Rapid assessment of genotype-by-environment interactions and heritability for growth rate in aquaculture species using in vitro fertilisation and DNA tagging

Commercial environments may receive only a fraction of expected genetic gains for growth rate as predicted from the selection environment. This fraction is result of undesirable genotype-by-environment interactions (GxE) and measured by the genetic correlation (rg) of growth between environments. Rapid estimates of genetic correlation achieved in one generation are notoriously difficult to estimate with precision. A new design is proposed where genetic correlations can be estimated by utilising artificial mating from cryopreserved semen and unfertilised eggs stripped from a single female. We compare a traditional phenotype analysis of growth to a threshold model where only the largest fish are genotyped for sire identification. The threshold model was robust to differences in family mortality differing up to 30%. The design is unique as it negates potential re-ranking of families caused by an interaction between common maternal environmental effects and growing environment. The design is suitable for rapid assessment of GxE over one generation with a true 0.70 genetic correlation yielding standard errors as low as 0.07. Different design scenarios were tested for bias and accuracy with a range of heritability values, number of half-sib families created, number of progeny within each full-sib family, number of fish genotyped, number of fish stocked, differing family survival rates and at various simulated genetic correlation levels.

Intermolecular Interactions of Noble-Gas-Containing Species

The importance of intermolecular interactions to chemistry, physics, and biology is difficult to overestimate. Without intermolecular forces, condensed phase matter could not form. The simplest way to categorize different types of intermolecular interactions is to describe them using van der Waals and hydrogen bonded (H-bonded) interactions. In the H-bond, the intermolecular interaction appears between a positively charged hydrogen atom and electronegative fragments and it originates from strong electrostatic interactions. H-bonding is important when considering the properties of condensed phase water and in many biological systems including the structure of DNA and proteins. Vibrational spectroscopy is a useful tool for studying complexes and the solvation of molecules. Vibrational frequency shift has been used to characterize complex formation. In an H-bonded system A∙∙∙H-X (A and X are acceptor and donor species, respectively), the vibrational frequency of the H-X stretching vibration usually decreases from its value in free H-X (red-shift). This frequency shift has been used as evidence for H-bond formation and the magnitude of the shift has been used as an indicator of the H-bonding strength. In contrast to this normal behavior are the blue-shifting H-bonds, in which the H-X vibrational frequency increases upon complex formation. In the last decade, there has been active discussion regarding these blue-shifting H-bonds. Noble-gases have been considered inert due to their limited reactivity with other elements. In the early 1930 s, Pauling predicted the stable noble-gas compounds XeF6 and KrF6. It was not until three decades later Neil Bartlett synthesized the first noble-gas compound, XePtF6, in 1962. A renaissance of noble-gas chemistry began in 1995 with the discovery of noble-gas hydride molecules at the University of Helsinki. The first hydrides were HXeCl, HXeBr, HXeI, HKrCl, and HXeH. These molecules have the general formula of HNgY, where H is a hydrogen atom, Ng is a noble-gas atom (Ar, Kr, or Xe), and Y is an electronegative fragment. At present, this class of molecules comprises 23 members including both inorganic and organic compounds. The first and only argon-containing neutral chemical compound HArF was synthesized in 2000 and its properties have since been investigated in a number of studies. A helium-containing chemical compound, HHeF, was predicted computationally, but its lifetime has been predicted to be severely limited by hydrogen tunneling. Helium and neon are the only elements in the periodic table that do not form neutral, ground state molecules. A noble-gas matrix is a useful medium in which to study unstable and reactive species including ions. A solvated proton forms a centrosymmetric NgHNg+ (Ng = Ar, Kr, and Xe) structure in a noble-gas matrix and this is probably the simplest example of a solvated proton. Interestingly, the hypothetical NeHNe+ cation is isoelectronic with the water-solvated proton H5O2+ (Zundel-ion). In addition to the NgHNg+ cations, the isoelectronic YHY- (Y = halogen atom or pseudohalogen fragment) anions have been studied with the matrix-isolation technique. These species have been known to exist in alkali metal salts (YHY)-M+ (M = alkali metal e.g. K or Na) for more than 80 years. Hydrated HF forms the FHF- structure in aqueous solutions, and these ions participate in several important chemical processes. In this thesis, studies of the intermolecular interactions of HNgY molecules and centrosymmetric ions with various species are presented. The HNgY complexes show unusual spectral features, e.g. large blue-shifts of the H-Ng stretching vibration upon complexation. It is suggested that the blue-shift is a normal effect for these molecules, and that originates from the enhanced (HNg)+Y- ion-pair character upon complexation. It is also found that the HNgY molecules are energetically stabilized in the complexed form, and this effect is computationally demonstrated for the HHeF molecule. The NgHNg+ and YHY- ions also show blue-shifts in their asymmetric stretching vibration upon complexation with nitrogen. Additionally, the matrix site structure and hindered rotation (libration) of the HNgY molecules were studied. The librational motion is a much-discussed solid state phenomenon, and the HNgY molecules embedded in noble-gas matrices are good model systems to study this effect. The formation mechanisms of the HNgY molecules and the decay mechanism of NgHNg+ cations are discussed. A new electron tunneling model for the decay of NgHNg+ absorptions in noble-gas matrices is proposed. Studies of the NgHNg+∙∙∙N2 complexes support this electron tunneling mechanism.

