Conceptual analysis of methods applied to assessment of diversity within and distance between populations with asexual or mixed mode of reproduction

Measures of diversity within populations, and distance between populations, are compared for organisms with an asexual or mixed mode of reproduction. Examples are drawn from studies of plant pathogenic fungi based on binary traits including presence/absence of DNA bands or virulence/avirulence to differential hosts. Commonly used measures of population diversity or genetic distance consider either genotype frequencies or allele frequencies. Kosman's diversity and distance measures are the most suitable for populations with an asexual or mixed mode of reproduction, because by considering genetic patterns of all individuals they take into account not just the genotype frequencies but also the genetic similarities between genotypes in the populations. The Kosman distance and diversity measures for populations can be calculated using different measures of dissimilarity between individuals (the simple mismatch, Jaccard and Dice coefficients of dissimilarity). Kosman's distances based on the simple mismatch and Jaccard dissimilarities are metrics. Comparisons of diversity indices for hypothetical examples as well as for actual data sets are presented to demonstrate that inferences from diversity analysis of populations can be driven by techniques of diversity and distance assessments and not only data driven.     

Informativeness of genetic markers for pairwise relationship and relatedness inference

Measuring the information content of markers in relationship/relatedness inferences is important in selecting highly informative markers to attain a given statistical power with the minimal genotyping effort. Using information-theoretic principles, I introduce the informativeness for relationship (I(R)) and the informativeness for relatedness (I(r)) to measure the amount of information provided by markers in inferring pairwise relationships (R) and relatedness (r), respectively. I also propose a fast and accurate algorithm to calculate the power (PW(R)) of a set of markers in differentiating two candidate relationships, and the reciprocal of the mean squared deviations of relatedness estimates (RMSD) to measure the amount of information of markers actually used by an estimator in estimating relatedness. All of the four measurements (I(R), I(r), PW(R), RMSD) apply to dominant and codominant markers, haploid and diploid individuals, and take into account of mutations and typing errors in data. The statistical properties of the four measurements and their relationships are investigated analytically and are examined by applying these methods to simulated and empirical data.     

Using AFLP markers and the Geneland program for the inference of population genetic structure

The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the computer program Geneland designed to infer population structure has been adapted to deal with dominant markers; and (ii) we use Geneland for numerical comparison of dominant and codominant markers to perform clustering. AFLP markers lead to less accurate results than bi-allelic codominant markers such as single nucleotide polymorphisms (SNP) markers but this difference becomes negligible for data sets of common size (number of individuals n≥100, number of markers L≥200). The latest Geneland version (3.2.1) handling dominant markers is freely available as an R package with a fully clickable graphical interface. Installation instructions and documentation can be found on http://www2.imm.dtu.dk/~gigu/Geneland.     

COLONY: a program for parentage and sibship inference from multilocus genotype data

Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface.     

Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis

This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1-0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.     

Gene-assisted selection for high molecular weight glutenin subunits in wheat doubled haploid breeding programs

Molecular markers based on DNA sequence variations of the coding and/or promoter regions of the wheat (Triticum aestivum L.) HMW glutenin genes located at the Glu-1 loci were developed. Markers characteristic of alleles Glu-A1-1a (encoding Ax1 subunit) and Glu-A1-1c (encoding Ax2* subunit) at the Glu-A1 locus, alleles Glu-B1ak (encoding Bx7* subunit) and Glu-B1al for overexpressed Bx7 subunit at the Glu-B1 locus and alleles Glu-D1-1a (encoding Dx2 subunit) and Glu-D1-1d (encoding Dx5 subunit) at the Glu-D1 locus were tested using genomic DNA of haploid leaf tissue. A method for simultaneously extracting DNA from 96 haploid leaf tissue pieces is described. Two of the developed markers were dominant and two were co-dominant. A F₁-derived population segregating for all HMW glutenin genes was used to test the validity of the markers and their usefulness in doubled haploid breeding programs. SDS-PAGE analysis of seed storage protein was performed on seeds from the doubled haploid lines. A total of 299 lines were tested with the DNA markers on the haploid tissue and validated by protein analysis of the corresponding DH seeds. PCR markers and SDS-PAGE analysis showed between 2 and 8.5% discrepancies depending on the marker. Applications of DNA markers for gene-assisted-selection of haploid tissue and use in breeding programs are discussed. Advantages and disadvantages of dominant and co-dominant markers are outlined.     

