Genetic structure in natural populations of flukes and snails: a practical approach and review

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. 27-40 ◽  
Author(s):  
P. JARNE ◽  
A. THÉRON
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Mating System ◽  
Natural Populations ◽  
Structured Populations ◽  
Biological Traits ◽  
Migration Rates ◽  
External Data ◽  
Selective Interference ◽  
Host Parasite

Several aspects of the coevolutionary dynamics in host-parasite systems may be better quantified based on analyses of population structure using neutral genetic markers. This includes, for example, the migration rates of hosts and parasites. In this respect, the current situation, especially in fluke-snail systems is unsatisfactory, since basic population genetics data are lacking and the appropriate methodology has rarely been used. After reviewing the forces acting on population structure (e.g. genetic drift or the mating system) and how they can be analysed in models of structured populations, we propose a simplified, indicative framework for conducting analyses of population structure in hosts and parasites. This includes consideration of markers, sampling, data analysis, comparison of structure in hosts and parasites and use of external data (e.g. from population dynamics). We then focus on flukes and snails, highlighting important biological traits with regard to population structure. The few available studies indicate that asexual amplification of flukes within snails strongly influences adult flukes populations. They also show that the genetic structure among populations in strongly affected by traits in other than snails (e.g. definitive host dispersal behaviour), as snails populations have limited migration. Finally more studies would allow us to deepen our current understanding of selective interference between flukes and snails (e.g. manipulation of host mating system by parasites), and evaluate how this affect population structure at neutral markers.

scholarly journals Genetic structure of natterjack toad (Epidalea calamita) populations in Flanders, Belgium, and its implications for conservation

2019 ◽  
Vol 40 (2) ◽  
pp. 193-205
Author(s):  
Joke Maes ◽  
Arend Raoul Van Oosten ◽  
Natalie Van Houtte ◽  
Erik Matthysen
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Habitat Management ◽  
Natural Populations ◽  
Conservation Priorities ◽  
Evolutionary Potential ◽  
Isolated Populations ◽  
Genetic Population ◽  
Wide Range ◽  
Epidalea Calamita

Abstract Unique evolutionary potential could be lost when a population goes extinct or when individuals are translocated to other existing populations. Therefore, in order to identify priorities and to predict the efficiency and consequences of conservation actions, information is needed on the genetic structure of natural populations. In the urbanized and diverse landscapes of Flanders, Belgium, natterjack toad (Epidalea calamita) populations have been declining over the last decades. Therefore, this species is subjected to a wide range of different types of conservation measures (e.g. habitat management, corridor development, translocations). However, more information is needed on its genetic population structure. In this study, we sampled egg clutches from six populations and studied their genetic structure with six microsatellite markers. In total, 184 samples from 99 different egg strings were genotyped. Observed heterozygosity was generally high, even for the small and isolated populations (overall mean HO = 0.43). The weak clustering by the Bayesian analyses (STRUCTURE, Adegenet and BAPS) does not allow us to make strong conclusions on the population structure. However, the significant ΦST values between the populations underline the importance of genetic information when conservation priorities are discussed. Unique evolutionary potential could be lost when one or more natterjack toad populations would go extinct, and translocation of individuals to other existing populations should be considered with caution.

scholarly journals Temporal migration rates affect the genetic structure of populations in the biennial Erysimum mediohispanicum with reproductive asynchrony

AoB Plants ◽  
2020 ◽  
Vol 12 (4) ◽  
Author(s):  
A Jesús Muñoz-Pajares ◽  
Mohamed Abdelaziz ◽  
F Xavier Picó
Keyword(s):  
Genetic Structure ◽  
Genetic Parameters ◽  
Natural Populations ◽  
Geographic Population ◽  
Migration Rates ◽  
Microsatellites Markers ◽  
Genetic Structure Of Populations ◽  
Population Genetic Parameters ◽  
Genetic Simulation ◽  
Shed Light

Abstract Migration is a process with important implications for the genetic structure of populations. However, there is an aspect of migration seldom investigated in plants: migration between temporally isolated groups of individuals within the same geographic population. The genetic implications of temporal migration can be particularly relevant for semelparous organisms, which are those that reproduce only once in a lifetime after a certain period of growth. In this case, reproductive asynchrony in individuals of the same population generates demes of individuals differing in their developmental stage (non-reproductive and reproductive). These demes are connected by temporal migrants, that is, individuals that become annually asynchronous with respect to the rest of individuals of their same deme. Here, we investigated the extent of temporal migration and its effects on temporal genetic structure in the biennial plant Erysimum mediohispanicum. To this end, we conducted two independent complementary approaches. First, we empirically estimated temporal migration rates and temporal genetic structure in four populations of E. mediohispanicum during three consecutive years using nuclear microsatellites markers. Second, we developed a demographic genetic simulation model to assess genetic structure for different migration scenarios differing in temporal migration rates and their occurrence probabilities. We hypothesized that genetic structure decreased with increasing temporal migration rates due to the homogenizing effect of migration. Empirical and modelling results were consistent and indicated a U-shape relationship between genetic structure and temporal migration rates. Overall, they indicated the existence of temporal genetic structure and that such genetic structure indeed decreased with increasing temporal migration rates. However, genetic structure increased again at high temporal migration rates. The results shed light into the effects of reproductive asynchrony on important population genetic parameters. Our study contributes to unravel the complexity of some processes that may account for genetic diversity and genetic structure of natural populations.