The community of medium-sized carnivores: the interactions between species, habitats and rabies

The composition of the carnivore community influences the different forms of inter-specific interactions. Furthermore, inter-specific interactions of carnivores have important implications for intra-guild competition, epidemiology and strategies of species-specific population management. Zoonooses, such as rabies, are diseases that can be transmitted from wildlife to people. Knowing the ecological characteristics of the species helps us to choose the right preventive actions and to time them accurately. In this thesis, I have studied how raccoon dogs Nyctereutes procyonoides, European badgers Meles meles, red foxes Vulpes vulpes and domestic cats Felis silvestris catus act as members of carnivore community, and how these interactions relate to the transmission risk of rabies. In the study area, these species form a community of medium-sized and rather generalist predators. They live in the same areas, in spatially and temporally overlapping home ranges and use the same habitats and dens and even have similar diets. However, there is no direct evidence of competition. Shared dens point to good tolerance of other species. Numerous observations of animals moving in each other’s proximity give similar clues. However, overlapping home ranges and similar habitat preferences lead to frequent inter-specific contacts, which increase the risk of possible rabies transmission. Also, the new insight of habitat use gained by this study illustrates the similar favouring of deciduous forests and fields by these sympatric medium-sized carnivores, creating a basis for contact zones, i.e. risky habitats for rabies transmission and spread. This study is so far the only simultaneous radio tracking study of raccoon dogs, badgers, foxes and cats. These results give new insight of the interactions in the carnivore community, as well as of the behaviour of each individual species. Also, these results have significant implications for the planning of rabies control. In order to reach viable management decisions, not only one or two species should be taken into consideration, but the whole community. In particular, this changes the perspective to inter-specific contacts, animal densities, densities of individuals susceptible to diseases and the magnitude of preventive actions. Rabies should be considered as a multi-vector disease, at least in Finland and the Baltic states. It is of interest for disease management to be able to model an epizootic with local parameters to reflect the real situation and also to suite best the local management needs.

Interactions between oppositely-charged vs. those between like-charged species in crystal of aminoacetonitrile picrate: a charge density investigation

Energy and charge aspects of two types of ion association - between oppositely-charged and between like-charged species - were quantified using the topological analysis of the electron density function derived from the low-temperature X-ray diffraction experiment for a crystal of aminoacetonitrile picrate (sp. gr. Cmca, Z = 8, R = 0.0187), providing an experimental evidence of their ``equal rights'' in crystal packing formation.

A Review of Interactions Between Hawaii's Fisheries and Protected Species

Several fisheries in Hawaii are known to have interactions with protected cetaceans, seabirds, marine turtles, or seals. Handline fisheries for bottomfish, tuna, and mackerel scad lose bait and catch to bottlenose dolphins, rough-toothed dolphins, and Hawaiian monk seals. Troll fisheries for billfish lose live bait to bottlenose dolphins, rough-toothed dolphins, albatrosses, and boobies; these fisheries may also lose catch to false killer whales. A longline fishery for tuna and billfish has burgeoned in Hawaii since 1987, resulting in interactions with protected species; marine turtles, seabirds, and monk seals take bait and are known to become hooked, and false killer whales may take catch. Research on deterrents or alternative fishing methods has been limited, and interactions have been reduced primarily through management and regulatory actions. These include area closures and gear requirements. An observer program has also been established for the bottomfish and longline fisheries.

Allelopathic interactions between the macroalga Ulva pertusa and eight microalgal species

HETEROSIGMA-AKASHIWO RAPHIDOPHYCEAE; CENTRAL VENICE LAGOON; ALEXANDRIUM-TAMARENSE; RED-TIDE; COASTAL LAGOONS; PHYTOPLANKTON; GROWTH; BAY; DINOFLAGELLATE; COMPETITION

Interactions between multiple large macrofauna species and nematode communities — Mechanisms for indirect impacts of trawling disturbance

Highlights •We exposed meiofauna to 7 different large macrofauna species at high and low densities. •Macrofauna presence altered nematode community structure and reduced their abundance. •Macrofauna species had similar effects by reducing the few dominant nematode species. •Meio–macrofauna resource competition and spatial segregation are the main drivers. •Trawling effects on macrofauna affect nematode communities indirectly. Diverse assemblages of infauna in sediments provide important physical and biogeochemical services, but are under increasing pressure by anthropogenic activities, such as benthic trawling. It is known that trawling disturbance has a substantial effect on the larger benthic fauna, with reductions in density and diversity, and changes in community structure, benthic biomass, production, and bioturbation and biogeochemical processes. Largely unknown, however, are the mechanisms by which the trawling impacts on the large benthic macro- and megafauna may influence the smaller meiofauna. To investigate this, a mesocosm experiment was conducted whereby benthic nematode communities from a non-trawled area were exposed to three different densities (absent, low, normal) of 7 large (> 10 mm) naturally co-occurring, bioturbating species which are potentially vulnerable to trawling disturbance. The results showed that total abundances of nematodes were lower if these large macrofauna species were present, but no clear nematode abundance effects could be assigned to the macrofauna density differences. Nematode community structure changed in response to macrofauna presence and density, mainly as a result of the reduced abundance of a few dominant nematode species. Any detectable effects seemed similar for nearly all macrofauna species treatments, supporting the idea that there may be a general indirect, macrofauna-mediated trawling impact on nematode communities. Explanations for these results may be, firstly, competition for food resources, resulting in spatial segregation of the meio- and macrobenthic components. Secondly, different densities of large macrofauna organisms may affect the nematode community structure through different intensities of bioturbatory disturbance or resource competition. These results suggest that removal or reduced densities of larger macrofauna species as a result of trawling disturbance may lead to increased nematode abundance and hints at the validity of interference competition between large macrofauna organisms and the smaller meiofauna, and the energy equivalence hypothesis, where a trade-off is observed between groups of organisms that are dependent on a common source of energy.

Invader-invader interactions in relation to environmental heterogeneity leads to zonation of two invasive amphipods, Dikerogammarus villosus (Sowinsky) and Gammarus tigrinus Sexton: amphipod pilot species project (AMPIS) report 6

As biological invasions continue, interactions occur not only between invaders and natives, but increasingly new invaders come into contact with previous invaders. Whilst this can lead to species replacements, co-existence may occur, but we lack knowledge of processes driving such patterns. Since environmental heterogeneity can determine species richness and co-existence, the present study examines habitat use and its mediation of the predatory interaction between invasive aquatic amphipods, the Ponto-Caspian Dikerogammarus villosus and the N. American Gammarus tigrinus. In the Dutch Lake IJsselmeer, we found broad segregation of D. villosus and G. tigrinus by habitat type, the former predominating in the boulder zone and the latter in the soft sediment. However, the two species co-exist in the boulder zone, both on the short and longer terms. We used an experimental simulation of habitat heterogeneity and show that both species utilize crevices, different sized holes in a plastic grid, non-randomly. These amphipods appear to optimise the use of holes with respect to their 'C-shape' body size. When placed together, D. villosus adults preyed on G. tigrinus adults and juveniles, while G. tigrinus adults preyed on D. villosus juveniles. Juveniles were also predators and both species were cannibalistic. However, the impact on G. tigrinus of the superior intraguild predator, D. villosus, was significantly reduced where experimental grids were present as compared to absent. This mitigation of intraguild predation between the two species in complex habitats may explain the co-existence of these two invasive species.

