Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (N _e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N _e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N _e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N _e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N _e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N _e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N _e confidence intervals. The magnitude of N _e/N _ramets and N _e/N _genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N _e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N _e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.

Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift

Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced.

Selfing rate variation within species is unrelated to life-history traits or geographic range position

PREMISE

In plants, populations and species vary widely along the continuum from outcrossing to selfing. Life-history traits and ecological circumstances influence among-species variation in selfing rates, but their general role in explaining intraspecific variation is unknown. Using a database of plant species, we test whether life-history traits, geographic range position, or abundance predict selfing rate variation among populations.

METHODS

We identified species where selfing rates were estimated in at least three populations at known locations. Two key life-history traits (generation time and growth form) were used to predict within-species selfing rate variation. Populations sampled within a species' native range were assessed for proximity to the nearest edge and abundance. Finally, we conducted linear and segmented regressions to determine functional relationships between selfing rate and geographic range position within species.

RESULTS

Selfing rates for woody species varied less than for herbs, which is explained by the lower average selfing rate of woody species. Relationships between selfing and peripherality or abundance significantly varied among species in their direction and magnitude. However, there was no general pattern of increased selfing toward range edges. A power analysis shows that tests of this hypothesis require studying many (i.e., 40+) populations.

CONCLUSIONS

Intraspecific variation in plant mating systems is often substantial yet remains difficult to explain. Beyond sampling more populations, future tests of biogeographic hypotheses will benefit from phylogeographic information concerning specific range edges, the study of traits influencing mating system (e.g., herkogamy), and measures of abundance at local scales (e.g., population density).

How and When Does Outcrossing Occur in the Predominantly Selfing Species Medicago truncatula?

Empirical studies on natural populations of Medicago truncatula revealed selfing rates higher than 80%, but never up to 100%. Similarly, several studies of predominantly selfing species show variability in the level of residual outcrossing between populations and also between temporal samples of the same population. However, these studies measure global selfing rates at the scale of the population and we do not know whether there is intra-population variation and how outcrossing events are distributed, between genotypes, plants, flowers, or seeds. Theoretical studies predict the maintenance of residual outcrossing in highly selfing species due to environmental (e.g., pollen biology) and/or genetic determinants and decompositions of the variation in outcrossing rate using experimental data can be very informative to test these hypotheses. Here, we focus on one natural population of M. truncatula in order to describe precisely its mating system. In particular, we investigated the determinants of the selfing rate by testing for seasonal variations (environmental determinism) and variations between genotypes (genetic determinism). We measured selfing rates in maternal progenies from plants collected widely across a natural population. For each plant, we collected pods from flowers produced at the beginning and at the end of the flowering season to test for a seasonal variation in the outcrossing rate. For each collected offspring, we also estimated the likelihood that it was issued from a self-fertilization event and assessed the genetic component of variation of this mating system measure. We found a significant, albeit small, increase in outcrossing rate in progenies collected at the end [t _m = 0.137 (SD = 0.025)] compared to those collected at the beginning [t _m = 0.083 (0.016)] of the flowering season. A significant between genotypes variation in selfing rate was also detected, resulting in a heritability of 9% for the rate of residual outcrossing. Altogether, our work shows that despite a predominantly selfing reproductive mode, M. truncatula displays variation in residual outcrossing rate, and that this trait is likely under a complex determinism combining environmental and genetic factors. We discuss the evolutionary implications of our results for the population.

More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast

Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilisation should have greater population structure than outcrossed species; however, demographic dynamics may affect this scenario. The mangrove killifish clade is composed of the two only known examples of self-fertilising species among vertebrates (Kryptolebias marmoratus and Kryptolebias hermaphroditus). A third species in this clade, Kryptolebias ocellatus, inhabits mangrove forests in southeast Brazil; however, its mating system and patterns of genetic structure have been rarely explored. Here, we examined the genetic structure and phylogeographic patterns of K. ocellatus along its distribution, using mitochondrial DNA and microsatellites to compare its patterns of genetic structure with the predominantly selfing and often-syntopic, K. hermaphroditus. Our results indicate that K. ocellatus reproduces mainly by outcrossing, with no current evidence of selfing, despite being an androdioecious species. Our results also reveal a stronger population subdivision in K. ocellatus compared to K. hermaphroditus, contrary to the theoretical predictions based on reproductive biology of the two species. Our findings indicate that, although morphologically similar, K. ocellatus and K. hermaphroditus had remarkably different evolutionary histories when colonising the same mangrove areas in southeastern Brazil, with other factors (e.g., time of colonisation, dispersal/establishment capacity) having more profound effects on the current population structuring of those species than differences in mating systems.

