Parentage and sibship exclusions: higher statistical power with more family members

Parentage exclusion probabilities are now routinely calculated in genetic marker-assisted parentage analyses to indicate the statistical power of the analyses achievable for a given set of markers, and to measure the informativeness of a set of markers for parentage inference. Previous formulas invariably assume that parentage is to be sought for a single offspring, while in practice multiple full siblings might be sampled (for example, seeds, eggs or young from a pair of monogamous parents) and their father, mother or both are to be assigned among a number of candidates. In this study, I derive formulas for parentage exclusion probabilities for an arbitrary number (n) of fullsibs, which reduce to previous equations for the special case of n=1. I also derive sibship exclusion probabilities, and investigate the power of differentiating half-sib, avuncular and grandparent-grandoffspring relationships using unlinked autosomal markers among different numbers of tested individuals. Applications of the formulas are demonstrated using both theoretical and empirical data sets of allele frequencies. The results from the study highlight the conclusion that the power of genealogical relationship inferences can be enhanced enormously by analysing multiple individuals for a given set of markers. The equations derived in this study allow more accurate determination of marker information and of the power of a parentage/sibship analysis. In addition, they can be used to guide experimental designs of parentage analyses in selecting markers and determining the number of offspring to be sampled and genotyped.     

Estimating pairwise relatedness from dominant genetic markers

Knowledge of the genetic relatedness between a pair of individuals is important in many research areas of quantitative genetics, conservation genetics, evolution and ecology. Many estimators have been developed to estimate such pairwise relatedness (r) using codominant markers, such as microsatellites and enzymes. In contrast, only two estimators are proposed to use dominant markers, such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), in relatedness inference. They are both biased estimators, and their statistical properties and robustness to the sampling errors in allele frequency have not been investigated. In this short paper, I propose two new pairwise relatedness estimators for dominant markers, and compare them in precision, accuracy and robustness to sampling with the two previous estimators using simulations. It was found that the new estimator based on the least squares approach is unbiased when allele frequencies are known or estimated from a sample without correcting for sampling effects. It has, however, a low precision and as a result, an intermediate overall performance among the four estimators in terms of the mean squared deviation (MSD) of estimates from actual values of r. The new estimator based on a similarity index is slightly biased but has generally the lowest MSD among the four estimators compared, regardless of the number of loci, type of actual relationships, allele frequencies known or estimated from samples. Simulations also show that the confidence intervals estimated by bootstrapping are appropriate for different estimators provided that the number of loci used in the estimation is not small.     

Informativeness of genetic markers for inference of ancestry

Inference of individual ancestry is useful in various applications, such as admixture mapping and structured-association mapping. Using information-theoretic principles, we introduce a general measure, the informativeness for assignment (I(n)), applicable to any number of potential source populations, for determining the amount of information that multiallelic markers provide about individual ancestry. In a worldwide human microsatellite data set, we identify markers of highest informativeness for inference of regional ancestry and for inference of population ancestry within regions; these markers, which are listed in online-only tables in our article, can be useful both in testing for and in controlling the influence of ancestry on case-control genetic association studies. Markers that are informative in one collection of source populations are generally informative in others. Informativeness of random dinucleotides, the most informative class of microsatellites, is five to eight times that of random single-nucleotide polymorphisms (SNPs), but 2%-12% of SNPs have higher informativeness than the median for dinucleotides. Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry.     

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.     

Profiling phylogenetic informativeness

The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic informativeness is equivalent for all rates when integrated across all of history, an informativeness profile across history is derived. Calculation of the informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.     

SSRs,SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of <Emphasis Type="Italic">Eucalyptus grandis</Emphasis>

Simple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihood-based estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.     

Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests

Nine microsatellite DNA markers (simple sequence repeats, SSRs) were used to estimate pairwise relationships among 597 Scots pine (Pinus sylvestris) trees as well as to generate a sibship structure for quantitative genetic parameters’ estimation comparison. The studied trees were part of an open-pollinated progeny test of 102 first-generation parents. Three methods were used to estimate variance components and heritabilities, namely, structured pedigree (half- and full-sib), marker-based pairwise relationships (four pairwise estimators), and a combined pedigree and marker-based relationship. In each of the three methods, the same animal model was used to compute variances except when marker-based relationship was used wherein we substituted the average numerator relationship matrix (i.e., pedigree-based matrix) with that computed based on markers’ pairwise relationships. Our results showed a high correlation in estimated breeding values between the pedigree (full-sib) and the combined marker-pedigree estimates. The marker-based relationship method produced high correlations when individual site data were analyzed. In contrast, the marker-based relationship method resulted in a significant decrease in both variance estimation and their standard errors which were in concordance with earlier published results; however, no estimates were produced when across-site analyses were attempted. We concluded that the combined pedigree method is the best approach as it represents the historical (pairwise) and contemporary (pedigree) relationships among the tested individuals, a situation that cannot be attained by any of the used methods individually. This method is dependent on the number and informativeness of the markers used.     

Efficient substructure RMSD query algorithms.

Protein structure analysis is a very important research topic in the molecular biology of the post-genomic era. The root mean square deviation (RMSD) is the most frequently used measure for comparing two protein three-dimensional (3-D) structures. In this paper, we deal with two fundamental problems related to the RMSD. We first deal with a problem called the "range RMSD query" problem. Given an aligned pair of structures, the problem is to compute the RMSD between two aligned substructures of them without gaps. This problem has many applications in protein structure analysis. We propose a linear-time preprocessing algorithm that enables constant-time RMSD computation. Next, we consider a problem called the "substructure RMSD query" problem, which is a generalization of the above range RMSD query problem. It is a problem to compute the RMSD between any substructures of two unaligned structures without gaps. Based on the algorithm for the range RMSD problem, we propose an O(nm) preprocessing algorithm that enables constant-time RMSD computation, where n and m are the lengths of the given structures. Moreover, we propose O(nm log r/r)-time and O(nm/r)-space preprocessing algorithm that enables O(r) query, where r is an arbitrary integer such that 1 < or = r < or = min(n, m). We also show that our strategy also works for another measure called the unit-vector root mean square deviation (URMSD), which is a variant of the RMSD.     

Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in <Emphasis Type="Italic">Musa</Emphasis>

Diversity Arrays Technology (DArT) is a DNA hybridisation-based molecular marker technique that can detect simultaneously variation at numerous genomic loci without sequence information. This efficiency makes it a potential tool for a quick and powerful assessment of the structure of germplasm collections. This article demonstrates the usefulness of DArT markers for genetic diversity analyses of Musa spp. genotypes. We developed four complexity reduction methods to generate DArT genomic representations and we tested their performance using 48 reference Musa genotypes. For these four complexity reduction methods, DArT markers displayed high polymorphism information content. We selected the two methods which generated the most polymorphic genomic representations (PstI/BstNI 16.8%, PstI/TaqI 16.1%) to analyze a panel of 168 Musa genotypes from two of the most important field collections of Musa in the world: Cirad (Neufchateau, Guadeloupe), and IITA (Ibadan, Nigeria). Since most edible cultivars are derived from two wild species, Musa acuminata (A genome) and Musa balbisiana (B genome), the study is restricted mostly to accessions of these two species and those derived from them. The genomic origin of the markers can help resolving the pedigree of valuable genotypes of unknown origin. A total of 836 markers were identified and used for genotyping. Ten percent of them were specific to the A genome and enabled targeting this genome portion in relatedness analysis among diverse ploidy constitutions. DArT markers revealed genetic relationships among Musa genotype consistent with those provided by the other markers technologies, but at a significantly higher resolution and speed and reduced cost.     

