wheat in the Fertile Crescent. There has long been speculation that barley was domesticated more than once. We use differences in haplotype frequency among geographic regions at multiple loci to infer at least two domestications of barley; one within the Fertile Crescent and a second 1,500-3,000 km farther east. The Fertile Crescent domestication contributed the majority of diversity in European and American cultivars, whereas the second domestication contributed most of the diversity in barley from Central Asia to the Far East.

Background selection at the chitin synthase II (chs2) locus in Paracoccidioides brasiliensis species complex

In fungi, chitin synthases have been classified into five classes according to differences in regions of high sequence conservation. The current investigation was initiated to examine the causes for the polymorphism patterns found in a class II chitin synthase gene (chs2) of Paracoccidioides brasiliensis, in an attempt to determine the evolutionary forces affecting the chitin synthesis metabolic pathway. Neutrality tests were applied to the chs2 sequences exhibited by P. brasiliensis species complex. According to these tests and based on non-synonymous differences, P. brasiliensis data rejected the null hypothesis for a pure drift mutational process owing to a large excess of unique polymorphisms. In contrast, the synonymous and intron site differences did not reject the null hypothesis. This pattern appears consistent with weak selection against most amino acid changes, in which the effect of background selection was not detectable at synonymous nor at intron sites.

Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity

Recombination occurs through both homologous crossing over and homologous gene conversion during meiosis. The contribution of recombination relative to mutation is expected to be dramatically reduced in inbreeding organisms. We report coalescent-based estimates of the recombination parameter (rho) relative to estimates of the mutation parameter (theta) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of rho/theta are much greater than expected, with a mean rho/theta approximately 1.5, similar to estimates from outcrossing species. We also estimate rho with and without the contribution of gene conversion. Genotyping errors can mimic the effect of gene conversion, upwardly biasing estimates of the role of conversion. Thus we report a novel method for identifying genotyping errors in nucleotide sequence data sets. We show that there is evidence for gene conversion in many large nucleotide sequence data sets including our data that have been purged of all detectable sequencing errors and in data sets from Drosophila melanogaster, D. simulans, and Zea mays. In total, 13 of 27 loci show evidence of gene conversion. For these loci, gene conversion is estimated to contribute an average of twice as much as crossing over to total recombination.

Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon

DNA variation in the alcohol dehydrogenase (Adh2) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species. A dimorphic pattern was detected in the Adh2 region of O. rufipogon. The silent nucleotide diversity (pi) in the Adh2 region in O. rufipogon was 0.011, which was higher than that of the Adh1 region in O. rufipogon. Especially, a high nucleotide diversity was detected at synonymous sites of the catalytic domain 1. Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region, indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types. On the other hand, the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region. The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region. This result suggests purifying selection on the replacement sites of the Adh2 region, as detected for the Adh1 region. Significant linkage disequilibria (16.4% of the tests) were detected between the Adh1 and Adh2 regions. Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region, significant interlocus linkage disequilibria were detected. The close physical distance and/or epistasis between the two Adh regions could be invoked to explain these nonrandom associations.

Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor

Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species.

Molecular phylogeny and evolution of alcohol dehydrogenase (Adh) genes in legumes

BACKGROUND

Nuclear genes determine the vast range of phenotypes that are responsible for the adaptive abilities of organisms in nature. Nevertheless, the evolutionary processes that generate the structures and functions of nuclear genes are only now be coming understood. The aim of our study is to isolate the alcohol dehydrogenase (Adh) genes in two distantly related legumes, and use these sequences to examine the molecular evolutionary history of this nuclear gene.

RESULTS

We isolated the expressed Adh genes from two species of legumes, Sophora flavescens Ait. and Wisteria floribunda DC., by a RT-PCR based approach and found a new Adh locus in addition to homologues of the Adh genes found previously in legumes. To examine the evolution of these genes, we compared the species and gene trees and found gene duplication of the Adh loci in the legumes occurred as an ancient event.

CONCLUSION

This is the first report revealing that some legume species have at least two Adh gene loci belonging to separate clades. Phylogenetic analyses suggest that these genes resulted from relatively ancient duplication events.

Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization

High levels of inbreeding cause populations to become composed of homozygous, inbred lines. High levels of homozygosity limit the effectiveness of recombination, and therefore, retard the rate of decay of linkage (gametic phase) disequilibrium (LD) among mutations. Inbreeding and recombination interact to shape the expected pattern of LD. The actual extent of nucleotide sequence level LD within inbreeding species has only been studied in Arabidopsis, a weedy species whose global range has recently expanded. In the present study, we examine the levels of LD within and between 18 nuclear genes in 25 accessions from across the geographic range of wild barley, a species with a selfing rate of approximately 98%. In addition to examination of intralocus LD, we employ a resampling method to determine whether interlocus LD exceeds expectations. We demonstrate that, for the majority of wild barley loci, intralocus LD decays rapidly, i.e., at a rate similar to that observed in the outcrossing species, Zea mays (maize). Excess interlocus LD is observed at 15% of two-locus combinations; almost all interlocus LD involves loci with significant geographic structuring of mutational variation.

Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives

Gene flow is a potential concern associated with the use of transgenic crops because it could affect genetic diversity of related landraces and wild relatives. This concern has taken on added importance with the looming introduction of transgenic crops in centers of crop domestication (Mexico, China) and those producing pharmaceutical compounds. For gene flow to take place among cultivars and their wild relatives, several steps have to be fulfilled, including the presence of cultivars or wild relatives within pollen or seed dispersal range, the ability to produce viable and fertile hybrids, at least partial overlap in flowering time, actual gene flow by pollen or seed, and the establishment of crop genes in the domesticated or wild recipient populations. In contrast with domestication genes, which often make crops less adapted to natural ecosystems, transgenes frequently represent gains of function, which might release wild relatives from constraints that limit their fitness. In most sexually reproducing organisms, the chromosomal region affected by selection of a single gene amounts to a small percentage of the total genome size. Because of gene flow, the level of genetic diversity present in the domesticated gene pool becomes a crucial factor affecting the genetic diversity of the wild gene pool. For some crops, such as cotton and maize, the introduction of transgenic technologies has led to a consolidation of the seed industry and a reduction in the diversity of the elite crop gene pool. Thus, diversity in improved varieties grown by farmers needs to be monitored. Several areas deserve further study, such as the actual magnitude of gene flow and its determinants in different agroecosystems, the long-term effects of gene flow on genetic diversity both across gene pools and within genomes, the expression of transgenes in new genetic backgrounds, and the effects of socio-economic factors on genetic diversity.

DNA diversity in Hawaiian endemic plant Schiedea globosa

This is the first report of a study devoted to the population genetics of speciation in the endemic Hawaiian plant genus Schiedea (Caryophyllaceae). Here, we report the estimates of DNA sequence diversity and divergence in a newly isolated nuclear gene from Maui and Oahu Schiedea globosa populations. Overall, the species-wide average heterozygosity per silent site is pi = 0.3%. The silent DNA diversity on the older island of Oahu (pi = 0.24%) is almost twice as high as on the younger Maui (pi = 0.14%). Consistent with this, the haplotype phylogeny suggests a more recent origin of the Maui populations. There is no significant isolation between the two Maui populations (F(st)=0.027), while isolation between the two islands is high (F(st)=0.57, P<0.0001). Pairwise mismatch distributions suggest population growth approximately 660 and 310 thousand generations ago for the Oahu and the Maui populations, respectively, which may be the minimal age for these populations. This is consistent with a fairly neutral frequency spectrum (Tajima's D is 0.34 and -0.94 for the Oahu and the Maui populations, respectively), suggesting that both populations are sufficiently old to have recovered from any initial founder effects. Relatively high nuclear DNA diversity in the S. globosa populations illustrates the usefulness of a DNA sequence-based approach to the population genetics of island plant populations.

Genetic diversity associated with variation in silage corn digestibility for three O-methyltransferase genes involved in lignin biosynthesis

Polymorphisms within three candidate genes for lignin biosynthesis were investigated to identify alleles useful for the improvement of maize digestibility. The allelic diversity of two caffeoyl-CoA 3-O-methyltransferase genes, CCoAOMT2 and CCoAOMT1, as well as that of the aldehyde O-methyltransferase gene, AldOMT, was evaluated for 34 maize lines chosen for their varying degrees of cell wall digestibility. Frequency of nucleotide changes averaged one SNP every 35 bp. Ninety-one indels were identified in non-coding regions and only four in coding regions. Numerous distinct and highly diverse haplotypes were identified at each locus. Numerous sites were in linkage disequilibrium that declined rapidly within a few hundred bases. For F4, an early flint French line with high cell wall digestibility, the CCoAOMT2 first exon presented many non-synonymous polymorphisms. Notably we found an 18-bp indel, which resembled a microsatellite and was associated with cell wall digestibility variation. Additionally, the CCoAOMT2 gene co-localized with a QTL for cell wall digestibility and lignin content. Together, these results suggest that genetic diversity investigated on a broader genetic basis could contribute to the identification of favourable alleles to be used in the molecular breeding of elite maize germplasm.

