, Jost's D,and FST are similarly constrained by allele frequencies: A mathematical,simulation, and empirical study

Statistics and Jost's D have been proposed for replacing F_ST as measures of genetic differentiation. A principal argument in favour of these statistics is the independence of their maximal values with respect to the subpopulation heterozygosity H_S, a property not shared by F_ST. Nevertheless, it has been unclear if these alternative differentiation measures are constrained by other aspects of the allele frequencies. Here, for biallelic markers, we study the mathematical properties of the maximal values of and D, comparing them to those of F_ST. We show that and D exhibit the same peculiar frequency‐dependence phenomena as F_ST, including a maximal value as a function of the frequency of the most frequent allele that lies well below one. Although the functions describing , D, and F_ST in terms of the frequency of the most frequent allele are different, the allele frequencies that maximize them are identical. Moreover, we show using coalescent simulations that when taking into account the specific maximal values of the three statistics, their behaviours become similar across a large range of migration rates. We use our results to explain two empirical patterns: the similar values of the three statistics among North American wolves, and the low D values compared to and F_ST in Atlantic salmon. The results suggest that the three statistics are often predictably similar, so that they can make quite similar contributions to data analysis. When they are not similar, the difference can be understood in relation to features of genetic diversity.     

Variability of the Ramularia collo‐cygni Population in Central Europe

The genetic structure of the fungal barley pathogen Ramularia collo‐cygni (Rcc) population in Central Europe involving the isolates from the Czech Republic, the Slovak Republic, Germany and Swiss was determined using amplified fragment length polymorphism (AFLP) analysis. One hundred and eighty‐four markers were chosen to determine genetic and genotypic diversity and to test the hypothesis of random mating and population differentiation of Rcc isolates. Among the 337 isolates collected, the overall gene diversity was moderate ( = 0.216). The level of multilocus genotypic diversity was higher within populations than among them. All individuals had unique multilocus genotypes. Genetic differentiation was significant among populations in localities, but at a moderate level (θ = 0.12; P < 0.001), suggesting that gene flow is occurring among populations. The isolates from all twelve clusters produced by Structure were found in all local populations, although at different frequencies. Therefore, the inferred clusters did not represent geographical populations. Although the null hypothesis of random mating in Rcc populations was rejected, the high level of genotypic diversity suggests that the Rcc population structure appears to be generated by a mixed reproductive system including both asexual and sexual reproduction, along with a rather high migration rate.     

Estimators for QST and coalescence times

Comparisons of to can provide insights into the evolutionary processes that lead to differentiation, or lack thereof, among the phenotypes of different groups (e.g., populations, species), and these comparisons have been performed on a variety of taxa, including humans. Here, I show that for neutrally evolving (i.e., by genetic drift, mutation, and gene flow alone) quantitative characters, the two commonly used estimators have somewhat different interpretations in terms of coalescence times, particularly when the number of groups that have been sampled is small. A similar situation occurs for estimators. Consequently, when observations come from only a small number of groups, which is not an unusual situation, it is important to match estimators appropriately when comparing to .     

Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups

Accurate estimates of heritability () are necessary to assess adaptive responses of populations and evolution of fitness‐related traits in changing environments. For plants, estimates generally rely on maternal progeny designs, assuming that offspring are either half‐sibs or unrelated. However, plant mating systems often depart from half‐sib assumptions, this can bias estimates. Here, we investigate how to accurately estimate in nonmodel species through the analysis of sibling designs with a moderate genotyping effort. We performed simulations to investigate how microsatellite marker information available for only a subset of offspring can improve estimates based on maternal progeny designs in the presence of nonrandom mating, inbreeding in the parental population or maternal effects. We compared the basic family method, considering or not adjustments based on average relatedness coefficients, and methods based on the animal model. The animal model was used with average relatedness information, or with hybrid relatedness information: associating one‐generation pedigree and family assumptions, or associating one‐generation pedigree and average relatedness coefficients. Our results highlighted that methods using marker‐based relatedness coefficients performed as well as pedigree‐based methods in the presence of nonrandom mating (i.e. unequal male reproductive contributions, selfing), offering promising prospects to investigate in situ heritabilities in natural populations. In the presence of maternal effects, only the use of pairwise relatednesses through pedigree information improved the accuracy of estimates. In that case, the amount of father‐related offspring in the sibling design is the most critical. Overall, we showed that the method using both one‐generation pedigree and average relatedness coefficients was the most robust to various ecological scenarios.     