Genetic characterization of Salix alba L. and Salix fragilis L. by means of different PCR-derived marker systems

Abstract

Salix alba L. and Salix fragilis L. are two closely related willow species whose phenotypic features, showing a large and continuous variation, have a low diagnostic value for identifying pure species and interspecific hybrids. In this paper, the effectiveness of different multilocus PCR-based molecular markers, such as I-SSRs, RAPDs and AFLPs in detecting genetic polymorphisms able to discriminate the two willow species was evaluated by analysing a set of 12 reference samples. Three genetic similarity indexes, Dice, Jaccard and Simple Matching coefficient, were used for all possible pairwise comparisons of individuals, revealing the same trend of variation within and between species when different marker systems were used. Cluster analysis, based on Dice genetic similarity coefficient, clustered the individuals of S. alba and S. fragilis into two distinct subgroups, indicating that the gene pools are well differentiated. Moreover, a number of private alleles for each marker system allowed the discrimination of the two species because always present only in one of the two. The utility of different marker systems in discriminating willow species was evaluated by the Polymorphism Information Content (PIC) and the Marker Index (MI) parameters. The variation of Dice's indexes obtained from a different number of experiments in relation to the marker systems is discussed.     

Development of EST-PCR markers and monitoring their intrapopulational genetic variation in Picea abies (L.) Karst.

Fifteen cDNA sequences are reported for the European coniferous forest tree species Norway spruce [Picea abies (L.) Karst.], including the results of similarity searches in public electronic databases. The sequences were subsequently employed for the design of specific primer pairs and PCR-based amplification of genomic fragments. For seven primer pairs, polymorphic EST-PCR markers were identified among 18 trees. Their mode of inheritance was verified by analysing single-tree offspring and studying segregation among haploid endosperms in comparison to diploid tissue. Codominant inheritance was indicated for six markers, while one marker was apparently dominant. Variation of the six codominant EST markers was tested by genotyping 110 randomly selected trees in a Bavarian Norway spruce population. For comparison, the same trees were genotyped at 18 enzyme coding gene loci. There were 3.33 alleles per locus for EST markers and 3.00 for isoenzyme gene markers. In general, a trend to more even frequency distributions and larger intrapopulational variation, including observed heterozygosities, was indicated more for EST markers than for isoenzyme gene markers. The benefits of these newly developed EST-PCR markers are outlined with respect to population genetics and ecological genetics. Received: 29 April 2000 / Accepted: 25 August 2000     

Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations

In F₂ populations, gametic and zygotic selection may affect the analysis of linkage in different ways. Therefore, specific likelihood equations have to be developed for each case, including dominant and codominant markers. The asymptotic bias of the classical estimates are derived for each case, in order to compare them with the standard errors of the suggested estimates. We discuss the utility and the efficiency of a previous model developed for dominant markers. We show that dominant markers provide very poor information in the case of segregation distortion and, therefore, should be used with circumspection. On the other hand, the estimation of recombination fractions between codominant markers is less affected by selection than is that for dominant markers. We also discuss the analysis of linkage between dominant and codominant markers.     

The relationship between species replacement,dissimilarity derived from nestedness,and nestedness

Aim Beta diversity can be partitioned into two components: dissimilarity due to species replacement and dissimilarity due to nestedness ( Baselga, 2010 , Global Ecology and Biogeography, 19 , 134–143). Several contributions have challenged this approach or proposed alternative frameworks. Here, I review the concepts and methods used in these recent contributions, with the aim of clarifying: (1) the rationale behind the partitioning of beta diversity into species replacement and nestedness‐resultant dissimilarity, (2) how, based on this rationale, numerators and denominators of indices have to match, and (3) how nestedness and nestedness‐resultant dissimilarity are related but different concepts. Innovation The rationale behind measures of species replacement (turnover) dictates that the number of species that are replaced between sites (numerator of the index) has to be relativized with respect to the total number of species that could potentially be replaced (denominator). However, a recently proposed partition of Jaccard dissimilarity fails to do this. In consequence, this partition underestimates the contribution of species replacement and overestimates the contribution of richness differences to total dissimilarity. I show how Jaccard dissimilarity can be partitioned into meaningful turnover and nestedness components, and extend these new indices to multiple‐site situations. Finally the concepts of nestedness and nestedness‐resultant dissimilarity are discussed. Main conclusions Nestedness should be assessed using consistent measures that depend both on paired overlap and matrix filling, e.g. NODF, whereas beta‐diversity patterns should be examined using measures that allow the total dissimilarity to be separated into the components of dissimilarity due to species replacement and dissimilarity due to nestedness. In the case of multiple‐site dissimilarity patterns, averaged pairwise indices should never be used because the mean of the pairwise values is unable to accurately reflect the multiple‐site attributes of dissimilarity.     

