Sarah Geldof

Bio: Sarah Geldof is an academic researcher from Katholieke Universiteit Leuven. The author has contributed to research in topics: Population & Schistosoma mansoni. The author has an hindex of 7, co-authored 9 publications receiving 500 citations.

Bidirectional introgressive hybridization between a cattle and human schistosome species.

Abstract: Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions, caused by parasitic flatworms of the genus Schistosoma (subclass Digenea). Following major water development schemes in the 1980s, schistosomiasis has become an important parasitic disease of children living in the Senegal River Basin (SRB). During molecular parasitological surveys, nuclear and mitochondrial markers revealed unexpected natural interactions between a bovine and human Schistosoma species: S. bovis and S. haematobium, respectively. Hybrid schistosomes recovered from the urine and faeces of children and the intermediate snail hosts of both parental species, Bulinus truncatus and B. globosus, presented a nuclear ITS rRNA sequence identical to S. haematobium, while the partial mitochondrial cox1 sequence was identified as S. bovis. Molecular data suggest that the hybrids are not 1st generation and are a result of parental and/or hybrid backcrosses, indicating a stable hybrid zone. Larval stages with the reverse genetic profile were also found and are suggested to be F1 progeny. The data provide indisputable evidence for the occurrence of bidirectional introgressive hybridization between a bovine and a human Schistosoma species. Hybrid species have been found infecting B. truncatus, a snail species that is now very abundant throughout the SRB. The recent increase in urinary schistosomiasis in the villages along the SRB could therefore be a direct effect of the increased transmission through B. truncatus. Hybridization between schistosomes under laboratory conditions has been shown to result in heterosis (higher fecundity, faster maturation time, wider intermediate host spectrum), having important implications on disease prevalence, pathology and treatment. If this new hybrid exhibits the same hybrid vigour, it could develop into an emerging pathogen, necessitating further control strategies in zones where both parental species overlap.

Divergent selection as revealed by P(ST) and QTL-based F(ST) in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient.

Abstract: Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P(ST) (a phenotypic alternative for Q(ST)) and neutral F(ST). However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F(ST) at only one of two QTL was detected as an outlier, although F(ST) at both loci correlated significantly with P(ST). No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P(ST) were observed.

Modeling genetic connectivity in sticklebacks as a guideline for river restoration

Abstract: Estimating genetic connectivity in disturbed riverine landscapes is of key importance for river restoration. However, few species of the disturbed riverine fauna may provide a detailed and basin-wide picture of the human impact on the population genetics of riverine organisms. Here we used the most abundant native fish, the three-spined stickleback (Gasterosteus aculeatus L.), to detect the geographical determinants of genetic connectivity in the eastern part of the Scheldt basin in Belgium. Anthropogenic structures came out as the strongest determinant of population structure, when evaluated against a geographically well-documented baseline model accounting for natural effects. These barriers not only affected genetic diversity, but they also controlled the balance between gene flow and genetic drift, and therefore may crucially disrupt the population structure of sticklebacks. Landscape models explained a high percentage of variation (allelic richness: adjusted R2 = 0.78; pairwise FST: adjusted R2 = 0.60), and likely apply to other species as well. River restoration and conservation genetics may highly benefit from riverine landscape genetics, including model building, the detection of outlier populations, and a specific test for the geographical factors controlling the balance between gene flow and genetic drift.

Guidelines for restoring connectivity around water mills: a population genetic approach to the management of riverine fish

Abstract: Summary 1. While freshwater systems provide important goods and services for society, they are threatened by human activity. Fragmentation is one of the most serious ecological concerns in the riverine environment. 2. Historical and cultural values may conflict with nature restoration. Here we use the Zwalm sub-basin (Scheldt basin, Belgium) as a case study for reconciling the restoration of the native fish fauna with the preservation of historical water mills (320‐1000 years old). 3. We assessed the genetic structure of a barrier-sensitive species, the three-spined stickleback Gasterosteus aculeatus , to estimate the impact of fragmentation on a local to catchment scale. We show how population genetic approaches may be used to generate guidelines for restoration and management, and advance the science of river restoration. 4. Dispersal was lower in above- than in below-mill populations, and water mills provoked an average loss of almost 4% of the genetic variation. This loss accumulated to 40% over the entire system (~23 km, 13 barriers). The impact of individual mills strongly increased with upstream distance and water mill height. One mill provoked significant genetic differentiation, despite the presence of a fish passage. 5. This detailed picture of the genetic connectivity in stickleback is indicative for the basin’s depauperate fauna. Many species share the same migratory pathways and barriers to dispersal. The physical properties of the water mills are likely to have similar effects on species with a similar genetic structure to stickleback. 6. Synthesis and applications . Population genetic studies may be particularly useful during the planning of river restoration and associated ecological studies. In the case of the Zwalm sub-basin, we propose a number of management actions, such as building new fish passages and translocating individuals to above-mill populations. These will counter the negative impact of the water mills on the genetic variation in aquatic fauna, whilst retaining their cultural‐economical value and limiting the restoration costs. Simulations suggest that reassessment of stickleback genetic structure after a decade should reveal whether or not restoration actions have been effective.

