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

Cryptic intraspecific variation in sex determination in Caenorhabditis elegans revealed by mutations

Sex determination mechanisms (SDMs) show striking diversity and appear to evolve rapidly. Although interspecific comparisons and studies of ongoing major transitions in sex determination (such as the establishment of new sex chromosomes) have shed light on how SDMs evolve, comparatively little attention has been paid to intraspecific variation with less drastic effects. In this study, I used mutant strains carrying a temperature-sensitive sex determination mutation, along with a second null mutation, in different wild genetic backgrounds to uncover hidden variation in the SDM of the model nematode Caenorhabditis elegans. I then used quantitative trait locus (QTL) mapping to begin to investigate its genetic basis. I identified several QTLs, and although this variation apparently involved genotype-by-temperature interactions, QTL effects were generally consistent across temperatures. These QTLs collectively and individually explained a relatively large fraction of the variance in tail morphology (a sexually dimorphic trait), and two QTLs contained no genes known to be involved in somatic sex determination. These results show the existence of within-species variation in sex determination in this species, and underscore the potential for microevolutionary change in this important developmental pathway.

A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

BACKGROUND

The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

RESULTS

We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3.

CONCLUSIONS

We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.

Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the nematode Caenorhabditis briggsae

New genomic resources and genetic tools of the past few years have advanced the nematode genus Caenorhabditis as a model for comparative biology. However, understanding of natural genetic variation at molecular and phenotypic levels remains rudimentary for most species in this genus, and for C. briggsae in particular. Here we characterize phenotypic variation in C. briggsae's sensitivity to the potentially important and variable environmental toxin, ethanol, for globally diverse strains. We also quantify nucleotide variation in a new sample of 32 strains from four continents, including small islands, and for the closest-known relative of this species (C. sp. 9). We demonstrate that C. briggsae exhibits little heritable variation for the effects of ethanol on the norm of reaction for survival and reproduction. Moreover, C. briggsae does not differ significantly from C. elegans in our assays of its response to this substance that both species likely encounter regularly in habitats of rotting fruit and vegetation. However, we uncover drastically more molecular genetic variation than was known previously for this species, despite most strains, including all island strains, conforming to the broad biogeographic patterns described previously. Using patterns of sequence divergence between populations and between species, we estimate that the self-fertilizing mode of reproduction by hermaphrodites in C. briggsae likely evolved sometime between 0.9 and 10 million generations ago. These insights into C. briggsae's natural history and natural genetic variation greatly expand the potential of this organism as an emerging model for studies in molecular and quantitative genetics, the evolution of development, and ecological genetics.

Evolution of Caenorhabditis mitochondrial genome pseudogenes and Caenorhabditis briggsae natural isolates

Although most metazoan mitochondrial genomes are highly streamlined and encode little noncoding DNA outside of the "AT" region, the accumulation of mitochondrial pseudogenes and other types of noncoding DNA has been observed in a growing number of animal groups. The nematode species Caenorhabditis briggsae harbors two mitochondrial DNA (mtDNA) pseudogenes, named Psinad5-1 and Psinad5-2, presumably derived from the nad5 protein-coding gene. Here, we provide an in-depth analysis of mtDNA pseudogene evolution in C. briggsae natural isolates and related Caenorhabditis species. Mapping the observed presence and absence of the pseudogenes onto phylogenies suggests that Psinad5-1 originated in the ancestor to C. briggsae and its recently discovered outcrossing relative species Caenorhabditis sp. 5 and Caenorhabditis sp. 9. However, Psinad5-1 was not detected in Caenorhabditis sp. 9 natural isolates, suggesting a lineage-specific loss of this pseudogene in this species. Our results corroborated the previous finding that Psinad5-2 originated within C. briggsae. The observed pattern of mitochondrial pseudogene gain and loss in Caenorhabditis was inconsistent with predictions of the tandem duplication-random loss model of mitochondrial genome evolution and suggests that intralineage recombination-like mechanisms might play a major role in Caenorhabditis mtDNA evolution. Natural variation was analyzed at the pseudogenes and flanking mtDNA sequences in 141 geographically diverse C. briggsae natural isolates. Although phylogenetic analysis placed the majority of isolates into the three previously established major intraspecific clades of C. briggsae, two new and unexpected haplotypes fell outside of these conventional groupings. Psinad5-2 copy number variation was observed among C. briggsae isolates collected from the same geographic site. Patterns of nucleotide diversity were analyzed in Psinad5-1 and Psinad5-2, and confidence intervals were found to overlap values from synonymous sites in protein-coding genes, consistent with neutral expectations. Our findings provide new insights into the mode and tempo of mitochondrial genome and pseudogene evolution both within and between Caenorhabditis nematode species.

Mating-system variation, demographic history and patterns of nucleotide diversity in the Tristylous plant Eichhornia paniculata

Inbreeding in highly selfing populations reduces effective size and, combined with demographic conditions associated with selfing, this can erode genetic diversity and increase population differentiation. Here we investigate the role that variation in mating patterns and demographic history play in shaping the distribution of nucleotide variation within and among populations of the annual neotropical colonizing plant Eichhornia paniculata, a species with wide variation in selfing rates. We sequenced 10 EST-derived nuclear loci in 225 individuals from 25 populations sampled from much of the geographic range and used coalescent simulations to investigate demographic history. Highly selfing populations exhibited moderate reductions in diversity but there was no significant difference in variation between outcrossing and mixed mating populations. Population size interacted strongly with mating system and explained more of the variation in diversity within populations. Bayesian structure analysis revealed strong regional clustering and selfing populations were highly differentiated on the basis of an analysis of F(st). There was no evidence for a significant loss of within-locus linkage disequilibrium within populations, but regional samples revealed greater breakdown in Brazil than in selfing populations from the Caribbean. Coalescent simulations indicate a moderate bottleneck associated with colonization of the Caribbean from Brazil approximately 125,000 years before the present. Our results suggest that the recent multiple origins of selfing in E. paniculata from diverse outcrossing populations result in higher diversity than expected under long-term equilibrium.

