Levels of genetic polymorphism: marker loci versus quantitative traits

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species

Phenotypic robustness can increase phenotypic variability after non-genetic perturbations in gene regulatory circuits

Non-genetic perturbations, such as environmental change or developmental noise, can induce novel phenotypes. If an induced phenotype confers a fitness advantage, selection may promote its genetic stabilization. Non-genetic perturbations can thus initiate evolutionary innovation. Genetic variation that is not usually phenotypically visible may play an important role in this process. Populations under stabilizing selection on a phenotype that is robust to mutations can accumulate such variation. After non-genetic perturbations, this variation can become a source of new phenotypes. We here study the relationship between a phenotype's robustness to mutations and a population's potential to generate novel phenotypic variation. To this end, we use a well-studied model of transcriptional regulation circuits. Such circuits are important in many evolutionary innovations. We find that phenotypic robustness promotes phenotypic variability in response to non-genetic perturbations, but not in response to mutation. Our work suggests that non-genetic perturbations may initiate innovation more frequently in mutationally robust gene expression traits.Comment: 11 pages, 5 figure

Statistics of selectively neutral genetic variation

Random models of evolution are instrumental in extracting rates of microscopic evolutionary mechanisms from empirical observations on genetic variation in genome sequences. In this context it is necessary to know the statistical properties of empirical observables (such as the local homozygosity for instance). Previous work relies on numerical results or assumes Gaussian approximations for the corresponding distributions. In this paper we give an analytical derivation of the statistical properties of the local homozygosity and other empirical observables assuming selective neutrality. We find that such distributions can be very non-Gaussian.Comment: 4 pages, 4 figure

Genetic Variation of Dacrycarpus Imbricatus in Bromo Tengger Semeru National Park, East Java Based on TrnL (UAA) Intron Region

The conservation of Jamuju Dacrycarpus imbricatus (Blume) de Laub. in Java Island has been considered important. One of the the limitation of such program is related to the viability data on the genetic diversity of species target. The aim of study was to determine genetic variation of D. imbricatus in Bromo Tengger Semeru Park, East Java based on trnL (UAA) intron region. DNA sample was collected from several D. imbricatus seedling population in Bromo Tengger Semeru National Park (BTSNP) in East Java. DNA was isolated and amplified using PCR. Genetic variation was estimated using trnL (UAA) intron sequences. This study confirm that D. imbricatus in Bromo Tengger Semeru has low genetic diversity. Based on the phylogenetic tree, D. imbricatus population from Bromo Tengger Semeru Park is closely related to D. imbricatus from Sabah-Malaysia and Hainan-China with 100 % similarity value. These data implies that population and habitat management of D. imbricatus in Bromo Tengger Semeru should be designed to enhance the population survival in the future

Genetic Variation of Leafhopper, Nephotettix Virescens Distant Active Transmitters From Endemic and Non Endemic Areas of Rice Tungro Disease Based on RAPD Marker

Genetic variation of leafhopper, Nephotettix virescens Distant active transmitters from endemic and non endemic areas of rice tungro disease based on RAPD marker. Leafhopper, Nephotettix virescens Distant (Hemiptera: Cicadellidae) plays an important role as a vector of rice tungro virus. However, the characters of N. virescens as a vector from endemic and non-endemic areas of tungro disease in Indonesia have not been well characterized and also available information is limited. The objective of this research was to study the character of N. virescens active transmitter from endemic and non-endemic of areas tungro disease based on RAPD markers. The N. virescens were collected from endemic area of Klaten (Central Java), Sleman (Yogyakarta) and non endemic area of Purwodadi (Central Java) Ngawi (East Java), and Pacitan (East Java). The N. virescens active transmitters were identified by their ability to transmit the virus based on Standard Evaluation System for Rice Tungro Virus, issued by IRRI. The genetic variations of N. virescens active transmitters were determined by using RAPD-PCR marker. Result of the research showed that three primers, OPB01, OPB10 and OPC08 amplified successfully of DNA template of N. virescens through RAPD-PCR technique. Based on the dendrogram, there were initial facts of possible genetic differences between the populations of N. virescens from endemic and non endemic areas of rice tungro disease. The N. virescens from endemic area of Klaten and Sleman are similar genetically but different from the N. virescens non endemic of Purwodadi, Pacitan and Ngawi

Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from mahoe (Melicytus ramiflorus)

Sourcing plant species of local provenance (eco-sourcing) has become standard practice in plant community restoration projects. Along with established ecological restoration practices, knowledge of genetic variation in existing and restored forest fragments is important for ensuring the maintenance of natural levels of genetic variation and connectivity (gene flow) among populations. The application of restoration genetics often employs anonymous ‘fingerprinting’ markers in combination with limited sample sizes due to financial constraints. Here, we used two such marker systems, AFLPs and ISSRs, to estimate population-level genetic variation of a frequently used species in restoration projects in New Zealand, māhoe (Melicytus ramiflorus, Violaceae). We examined two rural and two urban forest fragments, as potential local source populations, to determine whether the māhoe population at the recently (re)constructed ecosystem at Waiwhakareke Natural Heritage Park (WNHP), Hamilton, New Zealand reflects the genetic variation observed in these four potential source populations. Both marker systems produced similar results and indicated, even with small population sizes, that levels of genetic variation at WNHP were comparable to in situ populations. However, the AFLPs did provide finer resolution of the population genetic structure than ISSRs. ISSRs, which are less expensive and technically less demanding to generate than AFLPs, may be sufficient for restoration projects where only a broad level of genotypic resolution is required. We recommend the use of AFLPs when species with a high conservation status are being used due to the greater resolution of this technique

Genetic Covariance Structure of Reading, Intelligence and Memory in Children

This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained by a common genetic factor for reading performance, IQ, WM and STM and a genetic factor that only influenced reading performance and verbal memory. Genetic variation explained 83% of the variation in reading performance; most of this genetic variance was explained by variation in IQ and memory performance. We hypothesize, based on these results, that children with reading problems possibly can be divided into three groups: (1) children low in IQ and with reading problems; (2) children with average IQ but a STM deficit and with reading problems; (3) children with low IQ and STM deficits; this group may experience more reading problems than the other two

Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management

Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives