Genetic Analysis Of Natural Populations Research Articles

Genetic Analysis of Plant Pathogens Natural Populations.

Population genetics allow to address fundamental questions about the biology of plant pathogens. By testing specific hypotheses, population genetics provide insights into the population genetic variability of pathogens across different geographical areas, time, and associated plant hosts, as well as on the structure and differentiation of populations, and on the possibility that a population is introduced and from where it has originated. In this chapter, basic concepts of population genetics are introduced, as well as the five evolutionary factors affecting populations, that is, mutations, recombination, variation in population size, gene flow, and natural selection. A step-by-step workflow, from sampling to data analysis, on how to perform a genetic analysis of natural populations of plant pathogens is discussed. Increased knowledge of the population biology of pathogens is pivotal to improve management strategies of diseases in agricultural and forest ecosystems.

Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon.

Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

Western European Populations of the Ichneumonid Wasp Hyposoter didymator Belong to a Single Taxon

Hyposoter didymator (Hymenoptera, Ichneumonidae) is a generalist solitary endoparasitoid of noctuid larvae. In the present work, we tested whether populations of H. didymator were divided in several genetically distinct taxa as described for many other generalist parasitoid species, and whether differences in H. didymator parasitism rates were explained by the insect host species and/or by the plant on which these hosts were feeding on. The genetic analysis of natural populations collected in different regions in France and Spain on seven different insect hosts and seven different host plants (775 individuals) showed that H. didymator populations belong to a unique single taxon. However, H. didymator seems to be somewhat specialized. Indeed, in the fields it more often parasitized Helicoverpa armigera compared to the other host species collected in the present work. Also, H. didymator parasitism rates in field conditions and semi-field experimental studies were dependent on the host plants on which H. armigera larvae are feeding. Still, H. didymator can occur occasionally on non-preferred noctuid species. One hypothesis explaining the ability of H. didymator to switch hosts in natura could be related to fluctuating densities of the preferred host over the year; this strategy would allow the parasitoid to avoid seasonal population collapses.

Landscape genetics structure of European sweet chestnut (Castanea sativa Mill): indications for conservation priorities

Sweet chestnut is a tree of great economic (fruit and wood production), ecological, and cultural importance in Europe. A large-scale landscape genetic analysis of natural populations of sweet chestnut across Europe is applied to (1) evaluate the geographic patterns of genetic diversity, (2) identify spatial coincidences between genetic discontinuities and geographic barriers, and (3) propose certain chestnut populations as reservoirs of genetic diversity for conservation and breeding programs. Six polymorphic microsatellite markers were used for genotyping 1608 wild trees sampled in 73 European sites. The Geostatistical IDW technique (ArcGIS 9.3) was used to produce maps of genetic diversity parameters (He, Ar, PAr) and a synthetic map of the population membership (Q value) to the different gene pools. Genetic barriers were investigated using BARRIER 2.2 software and their locations were overlaid on a Digital Elevation Model (GTOPO30). The DIVA-GIS software was used to propose priority areas for conservation. High values of genetic diversity (He) and allelic richness (Ar) were observed in the central area of C. sativa’s European distribution range. The highest values of private allelic richness (PAr) were found in the eastern area. Three main gene pools and a significant genetic barrier separating the eastern from the central and western populations were identified. Areas with high priority for genetic conservation were indicated in Georgia, eastern Turkey, and Italy. Our results increase knowledge of the biogeographic history of C. sativa in Europe, indicate the geographic location of different gene pools, and identify potential priority reservoirs of genetic diversity.

Population Genomics of Fungal and Oomycete Pathogens.

We are entering a new era in plant pathology in which whole-genome sequences of many individuals of a pathogen species are becoming readily available. Population genomics aims to discover genetic mechanisms underlying phenotypes associated with adaptive traits such as pathogenicity, virulence, fungicide resistance, and host specialization, as genome sequences or large numbers of single nucleotide polymorphisms become readily available from multiple individuals of the same species. This emerging field encompasses detailed genetic analyses of natural populations, comparative genomic analyses of closely related species, identification of genes under selection, and linkage analyses involving association studies in natural populations or segregating populations resulting from crosses. The era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. This review focuses on conceptual and methodological issues as well as the approaches to answering questions in population genomics. The major steps start with defining relevant biological and evolutionary questions, followed by sampling, genotyping, and phenotyping, and ending in analytical methods and interpretations. We provide examples of recent applications of population genomics to fungal and oomycete plant pathogens.