Rapid sequence evolution of transcription factors controlling neuron differentiation in Caenorhabditis

Whether phenotypic evolution proceeds predominantly through changes in regulatory sequences is a controversial issue in evolutionary genetics. Ample evidence indicates that the evolution of gene regulatory networks via changes in cis-regulatory sequences is an important determinant of phenotypic diversity. However, recent experimental work suggests that the role of transcription factor (TF) divergence in developmental evolution may be underestimated. In order to help understand what levels of constraints are acting on the coding sequence of developmental regulatory genes, evolutionary rates were investigated among 48 TFs required for neuronal development in Caenorhabditis elegans. Allelic variation was then sampled for 28 of these genes within a population of the related species Caenorhabditis remanei. Neuronal TFs are more divergent, both within and between species, than structural genes. TFs affecting different neuronal classes are under different levels of selective constraints. The regulatory genes controlling the differentiation of chemosensory neurons evolve particularly fast and exhibit higher levels of within- and between-species nucleotide variation than TFs required for the development of several neuronal classes and TFs required for motorneuron differentiation. The TFs affecting chemosensory neuron development are also more divergent than chemosensory genes expressed in the neurons they differentiate. These results illustrate that TFs are not as highly constrained as commonly thought and suggest that the role of divergence in developmental regulatory genes during the evolution of gene regulatory networks requires further attention.

Evolution of the Caenorhabditis elegans genome

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Recombinational landscape and population genomics of Caenorhabditis elegans

Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolation from the remainder of the global population, whose members exhibit ample evidence of intercrossing and recombining. The population effective recombination rate, estimated from the pattern of linkage disequilibrium, is correlated with the estimated meiotic recombination rate, but its magnitude implies that the effective rate of outcrossing is extremely low, corroborating reports of selection against recombinant genotypes. Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains.

C. elegans is a model system for diverse fields of biology, but its ability to serve as a model for quantitative trait gene mapping depends on its recombination rate in the laboratory and in nature. The latter is a function of how worms mate and migrate in the wild. We examined the patterns of recombination in a population that we put through thousands of meioses in the laboratory and in a collection of strains isolated from nature. The data suggest that meiotic recombination rate is highly regular in worms, with discrete domains whose boundaries we identify. The pattern in natural strains suggests that population structure, population size, outcrossing rate, and selection combine to suppress the overall effects of recombination. Moreover, some “wild” strains appear to be laboratory contaminants. Nevertheless, the history of recombination in wild worms is sufficient to permit correlations between genotype and phenotype to pinpoint the loci responsible for phenotypic variation.

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing of the genomes of C. elegans and a second hermaphrodite, C. briggsae, was facilitated in part by the low amount of natural heterozygosity, which typifies selfing species. Ongoing genome projects for gonochoristic Caenorhabditis species seek to approximate this condition by intense inbreeding prior to sequencing. Here we show that despite this inbreeding, the heterozygous fraction of the whole genome shotgun assemblies of three gonochoristic Caenorhabditis species, C. brenneri, C. remanei, and C. japonica, is considerable. We first demonstrate experimentally that independently assembled sequence variants in C. remanei and C. brenneri are allelic. We then present gene-based approaches for recognizing heterozygous regions of WGS assemblies. We also develop a simple method for quantifying heterozygosity that can be applied to assemblies lacking gene annotations. Consistently we find that approximately 10% and 30% of the C. remanei and C. brenneri genomes, respectively, are represented by two alleles in the assemblies. Heterozygosity is restricted to autosomes and its retention is accompanied by substantial inbreeding depression, suggesting that it is caused by multiple recessive deleterious alleles and not merely by chance. Both the overall amount and chromosomal distribution of heterozygous DNA is highly variable between assemblies of close relatives produced by identical methodologies, and allele frequencies have continued to change after strains were sequenced. Our results highlight the impact of mating systems on genome sequencing projects.

The causes of mutation accumulation in mitochondrial genomes

A fundamental observation across eukaryotic taxa is that mitochondrial genomes have a higher load of deleterious mutations than nuclear genomes. Identifying the evolutionary forces that drive this difference is important to understanding the rates and patterns of sequence evolution, the efficacy of natural selection, the maintenance of sex and recombination and the mechanisms underlying human ageing and many diseases. Recent studies have implicated the presumed asexuality of mitochondrial genomes as responsible for their high mutational load. We review the current body of knowledge on mitochondrial mutation accumulation and recombination, and conclude that asexuality, per se, may not be the primary determinant of the high mutation load in mitochondrial DNA (mtDNA). Very little recombination is required to counter mutation accumulation, and recent evidence suggests that mitochondrial genomes do experience occasional recombination. Instead, a high rate of accumulation of mildly deleterious mutations in mtDNA may result from the small effective population size associated with effectively haploid inheritance. This type of transmission is nearly ubiquitous among mitochondrial genomes. We also describe an experimental framework using variation in mating system between closely related species to disentangle the root causes of mutation accumulation in mitochondrial genomes.

Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes

Population genetics theory predicts that differences in breeding systems should be an important factor in the dynamics of selfish genetic elements, because of different intensities of selection on both hosts and elements. We examined population frequencies of transposable elements (TEs) in natural populations of the self-fertilizing nematode Caenorhabditis elegans and its outcrossing relative Caenorhabditis remanei. We identified a Tc1-like class of elements in the C. remanei genome with homology to the terminal inverted repeats of the C. elegans Tc1 transposon, which we name mTcre1. We measured levels of insertion polymorphism for all 32 Tc1 elements present in the genome sequence of the C. elegans N2 strain, and 16 mTcre1 elements from the genome sequence of the C. remanei PB4641 strain. We show that transposons are less polymorphic and segregate at higher frequencies in C. elegans compared with C. remanei. Estimates of the intensity of selection based on the population frequencies of polymorphic elements suggest that transposons are selectively neutral in C. elegans, but subject to purifying selection in C. remanei. These results are consistent with a reduced efficacy of natural selection against TEs in selfing populations, but may in part be explained by non-equilibrium TE dynamics.

