Genetic parameters and provenance variation of Pinus radiata D. Don. ‘Eldridge collection’ in Australia 1: growth and form traits

Growth and form traits data were obtained from eight provenance trials of radiata pine (Pinus radiata D. Don) planted across the radiata pine plantation estate in southeast Australia. The genetic pool included 466 open-pollinated families collected from A?o Nuevo, Monterey and Cambria provenances on the Californian mainland coast in the USA and from Guadalupe and Cedros islands off the coast of Baja California in Mexico. Early survival of all provenances was around 90%, except for Cedros (<60%). Monterey and A?o Nuevo were the best performers at almost all sites. However, good growth performance of Cambria and good stem straightness of Guadalupe on some sites are important results, because the genetic base of the present Australian plantations evidently originated from only Monterey and A?o Nuevo. The average estimated single-site heritability for diameter at breast height was 0.22 and 0.32 at juvenile and mature ages, respectively. Heritability estimates for stem straightness and branching ranged from 0.23 to 0.55. Genetic correlation estimates between diameter at breast height (DBH) at juvenile and rotation ages were all >0.80. Estimates of between-site genetic and provenance correlations for DBH were often low, indicating high genotype by environment interaction across trials, consistent with previous Australian studies. However, there was minimal G × E among trials on high-altitude high-rainfall sites and among trials on low-altitude, low-rainfall sites.     

Genetic parameters and provenance variation of Pinus radiata D. Don. ‘Eldridge collection’ in Australia 2: wood properties

Provenance variation and genetic parameters for wood properties of mature radiata pine (Pinus radiata D. Don) were studied by sampling three provenance/progeny trials in southeast Australia. Among the mainland provenances, Monterey and Año Nuevo had higher density and modulus of elasticity (at one site) than Cambria. Basic density and predicted modulus of elasticity (MoE) for the island provenances, Guadalupe and Cedros, were ～20% higher at Billapaloola compared to mainland provenances grown at Green Hills and Salicki, differences that may or may not be linked to site differences. Heritability estimates of density, predicted MoE and microfibril angle were significant and $ {\bar{h}^2} $ ?>?0.45, suggesting moderate to strong genetic control. The estimated genetic correlations between diameter at breast height and wood properties in the current study were weaker (less negative) than the mean estimated from the current breeding population generation in radiata pine. Of the wood properties, density showed the strongest adverse genetic correlations with growth (mean r _A ?=??0.23?±?0.09). Selection for MoE may produce greater gain than selection for density because MoE had almost twice the estimated additive genetic coefficient of variation ( $ {\overline {\text{CV}}_A} $ ) compared to density. Estimated type B genetic correlations (r _B) for all wood quality traits were typically high, conforming to the trend that wood properties have low genotype-by-environment interaction (G?×?E). Significant differences in wood properties among provenances, families and/or individual trees provide an opportunity for breeding programmes to select superior trees for solid wood production that will combine superior growth with desirable wood traits.     

Genetic instability in protoclones of potato (Solanum tuberosum L. cv. ‘Bintje’): new types of variation after vegetative propagation

Summary The transmission of variation from protoplast-derived plants of tetraploid potato cultivar Bintje to tuber progeny was examined. The morphological alterations of a majority of the variant protoclones were transmitted to corresponding tuber progeny. Some of the normal and variant protoclones gave new phenotypes, or segregated into parental and new phenotypes after vegetative propagation. The ploidy levels of almost all these clones remained unchanged after propagation. It was concluded that the occurrence of variation after vegetative propagation was due to somatic segregation of chimeras resulting from gene mutations or chromosome structural rearrangements in only part of the regenerated plant. The origin of variation is discussed in the light of these results.     

