Genes and growth performance in crustacean species : a review of relevant genomic studies in crustaceans and other taxa

Global aquaculture has expanded rapidly to address the increasing demand for aquatic protein needs and an uncertain future for wild fisheries. To date, however, most farmed aquatic stocks are essentially wild and little is known about their genomes or the genes that affect important economic traits in culture. Biologists have recognized that recent technological advances including next generation sequencing (NGS) have opened up the possibility of generating genome wide sequence data sets rapidly from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', understanding gene function and genetic effects on expressed quantitative trait locus phenotypes will be fundamental to future knowledge development. Many factors can influence the individual growth rate in target species but of particular importance in agriculture and aquaculture will be the identification and characterization of the specific gene loci that contribute important phenotypic variation to growth because the information can be applied to speed up genetic improvement programmes and to increase productivity via marker-assisted selection (MAS). While currently there is only limited genomic information available for any crustacean species, a number of putative candidate genes have been identified or implicated in growth and muscle development in some species. In an effort to stimulate increased research on the identification of growth-related genes in crustacean species, here we review the available information on: (i) associations between genes and growth reported in crustaceans, (ii) growth-related genes involved with moulting, (iii) muscle development and degradation genes involved in moulting, and; (iv) correlations between DNA sequences that have confirmed growth trait effects in farmed animal species used in terrestrial agriculture and related sequences in crustacean species. The information in concert can provide a foundation for increasing the rate at which knowledge about key genes affecting growth traits in crustacean species is gained.

Quantitative genetic parameter estimates for body and carcass traits in a cultured stock of giant freshwater prawn (Macrobrachium rosenbergii) selected for harvest weight in Vietnam

We estimated the heritability and correlations between body and carcass weight traits in a cultured stock of giant freshwater prawn (GFP) (Macrobrachium rosenbergii) selected for harvest body weight in Vietnam. The data set consisted of 18,387 body and 1,730 carcass records, as well as full pedigree information collected over four generations. Variance and covariance components were estimated by restricted maximum likelihood fitting a multi-trait animal model. Across generations, estimates of heritability for body and carcass weight traits were moderate and ranged from 0.14 to 0.19 and 0.17 to 0.21, respectively. Body trait heritabilities estimated for females were significantly higher than for males whereas carcass weight trait heritabilities estimated for females and males were not significantly different (P>. 0.05). Maternal effects for body traits accounted for 4 to 5% of the total variance and were greater in females than in males. Genetic correlations among body traits were generally high in the mixed sexes. Genetic correlations between body and carcass weight traits were also high. Although some issues remain regarding the best statistical model to be fitted to GFP data, our results suggest that selection for high harvest body weight based on breeding values estimated by fitting an animal model to the data can significantly improve mean body and carcass weight in GFP.

Genetic response to combined family selection for improved mean harvest weight in giant freshwater prawn (Macrobrachium rosenbergii) in Vietnam

We estimated genetic changes in body and carcass weight traits in a giant freshwater prawn (GFP) (Macrobrachium rosenbergii) population selected for increased body weight at harvest in Vietnam. The data set consisted of 18,387 individual body and 1730 carcass weight records, as well as full pedigree information collected over four generations. Average selection response (per generation) in body weight at harvest (transformed to square root) estimated as the difference between the Selection line and the Control group was 7.4% calculated from least squares mean (LSMs), 7.0% from estimated breeding values (EBVs) and 4.4% calculated from EBVs between two consecutive generations. Favorable correlated selection responses (estimated from LSMs) were found for other body traits including: total length, cephalothorax length, abdominal length, cephalothorax width, and abdominal width (12.1%, 14.5%, 10.4%, 15.5% and 13.3% over three selection generations, respectively). Data in the second generation of selection showed positive correlated responses for carcass weight traits including: abdominal weight, exoskeleton-off weight, and telson-off weight of 8.8%, 8.6% and 8.8%, respectively. We conclude that body weight at harvest responded well to the application of combined (between and within) family selection and correlated responses in carcass weight traits were favorable.