High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in caenorhabditis

Almost all organismal function is controlled by pathways composed of interacting genetic components. The relationship between pathway structure and the evolution of individual pathway components is not completely understood. For the nematode Caenorhabditis elegans, chemosensory pathways regulate critical aspects of an individual's life history and development. To help understand how olfaction evolves in Caenorhabditis and to examine patterns of gene evolution within transduction pathways in general, we analyzed nucleotide variation within and between species across two well-characterized olfactory pathways, including regulatory genes controlling the fate of the cells in which the pathways are expressed. In agreement with previous studies, we found much higher levels of polymorphism within C. remanei than within the related species C. elegans and C. briggsae. There are significant differences in the rates of nucleotide evolution for genes across the two pathways but no particular association between evolutionary rate and gene position, suggesting that the evolution of functional pathways must be considered within the context of broader gene network structure. However, developmental regulatory genes show both higher levels of divergence and polymorphism than the structural genes of the pathway. These results show that, contrary to the emerging paradigm in the evolution of development, important structural changes can accumulate in transcription factors.

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements

To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced approximately 0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide.

Controlling population evolution in the laboratory to evaluate methods of historical inference

Natural populations of known detailed past demographic history are extremely valuable to evaluate methods of historical inference, yet are extremely rare. As an alternative approach, we have generated multiple replicate microsatellite data sets from laboratory-cultured populations of a gonochoric free-living nematode, Caenorhabditis remanei, that were constrained to pre-defined demographic histories featuring different levels of migration among populations or bottleneck events of different magnitudes. These data sets were then used to evaluate the performances of two recently developed population genetics methods, BayesAss+, that estimates recent migration rates among populations, and Bottleneck, that detects the occurrence of recent bottlenecks. Migration rates inferred by BayesAss+ were generally over-estimates, although these were often included within the confidence interval. Analyses of data sets simulated in-silico, using a model mimicking the laboratory experiments, produced less biased estimates of the migration rates, and showed increased efficiency of the program when the number of loci and sampled genotypes per population was higher. In the replicates for which the pre-bottleneck laboratory-cultured populations did not significantly depart from a mutation/drift equilibrium, an important assumption of the program Bottleneck, only a portion of the bottleneck events were detected. This result was confirmed by in-silico simulations mirroring the laboratory bottleneck experiments. More generally, our study demonstrates the feasibility, and highlights some of the limits, of the approach that consists in generating molecular genetic data sets by controlling the evolution of laboratory-reared nematode populations, for the purpose of validating methods inferring population history.

Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing

The evolution of self-fertilization can mediate pronounced changes in genomes as a by-product of a drastic reduction in effective population size and the concomitant accumulation of slightly deleterious mutations by genetic drift. In the nematode genus Caenorhabditis, a highly selfing lifestyle has evolved twice independently, thus permitting an opportunity to test for the effects of mode of reproduction on patterns of molecular evolution on a genomic scale. Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic model organism Caenorhabditis elegans. Despite evidence that weak selection on synonymous codon usage is pervasive in the history of all species in this genus, we find little difference among species in the patterns of codon usage bias and in replacement-site substitution. Applying a model of relaxed selection on codon usage to the C. elegans and C. briggsae lineages suggests that self-fertilization is unlikely to have evolved more than approximately 4 million years ago, which is less than a quarter of the time since they shared a common ancestor with outcrossing species. We conclude that the profound changes in mating behavior, physiology, and developmental mechanisms that accompanied the transition from an obligately outcrossing to a primarily selfing mode of reproduction evolved in the not-too-distant past.

Genome evolution in Caenorhabditis

Since the completion of the Caenorhabditis elegans genome sequence 10 years ago, efforts of the large community of C. elegans geneticists have resulted in a high-quality annotation of the structures and sequence relatedness of nearly all the protein encoding and RNA genes. Based on increasingly accurate gene counts in other species, it now appears that C. elegans has more functional genes than most insects and approximately the same number as most mammals. In the last few years, draft genome sequences for several other nematodes have been published (C. briggsae and Brugia malayi) or publicly released (C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Trichinella spiralis and Haemonchus contortus). Comparisons of gene content within the phylum and to other phyla reveal complex patterns of genome evolution. These patterns include substantial numbers of genes conserved across all the major metazoan phyla (core metazoan genes) and many nematode-specific genes and gene families. Nematode-specific genes are located predominantly on autosomal arms, which also have higher recombination rates. It appears that evolutionary innovations occur mostly in these regions, probably facilitated by higher recombination. Few of these genes have gross phenotypes when knocked down by RNAi, suggesting that many of them function in specific aspects of nematode biology that were not tested, including chemosensation, pathogen response and xenobiotic detoxification.

Beyond induced mutants: using worms to study natural variation in genetic pathways

Induced mutants in the nematode Caenorhabditis elegans are used to study genetic pathways of processes ranging from aging to behavior. The effects of such mutations are usually analyzed in a single wildtype background: N2. However, studies in other species demonstrate that the phenotype(s) of induced mutations can vary widely depending on the genetic background. Moreover, induced mutations in one genetic background do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Because other wildtype Caenorhabditis spp., including C. elegans, are now available, we review how current mapping resources and methodologies within and between species support the use of Caenorhabditis spp. for studying genetic variation, with a focus on pathways associated with human disease.