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations

BackgroundWe introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations.ResultsSequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n = 7) and wolves (n = 18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci were highly correlated.ConclusionWith an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.

Alleles In Space (AIS): Computer Software for the Joint Analysis of Interindividual Spatial and Genetic Information

Genetic analyses of natural populations have historically relied on statistical procedures based on the concept that distinct ‘‘populations’’ of a species exist across a landscape. Invariably, commonly used analyses reduce to approaches that treat collections of individuals (‘‘populations’’) as independent/causative variables and allele frequencies as dependent/ response variables. Examples of these procedures include Wright’s FST and its variants (Excoffier et al. 1992; Nei 1973; Slatkin 1995; Weir and Cockerham 1984), contingency table procedures (Raymond and Rousset 1995; Roff and Bentzen 1989), and measures of genetic distances among populations (e.g., Nei 1972, 1978; Reynolds et al. 1983). These analyses qualitatively or explicitly test null hypotheses of homogeneity of allele frequencies between or among populations. Although almost universally applied, the analyses mentioned above are not necessarily appropriate in many situations. For example, highly mobile organisms such as large mammals or birds can occupy continuous habitats over large spatial scales. Plants may also occupy large continuous habitats, as can species inhabiting marine or aquatic systems. In these cases, objectively designating groups of individuals at population levels for use in genetic analyses may prove difficult, if not impossible. Clearly, an important consideration in these situations is the spatial extent of the ‘‘populations’’ that are chosen for analyses. If groups of organisms are defined over larger than appropriate spatial scales, resulting measures of genetic differentiation may actually provide ambiguous or misleading results (Miller et al. 2002). To address many of these issues, I have developed a new software package entitled ‘‘Alleles In Space’’ (AIS). This program, rather than implementing methodology that relies on arbitrary groupings of individuals, instead has the ability to perform joint analyses of interindividual spatial and genetic information that can be applied at virtually any spatial scale. These approaches specifically lend themselves to analyses of genetic data when one or a few individuals are sampled from large numbers of collection sites. Moreover, the program is designed to handle a wide variety of genetic data types, including codominant marker systems, dominant marker systems, and DNA sequences. Thus AIS will likely be useful for elucidation of patterns in diverse study types ranging from local analyses of genetic structure, phylogeographical studies, and studies encompassing aspects of the emerging field of landscape genetics (Manel et al. 2003).

Evidence for bimodal hybrid zones between two species of char (Pisces: Salvelinus) in northwestern North America.

Dolly Varden (Salvelinus malma, Pisces: Salmonidae) and bull trout (Salvelinus confluentus) have widely overlapping, but largely parapatric ranges in watersheds in northwestern North America from Washington State to northern British Columbia. Genetic analysis of natural populations using diagnostic molecular markers revealed widespread local sympatry and hybridization with hybrids comprising 0-25% of the local samples. In a detailed analysis of hybridization using four nuclear DNA markers and mitochondrial DNA within the Thutade Lake watershed, northcentral British Columbia, hybrid genotypes constituted up to 9% of the population of juvenile char. There were significant deviations from Hardy-Weinberg, gametic, and cytonuclear equilibria, and local samples showed bimodal frequency distributions of genotypes. Pure parental and inferred backcross genotypes were most common, and F1 and F(n) hybrids were comparatively rare. Interspecific hybridization was asymmetrical, with most F1 hybrids (five of six) bearing S. confluentus mtDNA. The introgression of nuclear and mitochondrial alleles was asymmetrical, with S. confluentus mtDNA and Growth Hormone 2 introgressing into S. malma significantly more than either introgression of the three other nuclear loci, or introgression of S. malma alleles into S. confluentus. Substantial prezygotic isolation between the species likely depends on the large body size difference between them in sympatry: S. malma have small bodies and a stream resident life history (12-21 cm adult fork length at maturity), while S. confluentus are larger and adfluvial, i.e., they migrate to Thutade Lake where they grow to maturity before returning to tributary streams to spawn (40-90 cm at maturity). These traits may limit interspecific pairings because of size assortative pairing and size-dependent reproductive habitat use.

Quantitative genetic analysis of natural populations: old wine in a new but defective bottle?