Nucleotide polymorphism in the Adh1 locus region of the wild rice Oryza rufipogon

Nucleotide variation in the alcohol dehydrogenase (Adh1) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species. The estimated nucleotide diversity in the Adh1 locus region of O. rufipogon was 0.002, which was one of the lowest values detected in nuclear loci of plant species investigated so far. Tests of neutrality detected significantly negative deviation from the neutral mutation model for the coding region, especially for replacement sites. When each of the ADH1 domains was considered, significance was detected only for the catalytic domain 1. These results suggest purifying selection in the Adh1 coding region. In the phylogenetic tree of Oryza species based on Adh1 variation, cultivated rice O. sativa subspp. japonica and indica were included in the cluster of O. rufipogon. The genetic distance of the Adh1 region between O. rufipogon and O. sativa was as low as the nucleotide diversity of O. rufipogon. These results imply that O. rufipogon and O. sativa cannot be classified based on the nucleotide variation of Adh1. No replacement divergence between O. rufipogon and the other three A-genome species (O. glumaepatula, O. barthii and O. meridionalis) were detected, indicating that ADH1 is conserved in the A-genome species. On the other hand, between O. rufipogon and the E-genome species O. australiensis, replacement changes were detected only in the catalytic domain 1. The difference in replacement substitutions between the A- and E-genome species may be related to adaptive changes in the ADH1 domains, reflecting environmental differences where the species encounter anaerobic stress.

Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley

The Isa gene from barley--an intronless gene expressed in maternal tissues of the seed--has a likely role in defence against pathogens. The protein product--bi-functional alpha-amylase/subtilisin inhibitor--inhibits the seed's own amylase in addition to the bacterial protease subtilisin and fungal xylanase. Sixteen barley genotypes were targeted to amplify and sequence the Isa gene region to detect sequence polymorphisms, since little is known about genetic diversity at this locus. A total of 80 single nucleotide polymorphisms (SNPs) and 23 indels were detected in 2,164 bp of sequence containing the Isa transcript, promoter and 3' non-transcribed region (overall one SNP per 27 bp and one indel per 94 bp), with eight sequence-based haplotypes distinguishable amongst the 16 varieties. Sequencing a polymorphic region in the promoter in an additional 27 barley genotypes increased the number of sequence-based haplotypes discovered to 11. However there is low haplotype diversity amongst the cultivated barley varieties sampled, with most varieties represented by a single haplotype. There was minor amino acid diversity in the protein, with five out of ten SNP sites in the coding region predicted to produce amino acid substitutions. SNP analysis indicated a history of recombination events--a minimum of seven based on the initial eight haplotypes from the whole sequenced region. Most of the recombination events occurred in the highly polymorphic regions, the 3' non-transcribed region and sequences flanking a microsatellite in the Isa promoter.

Purifying selection and demographic expansion affect sequence diversity of the ligand-binding domain of a glutamate-gated chloride channel gene of Haemonchus placei