speed‐ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples

The genetic effective population size, N_e, can be estimated from the average gametic disequilibrium () between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed‐ne is a suite of matlab computer code functions to estimate from with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of estimators under various population genetic scenarios. speed‐ne was validated with data simulated under both time‐forward and time‐backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on , how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact . Estimators differed greatly in precision in the scenarios examined, and a widely employed estimator exhibited the largest variances among replicate data sets. speed‐ne implements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies. speed‐ne provides an open‐source extensible tool for estimation of from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare estimators.     

Purging putative siblings from population genetic data sets: a cautionary view

Interest has surged recently in removing siblings from population genetic data sets before conducting downstream analyses. However, even if the pedigree is inferred correctly, this has the potential to do more harm than good. We used computer simulations and empirical samples of coho salmon to evaluate strategies for adjusting samples to account for family structure. We compared performance in full samples and sibling‐reduced samples of estimators of allele frequency (), population differentiation () and effective population size (). Results: (i) unless simulated samples included large family groups together with a component of unrelated individuals, removing siblings generally reduced precision of and ; (ii) based on the linkage disequilibrium method was largely unbiased using full random samples but became increasingly upwardly biased under aggressive purging of siblings. Under nonrandom sampling (some families over‐represented), using full samples was downwardly biased; removing just the right ‘Goldilocks’ fraction of siblings could produce an unbiased estimate, but this sweet spot varied widely among scenarios; (iii) weighting individuals based on the inferred pedigree (to produce a best linear unbiased estimator, BLUE) maximized precision of when the inferred pedigree was correct but performed poorly when the pedigree was wrong; (iv) a variant of sibling removal that leaves intact small sibling groups appears to be more robust to errors in inferences about family structure. Our results illustrate the complex challenges posed by presence of family structure, suggest that no single optimal solution exists and argue for caution in adjusting population genetic data sets for the presence of putative siblings without fully understanding the consequences.     

DNA diversity of human populations from Eastern Europe and Siberia studied by multilocus DNA fingerprinting

We used DNA fingerprinting with M13 phage DNA as a probe to estimate the degree of genomic variability and genetic relationships in a heterogeneous group of 13 populations from Eastern Europe and Siberia. The popultaions belong to three language families: Indo-European (Slavonic: Russians, Byelorussians), Uralic (Finno-Ugric: Maris, Mordvinians, Udmurts), and Altaic (Turkic: Bashkirs, Tatars, Chuvashes, Yakuts). Multivariate statistical analyses were used (multidimensional scaling, cluster, and multiple correspondence analyses), and coefficients of gene differentiation (Gst) were evaluated. The level of interpopulation subdivision in the various ethnic groups appeared to be different: the Byelorussian populations revealed no regional differences, in contrast to the Bashkir populations, which formed a heterogeneous group. The populations subdivided into three general clusters: Slavonic populations formed a separate tight cluster characterized by a minimal level of interpopulation diversity, Bashkir and Yakut populations formed the second cluster, and the Finno-Ugric and several populations of the Turkic linguistic groups formed the third cluster. The robustness of these results obtained by different statistical data treatments reveals that multilocus DNA fingerprinting can be reliably used for population studies.Communicated by G. P. Georgiev     

NONSTATIONARY PATTERNS OF ISOLATION‐BY‐DISTANCE: INFERRING MEASURES OF LOCAL GENETIC DIFFERENTIATION WITH BAYESIAN KRIGING

Patterns of isolation‐by‐distance (IBD) arise when population differentiation increases with increasing geographic distances. Patterns of IBD are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate nonstationary patterns of IBD where the rate at which genetic differentiation accumulates varies across space. To characterize nonstationary patterns of IBD, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with two datasets: single nucleotide polymorphisms from human Swedish populations and dominant markers for alpine plant species.     

