Combining ability, genetic diversity and heterosis in relation to F1 performance of tropically adapted shrunken (sh2) sweet corn lines

With 6 tables Abstract The objectives of this study were to evaluate the importance of heterosis for agronomic and quality traits in shrunken (sh2) sweet corn, assess the usefulness of combining ability to predict the value of parents and their crosses for further genetic improvement and examine whether genetic divergence can predict heterosis or F1 performance. Ten genetically diverse shrunken (sh2) sweet corn inbred lines were used to generate 45 F1s. F1s and parents were evaluated for agronomic and quality traits across environments. Heterosis was more important for yield-related traits than it was for ear aspects and eating quality. Heterosis for most traits was mostly dependent on dominance genetic effects of parental lines. Parents and F1per se performance were highly correlated with general combining ability effects and mid-parent values, respectively, for most traits. Hybrid performance for flavour and plant height was significantly but weakly related to simple sequence repeat (SSR)-based genetic distance (GD). Phenotypic distance (PD), estimated from phenotypic traits was correlated with heterosis for total soluble solids, ear length and flavour. © 2012 State of Queensland.

Population Expansion and Genetic Structure in Carcharhinus brevipinna in the Southern Indo-Pacific

Background:Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. Methods and Findings:Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and FST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717–0.03508, p values ≤ 0.0013; pairwise FST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia’s east coast (pairwise ΦST = 0.01328, p < 0.015), and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04).Conclusions: The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific.

An inordinate fondness for Fusarium: Phylogenetic diversity of fusaria cultivated by ambrosia beetles in the genus Euwallacea on avocado and other plant hosts

Ambrosia beetle fungiculture represents one of the most ecologically and evolutionarily successful symbioses, as evidenced by the 11 independent origins and 3500 species of ambrosia beetles. Here we document the evolution of a clade within Fusarium associated with ambrosia beetles in the genus Euwallacea (Coleoptera: Scolytinae). Ambrosia Fusarium Clade (AFC) symbionts are unusual in that some are plant pathogens that cause significant damage in naive natural and cultivated ecosystems, and currently threaten avocado production in the United States, Israel and Australia. Most AFC fusaria produce unusual clavate macroconidia that serve as a putative food source for their insect mutualists. AFC symbionts were abundant in the heads of four Euwallacea spp., which suggests that they are transported within and from the natal gallery in mandibular mycangia. In a four-locus phylogenetic analysis, the AFC was resolved in a strongly supported monophyletic group within the previously described Cade 3 of the Fusarium solani species complex (FSSC). Divergence-time estimates place the origin of the AFC in the early Miocene similar to 21.2 Mya, which coincides with the hypothesized adaptive radiation of the Xyleborini. Two strongly supported clades within the AFC (Clades A and B) were identified that include nine species lineages associated with ambrosia beetles, eight with Euwallacea spp. and one reportedly with Xyleborus ferrugineus, and two lineages with no known beetle association. More derived lineages within the AFC showed fixation of the clavate (club-shaped) macroconidial trait, while basal lineages showed a mix of clavate and more typical fusiform macroconidia. AFC lineages consisted mostly of genetically identical individuals associated with specific insect hosts in defined geographic locations, with at least three interspecific hybridization events inferred based on discordant placement in individual gene genealogies and detection of recombinant loci. Overall, these data are consistent with a strong evolutionary trend toward obligate symbiosis coupled with secondary contact and interspecific hybridization. (C) 2013 Elsevier Inc. All rights reserved.

Sympatric prey responses to lethal top-predator control: predator manipulation experiments

