Population Differentiation In Daphnia Alters Community Assembly In Experimental Ponds

Most studies of community assembly ignore how genetic differentiation within species affects their colonization and extinction. However, genetic differentiation in ecologically relevant traits may be substantial enough to alter the colonization and extinction processes that drive community assembly. We measured significant molecular genetic and quantitative trait differentiation among three Daphnia pulex X pulicaria populations in southwestern Michigan ponds and investigated whether this differentiation could alter the assembly of pond zooplankton communities in experimental mesocosms. In this study, we monitored the invasion success of different D. pulex x pulicaria populations after their introduction into an established zooplankton community. We also monitored the invasion success of a diverse array of zooplankton species into different D. pulex x pulicaria populations. Zooplankton community composition depended on the D. pulex X pulicaria source population. Daphnia pulex X pulicaria from one population failed to invade zooplankton communities, while those from other populations successfully invaded similar communities. If population differentiation in other species plays a role in community assembly similar to that demonstrated in our study, assembly may be more sensitive to evolutionary processes than has been previously generally considered.Integrative Biolog

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations

Adaptive vs. neutral genetic diversity: implications for landscape genetics

Genetic diversity is important for the maintenance of the viability and the evolutionary or adaptive potential of populations and species. However, there are two principal types of genetic diversity: adaptive and neutral - a fact widely neglected by non-specialists. We introduce these two types of genetic diversity and critically point to their potential uses and misuses in population or landscape genetic studies. First, most molecular-genetic laboratory techniques analyse neutral genetic variation. This means that the gene variants detected do not have any direct effect on fitness. This type of genetic variation is thus selectively neutral and tells us nothing about the adaptive or evolutionary potential of a population or a species. Nevertheless, neutral genetic markers have great potential for investigating processes such as gene flow, migration or dispersal. Hence, they allow us to empirically test the functional relevance of spatial indices such as connectivity used in landscape ecology. Second, adaptive genetic variation, i.e. genetic variation under natural selection, is analysed in quantitative genetic experiments under controlled and uniform environmental conditions. Unfortunately, the genetic variation (i.e. heritability) and population differentiation at quantitative, adaptive traits is not directly linked with neutral genetic diversity or differentiation. Thus, neutral genetic data cannot serve as a surrogate of adaptive genetic data. In summary, neutral genetic diversity is well suited for the study of processes within landscapes such as gene flow, while the evolutionary or adaptive potential of populations or species has to be assessed in quantitative genetic experiments. Landscape ecologists have to mind these differences between neutral and adaptive genetic variation when interpreting the results of landscape genetic studie

The ecology and genetics of central and peripheral populations of Carduus defloratus