Complex cognitive interactions in a badly designed world : Investigating the underlying causes of collisions between distinct road users

Collisions between distinct road users (e.g. drivers and riders, drivers and cyclists) make a substantial contribution to the road trauma burden. Although evidence suggests different road users interpret the same road situations contrarily, it is not clear how their situation awareness differs, nor is it clear which differences might lead to conflicts. This article presents the findings from an on-road study which was conducted to examine driver, cyclist and motorcyclist situation awareness in different road environments. The findings suggest that drivers, motorcyclists, and cyclists develop markedly different situational understandings even when operating in the same road environments. Examination of these differences indicate that they are likely to be compatible along arterial roads, shopping strips and at roundabouts, but that they may create conflicts between the different road users at intersections. The key role of road design in supporting compatible situation awareness and behaviour across different road users is discussed.

Investigating the factors influencing cyclist awareness and behaviour : an on-road study of cyclist situation awareness

Situation awareness, ones understanding of ‘what is going on’, is a critical commodity for road users. Although the concept has received much attention in the driving context, situation awareness in vulnerable road users, such as cyclists, remains unexplored. This paper presents the findings from an exploratory on-road study of cyclist situation awareness, the aim of which was to explore how cyclists develop situation awareness, what their situation awareness comprises, and what the causes of degraded cyclist situation awareness may be. Twenty participants cycled a pre-defined urban on-road study route. A range of data were collected, including verbal protocols, forward scene video and rear video, and a network analysis procedure was used to describe and assess cyclist situation awareness. The analysis produced a number of key findings regarding cyclist situation awareness, including the potential for cyclists’ awareness of other road users to be degraded due to additional situation awareness and decision making requirements that are placed on them in certain road situations. Strategies for improving cyclists’ situation awareness are discussed.

Lane filtering and situation awareness in motorcyclists : an on-road proof of concept study

In Victoria, as in other jurisdictions, there is very little research on the potential risks and benefits of lane filtering by motorcyclists, particularly from a road safety perspective. This on-road proof of concept study aimed to investigate whether and how lane filtering influences motorcycle rider situation awareness at intersections and to address factors that need to be considered for the design of a larger study in this area. Situation awareness refers to road users’ understanding of ‘what is going on’ around them and is a critical commodity for safe performance. Twenty-five experienced motorcyclists rode their own instrumented motorcycle around an urban test route in Melbourne whilst providing verbal protocols. Lane filtering occurred in 27% of 43 possible instances in which there were one or more vehicles in the traffic queue and the traffic lights were red on approach to the intersection. A network analysis procedure, based on the verbal protocols provided by motorcyclists, was used to identify differences in motorcyclist situation awareness between filtering and non-filtering events. Although similarities in situation awareness across filtering and nonfiltering motorcyclists were found, the analysis revealed some differences. For example, filtering motorcyclists placed more emphasis on the timing of the traffic light sequence and on their own actions when moving to the front of the traffic queue, whilst non-filtering motorcyclists paid greater attention to traffic moving through the intersection and approaching from behind. Based on the results of this study, the paper discusses some methodological and theoretical issues to be addressed in a larger study comparing situation awareness between filtering and non-filtering motorcyclists.