Introduction Many prey species around the world are suffering declines due to a variety of interacting causes such as land use change, climate change, invasive species and novel disease. Recent studies on the ecological roles of top-predators have suggested that lethal top-predator control by humans (typically undertaken to protect livestock or managed game from predation) is an indirect additional cause of prey declines through trophic cascade effects. Such studies have prompted calls to prohibit lethal top-predator control with the expectation that doing so will result in widespread benefits for biodiversity at all trophic levels. However, applied experiments investigating in situ responses of prey populations to contemporary top-predator management practices are few and none have previously been conducted on the eclectic suite of native and exotic mammalian, reptilian, avian and amphibian predator and prey taxa we simultaneously assess. We conducted a series of landscape-scale, multi-year, manipulative experiments at nine sites spanning five ecosystem types across the Australian continental rangelands to investigate the responses of sympatric prey populations to contemporary poison-baiting programs intended to control top-predators (dingoes) for livestock protection. Results Prey populations were almost always in similar or greater abundances in baited areas. Short-term prey responses to baiting were seldom apparent. Longer-term prey population trends fluctuated independently of baiting for every prey species at all sites, and divergence or convergence of prey population trends occurred rarely. Top-predator population trends fluctuated independently of baiting in all cases, and never did diverge or converge. Mesopredator population trends likewise fluctuated independently of baiting in almost all cases, but did diverge or converge in a few instances. Conclusions These results demonstrate that Australian populations of prey fauna at lower trophic levels are typically unaffected by top-predator control because top-predator populations are not substantially affected by contemporary control practices, thus averting a trophic cascade. We conclude that alteration of current top-predator management practices is probably unnecessary for enhancing fauna recovery in the Australian rangelands. More generally, our results suggest that theoretical and observational studies advancing the idea that lethal control of top-predators induces trophic cascades may not be as universal as previously supposed.

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter- and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three nonrecombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

Novel species of Cercospora and Pseudocercospora (Capnodiales, Mycosphaerellaceae) from Australia

Novel species of Cercospora and Pseudocercospora are described from Australian native plant species. These taxa are Cercospora ischaemi sp. nov. on Ischaemum australe (Poaceae); Pseudocercospora airliensis sp. nov. on Polyalthia nitidissima (Annonaceae); Pseudocercospora proiphydis sp. nov. on Proiphys amboinensis (Amaryllidaceae); and Pseudocercospora jagerae sp. nov. on Jagera pseudorhus var. pseudorhus (Sapindaceae). These species were characterised by morphology and an analysis of partial nucleotide sequence data for the three gene loci, ITS, LSU and EF-1α. Recent divergence of closely related Australian species of Pseudocercospora on native plants is proposed.

Stochastic Filtering

The stochastic filtering has been in general an estimation of indirectly observed states given observed data. This means that one is discussing conditional expected values as being one of the most accurate estimation, given the observations in the context of probability space. In my thesis, I have presented the theory of filtering using two different kind of observation process: the first one is a diffusion process which is discussed in the first chapter, while the third chapter introduces the latter which is a counting process. The majority of the fundamental results of the stochastic filtering is stated in form of interesting equations, such the unnormalized Zakai equation that leads to the Kushner-Stratonovich equation. The latter one which is known also by the normalized Zakai equation or equally by Fujisaki-Kallianpur-Kunita (FKK) equation, shows the divergence between the estimate using a diffusion process and a counting process. I have also introduced an example for the linear gaussian case, which is mainly the concept to build the so-called Kalman-Bucy filter. As the unnormalized and the normalized Zakai equations are in terms of the conditional distribution, a density of these distributions will be developed through these equations and stated by Kushner Theorem. However, Kushner Theorem has a form of a stochastic partial differential equation that needs to be verify in the sense of the existence and uniqueness of its solution, which is covered in the second chapter.

Dynamic Instabilities in Slender Space Launch Vehicles under Propulsive Thrust and Aerodynamic Forces

A mechanics based linear analysis of the problem of dynamic instabilities in slender space launch vehicles is undertaken. The flexible body dynamics of the moving vehicle is studied in an inertial frame of reference, including velocity induced curvature effects, which have not been considered so far in the published literature. Coupling among the rigid-body modes, the longitudinal vibrational modes and the transverse vibrational modes due to asymmetric lifting-body cross-section are considered. The model also incorporates the effects of aerodynamic forces and the propulsive thrust of the vehicle. The effects of the coupling between the combustion process (mass variation, developed thrust etc.) and the variables involved in the flexible body dynamics (displacements and velocities) are clearly brought out. The model is one-dimensional, and it can be employed to idealised slender vehicles with complex shapes. Computer simulations are carried out using a standard eigenvalue problem within h-p finite element modelling framework. Stability regimes for a vehicle subjected to propulsive thrust are validated by comparing the results from published literature. Numerical simulations are carried out for a representative vehicle to determine the instability regimes with vehicle speed and propulsive thrust as the parameters. The phenomena of static instability (divergence) and dynamic instability (flutter) are observed. The results at low Mach number match closely with the results obtained from previous models published in the literature.