Ninety-five genomic sequences of the ligand-binding domain of glutamate-gated chloride channel genes of three populations of the parasitic nematode H. placei were evaluated for patterns of diversity, demography, and selection. These genes code for subunits of ion channels, which are involved in the mode of action of the most commonly used antiparasitic drugs, the macrocyclic lactones. An extremely high frequency of unique segregating sites in exons and introns was observed, with significantly negative neutrality tests in each population for noncoding, synonymous, and nonsynonymous sites. Several tests indicated that support for balancing selection, positive selection, and hitchhiking was lacking. McDonald-Kreitman tests using H. contortus or C. elegans as an outgroup revealed an extreme excess of replacement polymorphism, consistent with weak purifying selection. Although these tests agree that negative selection may explain the excess of replacement changes, an alternative interpretation is required for the significantly negative Fu and Li's D statistics based on silent and noncoding sites. These include homogeneous forces such as background selection and demographic expansion. The lack of population subdivision and the negative values of Tajima's D for this outbreeding parasitic nematode render background selection less likely than demographic expansion. Comparison of D statistics based on different site types using neutral coalescent simulations supported this interpretation. Although this statistic was more negative for nonsynonymous sites than for synonymous sites, most comparisons of the D statistic were not significantly different between mutation classes. A few significant site comparisons were also consistent with demographic expansion, because the observed test statistic ( D(neutral) - D(selected)) were low relative to the neutral expectations. Finally, previous mitochondrial studies also identified a demographic expansion of this parasitic nematode species, which lends further support to a scenario involving both demographic and purifying forces in the ligand-binding domain of H. placei.

Range expansion leading to departures from neutrality in the nonsymbiotic hemoglobin gene and the cpDNA trnL–trnF intergenic spacer in Trema dielsiana (Ulmaceae)

The population genetics and phylogeography of Trema dielsiana in Taiwan were inferred from genetic diversity at the nonsymbiotic hemoglobin gene and the trnL-trnF intergenic spacer of cpDNA. Reduced genetic variation was detected in these two unlinked genes. The gene genealogy of the hemoglobin locus recovered two lineages corresponding to the western and eastern regions of Taiwan. This pattern is compatible with a past fragmentation event revealed by phylogeographical analyses. To distinguish between selective departures from neutrality (i.e., heterogeneous processes) and demographic (homogeneous) processes, Hahn et al.'s heterogeneity test was conducted on the hemoglobin gene. Lack of significant differences in Tajima's D statistics between synonymous and nonsynonymous mutations indicates that homogeneous processes may have played a key role in governing the evolution of the functional locus. Significantly negative Tajima's D estimates for both overall exons and introns of the hemoglobin gene as well as for the cpDNA intergenic spacer support a phylogeographical hypothesis of range expansion after genetic bottlenecks. High level of genetic variation and a negative Tajima's D statistic suggests a possible northern refugium that may have harbored populations during the glacial maximum.

Transgene introgression from genetically modified crops to their wild relatives

Transgenes engineered into annual crops could be unintentionally introduced into the genomes of their free-living wild relatives. The fear is that these transgenes might persist in the environment and have negative ecological consequences. Are some crops or transgenic traits of more concern than others? Are there natural genetic barriers to minimize gene escape? Can the genetic transformation process be exploited to produce new barriers to gene flow? Questions abound, but luckily so do answers.

Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration

Mutations arise in a single individual and at a single point in time and space. The geographic distribution of mutations reflects both historical population size and frequency of migration. We employ coalescence-based methods to coestimate effective population size, frequency of migration, and level of recombination compatible with observed genealogical relationships in sequence data from nine nuclear genes in wild barley (Hordeum vulgare ssp. spontaneum), a highly self-fertilizing grass species. In self-fertilizing plants, gamete dispersal is severely limited; dissemination occurs primarily through seed dispersal. Also, heterozygosity is greatly reduced, which renders recombination less effective at randomizing genetic variation and causes larger portions of the genome to trace a similar history. Despite these predicted effects of this mating system, the majority of loci show evidence of recombination. Levels of nucleotide variation and the patterns of geographic distribution of mutations in wild barley are highly heterogeneous across loci. Two of the nine sampled loci maintain highly diverged, geographic region-specific suites of mutations. Two additional loci include region-specific haplotypes with a much shallower coalescence. Despite inbreeding, sessile growth habit, and the observation of geographic structure at almost half of sampled loci, parametric estimates of migration suggest that seed dispersal is sufficient for migration across the approximately 3,500-km range of the species. Recurrent migration is also evident based on the geographic distribution of mutational variation at some loci. At one locus a single haplotype has spread rapidly enough to occur, unmodified by mutation, across the range of the species.

Effects of inbreeding on the genetic diversity of populations

The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions.

Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sun-rock (11 genotypes), (ii) sun-soil (18 genotypes), (iii) shade-soil (11 genotypes), and (iv) shade-rock (14 genotypes). Fifty-four genotypes were tested for ecological-genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun-rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, G(ST) was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun-rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).