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

Background

Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated.

Results

Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo.

Conclusions

We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.

Structure of multilocus genetic diversity in predominantly selfing populations

Predominantly selfing populations are expected to have reduced effective population sizes due to nonrandom sampling of gametes, demographic stochasticity (bottlenecks or extinction-recolonization), and large scale hitchhiking (reduced effective recombination). Thus, they are expected to display low genetic diversity, which was confirmed by empirical studies. The structure of genetic diversity in predominantly selfing species is dramatically different from outcrossing ones, with populations often dominated by one or a few multilocus genotypes (MLGs) coexisting with several rare genotypes. Therefore, multilocus diversity indices are relevant to describe diversity in selfing populations. Here, we use simulations to provide analytical expectations for multilocus indices and examine whether selfing alone can be responsible for the high-frequency MLGs persistent through time in the absence of selection. We then examine how combining single and multilocus indices of diversity may be insightful to distinguish the effects of selfing, population size, and more complex demographic events (bottlenecks, migration, admixture, or extinction-recolonization). Finally, we examine how temporal changes in MLG frequencies can be insightful to understand the evolutionary trajectory of a given population. We show that combinations of selfing and small demographic sizes can result in high-frequency MLGs, as observed in natural populations. We also show how different demographic scenarios can be distinguished by the parallel analysis of single and multilocus indices of diversity, and we emphasize the importance of temporal data for the study of predominantly selfing populations. Finally, the comparison of our simulations with empirical data on populations of Medicago truncatula confirms the pertinence of our simulation framework.

Microsatellite evidence for obligate autogamy, but abundant genetic variation in the herbaceous monocarp Lobelia inflata (Campanulaceae)

Although high levels of self-fertilization (>85%) are not uncommon in nature, organisms reproducing entirely through selfing are extremely rare. Predominant selfers are expected to have low genetic diversity because genetic variation is distributed among rather than within lineages and is readily lost through genetic drift. We examined genetic diversity at 22 microsatellite loci in 105 individuals from a population of the semelparous herb Lobelia inflata L. and found (i) no evidence of heterozygosity through outcrossing, yet (ii) high rates of genetic polymorphism (2-4 alleles per locus). Furthermore, this genetic variation among lineages was associated with phenotypic traits (e.g. flower colour, size at first flower). Coupled with previous work characterizing the fitness consequences of reproductive timing, our results suggest that temporal genotype-by-environment interaction may maintain genetic variation and, because genetic variation occurs only among lineages, this simple system offers a unique opportunity for future tests of this mechanism.

The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula

Background

As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex plant phenotype and we know little about the pathways utilized by naturally tolerant plants. Legumes are important species in agricultural and natural ecosystems, since they engage in symbiotic nitrogen-fixation, but are especially vulnerable to salinity stress.

Results

Our studies of the model legume Medicago truncatula in field and greenhouse settings demonstrate that Tunisian populations are locally adapted to saline soils at the metapopulation level and that saline origin genotypes are less impacted by salt than non-saline origin genotypes; these populations thus likely contain adaptively diverged alleles. Whole genome resequencing of 39 wild accessions reveals ongoing migration and candidate genomic regions that assort non-randomly with soil salinity. Consistent with natural selection acting at these sites, saline alleles are typically rare in the range-wide species' gene pool and are also typically derived relative to the sister species M. littoralis. Candidate regions for adaptation contain genes that regulate physiological acclimation to salt stress, such as abscisic acid and jasmonic acid signaling, including a novel salt-tolerance candidate orthologous to the uncharacterized gene AtCIPK21. Unexpectedly, these regions also contain biotic stress genes and flowering time pathway genes. We show that flowering time is differentiated between saline and non-saline populations and may allow salt stress escape.

Conclusions

This work nominates multiple potential pathways of adaptation to naturally stressful environments in a model legume. These candidates point to the importance of both tolerance and avoidance in natural legume populations. We have uncovered several promising targets that could be used to breed for enhanced salt tolerance in crop legumes to enhance food security in an era of increasing soil salinization.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1160) contains supplementary material, which is available to authorized users.

Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula

Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50-75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.

Highest genetic diversity at the northern range limit of the rare orchid Isotria medeoloides

Populations in previously glaciated regions are often genetically depauperate in comparison with populations at lower latitudes, due either to bottlenecks experienced in post-glacial colonization or to contemporary genetic drift in small, peripheral populations. Populations of the rare self-fertilizing North American orchid Isotria medeoloides are largest in the previously glaciated region near the northern range limit, allowing us to examine the role of historical versus contemporary processes in determining population genetic diversity and structure. If contemporary processes predominate, genetic diversity should increase with increasing census size. In contrast, if sequential bottlenecks associated with colonization are paramount, diversity should decrease with latitude and be relatively insensitive to census size. We genotyped 299 individuals from 20 populations at four variable microsatellite loci to contrast genetic diversity and structure for populations in previously glaciated regions versus previously unglaciated regions. Populations were highly inbred (F=0.95) and highly differentiated (R(ST)=0.485). Across all sampled populations, genetic diversity decreased and genetic differentiation increased with declining population size. Small southern populations were especially differentiated and genetically depauperate. In the glaciated part of the range, genetic diversity increased as populations approached the northern range limit, demonstrating the centrality of contemporary processes for this post-glacial colonist.

Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula

Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.

Estimation of mating system parameters in an evolving gynodioecous population of cultivated sunflower (Helianthus annuus L.)

Cultivated plants have been molded by human-induced selection, including manipulations of the mating system in the twentieth century. How these manipulations have affected realized parameters of the mating system in freely evolving cultivated populations is of interest for optimizing the management of breeding populations, predicting the fate of escaped populations and providing material for experimental evolution studies. To produce modern varieties of sunflower (Helianthus annuus L.), self-incompatibility has been broken, recurrent generations of selfing have been performed and male sterility has been introduced. Populations deriving from hybrid-F1 varieties are gynodioecious because of the segregation of a nuclear restorer of male fertility. Using both phenotypic and genotypic data at 11 microsatellite loci, we analyzed the consanguinity status of plants of the first three generations of such a population and estimated parameters related to the mating system. We showed that the resource reallocation to seed in male-sterile individuals was not significant, that inbreeding depression on seed production averaged 15-20% and that cultivated sunflower had acquired a mixed-mating system, with ∼50% of selfing among the hermaphrodites. According to theoretical models, the female advantage and the inbreeding depression at the seed production stage were too low to allow the persistence of male sterility. We discuss our methods of parameter estimation and the potential of such study system in evolutionary biology.

Biased morph ratios and skewed mating success contribute to loss of genetic diversity in the distylous Pulmonaria officinalis

BACKGROUND AND AIMS

In heterostylous plant species, skewed morph ratios are not uncommon and may arise from a range of factors. Despite the recognized importance of skewed morph ratios on overall reproductive success within populations, little is known about the impact of skewed morph ratios on population genetic diversity and differentiation in heterostylous species. This study specifically aimed to clarify the effect of population size and morph bias on population genetic diversity and differentiation in the temperate forest herb Pulmonaria officinalis. This species is characterized by a distylous breeding system and shows morph-specific differences in reproductive success.

METHODS

Genetic diversity was determined for 27 P. officinalis populations in northern Belgium by using eight recently developed microsatellite markers. Multiple regressions were used to assess the relationship between genetic diversity, morph bias and population size, and F(ST)-values were calculated for short- and long-styled morphs separately to study genetic differentiation as a function of morph type.

KEY RESULTS

For all genetic measures used, morph bias was more important in explaining patterns of genetic diversity than population size, and in all cases patterns of population genetic diversity followed a quadratic function, which showed a symmetrical decrease in genetic diversity with increasing morph bias. However, probably due to the reproductive advantage of L-morphs relative to S-morphs, maximum genetic diversity was found in populations showing an excess of L-morphs (60·7 % L-morph). On the other hand, no significant difference in pairwise genetic distances between populations was observed between L- (0·107) and S-morphs (0·106).

CONCLUSIONS

Our results indicate that significant deviations from equal morph ratios not only affect plant reproductive success but also population genetic diversity of heterostylous plant species. Hence, when defining conservation measures for populations of heterostylous plant species, morph ratios should be considered as an important trait affecting their long-term population viability.

Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula

Background

We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual plants, and many instances of molecular adaptation have been reported for genes involved in flowering pathways. While perception of symbiotic microbes is also integral to adaptation in many plant species, very few reports of molecular adaptation exist for symbiotic genes. Here we used data from 57 individuals and 53 gene fragments to quantify the overall strength of both positive and purifying selection in M. truncatula and asked if footprints of positive selection can be detected at key genes of rhizobia recognition pathways.

Results

We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 5 genes involved in nitrogen-fixing bacteria recognition, 11 genes involved in flowering, and 37 genes used as control loci. We detected 1757 polymorphic sites yielding an average nucleotide diversity (pi) of 0.003 per site. Non-synonymous variation is under sizable purifying selection with 90% of amino-acid changing mutations being strongly selected against. Accessions were structured in two groups consistent with geographical origins. Each of these two groups harboured an excess of rare alleles, relative to expectations of a constant-sized population, suggesting recent population expansion. Using coalescent simulations and an approximate Bayesian computation framework we detected several instances of genes departing from selective neutrality within each group and showed that the polymorphism of two nodulation and four flowering genes has probably been shaped by recent positive selection.

Conclusion

We quantify the intensity of purifying selection in the M. truncatula genome and show that putative footprints of natural selection can be detected at different time scales in both flowering and symbiotic pathways.

Inbreeding depression and low between-population heterosis in recently diverged experimental populations of a selfing species

In fragmented populations, genetic drift and selection reduce genetic diversity, which in turn results in a loss of fitness or in a loss of evolvability. Genetic rescue, that is, controlled input of diversity from distant populations, may restore evolutionary potential, whereas outbreeding depression might counteract the positive effect of this strategy. We carried out self-pollination and crosses within and between populations in an experimental subdivided population of a selfing species, Triticum aestivum L., to estimate the magnitude of these two phenomena. Surprisingly, for a self-fertilizing species, we found significant inbreeding depression within each population for four of the six traits studied, indicating that mildly deleterious mutations were still segregating in these populations. The progeny of within- and between-population crosses was very similar, indicating low between-population heterosis and little outbreeding depression. We conclude that relatively large population effective sizes prevented fixation of a high genetic load and that local adaptation was limited in these recently diverged populations. The kinship coefficient estimated between the parents using 20 neutral markers was a poor predictor of the progeny phenotypic values, indicating that there was a weak link between neutral diversity and genes controlling fitness-related traits. These results show that when assessing the viability of natural populations and the need for genetic rescue, the use of neutral markers should be complemented with information about the presence of local adaptation in the subdivided population.

Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation

Genome-wide association studies rely upon segregating natural genetic variation, particularly the patterns of polymorphism and correlation between adjacent markers. To facilitate association studies in the model legume Medicago truncatula, we present a genome-scale polymorphism scan using existing Affymetrix microarrays. We develop and validate a method that uses a simple information-criteria algorithm to call polymorphism from microarray data without reliance on a reference genotype. We genotype 12 inbred M. truncatula lines sampled from four wild Tunisian populations and find polymorphisms at approximately 7% of features, comprising 31 419 probes. Only approximately 3% of these markers assort by population, and of these only 10% differentiate between populations from saline and non-saline sites. Fifty-two differentiated probes with unique genome locations correspond to 18 distinct genome regions. Sanger resequencing was used to characterize a subset of maker loci and develop a single nucleotide polymorphism (SNP)-typing assay that confirmed marker assortment by habitat in an independent sample of 33 individuals from the four populations. Genome-wide linkage disequilibrium (LD) extends on average for approximately 10 kb, falling to background levels by approximately 500 kb. A similar range of LD decay was observed in the 18 genome regions that assort by habitat; these LD blocks delimit candidate genes for local adaptation, many of which encode proteins with predicted functions in abiotic stress tolerance and are targets for functional genomic studies. Tunisian M. truncatula populations contain substantial amounts of genetic variation that is structured in relatively small LD blocks, suggesting a history of migration and recombination. These populations provide a strong resource for genome-wide association studies.