Effective population size and tests of neutrality at cytoplasmic genes inArabidopsis

Cytoplasmic genomes typically lack recombination, implying that genetic hitch-hiking could be a predominant force structuring nucleotide polymorphism in the chloroplast and mitochondria. We test this hypothesis by analysing nucleotide polymorphism data at 28 loci across the chloroplast and mitochondria of the outcrossing plantArabidopsis lyrata, and compare patterns with multiple nuclear loci, and the highly selfingArabidopsis thaliana. The maximum likelihood estimate of the ratio of effective population size at cytoplasmic relative to nuclear genes inA. lyratadoes not depart from the neutral expectation of 0·5. Similarly, the ratio of effective size inA. thalianais close to unity, the neutral expectation for a highly selfing species. The results are thus consistent with neutral organelle polymorphism in these species or with comparable effects of hitch-hiking in both cytoplasmic and nuclear genes, in contrast to the results of recent studies on gynodioecious taxa. The four-gamete test and composite likelihood estimation provide evidence for very low levels of recombination in the organelles ofA. lyrata, although permutation tests do not suggest that adjacent polymorphic sites are more closely linked than more distant sites across the two genomes, suggesting that mutation hotspots or very low rates of gene conversion could explain the data.

Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans

The nematode Oscheius tipulae belongs to the same family (Rhabditidae) as the model species Caenorhabditis elegans. Both species reproduce through self-fertilizing hermaphrodites and facultative males. Recent studies have shown that the self-fertile C. elegans and C. briggsae displayed a 20-fold lower genetic diversity than the male-female species C. remanei. Several explanations have been put forward to account for this difference, including their mode of reproduction and dynamic population structure. Here, we present the results of extensive worldwide sampling of O. tipulae, which we previously used as a laboratory organism for developmental genetics. We found that O. tipulae is much more widespread and common in soil throughout the world than Caenorhabditis species. We analysed 63 O. tipulae isolates from several continents using amplified fragment length polymorphism (AFLP). We found that O. tipulae harbours a 5-fold higher genetic diversity than C. elegans and C. briggsae. As in C. elegans, a high proportion of this diversity was found locally. Yet, we detected significant geographical differentiation, both at the worldwide scale with a latitudinal structure and between three localities in France. In summary, O. tipulae exhibited significantly higher levels of genetic diversity and large-scale geographical structure than C. elegans, despite their shared mode of reproduction. This species difference in genetic diversity may be explained by a number of other differences, such as population size, distribution, migration and dynamics. Due to its widespread occurrence and relatively high genetic diversity, O. tipulae may be a promising study species for evolutionary studies.

Multilocus patterns of polymorphism and selection across the X chromosome of Caenorhabditis remanei

Natural selection and neutral processes such as demography, mutation, and gene conversion all contribute to patterns of polymorphism within genomes. Identifying the relative importance of these varied components in evolution provides the principal challenge for population genetics. To address this issue in the nematode Caenorhabditis remanei, I sampled nucleotide polymorphism at 40 loci across the X chromosome. The site-frequency spectrum for these loci provides no evidence for population size change, and one locus presents a candidate for linkage to a target of balancing selection. Selection for codon usage bias leads to the non-neutrality of synonymous sites, and despite its weak magnitude of effect (N(e)s approximately 0.1), is responsible for profound patterns of diversity and divergence in the C. remanei genome. Although gene conversion is evident for many loci, biased gene conversion is not identified as a significant evolutionary process in this sample. No consistent association is observed between synonymous-site diversity and linkage-disequilibrium-based estimators of the population recombination parameter, despite theoretical predictions about background selection or widespread genetic hitchhiking, but genetic map-based estimates of recombination are needed to rigorously test for a diversity-recombination relationship. Coalescent simulations also illustrate how a spurious correlation between diversity and linkage-disequilibrium-based estimators of recombination can occur, due in part to the presence of unbiased gene conversion. These results illustrate the influence that subtle natural selection can exert on polymorphism and divergence, in the form of codon usage bias, and demonstrate the potential of C. remanei for detecting natural selection from genomic scans of polymorphism.

Comparative genetics of sex determination: masculinizing mutations in Caenorhabditis briggsae

The nematodes Caenorhabditis elegans and C. briggsae independently evolved self-fertile hermaphroditism from gonochoristic ancestors. C. briggsae has variably divergent orthologs of nearly all genes in the C. elegans sex determination pathway. Their functional characterization has generally relied on reverse genetic approaches, such as RNA interference and cross-species transgene rescue and more recently on deletion mutations. We have taken an unbiased forward mutagenesis approach to isolating zygotic mutations that masculinize all tissues of C. briggsae hermaphrodites. The screens identified loss-of-function mutations in the C. briggsae orthologs of tra-1, tra-2, and tra-3. The somatic and germline phenotypes of these mutations are largely identical to those of their C. elegans homologs, including the poorly understood germline feminization of tra-1(lf) males. This overall conservation of Cb-tra phenotypes is in contrast to the fem genes, with which they directly interact and which are significantly divergent in germline function. In addition, we show that in both C. briggsae and C. elegans large C-terminal truncations of TRA-1 that retain the DNA-binding domain affect sex determination more strongly than somatic gonad development. Beyond these immediate results, this collection of mutations provides an essential foundation for further comparative genetic analysis of the Caenorhabditis sex determination pathway.

Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae

Caenorhabditis elegans and C. briggsae have many parallels in terms of morphology, life history and breeding system. Both species also share similar low levels of molecular diversity, although the global sampling of natural populations has been limited and geographically biased. In this study, we describe the first cultured isolates of C. elegans and C. briggsae from sub-Saharan Africa. We characterize these samples for patterns of nucleotide polymorphism and vulva precursor cell lineage, and conduct a series of hybrid crosses in C. briggsae to test for genetic incompatibilities. The distribution of genetic diversity confirms a lack of geographic structure to C. elegans sequences but shows genetic differentiation of C. briggsae into three distinct clades that may correspond to three latitudinal ranges. Despite low levels of molecular diversity, we find considerable variation in cell division frequency in African C. elegans for the P3.p vulva precursor cell, and in African C. briggsae for P4.p, a variation that was not previously observed in this species. Hybrid crosses did not reveal major incompatibilities between C. briggsae strains from Africa and elsewhere, and there was some evidence of inbreeding depression. These new African isolates suggest that important ecological factors may be shaping the patterns of diversity in C. briggsae, and that despite many similarities between C. elegans and C. briggsae, there may be more subtle differences in their natural histories than previously appreciated.