Ihanne ja todellisuus : Jäsenyyteen sitoutuminen Suomen evankelis-luterilaisessa kirkossa 1960-luvulta 2000-luvulle

The subject of the study is the ideal and reality of commitment to membership in the Evangelical Lutheran Church of Finland from the 1960s to the 2000s. The research task is to ascertain what manner of commitment the Evangelical Lutheran Church of Finland expects from its members (the ideal) and how in reality membership of the Church is realized (empiria). The research object is also to study the extent to which the ideal of commitment evinced by the Church and the actual relation of commitment to the Church changed during the research period. Additionally, those factors were analysed which influence the relation between the ideal and reality of commitment. In the analysis of the ideal of commitment the research data are official documents of the Evangelical Lutheran Church of Finland. They include confessions of the Church, Catechisms, Christian doctrine, joint strategies and plans of the Church, likewise the Church Act and Church Order. The reality of commitment is explored on the basis of Church membership, participation in parish activity and the private practice of religion, likewise attitude to Christian faith. The empirical data of the study comprise Church statistics, material from Statistics Finland and relevant surveys implemented during the research period. The ideal of commitment alongside membership includes knowing the basic tenets of Christian faith and family life based on prayer and participation in liturgical cycles. A member of the Church is expected to take care of his/her faith by living in participation of the Word and sacrament, bearing responsibility for the parish and faithfully discharging his/her worldly obligations. There have been no major changes in the ideal of commitment during the research period. On the contrary, the reality of commitment has changed. Although the majority of Finns are still members of the Church, there has been a constant decline in their share of the population. The same can be stated with respect to parish life. This has its own strengths, among them Church rites, parish activity around feast days and also work with children and confirmation training. However, the general trend is towards a decline in participation. There has also been a decrease in commitment to belief in God as taught by the Church. On the other hand, private religious observance has not changed at all. From the perspective of commitment the Evangelical Lutheran Church of Finland exists in a state of tension between the theological ideal and sociological empiria. Matters exerting a particular influence over the relation between ideal and reality are communality and varying conceptions of the Church, likewise contextuality and the related private Christianity. Societal change poses a challenge to traditional Church communality. A decline in communality has in turn led to a decline in belonging to the Church. Weakening awareness of membership has undermined the handing down of the tradition among younger generations. Modernization has influence the identity of the Church and brought the Church to an internal divergence. This way it has been able to retain its structure as a folk church but at the same time it has lost its opportunities for the formation of a clear identity. The Church has adjusted to societal change by outward-directed activities (performance) alongside the purely religious message (function). The tension between an unchanged message and a changed operating environment has increased. The challenge of contextuality has led the Church to review parish life, the nature of teaching and activity and the language used by the Church, likewise the cultural modus. Increasingly privatized Christianity challenges above all the theology and teaching of the Church, but also the life of worship and relation to cultural life.

Thermal degradation of polystyrene

The importance of the study of thermal degradation of polymeric fuels arises from their role in the combustion of solid propellants. Estimation of the condensed-phase heat release during combustion can be facilitated by the knowledge of the enthalpy change associated with the polymer degradation process. Differential scanning calorimetry has been used to obtain enthalpy data. Kinetic studies on the polymeric degradation process have been carried out with the following objectives. The literature values of activation energies are quite diverse and differ from author to author. The present study has tried to locate possible reasons for the divergence in the reported activation energy values. A value of 30 kcal has been obtained and found to be independent of the technique employed. The present data on the kinetics support to chain-end initiation and unzipping process. The activation energies are further found to be independent of the atmosphere in which the degradation of polymer fuel is carried out. The degradation in air, N2, and O2 all yield a value of 30 kcal/mole for the activation energies.