Genetic Structure of Cochliobolus sativus Populations Sampled from Roots and Leaves of Barley and Wheat in North Dakota

Common root rot (CRR) and spot blotch, caused by Cochliobolus sativus (Ito and Kurib.) Drechsl. ex Dast., are important diseases of barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) worldwide. However, the population biology of C. sativus is still poorly understood. In this study, the genetic structure of three C. sativus populations, consisting of isolates sampled respectively from barley leaves (BL), barley roots (BR) and wheat roots (WR) in North Dakota, was analysed with amplified fragment length polymorphism (AFLP) markers. A total of 127 AFLP loci were generated among 208 C. sativus isolates analysed with three primer combinations. Gene diversity (H = 0.277–0.335) were high in all three populations. Genetic variation among C. sativus individuals within population accounted for 74%, whereas 26% of the genetic variation was explained among populations. Genetic differentiation was high (ØPT = 0.261, corrected = 0.39), whereas gene flow (Nm) ranged from 1.27 to 1.56 among the three populations analysed. The multilocus linkage disequilibrium (LD) (= 0.076–0.117) was moderate in C  sativus populations. Cluster analyses indicate that C. sativus populations differentiated according to the hosts (barley and wheat) and tissues (root and leaf) although generalists also exist in North Dakota. Crop breeding may benefit from combining genes for resistance against both specialists and generalists of C. sativus.     

Additive genetic variance for lifetime fitness and the capacity for adaptation in an annual plant

The immediate capacity for adaptation under current environmental conditions is directly proportional to the additive genetic variance for fitness, V_A(W). Mean absolute fitness, , is predicted to change at the rate , according to Fisher's Fundamental Theorem of Natural Selection. Despite ample research evaluating degree of local adaptation, direct assessment of V_A(W) and the capacity for ongoing adaptation is exceedingly rare. We estimated V_A(W) and in three pedigreed populations of annual Chamaecrista fasciculata, over three years in the wild. Contrasting with common expectations, we found significant V_A(W) in all populations and years, predicting increased mean fitness in subsequent generations (0.83 to 6.12 seeds per individual). Further, we detected two cases predicting “evolutionary rescue,” where selection on standing V_A(W) was expected to increase fitness of declining populations (< 1.0) to levels consistent with population sustainability and growth. Within populations, inter‐annual differences in genetic expression of fitness were striking. Significant genotype‐by‐year interactions reflected modest correlations between breeding values across years, indicating temporally variable selection at the genotypic level that could contribute to maintaining V_A(W). By directly estimating V_A(W) and total lifetime , our study presents an experimental approach for studies of adaptive capacity in the wild.     

Application of the\mathop m\limits^* - m method to the analysis of spatial patterns by changing the quadrat sizemethod to the analysis of spatial patterns by changing the quadrat size

A method for the analysis of spatial pattern using quadrats of different sizes is developed on the basis of the relationship of mean crowding () to mean density (m). The -on-m regression obtained by successive changes in quadrat size in a single population (unit-size relation) shows a characteristic pattern according to the type of distribution. By aid of the ρ-index proposed here, we can distinguish the random, aggregated and uniform distributions of the basic components (individual or group of individuals). The ρ serves as an index of spatial correlation between neighbouring quadrats, and it also provides information on the approximate area occupied by clump (colony), distribution pattern of individuals within clumps, and possibly the distribution pattern of clumps themselves. Even in a specified type of distribution, the unit-size relation is not necessarily identical with the relation for a series of populations at a particular quadrat size (series relation). The changes in the series relationship with successive changes of quadrat sizes are also considered for some basic patterns of distributions. The combined use of the unit-size and the series relations for a set of populations of the species under study may provide a satisfactory picture of the spatial pattern characteristic of the species. Application of the method is illustrated by using distribution data of several species of animals and plants. The advantage of the present method over other methods are discussed, and the formulae for determining the optimum quadrat unit in sampling surveys are given.     