Mating systems and the efficacy of selection at the molecular level

Mating systems are thought to play a key role in molecular evolution through their effects on effective population size (N(e)) and effective recombination rate. Because of reduced N(e), selection in self-fertilizing species is supposed to be less efficient, allowing fixation of weakly deleterious alleles or lowering adaptation, which may jeopardize their long-term evolution. Relaxed selection pressures in selfers should be detectable at the molecular level through the analyses of the ratio of nonsynonymous and synonymous divergence, D(n)/D(s), or the ratio of nonsynonymous and synonymous polymorphism, pi(n)/pi(s). On the other hand, selfing reveals recessive alleles to selection (homozygosity effect), which may counterbalance the reduction in N(e). Through population genetics models, this study investigates which process may prevail in natural populations and which conditions are necessary to detect evidence for relaxed selection signature at the molecular level in selfers. Under a wide range of plausible population and mutation parameters, relaxed selection against deleterious mutations should be detectable, but the differences between the two mating systems can be weak. At equilibrium, differences between outcrossers and selfers should be more pronounced using divergence measures (D(n)/D(s) ratio) than using polymorphism data (pi(n)/pi(s) ratio). The difference in adaptive substitution rates between outcrossers and selfers is much less predictable because it critically depends on the dominance levels of new advantageous mutations, which are poorly known. Different ways of testing these predictions are suggested, and implications of these results for the evolution of self-fertilizing species are also discussed.

Contrasting patterns of synonymous and nonsynonymous sequence evolution in asexual and sexual freshwater snail lineages

In asexual lineages, both synonymous and nonsynonymous sequence polymorphism may be reduced due to severe founder effects when asexual lineages originate. However, mildly deleterious (nonsynonymous) mutations may accumulate after asexual lineages are formed, because the efficiency of purifying selection is reduced even in the nonrecombining mitochondrial genome. Here we examine patterns of synonymous and nonsynonymous mitochondrial sequence polymorphism in asexual and sexual lineages of the freshwater snail Campeloma. Using clade-specific estimates, we found that synonymous sequence polymorphism was significantly reduced by 75% in asexuals relative to sexuals, whereas nonsynonymous sequence polymorphism did not differ significantly between sexuals and asexuals. Two asexual clades had high negative values for Tajima's D statistic. Coalescent simulations confirmed that various bottleneck scenarios can account for this result. We also used branch-specific estimates of the ratio of amino acid to silent substitutions, K(a)/K(s). Our study revealed that K(a)/K(s) ratios are six times higher in terminal branches of independent asexual lineages compared to sexuals. Coalescent-based reconstruction of gene networks for all sexual and asexual clades indicated that nonsynonymous mutations occurred at a higher frequency in recently derived asexual haplotypes. These findings suggest that patterns of synonymous and nonsynonymous nucleotide polymorphism in asexual snail lineages may be shaped by both severe founder effect and relaxed purifying selection.

Distinct patterns of genetic variation in Pristionchus pacificus and Caenorhabditis elegans, two partially selfing nematodes with cosmopolitan distribution

Hermaphroditism has evolved several times independently in nematodes. The model organism Caenorhabditis elegans and Pristionchus pacificus are self-fertile hermaphrodites with rare facultative males. Both species are members of different families: C. elegans belongs to the Rhabditidae and P. pacificus to the Diplogastridae. Also, both species differ in their ecology: C. elegans is a soil-dwelling nematode that is often found in compost heaps. In contrast, field studies in Europe and North America indicate that Pristionchus nematodes are closely associated with scarab beetles. In C. elegans, several recent studies have found low genetic diversity and rare out-crossing events. Little is known about diversity levels and population structure in free-living hermaphroditic nematodes outside the genus Caenorhabditis. Taking a comparative approach, we analyse patterns of molecular diversity and linkage disequilibrium in 18 strains of P. pacificus from eight countries and four continents. Mitochondrial sequence data of P. pacificus isolates reveal a substantially higher genetic diversity on a global scale when compared to C. elegans. A mitochondrial-derived hermaphrodite phylogeny shows little geographic structuring, indicating several worldwide dispersal events. Amplified fragment length polymorphism and single strand conformation polymorphism analyses demonstrate a high degree of genome-wide linkage disequilibrium, which also extends to the mitochondrial genome. Together, these findings indicate distinct patterns of genetic variation of the two species. The low level of genetic diversity observed in C. elegans might reflect a recent human-associated dispersal, whereas the P. pacificus diversity might reflect a long-lasting and ongoing insect association. Thus, despite similar lifestyle characteristics in the laboratory, the reproductive mode of hermaphroditism with rare facultative males can result in distinct genetic variability patterns in different ecological settings.

Impact of mating systems on patterns of sequence polymorphism in flowering plants

A fundamental challenge in population genetics and molecular evolution is to understand the forces shaping the patterns of genetic diversity within and among species. Among them, mating systems are thought to have important influences on molecular diversity and genome evolution. Selfing is expected to reduce effective population size, Ne, and effective recombination rates, directly leading to reduced polymorphism and increased linkage disequilibrium compared with outcrossing. Increased isolation between populations also results directly from selfing or indirectly from evolutionary changes, such as small flowers and low pollen output, leading to greater differentiation of molecular markers than under outcrossing. The lower effective recombination rate increases the likelihood of hitch-hiking, further reducing within-deme diversity of selfers and thus increasing their genetic differentiation. There are also indirect effects on molecular evolutionary processes. Low Ne reduces the efficacy of selection; in selfers, selection should thus be less efficient in removing deleterious mutations. The rarity of heterozygous sites in selfers leads to infrequent action of biased conversion towards GC, which tends to increase sequences' GC content in the most highly recombining genome regions of outcrossers. To test these predictions in plants, we used a newly developed sequence polymorphism database to investigate the effects of mating system differences on sequence polymorphism and genome evolution in a wide set of plant species. We also took into account other life-history traits, including life form (whether annual or perennial herbs, and woody perennial) and the modes of pollination and seed dispersal, which are known to affect enzyme and DNA marker polymorphism. We show that among various life-history traits, mating systems have the greatest influence on patterns of polymorphism.

Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny

To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.

Cytonuclear dynamics in selfing populations under selection

We develop a mathematical model to delimit the role of natural selection in maintaining nuclear and cytoplasmic polymorphisms in selfing populations. We provide explicit time-dependent solutions for joint cytonuclear frequencies under any combination of constant fertility, viability, and gametic selection and exact analytical conditions for the maintenance of polymorphisms under joint cytonuclear selection. The equilibrium structure is determined by the relative magnitude of echo fitnesses, defined as the rate at which individuals survive and produce offspring with their own genotype. Both nuclear and cytoplasmic polymorphisms can be maintained under biologically meaningful conditions, although the majority of the parameter combinations will lead to fixation. The theoretical framework developed here should be very useful in formally dissecting the form and strength of selection on cytonuclear genotypes in populations with negligible levels of outcrossing.

Evolution and Development: Anchors away!

Developmental mechanisms can evolve even when the trait they produce does not, and the nematode vulva has become a model organ for detecting such "developmental system drift". A new study reveals what may be the very earliest stages of this process by experimentally modifying key vulval signaling pathways in different species of Caenorhabditis, and carefully quantifying the results.

Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabditis remanei

Adaptive codon usage provides evidence of natural selection in one of its most subtle forms: a fitness benefit of one synonymous codon relative to another. Codon usage bias is evident in the coding sequences of a broad array of taxa, reflecting selection for translational efficiency and/or accuracy as well as mutational biases. Here, we quantify the magnitude of selection acting on alternative codons in genes of the nematode Caenorhabditis remanei, an outcrossing relative of the model organism C. elegans, by fitting the expected mutation-selection-drift equilibrium frequency distribution of preferred and unpreferred codon variants to the empirical distribution. This method estimates the intensity of selection on synonymous codons in genes with high codon bias as N(e)s = 0.17, a value significantly greater than zero. In addition, we demonstrate for the first time that estimates of ongoing selection on codon usage among genes, inferred from nucleotide polymorphism data, correlate strongly with long-term patterns of codon usage bias, as measured by the frequency of optimal codons in a gene. From the pattern of polymorphisms in introns, we also infer that these findings do not result from the operation of biased gene conversion toward G or C nucleotides. We therefore conclude that coincident patterns of current and ancient selection are responsible for shaping biased codon usage in the C. remanei genome.

Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions

The evolution of molecules, developmental circuits, and new species are all characterized by the accumulation of incompatibilities between ancestors and descendants. When specific interactions between components are necessary at any of these levels, this requires compensatory coevolution. Theoretical treatments of compensatory evolution that only consider the endpoints predict that it should be rare because intermediate states are deleterious. However, empirical data suggest that compensatory evolution is common at all levels of molecular interaction. A general solution to this paradox is provided by plausible neutral or nearly neutral intermediates that possess informational redundancy. These intermediates provide an evolutionary path between coadapted allelic combinations. Although they allow incompatible end points to evolve, at no point was a deleterious mutation ever in need of compensation. As a result, what appears to be compensatory evolution may often actually be "pseudocompensatory." Both theoretical and empirical studies indicate that pseudocompensation can speed the evolution of intergenic incompatibility, especially when driven by adaptation. However, under strong stabilizing selection the rate of pseudocompensatory evolution is still significant. Important examples of this process at work discussed here include the evolution of rRNA secondary structures, intra- and inter-protein interactions, and developmental genetic pathways. Future empirical work in this area should focus on comparing the details of intra- and intergenic interactions in closely related organisms.

Cumulative effects of spontaneous mutations for fitness in Caenorhabditis: role of genotype, environment and stress

It is often assumed that the mutation rate is an evolutionarily optimized property of a taxon. The relevant mutation rate is for mutations that affect fitness, U, but the strength of selection on the mutation rate depends on the average effect of a mutation. Determination of U is complicated by the possibility that mutational effects depend on the particular environmental context in which the organism exists. It has been suggested that the effects of deleterious mutations are typically magnified in stressful environments, but most studies confound genotype with environment, so it is unclear to what extent environmental specificity of mutations is specific to a particular starting genotype. We report a study designed to separate effects of species, genotype, and environment on the degradation of fitness resulting from new mutations. Mutations accumulated for >200 generations at 20 degrees in two strains of two species of nematodes that differ in thermal sensitivity. Caenorhabditis briggsae and C. elegans have similar demography at 20 degrees, but C. elegans suffers markedly reduced fitness at 25 degrees. We find little evidence that mutational properties differ depending on environmental conditions and mutational correlations between environments are close to those expected if effects were identical in both environments.

High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei

The common ancestor of the self-fertilizing nematodes Caenorhabditis elegans and C. briggsae must have reproduced by obligate outcrossing, like most species in this genus. However, we have only a limited understanding about how genetic variation is patterned in such male-female (gonochoristic) Caenorhabditis species. Here, we report results from surveying nucleotide variation of six nuclear loci in a broad geographic sample of wild isolates of the gonochoristic C. remanei. We find high levels of diversity in this species, with silent-site diversity averaging 4.7%, implying an effective population size close to 1 million. Additionally, the pattern of polymorphisms reveals little evidence for population structure or deviation from neutral expectations, suggesting that the sampled C. remanei populations approximate panmixis and demographic equilibrium. Combined with the observation that linkage disequilibrium between pairs of polymorphic sites decays rapidly with distance, this suggests that C. remanei will provide an excellent system for identifying the genetic targets of natural selection from deviant patterns of polymorphism and linkage disequilibrium. The patterns revealed in this obligately outcrossing species may provide a useful model of the evolutionary circumstances in C. elegans' gonochoristic progenitor. This will be especially important if self-fertilization evolved recently in C. elegans history, because most of the evolutionary time separating C. elegans from its known relatives would have occurred in a state of obligate outcrossing.