The aim of this thesis was to test several of the predictions of the abundant centre model (ACM) by comparing central and peripheral populations of the model species Carduus defloratus along a gradient from the centre towards the periphery of the distribution of the species. The ACM predicts that because of increasingly unfavorable and stressful conditions populations become less frequent, smaller, and less dense towards the range edges. Further predictions for peripheral populations derived from the model include lower reproduction of organisms, higher temporal variability of demographic transitions and of population growth rates, higher genetic differentiation among populations and lower within-population genetic diversity. Most of these predictions of the ACM were supported in C. defloratus. The size of populations, their density and reproduction, but also the proportion of seeds damaged by insects decreased from the distribution centre of the species towards the periphery. The number of flowering plants in a population influenced all components of reproduction. Plants in large populations initiated more seeds, aborted less seeds, and produced more and larger seeds per plant. This indicates pollen limitation and increased inbreeding in small, peripheral populations. The strongly reduced reproduction in combination with the lack of suitable, open rocky habitats and poor dispersal of the seeds limits the abundance of C. defloratus towards its northern range limit. Demographic studies in 14 populations of C. defloratus along the central-peripheral gradient did not indicate significant differences between peripheral and central populations in the asymptotic growth rate (λ) of the populations, of the temporal variability in λ, or in the extinction risk of populations of a certain size. However, the variability of several demographic transitions like seedling survival and stasis of vegetative plants decreased toward the periphery, but changes in these transitions compensated each other. These results are in contrast to the hypothesis of increasing demographic variability towards the periphery of the distribution of a species and an increased extinction risk of peripheral populations. Both population types differed significantly in particular demographic transitions, the contribution of particular transitions to λ, their stage structure, and the life span of plants. The fact that demographic features of C. defloratus showed clinal variation related to gradients in centrality and thus climate, suggest that it might be possible to predict general demographic features for individual populations based on their environment. An analysis of the genetic variability and genetic structure of 78 populations of C. defloratus based on AFLPs indicated that genetic variability within populations decreased towards the periphery whereas the genetic differentiation between populations increased. A strong increase of genetic differentiation between pairs of populations with their geographic distance (isolation by distance) indicated gene flow between neighbouring populations. The pattern found is likely to have been formed during the last glaciation, because the populations of C. defloratus outside of the Alps are very isolated and gene flow between them has been very unlikely for a long time. This result together with the small effect of current population size on genetic variability indicates that the population genetic structure of the long-lived species is mainly influenced by historical processes. Like the genetic diversity of molecular genetic markers, that of several quantitative traits decreased from the distribution centre towards the range margin. However, in contrast to the molecular genetic differentiation, the differentiation in quantitative traits did not increase towards the periphery. Quantitative and molecular genetic diversity were not correlated significantly and correlations between quantitative and molecular genetic differentiation were either weak or not significant. The quantitative genetic differentiation of several traits (QST) between 32 populations of C. deflorauts was stronger than the differentiation between molecular markers (PhiST) and some traits showed clinal variation with regard to environmental gradients, indicating that divergent selection acts on quantitative traits. The clinal variation in quantitative traits indicates that the observed differences are adaptive. The northern peripheral populations are likely to contain alleles that may become important for the adaptation of the species to a warmer climate. The northern range limit of C. defloratus rather results from lack of suitable open, rocky habitats than from poor adaptation to climatic conditions in the north. Altogether, the combination of different studies on a single model species and the results of this thesis contribute to a better understanding of the role of current and historic, and of demographic and genetic processes for the differentiation between central and peripheral populations. Moreover, these studies contribute to the discussion about the conservation value of small, peripheral populations in a time of climatic change

The ecology, genetics and evolution of two Saxifraga species with different fragmentation histories

