The population genetics of clonal and partially clonal diploids

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).     

cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms

Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, cloncase , for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The cloncase method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. three‐quarter of individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexual reproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonal organism (N_c = 998) was in good agreement with estimates obtained using methods based on temporal variations in allelic frequencies. The cloncase estimator presented herein is the first method allowing accurate inference of both sex frequency and effective population size from population data without knowledge of recombination or mutation rates. cloncase can be applied to population genetic data from any organism with cyclical parthenogenesis and should in particular be very useful for improving our understanding of pest and microbial population biology.     

Density-dependent population dynamics in clonal organisms: a modelling approach

1. Density dependence may act at several stages in an organisms life-cycle (e.g. on mortality, fecundity, etc.), but not all density-dependent processes necessarily regulate population size. In this paper I use a density manipulation experiment to determine the effects of density on the transition rates between different size classes of the clonal zoanthid Palythoa caesia Dana 1846. I then formulate a density-dependent matrix model of population dynamics of Palythoa , and perform a series of sensitivity analyses on the model to determine at what stage in the life-cycle regulation acts.
2. Seven of the 16 transition probabilities decreased with density, most of them being shrinkage (due to loss of tissue or fission) and stasis (the self–self transition) of medium and large colonies. The only probability to increase was for the stasis of large colonies. Recruitment was quadratically dependent on density, peaking at intermediate densities.
3. Equilibrium cover in the model was 84% and was reached in ≈40 years. To determine which density-dependent transitions were involved in population regulation, the strength of density dependence was varied in each independently. This sensitivity analysis showed that only changes in the probabilities of large colonies remaining large and producing medium colonies, were regulating.
4. These results suggest that regulation is primarily acting on fission of large colonies to produce intermediate-sized colonies, in combination with size specific growth rates. Fission rates decrease greatly with density, resulting in a greater proportion of large colonies at high densities and large colonies grow more slowly than small. Overall, this behaviour is very similar to that of clonal plants which have a phalanx type life history.     

Unicellular organisms and genetics

Abstract

Formation of asexual cysts can be induced in Gonyaulax polyedra by melatonin at 15 °C, or by its metabolite, 5‐methoxytryptamine, at 15 or 20 °C. When cells were exposed to a temperature of 10 °C, which holds the circadian oscillator(s), they were almost insensitive to melatonin, and the cyst‐inducing capacity of 5‐methoxy‐tryptamine was reduced to about 1/3. This desensitization was seen in various lighting conditions (LL, LD 16:8; LD 12:12; LD 11:13; DD). The reduction of cyst formation by decreased temperature was not due to a general incompetence of cells to encyst, because (a) low temperatures can lead to non‐photoperiodic cyst induction, and (b) both the MAO inhibitor tranylcypromine and the electroneutral Na+/H+ antiporter monensin lead to encystment in almost the entire cell population. After a 22‐h passage through the aperiodic state with a subsequent step‐up to 15 or 20 °C, the responsiveness to melatonin or 5‐methoxytryptamine, respectively, was approximately normal. Our results indicate that cyst formation via the short‐day/melatonin pathway requires an operating circadian oscillator.     

Comprehensive primer design for analysis of population genetics in non-sequenced organisms

Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.     

The population genetic structure of clonal organisms generated by exponentially bounded and fat-tailed dispersal

Long-distance dispersal (LDD) plays an important role in many population processes like colonization, range expansion, and epidemics. LDD of small particles like fungal spores is often a result of turbulent wind dispersal and is best described by functions with power-law behavior in the tails ("fat tailed"). The influence of fat-tailed LDD on population genetic structure is reported in this article. In computer simulations, the population structure generated by power-law dispersal with exponents in the range of -2 to -1, in distinct contrast to that generated by exponential dispersal, has a fractal structure. As the power-law exponent becomes smaller, the distribution of individual genotypes becomes more self-similar at different scales. Common statistics like GST are not well suited to summarizing differences between the population genetic structures. Instead, fractal and self-similarity statistics demonstrated differences in structure arising from fat-tailed and exponential dispersal. When dispersal is fat tailed, a log-log plot of the Simpson index against distance between subpopulations has an approximately constant gradient over a large range of spatial scales. The fractal dimension D2 is linearly inversely related to the power-law exponent, with a slope of approximately -2. In a large simulation arena, fat-tailed LDD allows colonization of the entire space by all genotypes whereas exponentially bounded dispersal eventually confines all descendants of a single clonal lineage to a relatively small area.     

Individual organisms as units of analysis: Bayesian-clustering alternatives in population genetics

Population genetic analyses traditionally focus on the frequencies of alleles or genotypes in 'populations' that are delimited a priori. However, there are potential drawbacks of amalgamating genetic data into such composite attributes of assemblages of specimens: genetic information on individual specimens is lost or submerged as an inherent part of the analysis. A potential also exists for circular reasoning when a population's initial identification and subsequent genetic characterization are coupled. In principle, these problems are circumvented by some newer methods of population identification and individual assignment based on statistical clustering of specimen genotypes. Here we evaluate a recent method in this genre--Bayesian clustering--using four genotypic data sets involving different types of molecular markers in non-model organisms from nature. As expected, measures of population genetic structure (F(ST) and phiST) tended to be significantly greater in Bayesian a posteriori data treatments than in analyses where populations were delimited a priori. In the four biological contexts examined, which involved both geographic population structures and hybrid zones, Bayesian clustering was able to recover differentiated populations, and Bayesian assignments were able to identify likely population sources of specific individuals.     