Redox regulation of plant stem cell fate

Despite the importance of stem cells in plant and animal development, the common mechanisms of stem cell maintenance in both systems have remained elusive. Recently, the importance of hydrogen peroxide (H₂O₂) signaling in priming stem cell differentiation has been extensively studied in animals. Here, we show that different forms of reactive oxygen species (ROS) have antagonistic roles in plant stem cell regulation, which were established by distinct spatiotemporal patterns of ROS‐metabolizing enzymes. The superoxide anion () is markedly enriched in stem cells to activate WUSCHEL and maintain stemness, whereas H₂O₂ is more abundant in the differentiating peripheral zone to promote stem cell differentiation. Moreover, H₂O₂ negatively regulates biosynthesis in stem cells, and increasing H₂O₂ levels or scavenging leads to the termination of stem cells. Our results provide a mechanistic framework for ROS‐mediated control of plant stem cell fate and demonstrate that the balance between and H₂O₂ is key to stem cell maintenance and differentiation.     

EXTINCTION-RECOLONIZATION DYNAMICS IN THE MYCOPHAGOUS BEETLE PHALACRUS SUBSTRIATUS

The population structure of the mycophagous beetle Phalacrus substriatus is characterized by many small, local populations interconnected by migration over a small spatial scale (10 × 75 m²). Each local P. substriatus population has a relatively short expected persistence time, but persistence of the species occurs due to a balance between frequent local extinctions and recolonizations. This nonequilibrium population structure can have profound effects on how the genetic variation is structured between and within populations. Theoretical models have stated that the genetic differentiation among local populations will be enhanced relative to an island model at equilibrium if the number of colonizers is less than approximately twice the number of migrants among local populations. To study these effects, a set of 50 local P. substriatus populations were surveyed over a four-year period to record any naturally occurring extinctions and recolonizations. The per population colonization and extinction rate were 0.237 and 0.275, respectively. Mark-recapture techniques were used to estimate a number of demographic parameters: local population size (N = 11.1), migration rate , number of colonizers (k = 4.0), and the probability of common origin of colonizers (φ = 0.5). The theoretically predicted level of differentiation among local populations (measured as Wright's F_ST) was 0.070. Genetic data obtained from an electrophoretic survey of seven polymorphic loci gave an estimated degree of differentiation of 0.077. There was thus a good agreement between the empirical results and the theoretical predictions. Young populations had significantly higher levels of differentiation than old, more established populations . The extinction-recolonization dynamics resulted in an overall increase in the genetic differentiation among local populations by c. 40%. The global effective population size was also reduced by c. 55%. The results give clear evidence to how nonequilibrium processes shape the genetic structure of populations.     

Genetic polymorphisms of α- and β-amylase isozymes in wild emmer wheat,Triticum dicoccoides,in Israel