One perfect worm

Recent studies show that local populations of the nematode Caenorhabditis elegans possess nearly as much genetic variation as that seen in existing worldwide collections. This suggests either wide-ranging migration and intense natural selection or recent dispersal, perhaps by human association. Either way, the effective population size of this ubiquitous model organism is unexpectedly small.

Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae

Caenorhabditis briggsae provides a natural comparison species for the model nematode C. elegans, given their similar morphology, life history, and hermaphroditic mode of reproduction. Despite C. briggsae boasting a published genome sequence and establishing Caenorhabditis as a model genus for genetics and development, little is known about genetic variation across the geographic range of this species. In this study, we greatly expand the collection of natural isolates and characterize patterns of nucleotide variation for six loci in 63 strains from three continents. The pattern of polymorphisms reveals differentiation between C. briggsae strains found in temperate localities in the northern hemisphere from those sampled near the Tropic of Cancer, with diversity within the tropical region comparable to what is found for C. elegans in Europe. As in C. elegans, linkage disequilibrium is pervasive, although recombination is evident among some variant sites, indicating that outcrossing has occurred at a low rate in the history of the sample. In contrast to C. elegans, temperate regions harbor extremely little variation, perhaps reflecting colonization and recent expansion of C. briggsae into northern latitudes. We discuss these findings in relation to their implications for selection, demographic history, and the persistence of self-fertilization.

Sampling from natural populations with RNAI reveals high outcrossing and population structure in Caenorhabditis elegans

Despite a nearly worldwide distribution in nature, Caenorhabditis elegans exhibits low levels of genetic polymorphism, possibly as an indirect consequence of low levels of outcrossing. In the laboratory, Caenorhabditis elegans males are produced at low rates and are steadily eliminated from cultures, so that reproduction happens largely through self-fertilization in hermaphrodites. C. elegans is increasingly the focus of evolutionary research; however, natural outcrossing rates are difficult to measure because mating tests with laboratory strains are usually required to identify C. elegans. We sampled natural populations of C. elegans with an RNA interference (RNAi) assay. Heterozygosities and polymorphism patterns revealed surprisingly high levels of population structure and outcrossing (approximately 22% of individuals are estimated to be the result of outcrossing and not self-fertilization). The finding of strong local population structure, together with low levels of diversity on local and global scales, suggests a metapopulation model of frequent extinction and recolonization of local populations. The occurrence of substantial outcrossing suggests that the extinction of local populations is probably not driven by the accumulation of harmful mutations.

Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques

Mitochondrial DNA (mtDNA) sequence data and amplified fragment length polymorphism (AFLP) patterns were compared for the lungworm Dictyocaulus viviparus, a nematode parasite of cattle. Eight individual D. viviparus samples from each of 8 herds in Sweden and 1 laboratory isolate were analysed, with the aim of describing the diversity and genetic structure in populations using different genetic markers on exactly the same DNA samples. There was qualitative agreement between the whole-genome AFLP data and the mtDNA sequence data, both indicating relatively strong genetic differentiation among the Swedish farms. However, the AFLP data detected much more genetic variation than did the mtDNA data, even after allowing for the different inheritance patterns of the markers, and indicated that there was much less differentiation among the populations. The mtDNA data therefore seemed to be more informative about the most recent history of the parasite populations, as the general patterns were less obscured by detailed inter-relationships among individual worms. The 4 mtDNA genes sequenced (1542 bp) showed consistent patterns, although there was more genetic variation in the protein-coding genes than in the structural RNA genes. Furthermore, there appeared to be at least 3 distinct genetic groups of D. viviparus infecting Swedish cattle, 1 of which was predominant and showed considerable differentiation between farms, but not necessarily within farms. Second, the 2 smaller genetic groups occurred on farms where the predominant group also occurred, suggesting that these farms have had multiple introductions of D. viviparus.

Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans

An understanding of the relative contributions of different evolutionary forces on an organism's genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, extending even between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using "scattered" samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is shaped largely by population subdivision due to self-fertilization coupled with long- and short-range migration between subpopulations.

High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations

BACKGROUND

Caenorhabditis elegans is a major model system in biology, yet very little is known about its biology outside the laboratory. In particular, its unusual mode of reproduction with self-fertile hermaphrodites and facultative males raises the question of its frequency of outcrossing in natural populations.

RESULTS

We describe the first analysis of C. elegans individuals sampled directly from natural populations. C. elegans is found predominantly in the dauer stage and with a very low frequency of males versus hermaphrodites. Whereas C. elegans was previously shown to display a low worldwide genetic diversity, we find by comparison a surprisingly high local genetic diversity of C. elegans populations; this local diversity is contributed in great part by immigration of new alleles rather than by mutation. Our results on heterozygote frequency, male frequency, and linkage disequilibrium furthermore show that selfing is the predominant mode of reproduction in C. elegans natural populations but that infrequent outcrossing events occur, at a rate of approximately 1%.

CONCLUSIONS

Our results give a first insight in the biology of C. elegans in the natural populations. They demonstrate that local populations of C. elegans are genetically diverse and that a low frequency of outcrossing allows for the recombination of these locally diverse genotypes.