DNA fingerprinting in clonal organisms

The use of DNA fingerprinting to identify members of the same clone in completely or partially asexual organisms requires that the individuals within a clone share a recent common ancestor. By considering the expected distributions of band–sharing values in asexual and sexual organisms, it is shown that DNA fingerprinting may be effective in distinguishing members of the same clone, provided that the frequency of sexual reproduction is considerably greater than the minisatellite mutation rate.     

Towards a population genetics of microorganisms: The clonal theory of parasitic protozoa

Over the past 15 years, molecular investigations, including the study of isozymes and DNA markers, have provided much information on the genetic variation, population structure, breeding system and other population characteristics of parasitic protozoa. For some parasitic protozoa, but not for others, the evidence indicates that their reproduction is prevailingly clonal. In this article, Michel Tibayrenc and Francisco Ayala propose that the issue of whether the predominant mode of reproduction of a given micro-organism is clonal or sexual can only be settled by population genetics information, and they summarize evidence favoring a clonal population structure for a number of parasitic protozoa.     

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.     

Population genetics of microbial organisms

Population data suggest that many parasitic protozoa (e.g. Trypanosoma, Leishmania, Entamoeba and Giardia) reproduce clonally, but this hypothesis has been highly controversial for Plasmodium falciparum. Although reproduction is predominantly clonal in the enteric bacteria Escherichia coli and Salmonella, the level of recombination affecting short (< 1 kb) regions of the chromosome is sufficient such that many genes are obviously mosaics of different ancestries. Transposable insertion sequences in E. coli are examples of selfish DNA whose short-term population dynamics are determined mainly by transposition and horizontal transmission among strains balanced against the regulation of transposition as a function of copy number, and negative effects on fitness. Occasional advantageous effects of transposable elements have also been documented.     

Sexual recombination punctuated by outbreaks and clonal expansions predicts Toxoplasma gondii population genetics

The cosmopolitan parasitic pathogen Toxoplasma gondii is capable of infecting essentially any warm-blooded vertebrate worldwide, including most birds and mammals, and establishes chronic infections in one-third of the globe’s human population. The success of this highly prevalent zoonosis is largely the result of its ability to propagate both sexually and clonally. Frequent genetic exchanges via sexual recombination among extant parasite lineages that mix in the definitive felid host produces new lines that emerge to expand the parasite’s host range and cause outbreaks. Highly successful lines spread clonally via carnivorism and in some cases sweep to pandemic levels. The extent to which sexual reproduction versus clonal expansion shapes Toxoplasma’s current, global population genetic structure is the central question this review will attempt to answer.     

Biological interactions among extant and fossil clonal organisms

Biological interactions among clonal marine organisms are an important aspect of their behavior and are important in the construction of biological reefs. The interactions addressed here are among crustose and erect coralline algae, sponges, corals, and bryozoans, and may involve clones of the same species (conspecific), or different species (heterospecific). Conspecific interactions may be either between modules or clones that are produced asexually from one propagule, genetically identical, or between clones that are sexually produced from two or more propagules that may or may not be genetically identical. Juxtaposed genetically identical clones generally fuse whereas non-identical clones may or may not fuse, depending on their relatedness and histocompatibility. Most heterospecific clonal interactions are spatially competitive and result in overgrowths or stand-offs. Clone fission/fragmentation may occur as a result of biotic or abiotic processes that initially degrade but may eventually restore or even enhance ability to gain space and/or nutrients. Self-overgrowths also occur, usually over dead, diseased, or senescent parts of the same clone.     

Molecular genetics and the management and conservation of marine organisms

Biochemical and molecular species identification techniques have a broad range of applications in the management and conservation of marine organisms. While species boundaries are not always clearly defined, phylogeneticists utilise autapomorphic characters to distinguish phylogenetic species. Genetic markers discriminate between marine taxa when traditional morphological distinctions are unclear. The applications of these techniques can be divided into four general categories. Firstly, compliance enforcement, which often depends on genetic identification techniques to enable officials to identify the species to which regulations pertain. Secondly, quality control applications, to allow for the testing of marine products to guard against fraudulent substitution with less valuable species, which is particularly pertinent since processing often obliterates identifiable features. Thirdly, a variety of applications to ecological and life-history studies and conservation management are reported. Here, the genetic identification techniques of species from cryptic life-cycle stages or of morphologically indistinct species are an indispensable tool for marine scientists, conservators and managers. Lastly, the application of genetic techniques for sourcing population origin is briefly discussed. The biochemical and molecular techniques applied to species identification all exploit phenotypic or genotypic polymorphisms that are sampled using either tertiary level protein based methods or primary level DNA based methods. In this review, examples of the applications along with the total protein, allozyme, serological, PCR and other DNA based methodologies are briefly described and some generalities with regard to their use are presented.     

Bacterial population genetics

Bacterial population genetics is the study of natural bacterial genetic diversity arising from evolutionary processes. The roles of molecular mistakes, restriction–modification, plasmids and gene transfer in bacteria are also important components of population genetics. These aspects are of considerable scientific importance from a fundamental perspective, because of the short generation times of bacteria, their microscopic cell size, the large population sizes bacteria can achieve and their different mechanisms of gene transfer.