Quantitative genetic analysis of natural populations: old wine in a new but defective bottle?

Genetic analysis of natural populations of the marine diazotrophic cyanobacterium Trichodesmium

The genetic diversity of Trichodesmium, a marine nitrogen-fixing non-heterocystous cyanobacterium of great ecological importance, was examined using the partial gene sequences of the small subunit ribosomal RNA (16S rDNA) gene and the regulatory gene hetR. Different species and morphotypes (fusiform and spherical colonies) of Trichodesmium were collected in the northern Caribbean Sea, the central Atlantic Ocean and southern Pacific Ocean. The trichome morphologies were observed with light microscopy before DNA extraction and PCR amplification. Phylogenetic analysis of 16S rDNA revealed that all cyanobacterial sequences from the colonies of Trichodesmium spp. were very closely related to the laboratory culture of Trichodesmium sp. NIBB 1067. The overall results from the hetR analysis were congruent with that of 16S rDNA, but the variation in nucleotide sequence between different species was higher within the hetR gene. The sequence data showed that three main clades were represented. One clade comprised sequences from Trichodesmium hildebrandtii Gomont and Trichodesmium thiebautii Gomont (including both its fusiform and spherical colony forms). Sequences from Trichodesmium contortum Wille and Trichodesmium tenue Wille constituted a second clade. The third clade contained Trichodesmium erythraeum Ehrenberg together with the two laboratory strains of this species, Trichodesmium sp. NIBB 1067 and Trichodesmium sp. IMS 101.

Genetic analysis of natural populations of the marine diazotrophic cyanobacterium Trichodesmium

The genetic diversity of Trichodesmium, a marine nitrogen-fixing non-heterocystous cyanobacterium of great ecological importance, was examined using the partial gene sequences of the small subunit ribosomal RNA (16S rDNA) gene and the regulatory gene hetR. Different species and morphotypes (fusiform and spherical colonies) of Trichodesmium were collected in the northern Caribbean Sea, the central Atlantic Ocean and southern Pacific Ocean. The trichome morphologies were observed with light microscopy before DNA extraction and PCR amplification. Phylogenetic analysis of 16S rDNA revealed that all cyanobacterial sequences from the colonies of Trichodesmium spp. were very closely related to the laboratory culture of Trichodesmium sp. NIBB 1067. The overall results from the hetR analysis were congruent with that of 16S rDNA, but the variation in nucleotide sequence between different species was higher within the hetR gene. The sequence data showed that three main clades were represented. One clade comprised sequences from Trichodesmium hildebrandtii Gomont and Trichodesmium thiebautii Gomont (including both its fusiform and spherical colony forms). Sequences from Trichodesmium contortum Wille and Trichodesmium tenue Wille constituted a second clade. The third clade contained Trichodesmium erythraeum Ehrenberg together with the two laboratory strains of this species, Trichodesmium sp. NIBB 1067 and Trichodesmium sp. IMS 101.

Molecular Ecology and Evolution: Approaches and Applications.

I: DNA fingerprinting and behavioral ecology.- Arbitrary primer mediated fingerprinting in plants: Case studies in plant breeding, taxonomy and phylogeny.- DNA amplification fingerprinting: A general tool with applications in breeding, identification and phylogenetic analysis of plants.- The analysis of simple repeat loci as applied in evolutionary and behavioral sciences.- Multilocus DNA fingerprinting and genetic relatedness in plants: A case study with banana and tomato.- Measuring reproductive success in insects.- Unravelling the components that underlie insect reproductive traits using a simple molecular approach.- Molecular analysis of kinship in birds: Interesting questions and useful techniques.- II: Population biology.- Molecular techniques in population genetics: A brief history.- Organization of genetic variation at the molecular level: Lessons from Drosophila.- The use of microsatellite analysis in population biology: Background, methods and potential applications.- The use of microsatellites for genetic analysis of natural populations.- PCR assays of variable nucleotide sites for identification of conservation units.- Concerted evolution and RAPping in mitochondrial VNTRs and the molecular geography of cricket populations.- Molecular markers and evolutionary processes in hermaphrodite freshwater snails.- Extinction and the formation of phylogenetic lineages: Diagnosing units of conservation management in the tiger beetle Cicindela dorsalis.- Perspective on conservation genetics.- III: Molecular systematics.- Advances in the theory and practice of DNA-hybridization as a systematic method.- Allozymes in mammalian population genetics and systematics: Indicative function of a marker system reconsidered.- Analysis of DNA from natural history museum collections.- Sources of ambiguity in nucleic acid sequence alignment.- Computational problems in molecular systematics.- The comparison of morphological and molecular data in phylogenetic systematics.- Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level.- Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates.- Bridging phylogenetics and population genetics with gene tree models.- IV: Speciation, development and genome organization.- The role of molecular genetics in speciation studies.- The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium.- The evolutionary ecology of Daphnia.- Diversity within diversity: Molecular approaches to studying microbial interactions with insects.- Evolutionary analysis of genes involved in early embryonic pattern formation in Drosophila.- Developmental genes and the origin and evolution of Metazoa.- To what extent does genetic information determine structural characteristics and document homologies?.- Evolution and multi-functionality of the chitin system.- Genome evolution: Between the nucleosome and the chromosome.- Individual genes underlying quantitative traits: Molecular and analytical methods.- Perspectives on future applications of experimental biology to evolution.

