P.H. van Tienderen

Dispersal, kinship and inbreeding in an island population of the Great Tit

We investigated the kinship structure of an island population of the Great Tit (Parus major). Kinship of birds could be inferred by comparing their family trees. Dispersal was also studied to explain the observed pattern of kinship.

The effects of inheritance in tetraploids on genetic diversity and population divergence

Polyploids are traditionally classified into allopolyploids and autopolyploids, based on their evolutionary origin and their disomic or multisomic mode of inheritance. Over the past decade it has become increasingly clear that there is a continuum between disomic and multisomic inheritance, with the rate of tetrasomy differing among species and among chromosomes within species. Here, we use a simple population genetic model to study the impact of the mode of inheritance on the genetic diversity and population divergence of tetraploids. We found that under almost strict disomic inheritance the tetraploid genome is divided into two separate subgenomes, such as found in classical allopolyploids. In those cases, assuming full tetrasomy in the analysis of polyploid genetic data will lead to an important bias in estimates of genetic diversity and population divergence. However, we found that even a low rate of allele exchange between the two subgenomes, at about one event per generation, is sufficient to homogenise the allele frequencies over the subgenomes, and the estimates become essentially unbiased. The inbreeding coefficient FIS can then be used to detect whether the estimates of diversity and divergence will be biased when full multisomy is assumed. Finally, we found that different summary statistics for measuring the strength of population differentiation are differentially affected by a deviation from full tetrasomy. Our model results provide several useful guidelines for the analysis of polyploid data, helping researchers to determine when their inferences are biased and which summary statistics to use.

Genetic differentiation between populations of Plantago lanceolata. 2. Phenotypic selection in a transplant experiment in three contrasting habitats.

(1) Populations of Plantago lanceolata were grown in a reciprocal-transplant experiment in an early-mown hayfield, a wet, late-mown hayfield and a pasture. At all three sites, populations and clones differed significantly in components of seed yield such as survival, incidence of flowering and seed set, and in annual seed yield. (2) Components of seed yield of transplants were correlated with the height of the surrounding vegetation. In the pasture, plants produced far more seeds in tall vegetation, which was probably due to a low local grazing intensity. In contrast, in the early-mown hayfield tall vegetation was associated with a lower lifetime seed yield. At all three sites, tall vegetation coincided with a low survival of transplants. (3) In the early-mown hayfield selection on timing of flowering and growth habit was found, which agreed with the expectations from the observed differences between populations. At all sites seed production varied above all because of differences in plant size, and no further direct effects of phenotypic traits on seed yield could be detected. (4) Specialization of clones to certain sites was tested by calculating correlations of seed-yield components across sites. No significant correlations were found between components of seed yield per clone across sites. This was probably due to the positive correlation of the mean plant size per clone at different sites. A trade-off between vegetative growth and reproduction is suggested as a possible cause.

Root Transcript Profiling of Two Rorippa Species Reveals Gene Clusters Associated with Extreme Submergence Tolerance

A comparison of submergence-induced transcriptomes of two flooding-tolerant Rorippa species with the relatively flooding-sensitive Arabidopsis identifies gene clusters potentially associated with tolerance. Complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. However, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus Rorippa, close relatives of Arabidopsis (Arabidopsis thaliana). We studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to submergence of two species, Rorippa sylvestris and Rorippa amphibia. We exploited the close relationship between Rorippa species and the model species Arabidopsis by using Arabidopsis GeneChip microarrays for whole-genome transcript profiling of roots of young plants exposed to a 24-h submergence treatment or air. A probe mask was used based on hybridization of genomic DNA of both species to the arrays, so that weak probe signals due to Rorippa species/Arabidopsis mismatches were removed. Furthermore, we compared Rorippa species microarray results with those obtained for roots of submerged Arabidopsis plants. Both Rorippa species could tolerate deep submergence, with R. sylvestris surviving much longer than R. amphibia. Submergence resulted in the induction of genes involved in glycolysis and fermentation and the repression of many energy-consuming pathways, similar to the low-oxygen and submergence response of Arabidopsis and rice (Oryza sativa). The qualitative responses of both Rorippa species to submergence appeared roughly similar but differed quantitatively. Notably, glycolysis and fermentation genes and a gene encoding sucrose synthase were more strongly induced in the less tolerant R. amphibia than in R. sylvestris. A comparison with Arabidopsis microarray studies on submerged roots revealed some interesting differences and potential tolerance-related genes in Rorippa species.