The influence of linkage and inbreeding on patterns of nucleotide sequence diversity at duplicate alcohol dehydrogenase loci in wild barley (Hordeum vulgare ssp. spontaneum)

Patterns of nucleotide sequence diversity are analyzed for three duplicate alcohol dehydrogenase loci (adh1-adh3) within a species-wide sample of 25 accessions of wild barley (Hordeum vulgare ssp. spontaneum). The adh1 and adh2 loci are tightly linked (recombination fraction <0.01) while the adh3 locus is inherited independently. Wild barley is predominantly self-fertilizing (approximately 98%), and as a consequence, effective recombination is restricted by the extreme reduction in heterozygosity. Large reductions in effective recombination, in turn, widen the conditions for linkage to influence nucleotide sequence diversity through the action of selective sweeps or background selection. These considerations would appear to predict (1) homogeneity in patterns of nucleotide sequence diversity, especially between closely linked loci, and (2) extensive linkage disequilibrium relative to random-mating species. In contrast to these expectations, the wild barley data reveal heterogeneity in patterns of nucleotide sequence diversity and levels of linkage disequilibrium that are indistinguishable from those observed at adh1 in maize, an outbreeding grass species.

Levels of DNA polymorphism vary with mating system in the nematode genus caenorhabditis

Self-fertilizing species often harbor less genetic variation than cross-fertilizing species, and at least four different models have been proposed to explain this trend. To investigate further the relationship between mating system and genetic variation, levels of DNA sequence polymorphism were compared among three closely related species in the genus Caenorhabditis: two self-fertilizing species, Caenorhabditis elegans and C. briggsae, and one cross-fertilizing species, C. remanei. As expected, estimates of silent site nucleotide diversity were lower in the two self-fertilizing species. For the mitochondrial genome, diversity in the selfing species averaged 42% of diversity in C. remanei. Interestingly, the reduction in genetic variation was much greater for the nuclear than for the mitochondrial genome. For two nuclear genes, diversity in the selfing species averaged 6 and 13% of diversity in C. remanei. We argue that either population bottlenecks or the repeated action of natural selection, coupled with high levels of selfing, are likely to explain the observed reductions in species-wide genetic diversity.

Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium)

Levels and patterns of nucleotide diversity vary widely among lineages. Because allopolyploid species contain duplicated (homoeologous) genes, studies of nucleotide diversity at homoeologous loci may facilitate insight into the evolutionary dynamics of duplicated loci. In this study, we describe patterns of sequence diversity from an alcohol dehydrogenase homoeologous locus pair (AdhC) in allotetraploid cotton (Gossypium, Malvaceae). These data are compared with equivalent information from another homoeologous alcohol dehydrogenase gene pair (AdhA, Small, Ryburn, and Wendel 1999. Mol. Biol. Evol. 16:491-501) which has an overall slower evolutionary rate than AdhC. As expected from the predicted correlation between nucleotide diversity and evolutionary rate, nucleotide diversity was higher for AdhC than for AdhA. In addition, nucleotide diversity is higher in the D-subgenome of allotetraploid cotton for AdhC, confirming earlier observations for AdhA. These observations indicate that for these two pairs of Adh loci, the null hypothesis of equivalent evolutionary dynamics for duplicated genes in allotetraploid cotton is rejected.

Plant molecular diversity and applications to genomics

Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.

Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses

We have applied a two-gene system based on the sequences of nuclear genes encoding multi-domain plastid acetyl-CoA carboxylase (ACCase) and plastid 3-phosphoglycerate kinase (PGK) to study grass evolution. Our analysis revealed that these genes are single-copy in most of the grass species studied, allowing the establishment of orthologous relationships between them. These relationships are consistent with the known facts of their evolution: the eukaryotic origin of the plastid ACCase, created by duplication of a gene encoding the cytosolic multi-domain ACCase gene early in grass evolution, and the prokaryotic (endosymbiont) origin of the plastid PGK. The major phylogenetic relationships among grasses deduced from the nucleotide sequence comparisons of ACCase and PGK genes are consistent with each other and with the milestones of grass evolution revealed by other methods. Nucleotide substitution rates were calculated based on multiple pairwise sequence comparisons. On a relative basis, with the divergence of the Pooideae and Panicoideae subfamilies set at 60 million years ago (MYA), events leading to the Triticum/Aegilops complex occurred at the following intervals: divergence of Lolium (Lolium rigidum) at 35 MYA, divergence of Hordeum (Hordeum vulgare) at 11 MYA and divergence of Secale (Secale cereale) at 7 MYA. On the same scale, gene duplication leading to the multi-domain plastid ACCase in grasses occurred at 129 MYA, divergence of grass and dicot plastid PGK genes at 137 MYA, and divergence of grass and dicot cytosolic PGK genes at 155 MYA. The ACCase and PGK genes provide a well-understood two-locus system to study grass phylogeny, evolution and systematics.

