Population genetics studies using microsatellites, and data on their molecular dynamics, are on the increase. But, so far, no consensus has emerged on which mutation model should be used, though this is of paramount importance for analysis of population genetic structure. However, this is not surprising given the variety of microsatellite molecular motifs. Null alleles may be disturbing for population studies, even though their presence can be detected through careful population analyses, while homoplasy seems of little concern, at least over short evolutionary scales. Interspecific studies show that microsatellites are poor markers for phylogenetic inference. However, these studies are fuelling discussions on directional mutation and the role of selection and recombination in their evolution. Nonetheless, it remains true that microsatellites may be considered as good, neutral mendelian markers.

Microsatellites, from molecules to populations and back

LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

Attempts to relate estimates of regional FST to gene flow and drift via Wright's (1931) equation FST ≈ 1/ (4Nm + 1) are often inappropriate because most natural sets of populations probably are not at equilibrium (McCauley 1993), as assumed by the island model upon which the equation is based, or ineffective because the influences of gene flow and drift are confounded in the product Nm. Evaluations of the association between genetic (FST ) and geographic distances separating all pairwise populations combinations in a region allows one to test for regional equilibrium, to evaluate the relative influences of gene flow and drift on population structure both within and between regions, and to visualize the behavior of the association across all degrees of geographic separation. Tests of the model using microsatellite data from 51 populations of eastern collared lizards (Crotaphytus collaris collaris) collected from four distinct geographical regions gave results highly consistent with predicted patterns of association based on regional differences in various historical and ecological factors that affect the amount of drift and gene flow. The model provides a prerequisite for and an alternative to regional FST analyses, which often simply assume regional equilibrium, thus potentially leading to erroneous and misleading inferences regarding regional population structure.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1999.tb04571.x

Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability

R ST, an analogue of FST, provides a convenient approach for estimating levels of genetic differentiation from microsatellite data. This paper examines current approaches for calculating estimates of RST and suggests a weighting scheme based on the transformation of allele sizes at loci across data sets. Combined within an analysis of variance framework this scheme yields an estimator of RST analogous to the θ estimator of FST. Software for the IBM‐PC is described which carries out such calculations and assesses the significance of RST or Nm estimates using bootstrap and permutation tests.

RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance

We investigated genetic population structure in wood frogs (Rana sylvatica) from a series of Prairie Pothole wetlands in the northern Great Plains. Amphibians are often thought to exist in demographic metapopulations, which require some movement between populations, yet genetic studies have revealed strong subdivision among populations, even at relatively fine scales (several km). Wood frogs are highly philopatric and studies of dispersal suggest that they may exhibit subdivision on a scale of approximately 1-2 km. We used microsatellites to examine population structure among 11 breeding assemblages separated by as little as 50 m up to approximately 5.5 km, plus one population separated from the others by 20 km. We found evidence for differentiation at the largest distances we examined and among a few neighbouring ponds, but most populations were strikingly similar in allele frequencies, suggesting high gene flow among all but the most distant populations. We hypothesize that the few significant differences among neighbouring populations at the finest scale may be a transient effect of extinction-recolonization founder events, driven by periodic drying of wetlands in this hydrologically dynamic landscape.

Microsatellite variation and fine‐scale population structure in the wood frog (Rana sylvatica)

Hermaphrodite tropical freshwater snails provide a good opportunity to study the effects of mating system and genetic drift on population genetic structure because they are self-fertile and they occupy transient patchily distributed habitats (ponds). Up to now the lack of detectable allozyme polymorphism prevented any intrapopulation studies. In this paper, we examine the consequences of selfing and bottlenecks on genetic polymorphism using microsatellite markers in 14 natural populations (under a hierarchical sampling design) of the hermaphrodite freshwater snail Bulinus truncatus. These population genetics data allowed us to discuss the currently available mutation models for microsatellite sequences. Microsatellite markers revealed an unexpectedly high levels of genetic variation with <=41 alleles for one locus and gene diversity of 0.20-0.75 among populations. The values of any estimator of F(is) indicate high selfing rates in all populations. Linkage disequilibria observed at all loci for some populations may also indicate high levels of inbreeding. The large extent of genetic differentiation measured by F(st), R(st) or by a test for homogeneity between genic distributions is explained by both selfing and bottlenecks. Despite a limited gene flow, migration events could be detected when comparing different populations within ponds.

