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The main objective of this project was to generate a large single nucleotide polymorphism (SNP) marker resource for later saturation of the genetic linkage map and fine mapping of quantitative trait loci (QTL). Another objective of this project was to learn more about basic crocodile biology, namely immune function and stress, and the underlying genetic function to evaluate their incorporation into CrocPLAN. This report describes the development of new phenotypic trait panels for farmed saltwater crocodiles. Among these is the major crocodilian stress hormone, corticosterone (CORT), which should be useful for the development of animal welfare standards and the eventual selection of individuals in the future. Immune assays, some of which have never been previously used in crocodilians, were employed in this project to assess immune function. These immune assays, which are relatively easy to perform and cheap, could be employed in any farming setting to assess immune function in the future. Levels of estradiol (ESTR) and testosterone (TEST) are also detailed in this report, for the first time in the saltwater crocodile. At the same time as trying to expedite industry adoption of genetic improvement programs, it was necessary to expand on the current selection criteria available to gain a deeper insight into the breeding objectives already defined from RIRDC Project US-109A. The traits added were corticosterone (the main crocodilian stress hormone), two immune parameters, two sex hormones (testosterone and estradiol), two behaviour characters and four skin quality traits. Simultaneously, some of these traits could be used to gauge current industry practices which are set out in the “Code of Practice on the humane treatment of wild and farmed Australian crocodiles”. I am pleased to report that the lowest levels of corticosterone ever reported in saltwater crocodiles were found certifying the recommendations set out in the “code of practice”.
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... Unexpectedly, crocodiles with higher growth rates had lower testosterone levels. The heritability of testosterone was calculated to be 0.22 (SE ± 0.20; Finger et al. 2015b) suggesting that testosterone could be a potential biomarker but requires the inclusion of behavioural observations before selection strategies can be developed. ...
... However, conducting bacterial killing assays is not without challenges. Thus, the strong negative genetic correlation of this trait and plasma testosterone (-0.80 ± 0.26) may prove useful as an alternative selection criterion (Finger et al. 2015b). ...
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In the last five decades, the Australian saltwater crocodile population has recovered from near extinction back to pre-hunting levels because of a highly successful conservation strategy. Farming has been crucial in the recovery by providing economic-incentives to landowners to conserve the species and its habitat. However, farming a species that has evolved little since the dinosaurs has unique challenges compared to traditional livestock species. The lack of selection and domestication (wild harvested eggs) equates to large phenotypic variation and, given the industry's infancy, has relied on developing husbandry approaches that balance the physiological needs of crocodiles and production outputs. This approach appears to have worked to satisfy the welfare needs of the crocodiles as well although improvements are continually being sought. Novel equipment and handling techniques have been developed to ensure safe working environments for staff whilst not compromising animal welfare. The primary product is the skin, which is also unique as skins/hides are normally a by-product of traditional farming operations. This brings more idiosyncratic challenges as buyers demand blemish-free skins that will produce flawless high-end fashion products. Overall, in a short period of time, the Australian crocodile industry has emerged as an economically-viable, sustainable conservation-based industry but still has many challenges ahead as we continue to learn about the husbandry and welfare requirements of these dinosaurian descendants.
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Profit from farmed crocodile is essentially a function of the returns and costs from the average lifetime productivity of the herd. The aim of a genetic improvement program is to improve the total economic value of the herd, and consequently maximise profit. To date, no research has been conducted to evaluate the potential of a genetic improvement program in the Australian crocodile industry. By implementing a selection program based on reproductive performance, juvenile growth rates and juvenile survival rates, the resultant superior breeding animals will increase the profitability of crocodile farms. The major benefits to the industry will be decreasing overhead costs by growing animals to marketable size in a quicker time, increasing profitability by offsetting some of the production costs per animal and increasing the number of animals obtained from the farm each year. The major aim of this project was to create a practical genetic improvement program for immediate adoption by the Australian crocodile industry, to be called CrocPLAN.
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This report summarises efforts to construct the first genetic linkage map for the saltwater crocodile (Crocodylus porosus), and subsequent investigation into the presence and positioning of quantitative trait loci (QTL) for economically important traits in farmed saltwater crocodiles. Linkage and QTL mapping exercises will contribute significantly to elucidation and characterisation of the crocodile genome, and represent an important first step towards the development of genetic improvement tools for implementation in industry breeding programs. One of the major objectives of this research was to generate the requisite genomic resources to carry out genetic mapping studies in saltwater crocodiles. As such, herein we describe the development of a microsatellite marker resource, a DNA resource, a first generation genetic linkage map, a refined karyotype for C.porosus, and a proof of principle QTL study identifying the first QTL for crocodilian, or indeed any other non-avian reptile.
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Biology and Evolution of Crocodylians is a comprehensive review of current knowledge about the world's largest and most famous living reptiles. Gordon Grigg's authoritative and accessible text and David Kirshner's stunning interpretive artwork and colour photographs combine expertly in this contemporary celebration of crocodiles, alligators, caimans and gharials. This book showcases the skills and capabilities that allow crocodylians to live how and where they do. It covers the biology and ecology of the extant species, conservation issues, crocodylian–human interaction and the evolutionary history of the group, and includes a vast amount of new information; 25 per cent of 1100 cited publications have appeared since 2007. Richly illustrated with more than 500 colour photographs and black and white illustrations, this book will be a benchmark reference work for crocodylian biologists, herpetologists and vertebrate biologists for years to come. Winner of the 2015 Whitley Medal.