Essays on Russia's Economic Transition

This study comprises an introductory section and three essays analysing Russia's economic transition from the early 1990s up to the present. The papers present a combination of both theoretical and empirical analysis on some of the key issues Russia has faced during its somewhat troublesome transformation from state-controlled command economy to market-based economy. The first essay analyses fiscal competition for mobile capital between identical regions in a transition country. A standard tax competition framework is extended to account for two features of a transition economy: the presence of two sectors, old and new, which differ in productivity; and a non-benevolent regional decision-maker. It is shown that in very early phase of transition, when the old sector clearly dominates, consumers in a transition economy may be better off in a competitive equilibrium. Decision-makers, on the other hand, will prefer to coordinate their fiscal policies. The second essay uses annual data for 1992-2003 to examine income dispersion and convergence across 76 Russian regions. Wide disparities in income levels have indeed emerged during the transition period. Dispersion has increased most among the initially better-off regions, whereas for the initially poorer regions no clear trend of divergence or convergence could be established. Further, some - albeit not highly robust - evidence was found of both unconditional and conditional convergence, especially among the initially richer regions. Finally, it is observed that there is much less evidence of convergence after the economic crisis of 1998. The third essay analyses industrial firms' engagement in provision of infrastructure services, such as heating, electricity and road maintenance. Using a unique dataset of 404 large and medium-sized industrial enterprises in 40 regions of Russia, the essay examines public infrastructure provision by Russian industrial enterprises. It is found that to a large degree engagement in infrastructure provision, as proxied by district heating production, is a Soviet legacy. Secondly, firms providing district heating to users outside their plant area are more likely to have close and multidimensional relations with the local public sector.

How terrorist campaigns end : The Rode Jeugd in the Netherlands and the Symbionese Liberation Army in the United States

This study explores the decline of terrorism by conducting source-based case studies on two left-wing terrorist campaigns in the 1970s, those of the Rode Jeugd in the Netherlands and the Symbionese Liberation Army in the United States. The purpose of the case studies is to bring more light into the interplay of different external and internal factors in the development of terrorist campaigns. This is done by presenting the history of the two chosen campaigns as narratives from the participants’ points of view, based on interviews with participants and extensive archival material. Organizational resources and dynamics clearly influenced the course of the two campaigns, but in different ways. This divergence derives at least partly from dissimilarities in organizational design and the incentive structure. Comparison of even these two cases shows that organizations using terrorism as a strategy can differ significantly, even when they share ideological orientation, are of the same size and operate in the same time period. Theories on the dynamics of terrorist campaigns would benefit from being more sensitive to this. The study also highlights that the demise of a terrorist organization does not necessarily lead to the decline of the terrorist campaign. Therefore, research should look at the development of terrorist activity beyond the lifespan of a single organization. The collective ideological beliefs and goals functioned primarily as a sustaining force, a lens through which the participants interpreted all developments. On the other hand, it appears that the role of ideology should not be overstated. Namely, not all participants in the campaigns under study fully internalized the radical ideology. Rather, their participation was mainly based on their friendship with other participants. Instead of ideology per se, it is more instructive to look at how those involved described their organization, themselves and their role in the revolutionary struggle. In both cases under study, the choice of the terrorist strategy was not merely a result of a cost-benefit calculation, but an important part of the participants’ self-image. Indeed, the way the groups portrayed themselves corresponded closely with the forms of action that they got involved in. Countermeasures and the lack of support were major reasons for the decline of the campaigns. However, what is noteworthy is that the countermeasures would not have had the same kind of impact had it not been for certain weaknesses of the groups themselves. Moreover, besides the direct impact the countermeasures had on the campaign, equally important was how they affected the attitudes of the larger left-wing community and the public in general. In this context, both the attitudes towards the terrorist campaign and the authorities were relevant to the outcome of the campaigns.