The aim of this thesis was to study the ecology, genetics and evolution of two congeneric species with different fragmentation histories. Saxifraga sponhemica is a glacial relict species of long-term fragmented lowland rock and scree habitats, and has been naturally rare for thousands of years with a disjunct distribution in Central Europe. Saxifraga granulata is a formerly common species of species-rich semi-natural grasslands that has become recently fragmented due to the intensification of agricultural practices. Fragmentation generally leads to loss of genetic diversity due to drift and inbreeding, reduced mean fitness and increased extinction rates of populations. Formerly common species are expected to be particularly susceptible to the recent anthropogenic fragmentation of their habitats. An analysis of the genetic diversity and the genetic structure of S. sponhemica populations based on RAPD-markers showed that in most populations considerable genetic variability has been preserved. An isolation by distance pattern of genetic differentiation suggested historical gene flow during the last glaciation when suitable habitats were much more abundant. Long-lived plant species can thus maintain historic genetic patterns despite the small size and strong isolation of populations. We grew plants form several families per population in a common garden to study the quantitative genetic variation within and among populations. We found several lines of evidence for divergent selection. Most population trait means were significantly related to climate gradients, indicating adaptation. Quantitative genetic differentiation increased with climatic distance and with geographical distance, even when neutral molecular divergence was controlled for, and quantitative genetic differentiation (QST) exceeded molecular genetic differentiation (FST) for some traits. Traits under strong selection showed little genetic variation within populations. The evolutionary potential of a population was not related to its size, the performance of the population or its neutral genetic diversity. However, performance in the common garden was lower for plants from populations with reduced molecular genetic variation, suggesting inbreeding depression due to genetic erosion. Studies of molecular and quantitative genetic variation may thus provide complementary insights important for the conservation of rare species. S. sponhemica does not appear to be genetically threatened in the short term, but populations are threatened by habitat destruction. A conservation measure could be to create new populations in suitable habitats with seeds from the same region to avoid local maladaptation. We also studied the RAPD molecular and the quantitative genetic structure of 19 populations of the declining grassland plant S. granulata in a geographically restricted area in Luxembourg and Germany. Differentiation for quantitative traits (QST) was slightly lower than differentiation for molecular markers (FST) suggesting homogenising selection for optimal trait values. Contrary to our expectations, the level of differentiation among fragmented S. granulata populations was low, and molecular genetic diversity was high and was not correlated with the size or the mean plant performance of populations. Gene flow by long distance dispersal or the longevity, clonality and polyploidy of S.granulata may have prevented genetic erosion due to drift. To avoid genetic erosion in the future, extant populations should be preserved and gene flow among populations should be maintained. Habitat fragmentation has led to increased inbreeding and inbreeding depression in many species. We investigated the effects of increased inbreeding and of intra- and interpopulation crosses on the reproduction and performance of S. granulata. Between population crosses may result in increased performance (heterosis), but may also lead to the disruption of coadapted gene complexes and to decreased performance (outbreeding depression). Inbreeding depression affected all traits in the F1 generation, but was stronger for traits expressed late during development and varied among families. Multiplicative fitness of the F2 generation after serial inbreeding was extremely low, but there was heterosis after crossing inbred lines. Outbreeding depression was however not observed in the F2. We also subjected the first generation of offspring to a fertilization and stress treatments (competition and defoliation). The adaptive plasticity of offspring from selfing and from interpopulation crosses in response to nutrient addition was reduced. Outbreeding depression was also observed in response to stress. The results suggest that continuous inbreeding may drastically reduce the fitness of plants, but effects may be environment-dependent. Overall, the results of this thesis advance knowledge on the role of time since habitat fragmentation, of historic connectivity among populations, and of life history traits such as longevity and clonality on the processes of selection and drift that shape the genetic variation within and among populations. It stresses the importance of using both molecular and quantitative genetic tools to gain complementary insight for the conservation of rare and endangered plant species. It shows how knowledge about the vulnerability to increased inbreeding and the potential risks of artificially increasing gene flow between populations of recently fragmented species contributes to their effective conservation

Genetic differentiation, effective population size and gene flow in marine fishes : implications for stock management

Many commercially exploited marine fish and mollusc species exhibit no or a low degree of genetic differentiation in neutral marker genes. This lack of genetic differentiation, typically attributed to high degree of gene flow in marine environments, has sometimes supported the thinking that genetically indistinguishable stocks can be managed as being one panmictic population. Recent comparative studies of neutral marker gene and quantitative trait differentiation in a wide variety of taxa - including several marine organisms - show that a high degree of genetic differentiation (as measured by Q_) in ecologically and economically important traits is a common place occurrence, even when the degree of differentiation in neutral marker genes (as measured by F_) is low or absent. In fact, among the empirical studies made so far, the outcome Q_>F_ is pervasive. This accords with the increasing evidence that natal homing and self-replenishment of local populations may be more common in marine habitats than previously anticipated. If so, the low degree of genetic differentiation in neutral genetic markers could be a simple consequence of the large effective population size (N_e) of many marine populations, effectively buffering them against differentiation due to genetic drift. However, genetic markers linked to parts of the genome under directional selection should readily diverge in allele frequencies especially when N_e is high. In fact, several recent studies have discovered that such loci provide a way to differentiate among stocks undifferentiated in neutral marker genes. Hence, the study of adaptive rather than neutral genetic differentiation among fish and shellfish populations might provide practical tools for stock identification and thereby contribute to improved fisheries policies.Special Revie

Estimators for QST and coalescence times.