Small variance in growth rates in annual plants has large effects on genetic drift

PREMISE OF THE STUDY

Effective population size (N(e)) is a critical index of the evolutionary capacity of populations. Low N(e) indicates that standing genetic diversity is susceptible to loss via stochastic processes (and inbreeding) and is, therefore, unavailable for natural selection to act upon. Reported N(e) in plant populations is often quite low. What biological and ecological factors might produce such low N(e) •

METHODS

We conducted a simulation model to test the effect of randomly assigned and autocorrelated growth rates of annual plants on plant-size distributions at the end of the growing season. Because plant size is directly correlated with reproductive output in annual plants, variation in plant size reflects variation in reproduction, and thus our modeled size distributions can be used to estimate N(e). •

KEY RESULTS

Randomly assigned growth rates had a negligble effect on N(e)/N. Autocorrelated growth rates decreased N(e)/N as the length of the growing season increased. This was the case even when the variance in growth rates was as low as 0.1% of the mean. •

CONCLUSIONS

While intrinsic plant biology can affect the degree of growth autocorrelation, ecological factors such as competition, herbivory, and abiotic stress can increase or decrease levels of growth autocorrelation. Ecological factors that increase growth autocorrelation can have significant effects on genetic drift within populations.

Epistasis in natural populations of a predominantly selfing plant

Populations of predominantly selfing plant species often show spatial genetic structure but little is known whether epistatic gene interactions are spatially structured. To detect a possible epistatic effect and a spatial scale at which it operates, we created artificial crosses between plants spanning a range of fixed distances from 1 to 400 m in three populations of wild barley. The self-pollinated and crossed progeny (F(1)) and two generations of segregated progeny (F(2) and F(3)) were tested in experimentally simulated population environments for relative performance (RP). The measured fitness traits included number of seeds, total seed weight and seed germination. For any of these traits, there was no association between RP of F(1), F(2) and F(3) plants and either pairwise kinship coefficients or crossing distance. In contrast, in all three populations, we found lower seed viability of outcrossed as compared with self-pollinated genotypes in the first generation of segregation. However, in the F(3) generation this outbreeding effect disappeared in the two populations and greatly decreased in the third population. For seed production, heterosis in F(1) and outbreeding depression in F(2) were observed only in the population with unusually high number of heterozygotes. Our findings support the view that in selfing species a spatial mosaic of various locally abundant genotypes represents not randomly fixed combinations of alleles but the co-adapted gene complexes that were sieved by selection, while heterozygotes are characteristic for the transient phase of this process, when segregation and purging of maladaptive genotypes have not yet occurred.

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish because they may result in similar phylogenetic patterns. We present a novel approach to evaluate whether ILS can be excluded as an explanation for incongruent patterns. This coalescence-based method uses molecular dating estimates of the duration of the putative ILS events to determine if invoking ILS as an explanation for incongruence would require unrealistically high effective population sizes. For four of the incongruent patterns identified within the Senecioneae, this approach indicates that ILS cannot be invoked to explain the observed incongruence. Alternatively, these patterns are more realistically explained by ancient hybridization events.

Using linked markers to estimate the genetic age of a volunteer population: a theoretical and empirical approach

Volunteers deriving from unharvested seeds of a crop can lead to persistent feral populations and participate in genetic exchanges across the agro-ecosystem, both between crop varieties and between crops and their wild relatives. A first step to understand the importance of volunteers is to characterize their capacity to reproduce autonomously for several generations. For that purpose, we constructed and evaluated a maximum-likelihood method to estimate the genetic age of a population deriving from one of the most common field crop type: an F1-hybrid variety. The method estimates the number of reproduction cycles that occurred since the cultivation of that variety. It makes use of genotypic data at a number of linked microsatellite loci pairs, thus exploiting the recombination of parental haplotypes, which is expected to occur as the population is reproducing. Estimates with moderate bias and variance were found for a broad range of parameter values in simulations, and the method revealed robust to some deviations from the assumptions of the underlying model. We propose a specific procedure to test the hypothesis of persistence, that is has a given volunteer population experienced more than one cycle of reproduction since the F1-hybrid state? The method was applied to both an experimental and a natural sunflower volunteer population and revealed promising, considering these ideal case studies. Possible further developments toward more complex natural systems are discussed.

Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus

The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size (Ne). The unexpectedly low Ne (73-386) and Ne/N ratio (10-3-10-4), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small Ne proves to be a common feature of F. serratus, then being abundant may not be enough for the species to weather future environmental changes.