Role of behaviour in biological invasions and species distributions; lessons from interactions between the invasive Gammarus pulex and the native G-duebeni (Crustacea : Amphipoda)

In attempting to understand the distributions of both introduced species and the native species on which they impact, there is a growing trend to integrate studies of behaviour with more traditional life history/ecological approaches. The question of what mechanisms drive the displacement of the freshwater amphipod Gammarus duebeni by the often introduced G pulex is presented as a case study Patterns of displacement are well documented throughout Europe, but the speed and direction of displacement between these species can be varied. From early studies proposing interspecific competition as causal in these patterns, I review research progress to date. I show there has been no evidence for interspecific competition operating, other than the field patterns themselves, a somewhat tautological argument. Rather, the increased recognition of behavioural attributes with respect to the cannibalistic and predatory nature of these species gave rise to a series of studies unravelling the processes driving field patterns. Both species engage in 'intraguild predation' (IGP), with moulting females particularly vulnerable to predation by congeneric males. G pulex is more able both to engage in and avoid this interaction with G duebeni. However, several factors mediate the strength and asymmetry of this IGP, some biotic (e.g. parasitism) and others abiotic (e.g. water chemistry). Further, a number of alternative hypotheses that may account for the displacement (hybridization; parasite transmission) have been tested and rejected. While interspecific competition has been modelled mathematically and found to be a weak interaction relative to IGP, mechanisms of competition between these Gammarus species remain largely untested empirically. Since IGP may be finely balanced in some circumstances, I conclude that the challenge to detect interspecific competition remains and we require assessment of its role, if any, in the interaction between these species. Appreciation of behavioural attributes and their mediation should allow us to more fully understand, and perhaps predict, species introductions and resultant distributions.

Trophic dynamics within a hybrid zone - interactions between an abundant cyprinid hybrid and sympatric parental species

1. Recent proliferation of hybridisation in response to anthropogenic ecosystem change, coupled with increasing evidence of the importance of ancient hybridisation events in the formation of many species, has moved hybridisation to the forefront of evolutionary theory.

2. In spite of this, the mechanisms (e. g. differences in trophic ecology) by which hybrids co-exist with parental taxa are poorly understood. A unique hybrid zone exists in Irish freshwater systems, whereby hybrid offspring off two non-native cyprinid fishes often outnumber both parental species.

3. Using stable isotope and gut content analyses, we determined the trophic interactions between sympatric populations of roach (Rutilus rutilus), bream (Abramis brama) and their hybrid in lacustrine habitats.

4. The diet of all three groups displayed little variation across the study systems, and dietary overlap was observed between both parental species and hybrids. Hybrids displayed diet, niche breadth and trophic position that were intermediate between the two parental species while also exhibiting greater flexibility in diet across systems.

Possible interactions between environmental factors in determining species optima

Questions: 1. Indicator values, such as those of Ellenberg, for different environmental factors are seen as independent. We tested for the presence of interactions between environmental factors ( soil moisture and reaction) to see if this assumption is simplistic. 2. How close are Ellenberg indicator values (IVs) related to the observed optima of species response curves in an area peripheral to those where they have been previously employed and 3. Can the inclusion of bryophytes add to the utility of IVs?

Location: South Uist, Outer Hebrides, Scotland, UK.

Methods: Two grids (ca. 2000 m x 2000 m) were sampled at 50-m intervals across the transition from machair to upland communities covering an orthogonal gradient of both soil pH ( reaction) and soil moisture content. Percentage cover data for vascular plants, bryophytes and lichens were recorded, along with pH and moisture content of the underlying sand/soil/peat. Reaction optima, derived from species response curves calculated using HOF models, were compared between wet and dry sites, and moisture optima between acidic and basic samples. Optima for the whole data set were compared to Ellenberg IVs to assess their performance in this area, with and without the inclusion of bryophytes.

Results: A number of species showed substantially different pH optima at high and low soil moisture contents (18% of those tested) and different soil moisture optima at high and low pH (49%). For a number of species the IVs were poor predictors of their actual distribution across the sampled area. Bryophytes were poor at explaining local variation in the environmental factors and also their inclusion with vascular plants negatively affected the strength of relationships.

Conclusions: A substantial number of species showed an interaction between soil moisture and reaction in determining their optima on the two respective gradients. It should be borne in mind that IVs such as Ellenberg's may not be independent of one another.