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Quantitative analysis of production traits in saltwater crocodiles (Crocodylus porosus): III. Juvenile survival
Abstract
Mortality records of 1302 juvenile crocodiles were available for analysis. Crocodiles that were slaughtered during this study were treated as censored (n = 2151). Additionally, records from animals that had neither died nor been slaughtered, i.e. were still alive in the production system (n = 1582), were censored at the last date of data collection. There were a total of 3733 censored records. The data were all full-sib records from 29 parental pairs from Janamba Croc Farm (Northern Territory, Australia), collected over nine consecutive years. Data were analysed using an extension of Cox's proportional hazards model to include frailty (random) terms to account for genetic effects. Heritability of log survival time for juvenile crocodile survival was 0.15 (SE 0.04). The probability of a juvenile crocodile surviving to day 400 was estimated to be only 51%. These results are the first to quantify juvenile survival in a captive breeding situation. Also, this is the first heritability estimate of crocodile survival and is a fundamental element in the development of a genetic improvement programme.
... Mortality data were collected in a similar manner described in Isberg et al. (2006) during routine feeding and cleaning procedures. The dead animal's clutch of origin was determined from the scute cuts and used to retrospectively determine the date of hatch (used to calculate age at death) and the origin of the clutch (captive breeding pen or wild egg collection area). ...
... animal model = 0.28-0.56) are higher than that previously estimated for crocodile survival (0.15; Isberg et al. 2006) and for any other domestic livestock species reported so far (sheep 0.08-0.33 (Riggio et al. 2008), 0.11 (Welsh et al. 2006); dairy 0.05-0.07 ...
Results/key findings
From the analyses presented herein, runtism constitutes 49% of deaths followed by deaths for no visible ailments (23%) and disease (12%). There were significant collection area and genetic effects, as well as time of hatch and number of hatchling effects. With the exception of runtism (0.71 SE 0.08), heritability was estimated to be 0.76 (SE 0.09) for all other causes of death using a Pair model due to confounding of the data. Additional data collection will rectify this situation allowing clutch to be included. The heritability estimates from the Animal model varied from 0.28 (SE 0.02) for deaths for no visible reason to 0.60 (SE 0.04) for runting. Crocodile breeding values estimated from these data show considerable variation which will allow producers to start selecting superior, and replacing inferior, animals from the higher risk mortality categories (runtism, no visible ailments and disease-related) to quickly ensure the economic impact of these causes of death are minimised.
Many of the findings in the histopathology study were expected due to the emaciated state of the runts that characterises the condition. However, the major findings were the presence of marked lymphoid atrophy, suggesting immunosuppression, and vacuolated adrenocortical cells due to chronic stress.
... Mortality data were collected in a similar manner described in Isberg et al. (2006) during routine feeding and cleaning procedures. The dead animal's clutch of origin was determined from the scute cuts and used to retrospectively determine the date of hatch (used to calculate age at death) and the origin of the clutch (captive breeding pen or wild egg collection area). ...
... animal model = 0.28-0.56) are higher than that previously estimated for crocodile survival (0.15; Isberg et al. 2006) and for any other domestic livestock species reported so far (sheep 0.08-0.33 (Riggio et al. 2008), 0.11 (Welsh et al. 2006); dairy 0.05-0.07 ...
... More than a theoretical curiosity, cohort selection has been rigorously demonstrated in experimental laboratory populations (Manton et al. 1981, Carey et al. 1992, Vaupel and Carey 1993). The underlying frailty heterogeneity has been documented in a variety of species, including crocodiles (Isberg et al. 2006), baboons (Bronikowski et al. 2002), birds (Wintrebert et al. 2005, Fox et al. 2006), wild plants (Beckage and Clark 2003, Landis et al. 2005), domestic animals (Ducrocq et al. 2000, Casellas et al. 2004), humans (Yashin et al. 1999, Garibotti et al. 2006), and British aristocrats (Doblhammer and Oeppen 2003). The taxonomic breadth of this list suggests that cohort selection may be a very common ecological phenomenon. ...