Genetic differentiation between populations of the ant Aphaenogaster ‘rudis’ in the Southeastern United States

Chromosomal and isozyme variation was examined in populations of the ant Aphaenogaster rudis. Georgian populations of this ant are referable to a lighter Coastal Plains or a darker Montane phenotype. Coastal Plains populations are fixed or nearly fixed for a null esterase allele, Es ⁰, whereas high activity allele frequencies characterise Montane populations. High Mdh-a ¹ frequencies (>0.5) are typical of Coastal Plains populations, but in Montane populations this allele is rarer (<0.3) or absent. Study of a narrow (approximately one kilometer wide) contact zone (Turner's Corner) between these two forms showed that Coastal Plains ants have n=20 as against n=22 for Montane ants there, that there was no chromosomal evidence of hybridization, but that the presence of low frequencies of the alternate Es alleles in both forms indicates that there is some introgression. The Montane phenotype is itself heterogeneous at Black Rock Mountain, where a further, 18-chromosome, cytotype shows marked microhabitat segregation from the sympatric 22-chromosome form and differs from it in allele frequencies at all four loci examined (Mdh-a, Mdh-b, Es, Amy). Average relative genetic distances (Nei's D_m) between populations within all forms are low (maximum of 0.03±0.01) compared with interform distances (minimum of 0.19±0.03), which are similar to distances between the rudis forms and both of fulva and treatae. Aphaenogaster fulva has a very similar karyotype to that of 18-chromosome rudis, in which some specimens show weak development of the taxonomic characters distinguishing fulva from rudis. However, fulva and 18-chromosome rudis differ markedly allozymically, especially in that Amy ⁵ and Amy ⁶ are the only amylase alleles in fulva and Amy ⁴ is the only amylase allele in 18-chromosome rudis. An Alachua County, Florida rudis-group population has a 22-chromosome karyotype different to that of Georgian rudis, but the genetic distance values suggest it may be most similar genetically to the Montane 22-chromosome form. Low-level gene flow between fulva and rudis-group populations is suggested by similarity of fulva and two different sympatric rudis-group populations in terms of Es alleles present.The Georgian 20- and 22-chromosome rudis karyotypes may possibly be related by Robertsonian changes, but the relationship between these and the 18-chromosome forms (18-chromosome rudis, fulva, and an 18-chromosome Florida isolate), treatae (n=21), and lamellidens (n=19), are obscure. A non-Robertsonian chromosome number polymorphism was found in one Coastal Plains population.No unequivocal evidence was found for an overall departure of genotype frequencies from those expected under the Hardy-Weinberg Law.The rudis cytotypes in Georgia are sibling species whose close morphological resemblance may reflect ecological but not genetic similarity.     

Intra- and interspecific variation in trophic ecology of ‘predatory’ ants in the subfamily Ponerinae

1. The characterisation of energy flow through communities is a primary goal of ecology. Furthermore, predator–prey interactions can influence both species abundance and community composition. The ant subfamily Ponerinae includes many predatory species that range from generalist insectivores to highly specialised hunters that target a single prey type. Given their high diversity and ubiquity in tropical ecosystems, measuring intra- and interspecific variation in their trophic ecology is essential for understanding the role of ants as predators of insect communities. 2. The stable isotopic composition of nitrogen of 22 species from the ant subfamily Ponerinae was measured, relative to plants and other predatory and herbivorous insects at two Atlantic Forest sites in Argentina. The study tested the general assumption that ponerine ants are all predatory, and examined intra- and interspecific variation in trophic ecology relative to habitat, body size and cytochrome c oxidase subunit 1 sequences (DNA barcoding). 3. Stable isotope analysis revealed that most ponerines occupy high trophic levels (primary and secondary predators), but some species overlapped with known insect herbivores. Species residing at low trophic levels were primarily arboreal and may rely heavily on nectar or other plant-based resources in their diet. In addition, larger species tend to occupy lower trophic positions than smaller species. 4. Although some of the species were divided into two or more genetic clusters by DNA barcoding analysis, these clusters did not correspond to intraspecific variation in trophic position; therefore, colony dietary flexibility most probably explains species that inhabit more than one trophic level.     

Phenotypic variation during micropropagation of the chimeralRhododendron ‘President Roosevelt’

The putative periclinal chimeraRhododendron xlimbatum President Roosevelt was used to study the origin of shoots in vitro. Genotypic segregation readily occurred in vitro. Numerous phenotypes were observed, although most shoots were either entirely green or maintained the original variegation pattern. Derivatives of the third apical layer were rarely involved in shoot formation. A reversed chimeral form was isolated. Adventitious shoots were usually miniaturized and rapidly proliferating, but axillary shoots had thicker stems, larger leaves and proliferated more slowly. Corolla tissue produced stunted, leafy shoots; no variegated shoots were produced from floret explants. In shoot tip cultures the addition of 40M 2iP without IBA resulted in the greatest number of shoots. Explant choice was the most critical factor for maintenance of foliar variegation.     