The use of microsatellites for genetic analysis of natural populations.

Microsatellites, tandemly repeated units of 2 to 5 bp are distributed throughout eukaryotic genomes. Length variation within microsatellites, caused by DNA slippage, can be amplified by PCR and used for DNA profiling. In this paper potential applications and limitations of this technique are discussed. Two case studies for pilot whales (Globicephala melas) and sheep (Ovis aries) exemplify the suitability of microsatellites for analyzing natural populations. Other currently available profiling techniques are compared to microsatellite analysis.

Genetic analysis of natural populations of Drosophila melanogaster in Japan. VI Differential regulation of duplicated amylase loci and degree of dominance of amylase activity in different environments.

The degrees of dominance of amylase activity, responsiveness to inducing (or repressive) environment, the activity of one allozyme relative to that of the other duplicated locus, and trans- or cis-action of controlling elements were investigated using 10 homozygous lines from a natural population in Japan. The main findings are: (1) Genetic variation in specific activity, responsiveness as well as relative activity of duplicated genes were found. (2) The degree of dominance of amylase activity drastically changed in different environments. The heterozygous amylase activity in starch food was almost the same as the parental value with lower activity (h=1.29±0.39, complete recessive). On the other hand, the enzyme activity of heterozygote in normal food was closer to the parent with higher activity (h=0.26 ±0.07, high dominance), indicating that the manner of amylase regulation is trans-action and also is affected by the environments. (3) The relative activity of one of the two duplicated amylase loci on the same chromosome was affected by an allozyme on the homologous chromosome. In other words, the regulation of duplicated amylase genes was trans-action and partially differentiated, but high correlation of the enzyme activity between the two duplicated genes on the same chromosome also indicated the coordinated regulation.

Genetic analysis of natural populations of Drosophila melanogaster in Japan. V Genetic variabilities of amylase activities in different developmental stages and theil relation to fitness.

Genetic variation of regulatory genes with respect to the amylase activities in different developmental stages (developmental inducibility) as well as the inducibility (S/N) which was studied in the previous reports (Yamazaki and Matsuo 1984), was found among 10 isogenic strains established from a natural population of Drosophila melanogaster. Net fitness of each of these 10 strains was obtained from interspecific competition experiments and the correlation between fitness and inducibilities of amylase was calculated; No correlation was obtained between developmental inducibility and fitness. On the other hand, a significant positive correlation was obtained between fitness and inducibility (S/N) (γp=0.48* and γg=0.95). This indicates that these two types of regulatory gene polymorphisms are different in nature, and that regulatory patterns of the enzymes which are found in different developmental stages under normal environments have little to do with adaptability of flies.

Genetic analysis of natural populations of Drosophila melanogaster in Japan. I. Protein polymorphism, lethal gene, sterility gene, inversion polymorphism and linkage disequilibrium.