Male sterility in triploid dandelions: asexual females vs asexual hermaphrodites

Male reproductive output, pollen in plants and sperm in animals has been shown to constitute a substantial cost for many organisms. In parthenogenetic hermaphrodites, selection is therefore expected to reduce the allocation of resources to male reproductive output. However, sustained production of pollen or sperm has been observed in numerous asexual hermaphrodites. We studied the widespread production of pollen by triploid asexual dandelions, Taraxacum sect. Ruderalia, comparing rare male sterile individuals with pollen producing asexuals. We found that individuals can show plasticity in the production of pollen, but that it is nevertheless possible to distinguish between (facultatively) male sterile asexuals and male fertile asexuals. Based on evidence from genetic markers and crosses, we conclude that the male sterility in asexual dandelions is caused by nuclear genes, in contrast to the cytoplasmically inherited male sterility previously found in sexual dandelions. Male sterile lineages did not produce more seeds per flower head, heavier seeds or seeds that were more viable. However, male sterile plants did produce more seed heads and hence more seeds than pollen producing ones, indicating that they were able to reallocate resources toward seed production. Considering the difference in seed production, it remains puzzling that not more asexual dandelions are male sterile.

Quantitative trait loci affecting growth-related traits in wild barley (Hordeum spontaneum) grown under different levels of nutrient supply.

The genetic basis of phenotypic plasticity of relative growth rate (RGR), its components and associated morphological traits was studied in relation to nutrient limitation. In all, 140 F3 lines from a cross, made between two Hordeum spontaneum (wild barley) accessions sampled in Israel, were subjected to growth analysis under two nutrient levels. Quantitative trait loci (QTLs) were detected for RGR and three of its components, leaf area ratio (LAR), specific leaf area and leaf mass fraction (LMF). Indications for close linkage (potential pleiotropy) were found, for example, for LAR and LMF. An interesting case is on chromosome 6, at which QTLs for RGR and seed mass were detected in the same region. These QTLs had opposite additive effects, supporting earlier results that plants growing from lighter seeds had a higher RGR. Only two QTLs were significant under both nutrient conditions, suggesting large QTL × environment interactions for most traits. For 21 out of 26 QTLs, however, the additive genetic effect was of identical sign in both nutrient environments, but reached the significance threshold in only one of them. Nevertheless, some QTLs detected in one of the two environments had virtually no effect in the other, and QTLs for plasticity were detected for RGR, LAR and LMF, as well as for some morphological traits. QTLs with opposite effects under high and low nutrients were not found. Thus, at the genetic level, there was no evidence for a trade-off between faster growth at high versus low nutrient levels.

Nuclear–Cytoplasmic male-sterility in diploid dandelions

Male-sterility was found in diploid dandelions from two widely separated populations from France, and its inheritance was analysed by crossing a diploid male-sterile dandelion to diploid sexuals and triploid apomicts. Nuclear genetic variation, found in full-sib families, segregated for male-fertility, partial male-sterility, and full male-sterility, and also segregated for small-sized versus normally sized pollen. The crossing results are best explained by a cytoplasmic male-sterility factor in combination with two dominant restorer genes. Involvement of the cytoplasmic male-sterility factor was further investigated by chloroplast haplotyping. Male-sterility was exclusively associated with a rare chloroplast haplotype (designated 16b). This haplotype was found in seven male-sterile plants and one (apparently restored) male-fertile individual but does not occur in 110 co-existing male-fertile plants and not in several hundreds of individuals previously haplotyped. Apomicts with cytoplasmic male sterility were generated in some test crosses. This raises the question as to whether the male sterility found in natural dandelion apomicts, is of cytoplasmic or of nuclear genetic nature. As many breeding systems in Taraxacum are involved in shaping population structure, it will be difficult to predict the evolutionary consequences of nuclear–cytoplasmic male-sterility for this species complex.