Comparisons of QST to FST can provide insights into the evolutionary processes that lead to differentiation, or lack thereof, among the phenotypes of different groups (e.g., populations, species), and these comparisons have been performed on a variety of taxa, including humans. Here, I show that for neutrally evolving (i.e., by genetic drift, mutation, and gene flow alone) quantitative characters, the two commonly used QST estimators have somewhat different interpretations in terms of coalescence times, particularly when the number of groups that have been sampled is small. A similar situation occurs for FST estimators. Consequently, when observations come from only a small number of groups, which is not an unusual situation, it is important to match estimators appropriately when comparing QST to FST

Molecular and Quantitative Genetic Differentiation in European Populations of Silene latifolia (Caryophyllaceae)

Background and Aims Among-population differentiation in phenotypic traits and allelic variation is expected as a consequence of isolation, drift, founder effects and local selection. Therefore, investigating molecular and quantitative genetic divergence is a pre-requisite for studies of local adaptation in response to selection under variable environmental conditions. Methods Among- and within-population variation were investigated in six geographically separated European populations of the white campion, Silene latifolia, both for molecular variation at six newly developed microsatellite loci and for quantitative variation in morphological and life-history traits. To avoid confounding effects of the maternal environment, phenotypic traits were measured on greenhouse-reared F1 offspring. Tests were made for clinal variation, and the correlations among molecular, geographic and phenotypic distances were compared with Mantel tests. Key Results The six populations of Silene latifolia investigated showed significant molecular and quantitative genetic differentiation. Geographic and phenotypic distances were significantly associated. Age at first flowering increased significantly with latitude and exhibited a Qst value of 0·17 in females and 0·10 in males, consistent with adaptation to local environmental conditions. By contrast, no evidence of isolation-by-distance and no significant association between molecular and phenotypic distances were found. Conclusions Significant molecular genetic divergence among populations of Silene latifolia, from the European native range is consistent with known limited seed and pollen flow distances, while significant quantitative genetic divergence among populations and clinal variation for age at first flowering suggest local adaptatio

Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs. molecular traits

Understanding the origin, maintenance and significance of phenotypic variation is one of the central issues in evolutionary biology. An ongoing discussion focuses on the relative roles of isolation and selection as being at the heart of genetically based spatial variation. We address this issue in a representative of a taxon group in which isolation is unlikely: a marine broadcast spawning invertebrate. During the free-swimming larval phase, dispersal is potentially very large. For such taxa, small-scale population genetic structuring in neutral molecular markers tends to be limited, conform expectations. Small-scale differentiation of selective traits is expected to be hindered by the putatively high gene flow. We determined the geographical distribution of molecular markers and of variation in a shell shape measure, globosity, for the bivalve Macoma balthica (L.) in the western Dutch Wadden Sea and adjacent North Sea in three subsequent years, and found that shells of this clam are more globose in the Wadden Sea. By rearing clams in a common garden in the laboratory starting from the gamete phase, we show that the ecotypes are genetically different; heritability is estimated at 23%. The proportion of total genetic variation that is between sites is much larger for the morphological additive genetic variation (QST = 0.416) than for allozyme (FST = 0.000–0.022) and mitochondrial DNA cytochrome-c-oxidase-1 sequence variation (ΦST = 0.017). Divergent selection must be involved and intraspecific spatial genetic differentiation in marine broadcast spawners is apparently not constrained by low levels of isolation.

Expression quantitative trait loci are highly sensitive to cellular differentiation state

Blood cell development from multipotent hematopoietic stem cells to specialized blood cells is accompanied by drastic changes in gene expression for which the triggers remain mostly unknown. Genetical genomics is an approach linking natural genetic variation to gene expression variation, thereby allowing the identification of genomic loci containing gene expression modulators (eQTLs). In this paper, we used a genetical genomics approach to analyze gene expression across four developmentally close blood cell types collected from a large number of genetically different but related mouse strains. We found that, while a significant number of eQTLs (365) had a consistent “static” regulatory effect on gene expression, an even larger number were found to be very sensitive to cell stage. As many as 1,283 eQTLs exhibited a “dynamic” behavior across cell types. By looking more closely at these dynamic eQTLs, we show that the sensitivity of eQTLs to cell stage is largely associated with gene expression changes in target genes. These results stress the importance of studying gene expression variation in well-defined cell populations. Only such studies will be able to reveal the important differences in gene regulation between different ce