Genetic parameters such as allozyme polymorphisms, lethal frequency, sterility frequency, inversion frequency and linkage disequilibrium were examined simultaneously in 780 second and third chromosomes, extracted from 2 natural populations of Drosophila melanogaster. The following results were obtained. 1) The average heterozygosities of 16 allozyme loci were 0.159 in the Akayu (AK) population and 0.181 in the Tanushimaru (TS) population. Little genetic differentiation was observed between populations (I=0.99). No linkage disequilibrium was observed between allozyme loci. 2) The frequency of the polymorphic inversion In(2L)t was 0.188 and 0.106 in the Akayu and Tanushimaru populations. That of the In(2R)NS was 0.115 and 0.049. That of the In(3L)P was 0.009 and 0.037, and that of the In(3R)P was 0.107 and 0.052. There were no significant linkage disequilibria between inversions. 3) The frequency of lethal carrying second chromosomes was 0.315 and 0.182 in the Akayu and Tanushimaru populations. Those on the third chromosome were found at a frequency of 0.327 and 0.305. The frequencies of sterile second chromosomes in Akayu were 0.147 and 0.127 in males and females, and of the third chromosomes, the respective frequencies were 0.093 and 0.084. Corresponding values for the Tanushimaru population were 0.091 and 0.07, and 0.0 and 0.084, respectively. Significant statistical associations were found between male and female sterility of the same shromosome, indicating pleiotropic gene action. 4) Negative or repulsion linkage disequilibria were found between inversions and allozymes, and between inversions. No evidence of frequency dependent selection with minority advantage was found.

Genetic analysis of natural populations of Poeciliopsis monacha

The genetic bases of seven polymorphic enzymes in Poeciliopsis monacha have been demonstrated through the analysis of allelic segregation in presumed heterozygotes captured in natural populations. Tests of linkage among loci revealed a significant association between two loci, Ldh-1 and Idh-2. Evidence for multiple insemination was detected in 23 percent of the females examined. Considering the limited number of markers available in the present study, it is probably that the actual frequency of multiple insemination is much higher.

Genetic Diversity in Liatris cylindracea

A genetically substructured population of the perennial, outbreeding herb, Liatris cylindracea was marked off into a grid with quadrat size that approximates the neighborhood size of Liatris. The plants were genotyped at 27 allozyme loci, 15 of which were polymorphic. The apportionment of genetic diversity within the population was determined by the Shannon information measure. Ninety-three percent of the total diversity is represented within each neighborhood. Five percent of the diversity is due to between neighborhoods, and about 2% is due to differences between sample rozs and columns. It is concluded that the subdivision of a population does not result in a loss of genetic diversity within neighborhoods. The properties of genetically subdivided populations have received considerable attention by theoreticians (e.g., Wright, 1943a; Kimura & Weiss, 1954; Maruyama, 1970). Because of the difficulty in the past of finding suitable single locus genetic markers, few experimental studies on genetic substructuring have been available. Now, with the advent of allozyme electrophoresis as a tool for the genetic analysis of natural populations, an increased number of studies on both animals (Selander 8c Yang, 1969; Workman gc Niswander, 1970; Neel gc Ward, 1972) and plants (Schaal, 1975) have indicated that populations of some organisms are genetically

Mendelian Genetics Today

The purpose of this first “Round-table Conference” could well be to present the historical development of human genetics from the early days of Mendelism to the elaboration of modern genetic research. The refinement of methodological possibilities and the unfolding of problems indicate to us the proper lines for further study. With this introduction I should like to restrict myself to a few remarks concerning the role of the gene analytical system of Gregor Mendel in human genetics. If as a result of corrent research the concept of the gene has undergone important alterations and is no longer the closed unit of the classical formulation, it still remains a useful concept for practical research. Every investigation of a genetically active factor immediately begins with the determination of a segregating unit or a mutating unit. Determining an allele relationship or a series of multiple alleles will remain the principal result. Quite often in human genetics it has not been possible to demonstrate these relationships as pseudoallelal or with other methods to achieve a differentiation of the gene concept into its subunits: the cistron, recon and muton. So far the objectives of human genetics the employment of the gene concept as classically formulated is methodologically necessary.The ideal goal of the gene analytical method is to determine the function of all genes which take part in the heredity of an organism, the preparation of theoretical chromosome maps for the various linkage groups, the determination of the relationships between the genes and their alleles to visible or measurable characteristics of the organism, and the establishment of relationships between phenotypic expression and dominance or epistasis. Its further area of interest is in the genetic analysis of natural populations, the question of spontaneous mutability, the problem of genetic diversity and the polymorphism caused by it in populations, and the equilibrium between all alleles. These questions lead necessarily to general problems of population dynamics, adaptation and evolution.