... Another reason to think so is that a number of common processes can generate persistent heterogeneity in both frailty and reproduction among individuals in a cohort. These include fine-scale spatial habitat heterogeneity (e.g., Gates and Gysel 1978, Boulding and Van Alstyne 1993, Menge et al. 1994, Winter et al. 2000, Franklin et al. 2000 2002, Bollinger and Gavin 2004, Landis et al. 2005), unequal allocation of parental care (e.g., Manser and Avey 2000, Johnstone 2004), maternal family effect (e.g., Fox et al. 2006 ), conditions during early development , including birth order effects (e.g., Lindstro¨mLindstro¨m 1999), persistent social rank (e.g., von Holst et al. 2002), and genetics (e.g., Yashin et al. 1999, Ducrocq et al. 2000, Gerdes et al. 2000, Casellas et al. 2004, Isberg et al. 2006). Thus, we would expect cohort selection to be quite common in nature. ...
Demographic heterogeneity--variation among individuals in survival and reproduction--is ubiquitous in natural populations. Structured population models address heterogeneity due to age, size, or major developmental stages. However, other important sources of demographic heterogeneity, such as genetic variation, spatial heterogeneity in the environment, maternal effects, and differential exposure to stressors, are often not easily measured and hence are modeled as stochasticity. Recent research has elucidated the role of demographic heterogeneity in changing the magnitude of demographic stochasticity in small populations. Here we demonstrate a previously unrecognized effect: heterogeneous survival in long-lived species can increase the long-term growth rate in populations of any size. We illustrate this result using simple models in which each individual's annual survival rate is independent of age but survival may differ among individuals within a cohort. Similar models, but with nonoverlapping generations, have been extensively studied by demographers, who showed that, because the more "frail" individuals are more likely to die at a young age, the average survival rate of the cohort increases with age. Within ecology and evolution, this phenomenon of "cohort selection" is increasingly appreciated as a confounding factor in studies of senescence. We show that, when placed in a population model with overlapping generations, this heterogeneity also causes the asymptotic population growth rate lambda to increase, relative to a homogeneous population with the same mean survival rate at birth. The increase occurs because, even integrating over all the cohorts in the population, the population becomes increasingly dominated by the more robust individuals. The growth rate increases monotonically with the variance in survival rates, and the effect can be substantial, easily doubling the growth rate of slow-growing populations. Correlations between parent and offspring phenotype change the magnitude of the increase in lambda, but the increase occurs even for negative parent-offspring correlations. The effect of heterogeneity in reproductive rate on lambda is quite different: growth rate increases with reproductive heterogeneity for positive parent-offspring correlation but decreases for negative parent-offspring correlation. These effects of demographic heterogeneity on lambda have important implications for population dynamics, population viability analysis, and evolution.
... May, 1973a;Lomnicki, 1978;Leigh, 1981;Shaffer, 1981;Lande, 1993;Uchmanski, 1999) are supported by data from natural populations (Dochtermann & Gienger, 2012). Demographic heterogeneity, among-individual variation in vital parameters such as survival and reproduction, is ubiquitous (Stover et al., 2012), resulting from fine-scale spatial habitat heterogeneity (e.g., Gates & Gysel, 1978;Boulding & Van Alstyne, 1993;Menge et al., 1994;Winter et al., 2000;Franklin et al., 2000;Manolis et al., 2002;Bollinger & Gavin, 2004;Landis et al., 2005), unequal allocation of parental care (e.g., Manser & Avey, 2000;Johnstone, 2004), maternal family effect (e.g., Fox et al., 2006;Pettorelli & Durant, 2007), conditions during early development, including birth order effects (e.g., Lindström, 1999), persistent social rank (e.g., von Holst et al., 2002), and genetics (e.g., Yashin et al., 1999;Ducrocq et al., 2000;Gerdes et al., 2000;Casellas et al., 2004;Isberg et al., 2006). The stability of population sizes is related to the probability of extinction Inchausti & Halley, 2003). ...
How to cite the article:Heininger K. Duality of stochasticity and natural selection: a cybernetic evolution theory. WebmedCentral ECOLOGY 2015;6(2):WMC004796
... The cost of this production system is considerable, and includes additional general husbandry, maintenance of water quality and feeding. In a similar way to that used in the cattle industry, AI, in combination with frozen semen in the crocodile, has the potential to reduce the need for males on farm and dramatically reduce production costs, Moreover, crocodile AI would greatly facilitate the transfer and delivery of selected genetics for improvements in production traits (Isberg et al. 2003(Isberg et al. , 2005a(Isberg et al. , 2005b(Isberg et al. , 2006a(Isberg et al. , 2006b. Semen, rather than crocodiles, can be shipped from farm to farm at a reduced cost, and semen from wild animals could be used to improve genetic vigour without bringing males into captivity. ...