Summary - and -amylase isozyme diversity was studied electrophoretically by thin-layer polyacrylamide gel isoelectrofocusing in the tetraploid wild emmer wheat, Triticum dicoccoides, the progenitor of all cultivated wheats. We analyzed 225 plants from 23 populations encompassing the ecological spectrum of T. dicoccoides in Israel. The results were as follows: (a) Band and multilocus genotype polymorphisms abound and vary within and between the four amylase components: malt, green (-amylases), and dry and germinating seeds (-amylases). (b) The number of bands of malt, green, and dry and germinating seeds were 20, 6, 11 and 13, respectively, generating 40, 6, 51, and 51 patterns or multilocus genotypes (MGP), respectively. The MGPs vary drastically within and between populations, from monomorphic in some populations with a single pattern to highly polymorphic ones, (c) Mean H _e values for malt, green, and germinating and dry seeds are 0.053, 0.055, 0.088, and 0.077, respectively; mean number of bands per individual was 11.8, 4.4, 7.6, and 4.0, respectively, (d) The percentages of 50 bands and 148 multilocus genotype patterns (MGP) (in parenthesis) were classified into widespread, sporadic, and localized: 84.4 (10.8), 8.9 (12.2), 6.7 (77.0), respectively. Notably, 89.2% of the patterns were not widespread, but sporadic and localized, (e) The mean value of genetic distances among populations (Nei's D) for the four amylase groups is D = 0.136, 0.175, 0.288 and 0.307, respectively, not displaying geographical correlates. (f) Most of the - and -amylase diversity is between populations (G _st = 68–75%). (g) Significant environmental correlates occur between either bands or patterns and climatic diversity (water and primarily temperature factors). (h) Significant associations of multilocus amylase bands occur across Israel. Like-wise, significant gametic phase disequilibria, D, occur within populations and are positively correlated with climatic variables, primarily that of temperature, (i) Discriminant analyses correctly classified (95–100%) the 23 wild emmer populations into their ecogeographical region and soil type. (j) Autocorrelation analysis showed that there is no correlation between bands and geographic distance and excluded migration as a major factor of amylase differentiation.These results suggest that diversifying climatic and edaphic natural selection rather than stochastisity or migration is the major evolutionary force driving amylase differentiation at both the single and multilocus levels. Furthermore, wild emmer harbors high levels of - and -amylase diversity both as single bands and as multilocus adaptive genetic patterns. These are exploitable both as genetic markers for quantitative loci (QTLs) and as adaptive genetic resources to improve wheat germination and growth through classical breeding and/or biotechnology.     

High‐throughput identification of protein mutant stability computed from a double mutant fitness landscape

The effect of a mutation on protein stability is traditionally measured by genetic construction, expression, purification, and physical analysis using low‐throughput methods. This process is tedious and limits the number of mutants able to be examined in a single study. In contrast, functional fitness effects can be measured in a high‐throughput manner by various deep mutational scanning tools. Using protein GB 1, we have recently demonstrated the feasibility of estimating the mutational stability effect ( G) of single‐substitution based on the functional fitness profile of all double‐substitutions. The principle is to identify genetic backgrounds that have an exhausted stability margin. The functional effect of an additional substitution on these genetic backgrounds can then be used to compute the mutational G based on the biophysical relationship between functional fitness and thermodynamic stability. However, to identify such genetic backgrounds, the approach described in our previous study required a benchmark dataset, which is a set of known mutational G. In this study, a benchmark‐independent approach is developed. The genetic backgrounds of interest are identified using k‐means clustering with the integration of structural information. We further demonstrated that a reasonable approximation of G can also be obtained without taking structural information into account. In summary, this study describes a novel method for computing G from double‐substitution functional fitness profiles alone, without relying on any known mutational G as a benchmark.     

The association between polyploidy and clonal reproduction in diploid and tetraploid Chamerion angustifolium

Clonal reproduction is associated with the incidence of polyploidy in flowering plants. This pattern may arise through selection for increased clonality in polyploids compared to diploids to reduce mixed‐ploidy mating. Here, we test whether clonal reproduction is greater in tetraploid than diploid populations of the mixed‐ploidy plant, Chamerion angustifolium, through an analysis of the size and spatial distribution of clones in natural populations using AFLP genotyping and a comparison of root bud production in a greenhouse study. Natural tetraploid populations (N = 5) had significantly more AFLP genotypes ( = 10.8) than diploid populations ( = 6.0). Tetraploid populations tended to have fewer ramets per genotype and fewer genotypes with >1 ramet. In a spatial autocorrelation analysis, ramets within genotypes were more spatially aggregated in diploid populations than in tetraploid populations. In the greenhouse, tetraploids allocated 90.4% more dry mass to root buds than diploids, but tetraploids produced no more root buds and 44% fewer root buds per unit root mass than diploids. Our results indicate that clonal reproduction is significant in most populations, but tetraploid populations are not more clonal than diploids, nor are their clones more spatially aggregated. As a result, tetraploids may be less sheltered from mixed‐ploidy mating and diploids more exposed to inbreeding, the balance of which could influence the establishment of tetraploids in diploid populations.     