/pdf/microsatellites-and-the-genetics-of-highly-selfing-4q9paeoo7e.pdf

Microsatellites and the Genetics of Highly Selfing Populations in the Freshwater Snail Bulinus truncatus

La caracterisation de schistosomes par la morphologie des oeufs intra-uterins des vers femelles et l'analyse des phenotypes des parasites observes pour la phosphatase acide apres separation electrophoretique suggere la presence de genes de S. bovis, parasite du betail domestique, chez des schistosomes issus de l'homme dans la region est du Niger et presumes appartenir a l'espece S. haematobium

/pdf/arguments-en-faveur-d-une-modification-du-genome-4ga43o71hl.pdf

Arguments en faveur d'une modification du génome (introgression) du parasite humain Schistosoma haematobium par des gènes de S. bovis , au Niger

Background Currently, the control of urinary schistosomiasis is mostly based on mass treatment. Characterization of Schistosoma haematobium transmission could lead to adding new methods to the control strategy. Methods We carried out malacological and cercariometrical surveys in irrigated perimeters of the Niger River valley. A semi-monthly follow-up was performed in three main sites of human-water contact in a village located at the border of the irrigated perimeter. Bulinids were collected during 20 min; after identification based on the shell morphology, their parasites were characterized by isoelectrofocalisation. The cercariometrical technique by differential filtration was used to evaluate the density of cercariae in every site with two 20 litres samples of water collected at various periods of the day (9, 12, 15 and 18 h). Results In the arm of the river, the cercariometry never showed cercariae whereas only some Bulinus truncatus, all negative, were collected. In the channels, B. truncatus and B. globosus were observed and highest density was found during the dry season. Only B. truncatus was naturally infested. Homozygote BB phenotype (characteristic of S. haematobium) was observed in all positive molluscs. Using cercariometry, more than two third of cercariae were collected at 3:00 PM. Conclusion Transmission of S. haematobium was primarily focused in the irrigating channels during the dry hot season at the beginning of afternoon. These results should lead to improve the output of S. haematobium control methods within irrigated areas.

Focalisation de la transmission de Schistosoma haematobium au sein des périmètres irrigués de la vallée du Niger (Niger) : importance des facteurs malacologiques

We investigated the genetic variability for phally polymorphism within and between natural populations of the hermaphrodite self-fertile freshwater snail Bulinus truncatus. Phally polymorphism is characterized by the co-occurrence in natural populations of regular hermaphrodite individuals (euphallic) and individuals deprived of the male copulatory organ (aphallic). The two morphs can both self-fertilize and outcross. However, aphallic individuals cannot outcross as males. We examined the variation of the aphally ratio in 22 natural populations from Niger over two successive years. During the second years, populations were sampled three times at 3 week intervals. The aphally ratio was highly variable among populations at a given sampling data and remained relatively stable over time. For 10 of these populations, one population from Corsica and two from Sardinia, we also estimated the between- and within- population variability, analysing the aphally ratio of 346 families under laboratory conditions. The aphally ratio varied significantly among populations and was highly correlated with the aphally ratio of the natural populations. Some within-population variability, associated with a high value of the broad sense heritability, was observed in four populations out of 13. In these populations, aphallic individuals produced significantly more aphallic offspring than euphallic individuals. Our results indicate a strong genetic basis for aphally, with large genetic differences among populations and some genetic variability for aphally within populations. We discuss the adaptive and stochastic factors that may shape the distribution of the genetic variability for aphally.

R. Labbo

Papers

Microsatellites and the Genetics of Highly Selfing Populations in the Freshwater Snail Bulinus truncatus

Arguments en faveur d'une modification du génome (introgression) du parasite humain Schistosoma haematobium par des gènes de S. bovis , au Niger

Focalisation de la transmission de Schistosoma haematobium au sein des périmètres irrigués de la vallée du Niger (Niger) : importance des facteurs malacologiques

Stability and genetic basis of variability of phally polymorphism in natural populations of the self-fertile freshwater snail Bulinus truncatus

Le risque bilharzien dans la région du barrage de Bagré, Burkina Faso