Conservation of Atlantic salmon by supplementary stocking of juvenile fish

Wild salmon stocks in the northern Baltic rivers became endangered in the second half of the 20th century, mainly due to recruitment overfishing. As a result, supplementary stocking was widely practised, and supplementation of the Tornionjoki salmon stock took place over a 25 year period until 2002. The stock has been closely monitored by electrofishing, smolt trapping, mark-recapture studies, catch samples and catch surveys. Background information on hatchery-reared stocked juveniles was also collected for this study. Bayesian statistics was applied to the data as this method offers the possibility of bringing prior information into the analysis and an advanced ability for incorporating uncertainty, and also provides probabilities for a multitude of hypotheses. Substantial divergences between reared and wild Tornionjoki salmon were identified in both demographic and phenological characteristics. The divergences tended to be larger the longer the duration spent in hatchery and the more favourable the hatchery conditions were for fast growth. Differences in environment likely induced most of the divergences, but selection of brood fish might have resulted in genotypic divergence in maturation age of reared salmon. Survival of stocked 1-year old juveniles to smolt varied from about 10% to about 25%. Stocking on the lower reach of the river seemed to decrease survival, and the negative effect of stocking volume on survival raises the concern of possible similar effects on the extant wild population. Post-smolt survival of wild Tornionjoki smolts was on average two times higher than that of smolts stocked as parr and 2.5 times higher than that of stocked smolts. Smolts of different groups showed synchronous variation and similar long-term survival trends. Both groups of reared salmon were more vulnerable to offshore driftnet and coastal trapnet fishing than wild salmon. Average survival from smolt to spawners of wild salmon was 2.8 times higher than that of salmon stocked as parr and 3.3 times higher than that of salmon stocked as smolts. Wild salmon and salmon stocked as parr were found to have similar lifetime survival rates, while stocked smolts have a lifetime survival rate over 4 times higher than the two other groups. If eggs are collected from the wild brood fish, stocking parr would therefore not be a sensible option. Stocking smolts instead would create a net benefit in terms of the number of spawners, but this strategy has serious drawbacks and risks associated with the larger phenotypic and demographic divergences from wild salmon. Supplementation was shown not to be the key factor behind the recovery of the Tornionjoki and other northern Baltic salmon stocks. Instead, a combination of restrictions in the sea fishery and simultaneous occurrence of favourable natural conditions for survival were the main reasons for the revival in the 1990 s. This study questions the effectiveness of supplementation as a conservation management tool. The benefits of supplementation seem at best limited. Relatively high occurrences of reared fish in catches may generate false optimism concerning the effects of supplementation. Supplementation may lead to genetic risks due to problems in brood fish collection and artificial rearing with relaxed natural selection and domestication. Appropriate management of fisheries is the main alternative to supplementation, without which all other efforts for long-term maintenance of a healthy fish resource fail.

The life cycle and genetic structure of the red alga Furcellaria lumbricalis on a salinity gradient

The life cycle and genetic diversity of the red alga Furcellaria lumbricalis (Hudson) Lamouroux were investigated in 15 populations in northern Europe. The occurrence of different life cycle phases and seasonality of reproduction were studied in four brackish populations in the northern Baltic Sea. Furthermore, a new method, based on genome screening with ISSR markers combined with a restriction-ligation method, was developed to discover microsatellite markers for population genetic analyses. The mitochondrial DNA cox2-3 spacer sequence and four microsatellite markers were used to examine the genetic diversity and differentiation of red algal populations in northern Europe. In addition, clonality and small-scale genetic structure of one Irish and four Baltic Sea populations were studied with microsatellite markers. It was discovered that at the low salinities of the northern Baltic Sea, only tetrasporophytes and males were present in the populations of F. lumbricalis and that winter was the main season for tetrasporangial production. Furthermore, the population occurring at the lowest salinity (3.6 practical salinity units, psu) did not produce spores. The size of the tetraspores was smaller in the Baltic Sea populations than that in the Irish population, and there were more deformed spores in the Baltic Sea populations than in the Irish populations. Studies with microsatellite markers indicated that clonality is a common phenomenon in the Baltic Sea populations of F. lumbricalis, although the proportion of clonal individuals varied among populations. Some genetic divergence occurred within locations both in Ireland and in the northern Baltic Sea. Even though no carpogonia were detected in the field samples during the study, the microsatellite data indicated that sexual reproduction occurs at least occasionally in the northern Baltic Sea. The genetic diversity of F. lumbricalis was highest in Brittany, France. Since no variation was discovered in the mtDNA cox2-3 spacer sequence, which is generally regarded as an informative phylogeographic marker in red algae, it can be assumed that the studied populations probably share the same origin.