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

Abstract: Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP–based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such regions in natural populations, and identifying new genomic regions and candidate genes of evolutionary significance.

Landscape genetics: where are we now?

Abstract: Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Individual dispersal, landscape connectivity and ecological networks.

Abstract: Connectivity is classically considered an emergent property of landscapes encapsulating individuals’ flows across space. However, its operational use requires a precise understanding of why and how organisms disperse. Such movements, and hence landscape connectivity, will obviously vary according to both organism properties and landscape features. We review whether landscape connectivity estimates could gain in both precision and generality by incorporating three fundamental outcomes of dispersal theory. Firstly, dispersal is a multi-causal process; its restriction to an ‘escape reaction’ to environmental unsuitability is an oversimplification, as dispersing individuals can leave excellent quality habitat patches or stay in poor-quality habitats according to the relative costs and benefits of dispersal and philopatry. Secondly, species, populations and individuals do not always react similarly to those cues that trigger dispersal, which sometimes results in contrasting dispersal strategies. Finally, dispersal is a major component of fitness and is thus under strong selective pressures, which could generate rapid adaptations of dispersal strategies. Such evolutionary responses will entail spatiotemporal variation in landscape connectivity. We thus strongly recommend the use of genetic tools to: (i) assess gene flow intensity and direction among populations in a given landscape; and (ii) accurately estimate landscape features impacting gene flow, and hence landscape connectivity. Such approaches will provide the basic data for planning corridors or stepping stones aiming at (re)connecting local populations of a given species in a given landscape. This strategy is clearly species- and landscape-specific. But we suggest that the ecological network in a given landscape could be designed by stacking up such linkages designed for several species living in different ecosystems. This procedure relies on the use of umbrella species that are representative of other species living in the same ecosystem.

Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis.

Abstract: Comparative studies of quantitative genetic and neutral marker differentiation have provided means for assessing the relative roles of natural selection and random genetic drift in explaining among-population divergence. This information can be useful for our fundamental understanding of population differentiation, as well as for identifying management units in conservation biology. Here, we provide comprehensive review and meta-analysis of the empirical studies that have compared quantitative genetic (QST) and neutral marker (FST) differentiation among natural populations. Our analyses confirm the conclusion from previous reviews – based on ca. 100% more data – that the QST values are on average higher than FST values [mean difference 0.12 (SD 0.27)] suggesting a predominant role for natural selection as a cause of differentiation in quantitative traits. However, although the influence of trait (life history, morphological and behavioural) and marker type (e.g. microsatellites and allozymes) on the variance of the difference between QST and FST is small, there is much heterogeneity in the data attributable to variation between specific studies and traits. The latter is understandable as there is no reason to expect that natural selection would be acting in similar fashion on all populations and traits (except for fitness itself). We also found evidence to suggest that QST and FST values across studies are positively correlated, but the significance of this finding remains unclear. We discuss these results in the context of utility of the QST–FST comparisons as a tool for inferring natural selection, as well as associated methodological and interpretational problems involved with individual and meta-analytic studies.

Evolutionary inference from QST

Abstract: Q(ST) is a commonly used metric of the degree of genetic differentiation among populations displayed by quantitative traits. Typically, Q(ST) is compared to F(ST) measured on putatively neutral loci; if Q(ST)=F(ST), this is taken as evidence of spatially heterogeneous and diversifying selection. This paper reviews the uses, assumptions and statistics of Q(ST) and F(ST) comparisons. Unfortunately, Q(ST)/F(ST) comparisons are statistically challenging. For a single trait, Q(ST) must be compared not to the mean F(ST) but to the distribution of F(ST) values. The sources of biases and sampling error for Q(ST) are reviewed, and a new method for comparing Q(ST) and F(ST) is suggested. Simulation results suggest that the distribution of neutral F(ST) and Q(ST) values are little affected by various deviations from the island model. Consequently, the distributions of Q(ST) and F(ST) are well approximated by the Lewontin-Krakauer prediction, even with realistic deviations from the island-model assumptions.