Genome and species relationships in genus<Emphasis Type="Italic"> Avena</Emphasis> based on RAPD and AFLP molecular markers

Species and genome relationships among 11 diploid (A and C genomes), five tetraploid (AB and AC genomes) and two hexaploid (ACD genome) Avena taxa were investigated using amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers. The two primer pairs used for the AFLP reactions produced a total of 354 polymorphic bands, while 187 reproducible bands were generated using ten RAPD primers. Genetic similarities amongst the entries were estimated using the Jaccard and Dice algorithms, and cluster analyses were performed using UPGMA and neighbor joining methods. Principle coordinate analysis was also applied. The highest cophenetic correlation coefficient was obtained for the Jaccard algorithm and UPGMA clustering method (r=0.99 for AFLP and r=0.94 for RAPD). No major clustering differences were present between phenograms produced with AFLPs and RAPDs. Furthermore, data produced with AFLPs and RAPDs were highly correlated (r=0.92), indicating the reliability of our results. All A genome diploid taxa are clustered together according to their karyotype. The AB genome tetraploids were found to form a subcluster within the A_s genome diploids (AFLPs), indicating their near-autoploid origin. The AC genome tetraploids are clustered to the ACD genome hexaploids. Finally, the C genome diploids form an outer branch, indicating the major genomic divergence between the A and C genomes in Avena.Communicated by J.S. Heslop-Harrison     

Development and characteristics of microsatellite markers in Pinus merkusii

Pinus merkusii is an important industrial species that is distributed only in Southeast Asia. We isolated 10 microsatellite markers from this species using a dual‐suppression‐polymerase chain reaction technique. Of these markers, five loci were codominant and polymorphic. The number of alleles per locus ranged from three to six and the expected heterozygosity ranged from 0.389 to 0.728. These microsatellite markers will be available for analysis on population genetics and mating patterns.     

Deterministic paternity exclusion using RAPD markers

The Random Amplified Polymorphic DNA (RAPD) technique can potentially provide hundreds of polymorphic markers for use by ecologists studying mating systems in natural populations. We consider here the implications of the dominance displayed by RAPD markers for deterministic paternity assignment. Our goal was to provide a means for assessing the costs associated with such a study for ecologists who might be considering the use of RAPD markers for paternity analysis. The theoretical expected proportion of offspring for which all males except the true father can be exlucded (P(ET)) is calculated for both dominant and codominant marker systems. The ability to assign paternity unambiguously generally increases with the number of loci and the frequency of the recessive allele (but only up to a point), and decreases with increasing sample size (number of individuals surveyed). The gain in P(ET) with decreasing sample size is unexpectedly slight. Not surprisingly, the performance of dominant markers at paternity exclusion is, in general, greatly exceeded by codominant markers, with the exception of the case in which the frequency of the recessive allele is high at all loci. In this case, codominant markers perform only slightly better than do dominant markers. Thus, a researcher should expect to score more than 50 RAPD loci for each offspring for most applications of paternity exclusion analysis.(ABSTRACT TRUNCATED AT 250 WORDS)     

Dominant vs. codominant genetic markers in the estimation of male mating success

Although a major component of fitness, male reproductive success is generally extremely difficult to estimate. As a result, genetic methods and maximum likelihood models have been developed to estimate male parentage, but all are limited in practice by the degree of genetic variation observable. Scoring individuals phenotypically at a large number of random loci exhibiting dominance (e.g. RAPD markers) may provide a means of detecting sufficient genetic variation. Dominance, however, represents a loss of information and therefore greater variation in the estimate of paternity. A mixture model describing mating in a population is presented to quantify the trade-off between marker types when estimates of male fertility are sought. A sample size 1.5-2.0 times greater is required for dominant markers under some conditions to obtain the same confidence in fertility estimates as for codominant markers, although with large sample sizes the fertility estimates are similar for either marker type. Since the number of dominant DN A markers is not limited in the same manner as is the number of codominant protein markers, one's confidence in the estimates can be increased above that possible from proteins by surveying additional loci. However, for a fixed sample size a trade-off exists between the number of progeny assayed per female and the number of loci surveyed. In many cases more progeny per female provide better estimates of fertility than more loci.     

The effective size of bryophyte populations

Bryophytes with their dominant haploid stage conform poorly to the life cycles generally treated in population genetical models. Here we make a detailed analysis of what effective sizes bryophyte model populations have as a function of their breeding system. It is found that the effective size is rarely much smaller than the scored number of haploid gametophytic individuals, even when the limited number of diploids (sporophytes) formed is taken into account. The most severe decrease in effective size occurs when unisexual gametophytic females produce only a small number of fertile diploid sporophytes in male biased populations; this effect is due to the restricted sampling of male gametophytic individuals that then occurs. It is shown that the harmonic mean of diploid sporophytes formed per haploid gametophytic individuals is the relevant measure in these calculations and not the standard (and generally larger) arithmetic mean.     