This review reports the current status of artificial breeding technology in the Crocodylia and the future requirements for the establishment of AI in the saltwater crocodile. Although there are challenges regarding safe restraint and immobilisation, semen collection of the saltwater crocodile by manual stimulation has proven effective in yielding sufficient volume and sperm concentrations for empirical and molecular analyses of sperm preservation and physiology. Nevertheless, there is still much to learn with respect to fundamental anatomy, physiology and behaviour in both sexes, but particularly in the female. Although lessons can be learned from successful AI in the alligator, the details of this research are not readily accessible. Future research needs to focus on the proximate factors of seasonality and the underlying control of the female’s annual reproductive cycle; this will require novel and innovative ways to collect blood samples without causing stress or injury, and ideally a dedicated crocodile research breeding colony. Because the saltwater crocodile is a farmed species, there is likely to be sufficient impetus for the application of assisted breeding technology to drive future productivity in the industry. These developments will also have benefits for the genetic and reproductive management of endangered captive populations.
... While harvesting eggs (and adults for breeding) from the wild has been an effective conservation strategy, it means that no selection for performance ability under intensive production systems can be undertaken. The opportunity is to exploit the genetic variation and Isberg et al. (2004;2005a;2005b;2006a;2006b) assessed the potential of implementing genetic improvement noting that there were substantial economic benefits to be gained. For example, survival heritability estimates for crocodiles are much higher (animal model = 0.28 -0.60) than those reported for many other production species (Isberg et al. 2009). ...
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.
... Populations are also demographically heterogeneous, with individuals varying in survival and reproduction (Kendall et al., 2011). Most structured population models incorporate some heterogeneity due to age, size, or major developmental stages (Kendall et al., 2011), but there are many other meaningful sources of demographic heterogeneity, including genetic variation (Gerdes et al., 2000;Isberg et al., 2006), conditions during early development (Loison et al., 1996), persistent social rank (von Holst et al., 2002), spatial habitat heterogeneity (Franklin et al., 2000;Manolis et al., 2002), and maternal effects (Fox et al., 2006). Spatial and temporal environmental variations result in phenotypic differences in individuals, and individuals may vary in their intrinsic vigor and fecundity (Kendall and Fox, 2002). ...
Small and declining populations of large mammals are vulnerable to stochastic events and can be at high risk of extinction. Population viability is also susceptible to the detrimental effects of low genetic diversity and inbreeding. The objective of this study was to do an assessment of three endangered caribou subpopulations using non-invasive genetic sampling to assess demographic population changes by combining capture-recapture modeling, familial pedigree networks, individual fitness and inbreeding coefficients. Three subpopulations of the Central Mountain caribou ecotype (Rangifer tarandus caribou) in Jasper National Park, Canada, were systematically surveyed over a 10-year period and fecal samples collected for DNA analyses. For the Tonquin, population size declined at a rate of 0.86 (95% CI 0.82, 0.91), the number of females decreased from 41 in 2006 to only 14 in 2015. The Brazeau and Maligne subpopulations also declined over the same period, from 22 to 11 individuals (11 and 5 females) in 2006, to 12 and 3 individuals (6 and 1 females) in 2015. The pedigree network confirmed limited interbreeding among subpopulations, varied fitness levels in both males and females, and evidence of inbreeding avoidance among high-fitness individuals. All population parameters pointed to a rapid population decline and low population sizes, putting them at high risk of extinction. The varying reproductive fitness observed amongst males and females was significant and should be considered in future population augmentation or reintroduction efforts. Improved connectivity among and with neighbouring subpopulations should also be considered to sustain or enhance genetic diversity.
... To achieve this objective, crocodile farming must remain economically viable. As such, previous studies have been conducted to understand the significant biotic and abiotic factors affecting various production traits including age at harvest (Isberg et al., 2005), juvenile survival (Isberg et al., 2006a) and number of scale rows (Isberg et al., 2006b;Miles et al., 2010). However, many of the factors that could underlie these production traits remain unknown. ...