Precision of methods for calculating identity-by-descent matrices using multiple markers

A rapid, deterministic method (DET) based on a recursive algorithm and a stochastic method based on Markov Chain Monte Carlo (MCMC) for calculating identity-by-descent (IBD) matrices conditional on multiple markers were compared using stochastic simulation. Precision was measured by the mean squared error (MSE) of the relationship coefficients in predicting the true IBD relationships, relative to MSE obtained from using pedigree only. Comparisons were made when varying marker density, allele numbers, allele frequencies, and the size of full-sib families. The precision of DET was 75–99% relative to MCMC, but was not simply related to the informativeness of individual loci. For situations mimicking microsatellite markers or dense SNP, the precision of DET was ≥ 95% relative to MCMC. Relative precision declined for the SNP, but not microsatellites as marker density decreased. Full-sib family size did not affect the precision. The methods were tested in interval mapping and marker assisted selection, and the performance was very largely determined by the MSE. A multi-locus information index considering the type, number, and position of markers was developed to assess precision. It showed a marked empirical relationship with the observed precision for DET and MCMC and explained the complex relationship between relative precision and the informativeness of individual loci.     

Factors affecting placental traits and relationships of placental traits with neonatal behaviour in goat

The relationships between placental characteristics and litter weight, factors affecting these characteristics, and the relationship between these characteristics and neonatal behaviour of goat kids were investigated in this study. The study was carried out over three consecutive years and animal material consisted of total 152 Turkish Saanen goats and their 230 kids. The results of the study demonstrated that there were positive correlations between litter weight (LW), cotyledon number (CN), placental weight (PW) (r=0.64 and 0.76, P<0.01), but there was negative correlation between LW and cotyledon density (CD) (r=-0.42, P<0.01). CD was negatively correlated with PW (r=-0.61, P<0.01). CN and PW were influenced by the parity of doe, birth type-sex combination, buck within years and year of the study. On the other hand, parity and birth type-sex combination had no effect on PE (P>0.05), but buck within year affected placental efficiency (P<0.01). CD was only influenced by the parity of doe (P<0.01). Duration of birth (D) was not significantly related with CD, but if CD declined, it prolonged (r=-0.23, P>0.05). There were strong relationships between CD and birth-to-standing (B-St), and CD and birth-to-suckling (B-Su) (r=-0.42 and -0.51, P=0.01 and P<0.01).The results of the present study have shown similarities to the findings of the studies in sheep. Further studies are required to investigate the basis of the relationship between CD and neonatal behaviour.     

Muscular strength and power are correlated with motor unit action potential amplitudes,but not myosin heavy chain isoforms in sedentary males and females

It remains unclear if the sizes of higher-threshold motor units (MU) are associated with muscular strength and power. Therefore, the purpose of this study was to examine sex-related differences in muscle cross-sectional area (mCSA), percent myosin heavy chain (%MHC) isoform expression, and the MU action potential amplitudes (MUAP_AMPS)-recruitment threshold (RT) relationships of the vastus lateralis and isometric peak torque, isokinetic peak torque and mean power at 1.05 rad·s⁻¹ of the leg extensors. Surface electromyographic decomposition techniques were used to quantify MUAP_AMPS recorded during isometric muscle actions at 70% of maximal voluntary contractions and regressed against RTs with the slopes calculated. Ultrasound images were used to measure mCSA. Males had greater slopes from the MUAP_AMP-RT relationship than the females (P < 0.05). The greater slopes likely reflected larger higher-threshold MUs for the males. The mCSAs and slopes from the relationships were strongly correlated with isometric and isokinetic peak torque and isokinetic mean power (r = 0.78–0.82), however, type I %MHC isoform was only moderately correlated with isometric peak torque (r = −0.54). The results indicated that sex-related differences in muscular strength and power were associated more so with the sizes of the higher-threshold MUs (slopes) and mCSA than MHC isoforms. The amount of cross-bridge activity within muscle fibers that comprise higher-threshold MUs may be the primary contributor to muscular strength and power rather than the contractile properties of the muscle.     