On-road driving studies to understand why drivers behave as they do at regional rail level crossings

Improving safety at rail level crossings is an important part of both road and rail safety strategies. While low in number, crashes between vehicles and trains at level crossings are catastrophic events typically involving multiple fatalities and serious injuries. Advances in driving assessment methods, such as the provision of on-road instrumented test vehicles with eye and head tracking, provide researchers with the opportunity to further understand driver behaviour at such crossings in ways not previously possible. This paper describes a study conducted to further understand the factors that shape driver behaviour at rail level crossings using instrumented vehicles. Twenty-two participants drove an On-Road Test Vehicle (ORTeV) on a predefined route in regional Victoria with a mix of both active (flashing lights with/without boom barriers) and passively controlled (stop, give way) crossings. Data collected included driving performance data, head checks, and interview data to capture driver strategies. The data from an integrated suite of methods demonstrated clearly how behaviour differs at active and passive level crossings, particularly for inexperienced drivers. For example, the head check data clearly show the reliance and expectancies of inexperienced drivers for active warnings even when approaching passively controlled crossings. These studies provide very novel and unique insights into how level crossing design and warnings shape driver behaviour.

Awesome foursome? The compatibility of situation awareness across drivers, riders, cyclists, and pedestrians

Collisions between distinct road users (e.g. drivers and motorcyclists) make a substantial contribution to the road trauma burden. Although evidence suggests distinct road users interpret the same road situations differently, it is not clear how road users’ situation awareness differs, nor is it clear which differences might lead to conflicts. This article presents the findings from an on-road study which examined driver, cyclist, motorcyclist and pedestrian situation awareness at intersections. The findings suggest that situation awareness at intersection is markedly different across the four road user groups studied, and that some of these differences may create conflicts between the different road users. The findings also suggest that the causes of the differences identified relate to road design and road user experience. In closing, the key role of road design and training in supporting safe interactions between distinct road users is discussed.

Interactions between cars and motorcycles testing underlying concepts through integration of on-road and simulator studies

We conducted on-road and simulator studies to explore the mechanisms underpinning driver-rider crashes. In Study 1 the verbal protocols of 40 drivers and riders were assessed at intersections as part of a 15km on-road route in Melbourne. Network analysis of the verbal transcripts highlighted key differences in the situation awareness of drivers and riders at intersections. In a further study using a driving simulator we examined in car drivers the influence of acute exposure to motorcyclists. In a 15 min simulated drive, 40 drivers saw either no motorcycles or a high number of motorcycles in the surrounding traffic. In a subsequent 45-60 min drive, drivers were asked to detect motorcycles in traffic. The proportion of motorcycles was manipulated so that there was either a high (120) or low (6) number of motorcycles during the drive. Those drivers exposed to a high number of motorcycles were significantly faster at detecting motorcycles. Fundamentally, the incompatible situation awareness at intersections by drivers and riders underpins the conflicts. Study 2 offers some suggestion for a countermeasure here, although more research around schema and exposure training to support safer interactions is needed.

Waiting for warning: Driver Situation awareness at rural rail level crossings

Driver behaviour at rail level crossings represents a key area for further research. This paper describes an on-road study comparing novice and experienced driver situation awareness at rural rail level crossings. Participants provided verbal protocols while driving a pre-determined rural route incorporating ten rail level crossings. Driver situation awareness was assessed using a network analysis approach. The analysis revealed key differences between novice and experienced drivers' situation awareness. In particular, the novice drivers seemed to be more reliant on rail level crossing warnings and their situation awareness was less focussed on the environment outside of the rail level crossing. In closing, the implications for rail level crossing safety are discussed.

Exploring schema-driven differences in situation awareness between road users : an on-road study of driver, cyclist and motorcyclist situation awareness

Collisions between different road users make a substantial contribution to road trauma. Although evidence suggests that different road users interpret the same road situations differently, it is not clear how road users' situation awareness differs, nor is it clear which differences might lead to conflicts. This article presents the findings from an on-road study conducted to examine driver, motorcyclist and cyclist situation awareness in different road environments. The findings suggest that, in addition to minor differences in the structure of different road users' situation awareness (i.e. amount of information and how it is integrated), the actual content of situation awareness in terms of road user schemata, the resulting interaction with the world and the information underpinning situation awareness is markedly different. Further examination indicates that the differences are likely to be compatible along arterial roads, shopping strips and at roundabouts, but that they may create conflicts between different road users at intersections. Interventions designed to support compatible situation awareness and behaviour between different road users are discussed. Practitioner Summary: Incompatible situation awareness plays a key role in collisions between different road users (e.g. drivers and motorcyclists). This on-road study examined situation awareness in drivers, motorcyclists and cyclists, identifying the key differences and potential conflicts that arise. The findings are used to propose interventions designed to enhance the compatibility of situation awareness between road users.