Temperature- and seed-batch-related variation in the kinetic behaviour of phytochrome under ‘high-irradiance-response’ conditions

The characteristics of the high-irradiance response (HIR) of plant photomorphogenesis are thought to be the result of the interaction of both the light and dark reactions of phytochrome. Thus any variation in the rates of the dark reactions may be expected to lead to variation in the characteristics of the HIR. We report here substantial differences in the rates of the dark reactions between different seed batches of a single species (Sinapis alba L.), and also between different organs of seedlings from each of the batches of seed. Calculations of phytochrome dynamics from the measured dark-reaction rates show that the behaviour of Pfr under HIR conditions will vary considerably according to seed batch and seedling organ. Much larger differences in dark-reaction rates, and the resulting phytochrome dynamics, were found between 25° and 10° C. These lead to the prediction that the HIR will be much reduced at the lower temperature, and may be absent in some cases.Abbreviations and symbols HIR high-irradiance response - Pfr far-red-absorbing form of phytochrome - Pr red-absorbing form of phytochrome - Ptot total phytochrome, Pr+Pfr - _ss Pfr/Ptot ratio which immediately establishes the phytochrome steady state     

Leaf characteristics and diurnal variation of chlorophyll fluorescence in leaves of the ‘bana’ vegetation of the amazon region

In six dominant species of the Amazonian ‘Bana’ vegetation, leaf blade characteristics, pigment composition, and chlorophyll (Chl) fluorescence parameters were measured in young and mature leaves under field conditions. Leaf δ¹³C was comparable in the six species, which suggested that both expanding and expanded leaves contained organic matter fixed under similar intercellular and ambient CO₂ concentration (C _i/C _a). High leaf C/N and negative δ¹⁵N values found in this habitat were consistent with the extreme soil N-deficiency. Analysis of Chl and carotenoids showed that expanding leaves had an incomplete development of photosynthetic antenna when compared to adult leaves. Dynamic inactivation of photosystem 2 (PS2) at midday was observed at both leaf ages as F_v/F_m decreased compared to predawn values. Adult leaves reached overnight F_v/F_m ratios typical of healthy leaves. Overnight recovery of F_v/F_m in expanding leaves was incomplete. F₀ remained unchanged from midday to predawn and F_v tended to increase from midday to predawn. The recovery from midday depression observed in adult leaves suggested an acclimatory down-regulation associated with photo-protection and non-damage of PS2.     

Genetic transformation of the apple scion cultivar ‘Delicious’ viaAgrobacterium tumefaciens

Transformed shoots of the major apple scion cultivar Delicious (Malus × domestica Borkh.) were obtained by cocultivation withAgrobacterium tumefaciens carrying disarmed plasmids. The transformation efficiency was influenced by the type of plasmid and by the inoculation temperature. Initial selection involved a callus stage followed by shoot regeneration. Shoot regeneration occurred only in the dark. Shoots grew in the light and were rooted in the presence of 100 mg l^–1 kanamycin. Of the range of plasmids tested, the cointegrates pGV 3850::1103neo and pGV 3850::1103gus gave a higher frequency of transformation than the binary vector pGV 3111 × pKIWI. Elongation of transformed shoots was enhanced by culture in a mixture of the cytokinins 6(--dimethylallylamino)purine and 6-benzyladenine. Up to 60% of the elongated shoots rooted in 100 mg l^–1 kanamycin. Transformation was indicated by kanamycin resistance, -glucuronidase assay, nopaline synthesis, and by integration of the T-DNA as judged by Southern analysis.     

Genetic and biochemical studies on perchloroethylene ‘in vitro’ and ‘in vivo’

Perchloroethylene (PCE) was tested in a diploid strain (D7) of the yeast Saccharomyces cerevisiae in suspension tests with and without a mammalian microsomal activation system (S9) and ‘in vivo’ by the intrasanguineous host-mediated assay. In addition, enzyme alteration studies were performed in mice non-pretreated or pretreated with phenobarbital + β-naphthoflavone. PCE did not induce any genetic effect either ‘in vitro’ or ‘in vivo’. In the suspension test, PCE was more toxic without metabolic activation and less toxic with mammalian microsomal activation. The enzymatic determinations showed an increase of the aminopyrine demethylase activity and of the level of cytochrome P-450.     