Towards a genome-based taxonomy for prokaryotes

The ranks higher than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16S rRNA gene sequences, but no definite standards exist for the absolute relatedness (measured by 16S rRNA or other means) between the ranks. Accordingly, it remains unknown how comparable the ranks are between different organisms. To gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced strains, using as a robust measure of relatedness the average amino acid identity (AAI) of the shared genes. Our results reveal that adjacent ranks (e.g., phylum versus class) frequently show extensive overlap in terms of genetic and gene content relatedness of the grouped organisms, and hence, the current system is of limited predictive power in this respect. The overlap between nonadjacent ranks (e.g., phylum versus family) is generally limited and attributable to clear inconsistencies of the taxonomy. In addition to providing means for standardizing taxonomy, our AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes. For instance, the 23S rRNA gene was found to be as good a marker as the 16S rRNA gene, while several of the widely distributed protein-coding genes, such as the RNA polymerase and gyrase subunits, show a strong phylogenetic signal, albeit less strong than the rRNA genes (0.78 > R2 > 0.69 for the protein-coding genes versus R2 = 0.84 for the rRNA genes). The AAI approach outlined here could contribute significantly to a genome-based taxonomy for all microbial organisms.     

Genome- and species-specific markers and genome relationships of diploid perennial species in Triticeae based on RAPD analyses.

Eight different genomes (E, H, I, P, R, St, W, and Ns) represented by 22 diploid species of the tribe Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique. The genome relationships were obtained based on 371 RAPD fragments produced with 30 primers. The four species of the genus Psathyrostachys (having various Ns genomes) were closely related. The genomes Ee and Eb had a similarly close relationship and were distinct from all other genomes analyzed. Genomes P, R, and St were grouped in one cluster and genomes H and I in another. Genome W had a distant relationship with all other genomes. These results agree with the conclusions from studies of chromosome pairing and isozyme and DNA sequence analyses. Twenty-nine and 11 RAPD fragments are considered to be genome- and species-specific markers, respectively. One to six genome-specific markers were identified for each genome. These RAPD markers are useful in studies of genome evolution, analysis of genome composition, and genome identification.     

Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium

Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models.     

The relationship between oxygen consumption and body acceleration in a range of species

The ability to measure the energy expenditure of free-ranging animals is of great importance but the techniques available each have their limitations. Recently, as an alternative to more established techniques, an integrated measure of body acceleration termed overall dynamic body acceleration (ODBA) has been used as a calibrated proxy for rate of oxygen consumption (V(O(2))) and hence metabolic rate. The present study tested the potential of this technique, firstly by expanding the range of species for which the V(O(2))-ODBA relationship has been defined and secondly by undertaking a validation exercise to explore the accuracy of predictions made using ODBA. V(O(2))-ODBA relationships during terrestrial locomotion were established for several bipedal and quadrupedal endotherms and compiled with similar relationships previously determined in other species. A model incorporating all of these species showed that ODBA is an excellent predictor of V(O(2)) but there is variation in the V(O(2))-ODBA relationship between species, and further variation within some species. Including measurements such as body mass and structural size in prediction equations might further improve the predictive power of the 'ODBA technique' and eliminate species-specific differences. In the validation exercise, estimate errors were calculated for the species-specific predictive equations. The use of ODBA to estimate V(O(2)) was valid across all species examined and may show a greater potential for estimating energy expenditure for individual animals than other techniques.     

Sweat rate prediction equations for outdoor exercise with transient solar radiation