Cultivation of the rhabditid Poikilolaimus oxycercus as a laboratory nematode for genetic analyses

Vulva formation is a paradigm for evolutionary developmental biology in nematodes. Not only do the number of vulval precursor cells (VPCs) differ between members in the Rhabditidae and Diplogastridae, they are also sculpted via different developmental mechanisms, either by cell fusion in most Rhabditidae or by programmed cell death in the Diplogastridae. In this context, the species Poikilolaimus oxycercus is the only known species in the family Rhabditidae to have a subset of the Pn.p cells commit programmed cell death during the patterning of the VPCs. Our current study introduces P. oxycercus as a new laboratory organism. There are discrete laboratory strains that are genetically polymorphic from each other as well as heterogeneous within each strain. In order to cultivate this gonochoristic nematode into an experimental model with a tractable genetic system, we produced two inbreeding tolerant, near-isogenic strains capable of producing viable progeny with each other. We also described P. oxycera's morphology by scanning electron microscopy (SEM), basic life history traits, hybrid viability, and mating behavior. P. oxycercus females have no preference for inter- or intra-strain matings, and can mate with multiple males in a relatively short time period, suggesting a propensity for maintaining heterozygosity through promiscuity. Interestingly, all sexes from three species in the genus Poikilolaimus show five 4',6-diamidino-2-phenylindole (DAPI) staining bodies in their germ line cells. This could indicate that Poikilolaimus species possess five bivalent chromosomes in their germ lines, in contrast to the hermaphroditic Caenorhabditis elegans or Pristionchus pacificus, which have six chromosomes.

Evolution: An Ecological Context for C. elegans

Despite low global diversity among natural populations of Caenorhabditis elegans, neighboring populations can be as genetically distinct as strains from different continents, probably owing to transient bottlenecks and ongoing dispersal as a dauer larva. Selfing predominates in the wild, but rare outcrossing may also play an important role.

The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species

We analyzed the effects of mating system and recombination rate on single nucleotide polymorphisms using 14 single-copy nuclear loci from single populations of five species of wild tomatoes (Solanum section Lycopersicon). The taxa investigated comprise two self-compatible (SC) and three self-incompatible (SI) species. The observed reduction in nucleotide diversity in the SC populations compared to the SI populations is much stronger than expected under the neutral effects of the mating system on effective population size. Importantly, outgroup sequences available for 11 of the 14 loci yield strong positive correlations between silent nucleotide diversity and silent divergence, indicative of marked among-locus differences in mutation rates and/or selective constraints. Furthermore, using a physical estimate of local recombination rates, we find that silent nucleotide diversity (but not divergence) is positively correlated with recombination rate in two of the SI species. However, this correlation is not nearly as strong as in other well-characterized species (in particular, Drosophila). We propose that nucleotide diversity in Lycopersicon is dominated mainly by differences in neutral mutation rates and/or selective constraints among loci, demographic processes (such as population subdivision), and background selection. In addition, we hypothesize that the soil seed bank plays an important role in the maintenance of the large genetic diversity in the SI species (in particular L. peruvianum).

The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection, whereas others claim that most between-species regulatory changes are neutral or nearly neutral. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences.

Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes

The sex determination gene fem-3 encodes one of the most divergent proteins yet described in the terrestrial nematode Caenorhabditis. Despite this rapid sequence change, however, FEM-3 is essential for male development in the three species surveyed thus far. It also participates in conserved protein-protein complexes with the transmembrane receptor TRA-2 and the phosphatase FEM-2 in these species. These interactions show strong species specificity, indicating that conserved residues are not sufficient for function and that compensatory evolution between binding partners is important. To shed further light on the nature of this coevolution, and to discern the extent of amino acid polymorphism allowed in FEM-3 and the domain of TRA-2 that binds it, we have examined intraspecific variation in the gonochoristic species Caenorhabditis remanei. Ten new complete Cr-fem-3 alleles from three regions of the United States are described. We also obtained sequences for the FEM-3-binding domain of TRA-2 for 9 of the same strains. These alleles were compared with each other, with the European founder alleles, and with the orthologous sequences from the congeners Caenorhabditis elegans and C. briggsae. We find that FEM-3 harbors abundant amino acid polymorphisms along its entire length. The majority (but not all) of these occur in nonconserved residues, and in at least one domain there is evidence for diversifying selection. The FEM-3-binding domain of TRA-2 is less polymorphic than FEM-3. Amino acids neither polymorphic nor conserved between species are candidates for residues mediating species-specific interaction of FEM-3 with its binding partners.

Molecular evolution of the GapC gene family in Amsinckia spectabilis populations that differ in outcrossing rate

Molecular evolutionary analysis of the glyceraldehyde 3-phosphate dehydrogenase (GapC) gene family was conducted in the plant genus Amsinckia (Boraginaceae), a group that exhibits marked variation in the mating system. GapC genes in this group differ from those of Arabidopsis thaliana in terms of both intron size and number. Phylogenetic and Southern hybridization analyses suggest the presence of multiple GapC loci, each defined by a set of base substitutions that are in strong linkage disequilibrium. One species of Amsinckia, A. spectabilis, was studied in some detail. This species consists of selfing (A. s. spectabilis) and outcrossing (A. s. microcarpa) varieties. Two selfing populations and one outcrossing population sample were analyzed in detail for variation at one of the members of this gene family. GapC3. A reduction in number of GapC3 haplotypes and level of genetic diversity was observed in the selfing populations of A. spectabilis. GapC3 in the outcrossing population (but not the two selfing populations) exhibited a significant departure from neutrality in the direction of an excess of singletons. These results are discussed in the context of forces acting on sequence evolution in populations with different mating systems.

Cloning and expression analysis ofpos-1 in the nematodesCaenorhabditis briggsae andCaenorhabditis remanei

The Caenorhabditis elegans pos-1 gene encodes a zinc-finger protein that is required for germline specification during embryogenesis. The maternally provided mRNA is translationally regulated both spatially and temporally during early development. We have cloned orthologs of pos-1 from C. briggsae and C. remanei, two Caenorhabditis species that have diverged from C. elegans by approximately 20-40 million years. Two regions in the 3' untranslated region are highly conserved among all three species. We find that the pos-1 RNA is expressed in the hermaphrodite and female gonads of C. briggsae and C. remanei but POS-1 protein is not detected at high levels in C. briggsae until the 2-cell stage of embryogenesis. The protein expression is restricted to the germline precursors of the embryo. We conclude that pos-1 appears to be translationally regulated in C. briggsae as it is in C. elegans and speculate the conserved 3' UTR sequences may be involved.