Molecular characterization of "Candidatus Parilichlamydia carangidicola," a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, "Candidatus Parilichlamydiaceae" fam. nov. (order Chlamydiales).

Three cohorts of farmed yellowtail kingfish (Seriola lalandi) from South Australia were examined for Chlamydia-like organisms associated with epitheliocystis. To characterize the bacteria, 38 gill samples were processed for histopathology, electron microscopy, and 16S rRNA amplification, sequencing, and phylogenetic analysis. Microscopically, the presence of membrane-enclosed cysts was observed within the gill lamellae. Also observed was hyperplasia of the epithelial cells with cytoplasmic vacuolization and fusion of the gill lamellae. Transmission electron microscopy revealed morphological features of the reticulate and intermediate bodies typical of members of the order Chlamydiales. A novel 1,393-bp 16S chlamydial rRNA sequence was amplified from gill DNA extracted from fish in all cohorts over a 3-year period that corresponded to the 16S rRNA sequence amplified directly from laser-dissected cysts. This sequence was only 87% similar to the reported "Candidatus Piscichlamydia salmonis" (AY462244) from Atlantic salmon and Arctic charr. Phylogenetic analysis of this sequence against 35 Chlamydia and Chlamydia-like bacteria revealed that this novel bacterium belongs to an undescribed family lineage in the order Chlamydiales. Based on these observations, we propose this bacterium of yellowtail kingfish be known as "Candidatus Parilichlamydia carangidicola" and that the new family be known as "Candidatus Parilichlamydiaceae."

Molecular characterization of "Candidatus Similichlamydia latridicola" gen. nov., sp. nov. (Chlamydiales: "Candidatus Parilichlamydiaceae"), a novel Chlamydia-like epitheliocystis agent in the striped trumpeter, Latris lineata (Forster)

Histological analysis of gill samples taken from individuals of Latris lineata reared in aquaculture in Tasmania, Australia, and those sampled from the wild revealed the presence of epitheliocystis-like basophilic inclusions. Subsequent morphological, in situ hybridization, and molecular analyses were performed to confirm the presence of this disease and discovered a Chlamydia-like organism associated with this condition, and the criteria set by Fredericks and Relman's postulates were used to establish disease causation. Three distinct 16S rRNA genotypes were sequenced from 16 fish, and phylogenetic analyses of the nearly full-length 16S rRNA sequences generated for this bacterial agent indicated that they were nearly identical novel members of the order Chlamydiales. This new taxon formed a well-supported clade with "Candidatus Parilichlamydia carangidicola" from the yellowtail kingfish (Seriola lalandi). On the basis of sequence divergence over the 16S rRNA region relative to all other members of the order Chlamydiales, a new genus and species are proposed here for the Chlamydia-like bacterium from L. lineata, i.e., "Candidatus Similichlamydia latridicola" gen. nov., sp. nov.

An evaluation of the culture performance of two Macrobrachium species in Vanuatu: the exotic M. rosenbergii and the indigenous M. lar

Fisheries and aquaculture are important for food security, income generation and are critical to long term sustainability of many countries. Freshwater prawns have been harvested in the streams and creeks in Vanuatu, however due to over-exploitation catches have declined in recent years. To satisfy high demand for this product, Vanuatu government intends to establish economically viable small-scale aquaculture industries. The current project showed that wild Macrobrachium lar in Vanuatu constitute a single population for management purposes and that M. rosenbergii grows much faster than M. lar in simple pond grow-out systems, hence is a better species for culture in Vanuatu.