We investigated the validity of employing a fuzzy piecewise prediction equation (PW) [Gonzalez et al. J Appl Physiol 107: 379-388, 2009] defined by sweat rate (m(sw), g·m(-2)·h(-1)) = 147 + 1.527·(E(req)) - 0.87·(E(max)), which integrates evaporation required (E(req)) and the maximum evaporative capacity of the environment (E(max)). Heat exchange and physiological responses were determined throughout the trials. Environmental conditions were ambient temperature (T(a)) = 16-26°C, relative humidity (RH) = 51-55%, and wind speed (V) = 0.5-1.5 m/s. Volunteers wore military fatigues [clothing evaporative potential (i(m)/clo) = 0.33] and carried loads (15-31 kg) while marching 14-37 km over variable terrains either at night (N = 77, trials 1-5) or night with increasing daylight (N = 33, trials 6 and 7). PW was modified (Pw,sol) for transient solar radiation (R(sol), W) determined from measured solar loads and verified in trials 6 and 7. PW provided a valid m(sw) prediction during night trials (1-5) matching previous laboratory values and verified by bootstrap correlation (r(bs) of 0.81, SE ± 0.014, SEE = ± 69.2 g·m(-2)·h(-1)). For trials 6 and 7, E(req) and E(max) components included R(sol) applying a modified equation Pw,sol, in which m(sw) = 147 + 1.527·(E(req,sol)) - 0.87·(E(max)). Linear prediction of m(sw) = 0.72·Pw,sol + 135 (N = 33) was validated (R(2) = 0.92; SEE = ±33.8 g·m(-2)·h(-1)) with PW β-coefficients unaltered during field marches between 16°C and 26°C T(a) for m(sw) ≤ 700 g·m(-2)·h(-1). PW was additionally derived for cool laboratory/night conditions (T(a) < 20°C) in which E(req) is low but E(max) is high, as: PW,cool (g·m(-2)·h(-1)) = 350 + 1.527·E(req) - 0.87·E(max). These sweat prediction equations allow valid tools for civilian, sports, and military medicine communities to predict water needs during a variety of heat stress/exercise conditions.     

Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ?K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.     

Microsatellite diversity and fitness in stranded juvenile harp seals (Phoca groenlandica)

A positive relationship between genetic diversity at neutral markers and juvenile survival has been demonstrated for many vertebrate populations, although the correlation is typically weak and the explanation for it remains controversial. We assessed variation at 9-12 microsatellite loci in 65 juvenile harp seals (Phoca groenlandica) that stranded in poor condition around Long Island, NY, from 2001 to 2004. Compared with seals that died, surviving individuals had slightly higher measures of mean d(2), which reflects the size difference between alleles within an individual and provides an index of outbreeding. In contrast, there were no significant differences between survivors and nonsurvivors in heterozygosity or estimates of internal relatedness. This pattern is attributed to the fact that these microsatellite markers were exceptionally variable in this species (9-22 alleles per locus), and all individuals were heterozygous at most loci. Under these circumstances, mean d(2) may provide a powerful measure for assessing diversity-fitness correlations.     

Gene recombination and segregation of resistance factor R in Escherichia coli

Hashimoto, Hajime (Osaka University, Osaka, Japan), and Yukinori Hirota. Gene recombination and segregation of resistance factor R in Escherichia coli. J. Bacteriol. 91:51-62. 1966.-Independent chloramphenicol-sensitive (CM(s)) mutants of the drug-resistance factor R were isolated. Introduction of two different R factor CM(s) mutants into a single bacterium, by conjugation or transduction, gave chloramphenicol-resistant (CM(r)) colonies when such strains were plated on a medium containing chloramphenicol (Cm). These CM(r) colonies resulted from recombination between two R factors contained within the same cell. Most of the CM(r) colonies were heterogeneous, and segregation of drug-resistance markers was observed among the progeny. Segregated bacteria which still carried the recombinant R factor were stable for resistance to Cm as well as for other markers of R. All the markers of recombinant R factors were cotransducible with high coincidence and at the same frequency as wild-type R. Sensitive mutants of R which had lost all the resistance markers of the R factor were found also. A mutation of R, referred to as SMA, which was sensitive to streptomycin and sulfanilamide, was capable of reverting to resistance to both of these drugs simultaneously. The sensitive alleles for SMA, CM, and TC were shown to be recessive to the resistance alleles. Mutants of R having multisite mutations or deletions in the CM gene were isolated and used to analyze the pattern of linked segregation of unselected markers of the recombinant R factor. The drug resistance factor R was shown to have two linkage groups, CM-SMA and TC-m.