Breeding systems and genome evolution

The profound effects of inbreeding and other non-recombining breeding systems on genetic variability and molecular evolution are now beginning to be understood. Theoretical models predict how such populations are expected to differ from outcrossed populations, and DNA sequence data are being collected and used to test the predictions.

Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea)

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141-147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum)

Patterns of nucleotide sequence diversity in the predominantly self-fertilizing species Hordeum vulgare subspecies spontaneum (wild barley) are compared between the putative alcohol dehydrogenase 3 locus (denoted "adh3") and alcohol dehydrogenase 1 (adh1), two related but unlinked loci. The data consist of a sequence sample of 1,873 bp of "adh3" drawn from 25 accessions that span the species range. There were 104 polymorphic sites in the sequenced region of "adh3." The data reveal a strong geographic pattern of diversity at "adh3" despite geographic uniformity at adh1. Moreover, levels of nucleotide sequence diversity differ by nearly an order of magnitude between the two loci. Genealogical analysis resolved two distinct clusters of "adh3" alleles (dimorphic sequence types) that coalesce roughly 3 million years ago. One type consists of accessions from the Middle East, and the other consists of accessions predominantly from the Near East. The two "adh3" sequence types are characterized by a high level of differentiation between clusters ( approximately 2.2%), which induces an overall excess of intermediate frequency variants in the pooled sample. Finally, there is evidence of intralocus recombination in the "adh3" data, despite the high level of self-fertilization characteristic of wild barley.

Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum)

Patterns of nucleotide sequence diversity in the predominantly self-fertilizing species Hordeum vulgare subspecies spontaneum (wild barley) are compared between the putative alcohol dehydrogenase 3 locus (denoted "adh3") and alcohol dehydrogenase 1 (adh1), two related but unlinked loci. The data consist of a sequence sample of 1,873 bp of "adh3" drawn from 25 accessions that span the species range. There were 104 polymorphic sites in the sequenced region of "adh3." The data reveal a strong geographic pattern of diversity at "adh3" despite geographic uniformity at adh1. Moreover, levels of nucleotide sequence diversity differ by nearly an order of magnitude between the two loci. Genealogical analysis resolved two distinct clusters of "adh3" alleles (dimorphic sequence types) that coalesce roughly 3 million years ago. One type consists of accessions from the Middle East, and the other consists of accessions predominantly from the Near East. The two "adh3" sequence types are characterized by a high level of differentiation between clusters ( approximately 2.2%), which induces an overall excess of intermediate frequency variants in the pooled sample. Finally, there is evidence of intralocus recombination in the "adh3" data, despite the high level of self-fertilization characteristic of wild barley.

Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium)

Nuclear-encoded genes exist in families of various sizes. To further our understanding of the evolutionary dynamics of nuclear gene families we present a characterization of the structure and evolution of the alcohol dehydrogenase (Adh) gene family in diploid and tetraploid members of the cotton genus (Gossypium, Malvaceae). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members, and Southern hybridization analyses were used to document variation in gene copy number. Adh gene copy number varies among Gossypium species, with diploids containing at least seven Adh loci in two primary gene lineages. Allotetraploid Gossypium species are inferred to contain at least 14 loci. Intron lengths vary markedly between loci, and one locus has lost two introns usually found in other plant Adh genes. Multiple examples of apparent gene duplication events were observed and at least one case of pseudogenization and one case of gene elimination were also found. Thus, Adh gene family structure is dynamic within this single plant genus. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution.

Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana

An approximately 1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity theta(TOTAL) = 0.004, theta(SIL) = 0. 005 was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana

Nucleotide variation at the alcohol dehydrogenase locus (Adh) was studied in the outcrossing Arabidopsis lyrata, a close relative of the selfing Arabidopsis thaliana. Overall, estimated nucleotide diversity in the North American ssp. lyrata and two European ssp. petraea populations was 0.0038, lower than the corresponding specieswide estimate for A. thaliana at the same set of nucleotide sites. The distribution of segregating sites across the gene differed between the two species. Estimated sequence diversity within an A. lyrata population with a large sample size (0.0023) was much higher than has previously been observed for A. thaliana. This North American population has an excess of sites at intermediate frequencies compared with neutral expectation (Tajima's D = 2.3, P < 0.005), suggestive of linked balancing selection or a recent population bottleneck. In contrast, an excess of rare polymorphisms has been found in A. thaliana. Polymorphism within A. lyrata and divergence from A. thaliana appear to be correlated across the Adh gene sequence. The geographic distribution of polymorphism was quite different from that of A. thaliana, for which earlier studies of several genes found low within-population nucleotide site polymorphism and no overall continental differentiation of variation despite large differences in site frequencies between local populations. Differences between the outcrossing A. lyrata and the selfing A. thaliana reflect the impact of differences in mating system and the influence of bottlenecks in A. thaliana during rapid colonization on DNA sequence polymorphism. The influence of additional variability-reducing mechanisms, such as background selection or hitchhiking, may not be discernible.

Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization

It is shown that partial self-fertilization can be introduced into neutral population genetic models with recombination as a simple change in the scaling of the parameters. This means that statistical and computational methods that have been developed under the assumption of random mating can be used without modification, provided the appropriate parameter changes are made. An important prediction is that all forms of linkage disequilibrium will be more extensive in selfing species. The implications of this are discussed.

Evolution of genes and taxa: a primer

The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction--parsimony, distance and maximum likelihood--differ in their use of these models. All three face similar problems in finding optimal--and reliable--solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.

DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus

A study of DNA polymorphism and divergence was conducted for the cytosolic phosphoglucose isomerase (PGI:E.C.5.3.1.9) gene of five species of the mustard genus Leavenworthia: Leavenworthia stylosa, L. alabamica, L. crassa, L. uniflora, and L. torulosa. Sequences of an internal 2.3-kb PgiC gene region spanning exons 6-16 were obtained from 14 L. stylosa plants from two natural populations and from one to several plants for each of the other species. The level of nucleotide polymorphism in L. stylosa PgiC gene was quite high (pi = 0.051, theta = 0.052). Although recombination is estimated to be high in this locus, extensive haplotype structure was observed for the entire 2.3-kb region. The L. stylosa sequences fall into at least two groups, distinguished by the presence of several indels and nucleotide substitutions, and one of the three charge change nucleotide replacements within the region sequenced correlates with the haplotypes. The differences between the haplotypes are older than between the species, and the haplotypes are still segregating in at least two of five species studied. There is no evidence of recent or ancient population subdivision that could maintain distinct haplotypes. The age of the haplotypes and the results of Kelly's Z(nS) and Wall's B and Q tests with recombination suggest that the haplotypes are maintained due to balancing selection at or near this locus.

Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana

Molecular variation in genes that regulate development provides insights into the evolutionary processes that shape the diversification of morphogenetic pathways. Intraspecific sequence variation at the APETALA3 and PISTILLATA floral homeotic genes of Arabidopsis thaliana was analyzed to infer the extent and nature of diversity at these regulatory loci. Comparison of AP3 and PI diversity with three previously studied genes revealed several features in the patterning of nucleotide polymorphisms common between Arabidopsis nuclear loci, including an excess of low-frequency nucleotide polymorphisms and significantly elevated levels of intraspecific replacement variation. This pattern suggests that A. thaliana has undergone recent, rapid population expansion and now exists in small, inbred subpopulations. The elevated intraspecific replacement levels may thus represent slightly deleterious polymorphisms that differentiate distinct ecotypes. The distribution of replacement and synonymous changes in AP3 and PI core and noncore functional domains also indicates differences in the patterns of molecular evolution between these interacting floral regulatory genes.

The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia

To test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.

Sequence variation: looking for effects of genetic linkage

Selection at linked loci probably reduces the variability of genes in regions of infrequent recombination. Detailed sequence information is needed to test possible causes of this effect; such information is now becoming available, but its interpretation can be difficult.