Ecology of Plantago Populations

The performance of plants in the field differs due to the environmental conditions and genetic variation between plants. Demographic studies provide basic material for investigations of the ecophysiological aspects of the adaptation to the environment and of the selection processes which have given rise to adaptation. The demographic work in the project includes a comparison on different levels: between species, between populations of a single species and, in some cases, comparison between spatial subdivisions within a single population. The last mentioned studies have been carried out to determine the scale on which genetic differentiation occurs and will be treated in Chapter 7. They are essential to define accurately a population. Theoretically a population can be defined as a group of individuals which (potentially) interbreed, and which is more or less separated from other groups (Bakker 1964). The results of the detailed studies showed that inhomogeneity in the habitat or variation in the management of the vegetation can cause genetic variation between the local plant groups. When demographic plots are chosen in a relatively homogeneous vegetation, with greatest distances in the order of metres, no genetically determined variation between the plots can be expected. Thus plots with a distance of in most cases less than 10 m (in the two Achterberg sites maximally 25 m) in a visually homogeneous vegetation as used in our demographic studies were regarded as representing a single population.

Within-population variability in morphology and life history of Plantago major L. ssp. pleiosperma Pilger in relation to environmental heterogeneity

SummaryAn attempt was made to relate variation in life-history characteristics within a population of Plantago major ssp. pleiosperma to small-scale environmental variability. At a beach plain, embanked in 1966, a mosaic environment was distinguished with spatial variability in vegetation structure as well as in nutrient availability and water content of the soil. Differences between three subsites in comtemporary selection were demonstrated, e.g. in shoot morphology and allocation to reproductive tissue. The effects of nutrient supply and waterlogging on morphology and life history were studied on lines from the three subsites in a greenhouse. For most of the traits high levels of phenotypic plasticity were observed, covering almost entirely the observed phenotypic variability at the beach plain. In all treatments lines from the shrubs had, however, a higher leaf-area ratio as well as delayed flowering when compared to lines from more open subsites. In addition, in a reciprocal transplant experiment it was demonstrated that lines from the shrubs had larger shoots with e.g. broader leaves in the shady environment of the shrubs than other lines.From the experiments no indications were obtained that lines from any subsite were especially adapted to specific levels of nutrient supply or water content of the soil. With respect to these environmental factors P. major ssp. pleisoperma might occur and reproduce at all subsites by means of phenotypic plasticity, e.g. in plant form. However, it is suggested that spatial variability in vegetation structure caused a population subdivision in allocation patterns, leaf form and life history at the beach plain, over distances of about 15–25 m. This differentation occurred during primary succession over a period of twenty years.

Inheritance in tetraploid yeast revisited: segregation patterns and statistical power under different inheritance models.

In their recent article, Albertin et al. (2009) suggest an autotetraploid origin of 10 tetraploid strains of baker’s yeast (Saccharomyces cerevisiae), supported by the frequent observation of double reduction meiospores. However, the presented inheritance results were puzzling and seemed to contradict the authors’ interpretation that segregation ratios support a tetrasomic model of inheritance. Here, we provide an overview of the expected segregation ratios at the tetrad and meiospore level given scenarios of strict disomic and tetrasomic inheritance, for cases with and without recombination between locus and centromere. We also use a power analysis to derive adequate sample sizes to distinguish alternative models. Closer inspection of the Albertin et al. data reveals that strict disomy can be rejected in most cases. However, disomic inheritance with strong but imperfect preferential pairing could not be excluded with the sample sizes used. The possibility of tetrad analysis in tetraploid yeast offers a valuable opportunity to improve our understanding of meiosis and inheritance of tetraploids.