scholarly journals A stochastic model of selection on selfing rates in structured populations

1995 ◽  
Vol 65 (3) ◽  
pp. 209-222 ◽  
Author(s):  
J. Ronfort ◽  
D. Couvet
Keyword(s):  
Population Structure ◽  
Stochastic Model ◽  
Mating System ◽  
Inbreeding Depression ◽  
Structured Populations ◽  
Empirical Literature ◽  
Mixed Mating ◽  
Selfing Rate ◽  
Mixed Mating System ◽  
Biparental Inbreeding

SummaryPrevious theoretical studies of the evolution of the selfing rate have shown that mixed mating systems are not evolutionary stable states. Such models have, however, not included the effects of population structure and thus biparental inbreeding together with the evolution of selfing rates and inbreeding depression. In order to examine selection on selfing rates in structured populations, a stochastic model simulating a finite population with partial selfing and restricted pollen and seed dispersal has been developed. Selection on the mating system was followed by introducing modifiers affecting the selfing rate. The major result was that, with density dependent recruitment, a process which maintains the population structure necessary for biparental inbreeding to occur, a mixed mating system could be maintained. This result was associated with an increase of the mutation load with high selfing rates, and the selected selfing rate depended on the degree of population structure rather than on the initial selfing rate. With low dominance of deleterious alleles, complete allogamy can be selected for. Further studies showed that the more general condition of spatial heterogeneity of recruitment can lead to similar results, the most important condition being the maintenance of genetic structure within populations. A brief survey of the empirical literature shows that a positive relationship between the magnitude of inbreeding depression and the inbreeding coefficient within populations has been observed, in support of the present model.

scholarly journals Environmental Patterns Are Imposed on the Population Structure ofEscherichia coliafter Fecal Deposition

2010 ◽  
Vol 77 (1) ◽  
pp. 211-219 ◽  
Author(s):  
Peter W. Bergholz ◽  
Jesse D. Noar ◽  
Daniel H. Buckley
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Environmental Gradients ◽  
Natural Populations ◽  
Genomic Diversity ◽  
Source Analysis ◽  
Ecological Processes ◽  
New Host ◽  
E Coli ◽  
Landscape Genetic

ABSTRACTThe intestinal microbeEscherichia coliis subject to fecal deposition in secondary habitats, where it persists transiently, allowing for the opportunity to colonize new hosts. Selection in the secondary habitat can be postulated, but its impact on the genomic diversity ofE. coliis unknown. Environmental selective pressure on extrahostE. colican be revealed by landscape genetic analysis, which examines the influences of dispersal processes, landscape features, and the environment on the spatiotemporal distribution of genes in natural populations. We conducted multilocus sequence analysis of 353E. coliisolates from soil and fecal samples obtained in a recreational meadow to examine the ecological processes controlling their distributions. Soil isolates, as a group, were not genetically distinct from fecal isolates, with only 0.8% of genetic variation and no fixed mutations attributed to the isolate source. Analysis of the landscape genetic structure ofE. colipopulations showed a patchy spatial structure consistent with patterns of fecal deposition. Controlling for the spatial pattern made it possible to detect environmental gradients of pH, moisture, and organic matter corresponding to the genetic structure ofE. coliin soil. Ecological distinctions amongE. colisubpopulations (i.e.,E. colireference collection [ECOR] groups) contributed to variation in subpopulation distributions. Therefore, while fecal deposition is the major predictor ofE. colidistributions on the field scale, selection imposed by the soil environment has a significant impact onE. colipopulation structure and potentially amplifies the occasional introduction of stress-tolerant strains to new host individuals by transmission through water or food.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Average Number of Nucleotide Differences in a Sample From a Single Subpopulation: A Test for Population Subdivision

Genetics ◽  
1987 ◽  
Vol 117 (1) ◽  
pp. 149-153
Author(s):  
Curtis Strobeck
Keyword(s):  
Monte Carlo Simulation ◽  
Population Structure ◽  
Random Mating ◽  
Population Subdivision ◽  
Expected Number ◽  
Migration Rates ◽  
Mating Population ◽  
Unbiased Estimates ◽  
Increasing Function ◽  
Stepping Stone Model

ABSTRACT Unbiased estimates of θ = 4Nµ in a random mating population can be based on either the number of alleles or the average number of nucleotide differences in a sample. However, if there is population structure and the sample is drawn from a single subpopulation, these two estimates of θ behave differently. The expected number of alleles in a sample is an increasing function of the migration rates, whereas the expected average number of nucleotide differences is shown to be independent of the migration rates and equal to 4N  Tµ for a general model of population structure which includes both the island model and the circular stepping-stone model. This contrast in the behavior of these two estimates of θ is used as the basis of a test for population subdivision. Using a Monte-Carlo simulation developed so that independent samples from a single subpopulation could be obtained quickly, this test is shown to be a useful method to determine if there is population subdivision.

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