Multipoint genetic mapping of quantitative trait loci with dominant markers in outbred populations

We present a multipoint algorithm for mapping quantitative trait loci (QTLs) using dominant markers. The algorithm is designed for outbred populations and is particularly suited for large families. The algorithm works with either codominant or dominant markers, either of which may be interspersed within the same linkage map. Concurrently, the algorithm also partitions dominance variance at the QTL. Computer simulations show that with large families, QTL mapping with dominant markers can be almost as powerful as with bi-allelic, codominant markers. Yet despite this, other situations show a large standard deviation in the estimate of the QTL position, thus making QTL mapping with dominant markers in outbred populations a useful detection tool, albeit limited in its resolution. This revised version was published online in July 2006 with corrections to the Cover Date.     

Template mixing: a method of enhancing detection and interpretation of codominant RAPD markers

Ten codominant RAPD markers, ranging in size from about 300 to about 1350 bp, were identified in mapping populations of chickpea (Cicer arietinum L.) and diploid strawberry (Fragaria vesca L.). A distinguishing feature of all ten markers, and perhaps of codominant RAPD markers in general, was the presence in heterozygous individuals of a non-parental, heteroduplex band migrating more slowly than either of the respective parental bands. This non-parental band could also be generated by mixing parental DNAs before PCR (template mixing). As a means of identifying primers likely to detect codominant RAPD markers, parental and mixed-template (parent-parent) PCR-product gel lanes were compared for 20 previously untested RAPD primers (10-base oligomers). Four primers that produced a total of five non-parental, heteroduplex bands in mixed-template reactions were selected, and then used to detect a total of five segregating, codominant markers and nine dominant markers in the respective F₂ mapping population, a codominant marker frequency of 35.7%. When closely migrating fast and slow bands of codominant RAPDs were difficult to differentiate, parent-progeny template mixing was used to deliberately generate heteroduplex bands in fast- or slow-band F₂ homozygotes, respectively, allowing confirmation of marker phenotype.     

A family of functional dissimilarity measures for presence and absence data

Plot‐to‐plot dissimilarity measures are considered a valuable tool for understanding the complex ecological mechanisms that drive community composition. Traditional presence/absence coefficients are usually based on different combinations of the matching/mismatching components of the 2 × 2 contingency table. However, more recently, dissimilarity measures that incorporate information about the degree of functional differences between the species in both plots have received increasing attention. This is because such “functional dissimilarity measures” capture information on the species' functional traits, which is ignored by traditional coefficients. Therefore, functional dissimilarity measures tend to correlate more strongly with ecosystem‐level processes, as species influence these processes via their traits. In this study, we introduce a new family of dissimilarity measures for presence and absence data, which consider functional dissimilarities among species in the calculation of the matching/mismatching components of the 2 × 2 contingency table. Within this family, the behavior of the Jaccard coefficient, together with its additive components, species replacement, and richness difference, is examined by graphical comparisons and ordinations based on simulated data.     

Haploidy, diploidy and evolution of antifungal drug resistance in Saccharomyces cerevisiae

We tested the hypothesis that the time course of the evolution of antifungal drug resistance depends on the ploidy of the fungus. The experiments were designed to measure the initial response to the selection imposed by the antifungal drug fluconazole up to and including the fixation of the first resistance mutation in populations of Saccharomyces cerevisiae. Under conditions of low drug concentration, mutations in the genes PDR1 and PDR3, which regulate the ABC transporters implicated in resistance to fluconazole, are favored. In this environment, diploid populations of defined size consistently became fixed for a resistance mutation sooner than haploid populations. Experiments manipulating population sizes showed that this advantage of diploids was due to increased mutation availability relative to that of haploids; in effect, diploids have twice the number of mutational targets as haploids and hence have a reduced waiting time for mutations to occur. Under conditions of high drug concentration, recessive mutations in ERG3, which result in resistance through altered sterol synthesis, are favored. In this environment, haploids consistently achieved resistance much sooner than diploids. When 29 haploid and 29 diploid populations were evolved for 100 generations in low drug concentration, the mutations fixed in diploid populations were all dominant, while the mutations fixed in haploid populations were either recessive (16 populations) or dominant (13 populations). Further, the spectrum of the 53 nonsynonymous mutations identified at the sequence level was different between haploids and diploids. These results fit existing theory on the relative abilities of haploids and diploids to adapt and suggest that the ploidy of the fungal pathogen has a strong impact on the evolution of fluconazole resistance.     

57株毛头鬼伞遗传多样性分析

运用SRAP、RAPD、ISSR3种分子标记技术对来源不同地区的57株毛头鬼伞Coprinus comatus进行了遗传多样性分析,通过3种分子标记进行聚类分析,当相异系数D为0.48时,可以把57株毛头鬼伞分为4类:Ⅰ类包括Co0001;Ⅱ类包括Co0003;Ⅲ类包括Co0005;Ⅳ类包括其余54个菌种。供试的57个菌株间的相异系数范围从0–0.72,具有一定的遗传多态性。但其中有许多菌株两者之间的相异系数为0,说明毛头鬼伞菌种存在着比较严重的同种异名现象。