Article
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To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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Extremely poor growth of some individuals within a birth cohort (runting) is a significant problem in crocodile farming. We conducted a pathological investigation to determine if infectious disease is associated with runting in farmed saltwater crocodiles (Crocodylus porosus) and to look for evidence of other etiologies. In each of 2005 and 2007, 10 normal and 10 runt crocodiles, with an average age of 5.5 months and reared under identical conditions, were sampled. Laboratory testing included postmortem; histological examination of a wide variety of tissues (with quantitation of features that were noted subjectively to be different between groups); hematology; serum biochemistry (total protein, albumin, globulins, total calcium, phosphorus, and iron); bacterial culture of liver and spleen (2005 only); viral culture of liver, thymus, tonsil, and spleen using primary crocodile cell lines (2007 only); and serum corticosterone (2007 only). The only evidence of infectious disease was mild cutaneous poxvirus infection in 45% of normal and 40% of runt crocodiles and rare intestinal coccidia in 5% of normal and 15% of runt crocodiles. Bacterial and viral culture did not reveal significant differences between the 2 groups. However, runt crocodiles exhibited significant (P < .05) increases in adrenocortical cell cytoplasmic vacuolation and serum corticosterone, decreased production of bone (osteoporosis), and reduced lymphoid populations in the spleen, tonsil, and thymus. Runts also exhibited moderate anemia, hypoalbuminemia, and mild hypophosphatemia. Taken together, these findings suggest an association between runting and a chronic stress response (hyperactivity of the hypothalamic-pituitary-adrenal axis).
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The immune function of crocodilians is understudied but is of interest for medical, ecological and evolutionary purposes. Crocodiles share a common ancestor with birds, comprising the archosaurian lineage, so they are an important link in our understanding of immune system evolution. As top trophic carnivores, they inhabit temperate and tropical climates in their semi-aquatic environment. However, they are also ectothermic, whereby environmental temperatures affect their physiological processes, including immune function, adding to the complexity of research in this area. Anecdotal observations and recent research have augmented enthusiasm in the realm of crocodilian immunology. Despite comprising both adaptive and innate systems, most research has investigated the innate system, which comprises peptides, proteins and leucocytes functioning in defence. Herein, we provide an overview into the innate immune system of the crocodile and areas for further research.
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Minimising stress in farmed crocodiles is not only important for improving animal welfare, but may also improve skin blemish healing and infection resistance, which influence the quality of the final skin product. Forty near-harvest size saltwater crocodiles (1.6-1.8 m TL) from two Australian farms were sampled to evaluate the effect of different pen types (communal pens n=20; individual pens n=20) on stress as indicated by plasma corticosterone. Blood samples were taken within three minutes of immobilisation and analysed using a commercial enzyme immunoassay kit. There was no relationship with animal size (P=0.16), between farms (P=0.86), pen types (P=0.69), communal pens between farms (P=0.28) or individual pens between farms (P=0.24). Based on corticosterone levels, it appears that individual pens do not cause significantly more stress on harvest-size animals than communal pens. Individual pens meet their design specifications by achieving comparable healing rates of belly skin blemishes as communal pens without compromising animal welfare and minimising the possibility of new blemishes.
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Immune responsiveness, the ability of an organism to effectively respond immunologically following antigenic exposure, is an essential component of life history, as organisms require effective immune functionality in order to grow, survive and reproduce. However, immune status is also associated with concomitant trade-offs in these physiological functions. Herein we demonstrate the validation of phytohaemagglutinin (PHA) injection in saltwater crocodiles, Crocodylus porosus, to assess cellular immune responsiveness. Following injection of 2 mg mL–1 PHA into the hind toe webbing, we observed a peak swelling response 12 h after injection, with PHA inducing increased thickness compared with webs injected with phosphate-buffered saline (PBS) (F5,518 = 145.13, P < 0.001). Subsequent injections increased responsiveness relative to the primary injection response (F5,290 = 2.92, P = 0.029), suggesting that PHA exposure induced immunological memory, a tenet of acquired immunity. Histological examination revealed that PHA-injected toe webs displayed increased numbers of leukocytes (granulocytes, macrophages, and lymphocytes) relative to PBS-injected webs, with peak leukocytic infiltrate observed 12 h after injection. We suggest the use of PHA injection in crocodilians as a measure of cellular immune responsiveness in agricultural (production and animal welfare), ecological, and toxicological contexts.
Article
The electric stunner (e-stunner) is commonly used to handle Nile crocodiles (Crocodylus niloticus) on commercial farms in South Africa, but while it seems to improve handling and safety for the keepers, no information regarding physiological reactions to e-stunning is currently available. The aim of this study was therefore to compare various physiological parameters in farmed C niloticus captured either manually (noosing) or by using an e-stunner. A total of 45 crocodiles were captured at a South African farm by either e-stunning or noosing, and blood samples were taken immediately as well as four hours after capture. Parameters monitored were serum corticosterone, lactate, glucose, as well as alanine aminotransferase, alkaline phosphatase, aspartate aminotransferase and creatine kinase. Lactate concentrations were significantly higher in noosed compared with e-stunned animals (P<0.001). No other blood parameter differed significantly between the two methods of capture. In addition, recorded capture time confirmed that noosing takes significantly longer time compared with e-stunning (P<0.001), overall indicating that e-stunning seems to be the better option for restraint of especially large numbers of crocodiles in a commercial setup because it is quicker, safer and did not cause a significant increase in any of the parameters measured.