Seasonal variation in the form of iron in the liver of Spitsbergen reindeer: a Mössbauer spectroscopic study

Mössbauer spectra have been obtained from samples of the liver of Spitsbergen reindeer at different times of the year. Most of the iron is in a very similar form to that of the iron storage materials ferritin and haemosiderin. The data reflect the large differences in the amount of iron found in the liver at different times of the year and also indicate that there are only relatively small differences in the chemical and physical form of the iron found in the liver at different times of the year.     

Innatism in the Anthropology of A. L. Kroeber: A Critique of ‘the Boasian Paradigm’

Basing his analysis on Kroeber's ‘The superorganic’ (1917 Kroeber, A. L. 1917. The superorganic.. American Anthropologist, 19: 163–213. [Crossref] [Google Scholar]) and ‘Eighteen professions’ (1915 Kroeber, A. L. 1915. Eighteen professions.. American Anthropologist, 17: 283–88. [Crossref] [Google Scholar]), Derek Freeman has put forward the notion of a ‘Boasian paradigm’, whereby Kroeber is alleged to have perpetuated the biology/culture split suggested by Boas. I argue, instead, that there is a strong innatist element in Kroeber's writings throughout his long career; and that the articles noted above need to be placed in the social and intellectual contexts of their time, particularly the encroachment of the eugenics movement on social theory and its application to immigration restriction.     

Comprehensive Assessment of Genetic Sequence Variants in the Antioxidant ‘Master Regulator’ Nrf2 in Idiopathic Parkinson’s Disease

Parkinson’s disease (PD) is a complex neurodegenerative disorder influenced by a combination of genetic and environmental factors. The molecular mechanisms that underlie PD are unknown; however, oxidative stress and impairment of antioxidant defence mechanisms have been implicated as major contributors to disease pathogenesis. Previously, we have reported a PD patient-derived cellular model generated from biopsies of the olfactory mucosa, termed hONS cells, in which the NRF2-mediated antioxidant response pathway genes were among the most differentially-expressed. To date, few studies have examined the role of the NRF2 encoding gene, NFE2L2, and PD. In this study, we comprehensibly assessed whether rare and common NFE2L2 genetic variations modify susceptibility to PD using a large Australian case-control sample (PD=1338, controls=1379). We employed a haplotype-tagging approach that identified an association with the tagging SNP rs2364725 and PD (OR = 0.849 (0.760-0.948), P = 0.004). Further genetic screening in hONS cell lines produced no obvious pathogenic variants in the coding regions of NFE2L2. Finally, we investigated the relationship between xenobiotic exposures and NRF2 function, through gene-environment interactions, between NFE2L2 SNPs and smoking or pesticide exposure. Our results demonstrated a significant interaction between rs2706110 and pesticide exposure (OR = 0.597 (0.393-0.900), P = 0.014). In addition, we were able to identify some age-at-onset modifying SNPs and replicate an ‘early-onset’ haplotype that contains a previously identified ‘functional promoter’ SNP (rs6721961). Our results suggest a role of NFE2L2 genetic variants in modifying PD susceptibility and onset. Our findings also support the utility of testing gene-environment interactions in genetic studies of PD.     

Population Genetic Diversity in the Australian ‘Seascape’: A Bioregion Approach

Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a ‘hump’ in diversity across the range studied (−9.4 to −43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.     

Genetic ancestry of participants in the National Children’s Study

Background

The National Children’s Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, and health. Determination of the ancestry of these NCS participants is important for assessing the diversity of study participants and for examining the effect of ancestry on various health outcomes.

Results

We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites, by analyzing 30,000 markers on exome arrays, using the 1000 Genomes Project superpopulations as reference populations, and compared this with the measures of self-reported ethnicity and race. For 99% of the individuals, self-reported ethnicity and race agreed with the predicted superpopulation. NCS individuals self-reporting as Asian had genetic ancestry of either South Asian or East Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 33% matched the South Asian or East Asian groups, while these groups represented only 4.4% of the other reported categories.

Conclusions

Our data suggest that self-reported ethnicity and race have some limitations in accurately capturing Hispanic and South Asian populations. Overall, however, our data indicate that despite the complexity of the US population, individuals know their ancestral origins, and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.