Genetic differentiation of Rubus chamaemorus populations in the Czech Republic and Norway after the last glacial period

The population structure of cloudberry (Rubus chamaemorus L.), collected from Krkonose Mountains (the Czech Republic), continental Norway and Spitsbergen, was examined using microsatellite analyses (SSR). Among 184 individuals, 162 different genotypes were identified. The overall unbiased gene diversity was high (). A high level of genetic differentiation among populations (F_ST = 0.45; p < .01) indicated restricted gene flow between populations. Using a Bayesian approach, six clusters were found which represented the genetic structure of the studied cloudberry populations. The value of correlation index between genetic and geographical distances (r = .44) indicates that gene flow, even over a long distance, could exist. An exact test of population differentiation showed that Rubus chamaemorus populations from regions (Krkonose Mountains, continental Norway and Spitsbergen) are differentiated although some individuals within populations share common alleles even among regions. These results were confirmed by AMOVA, where the highest level of diversity was found within populations (70.8%). There was no difference between 87 pairs of populations (18.7%) mostly within cloudberry populations from continental Norway and from Spitsbergen. Based on obtained results, it is possible to conclude that Czech and Norwegian cloudberry populations are undergoing differentiation, which preserves unique allele compositions most likely from original populations during the last glaciation period. This knowledge will be important for the creation and continuation of in situ and ex situ conservation of cloudberry populations within these areas.     

Encapsulation and release of a bacterial carotenoid from hydrogel matrix: Characterization,kinetics and antioxidant study

Various natural polymers with hydrophilic properties have been used to form hydrogels for the encapsulation and delivery of nutrients and drugs in food and pharmaceutical industries. Among them, chitosan (ChiHG)‐ and alginate (AlgHG)‐ based hydrogels have been extensively explored for delivery of several nutraceuticals in recent years. Release of natural canthaxanthin (CX) obtained from Dietzia maris NITD (accession number: HM151403) has been investigated with emphasis on biomedical applications. Significant changes (P < 0.05) in degree of swelling and moisture content (% dry basis) were found after encapsulation of bacterial canthaxanthin (BCX), but the gel content remained unchanged. BCX encapsulation efficiency was calculated to be 55.92% and 60.45% in ChiHG and AlgHG, respectively. A noticeable change in heat of fusion d melting point was recorded in ChiHG and AlgHG after BCX encapsulation. Swelling and BCX release from gel matrix was performed under two different pH (1.2 and 7.4). The results showed that swelling of hydrogel and BCX release was facilitated at higher pH (7.4) than acidic pH (1.2). With regard to the release kinetics data, it was found that BCX is released from bothand AlgHG in a diffusion transport method. In addition, antioxidant activity of BCX encapsulated hydrogels was found significantly higher (P < 0.001) in terms of DPPH, ABTS, nitrite, hydroxyl radical scavenging and reducing power assay. These results indicated that BCX can be successfully encapsulated into a polymeric hydrogel to obtain a dynamic biomaterial that may be used in drug delivery applications in future.     

Population genomics from pool sequencing

Next generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator , nucleotide pairwise diversity Π, Tajima's D, Fu and Li's D and F, Fay and Wu's H, McDonald‐Kreitman and HKA tests and , corrected for sequencing errors and ascertainment bias. In a simulation study, we show that pool and individual θ estimates are highly correlated and discuss how the performance of the statistics vary with read depth and sample size in different evolutionary scenarios. As an application, we reanalyse sequences from Drosophila mauritiana and from an evolution experiment in Drosophila melanogaster. These methods are useful for population genetic projects with limited budget, study of communities of individuals that are hard to isolate, or autopolyploid species.