... CrocPLAN (Isberg et al., 2004) was the first multi-trait genetic improvement program developed for a crocodilian. Saltwater crocodile (Crocodylus porosus) production records from Janamba Crocodile Farm, Middle Point, Northern Territory, Australia were used to estimate crocodile breeding values (CBVs) for four breeding objectives: -reproductive output (Isberg et al., 2005a), -age at slaughter (Isberg et al., 2005b), -juvenile survival (Isberg et al., 2006a), and -number of scale rows (Isberg et al., 2006b). Whilst these breeding objectives allowed immediate implementation as a practical genetic selection tool with significant economic incentives for crocodile producers, further traits were of interest for potential inclusion. ...
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”.
... May, 1973a;Lomnicki, 1978;Leigh, 1981;Shaffer, 1981;Lande, 1993;Uchmanski, 1999) are supported by data from natural populations (Dochtermann & Gienger, 2012). Demographic heterogeneity, among-individual variation in vital parameters such as survival and reproduction, is ubiquitous (Stover et al., 2012), resulting from fine-scale spatial habitat heterogeneity (e.g., Gates & Gysel, 1978;Boulding & Van Alstyne, 1993;Menge et al., 1994;Winter et al., 2000;Franklin et al., 2000;Manolis et al., 2002;Bollinger & Gavin, 2004;Landis et al., 2005), unequal allocation of parental care (e.g., Manser & Avey, 2000;Johnstone, 2004), maternal family effect (e.g., Fox et al., 2006;Pettorelli & Durant, 2007), conditions during early development, including birth order effects (e.g., Lindström, 1999), persistent social rank (e.g., von Holst et al., 2002), and genetics (e.g., Yashin et al., 1999;Ducrocq et al., 2000;Gerdes et al., 2000;Casellas et al., 2004;Isberg et al., 2006). The stability of population sizes is related to the probability of extinction Inchausti & Halley, 2003). ...
Orthodox Darwinism assumes that environments are stable. There is an important difference between breeding (Darwin’s role model of evolution) and evolution itself: while in breeding the final goal is preset and constant, adaptation to varying biotic and abiotic environmental conditions is a moving target and selection can be highly fluctuating. Evolution is a cybernetic process whose Black Box can be understood as learning automaton with separate input and output channels. Cybernetics requires a closed signal loop: action by the system causes some change in its environment and that change is fed to the system via information (feedback) that enables the system to change its behavior. The input signal is given by a complex biotic and abiotic environment. Natural selection is the output/outcome of the learning automaton.
Environments are stochastic. Particularly, density- and frequency-dependent coevolutionary interactions generate chaotic and unpredictable dynamics. Stochastic environments coerce organisms into risky lotteries. Chance favors the prepared. The ‘Law of Requisite Variety’ holds that cybernetic systems must have internal variety that matches their external variety so that they can self-organize to fight variation with variation. Both conservative and diversifying bet-hedging are the risk-avoiding and -spreading insurance strategies in response to environmental uncertainty. The bet-hedging strategy tries to cover all bases in an often unpredictable environment where it does not make sense to “put all eggs into one basket”. In this sense, variation is the bad/worst-case insurance strategy of risk-aversive individuals. Variation is pervasive at every level of biological organization and is created by a multitude of processes: mutagenesis, epimutagenesis, recombination, transposon mobility, repeat instability, gene expression noise, cellular network dynamics, physiology, phenotypic plasticity, behavior, and life history strategy. Importantly, variation is created condition-dependently, when variation is most needed – in organisms under stress. The bet-hedging strategy also manifests in a multitude of life history patterns: turnover of generations, reproductive prudence, iteroparity, polyandry, and sexual reproduction.
Cybernetic systems are complex systems. Complexity is conceived as a system’s potential to assume a large number of states, i.e., variety. Complex systems have both stochastic and deterministic properties and, in fact, generate order from chaos. Non-linearity, criticality, self-organization, emergent properties, scaling, hierarchy and evolvability are features of complex systems. Emergent properties are features of a complex system that are not present at the lower level but arise unexpectedly from interactions among the system’s components. Only within an intermediate level of stochastic variation, somewhere between determined rigidity and literal chaos, local interactions can give rise to complexity. Stochastic environments change the rules of evolution. Lotteries cannot be played and insurance strategies not employed with single individuals. These are emergent population-level processes that exert population-level selection pressures generating variation and diversity at all levels of biological organization. Together with frequency and density-dependent selection, lottery- and insurance-dependent selection act on population-level traits.
The duality of stochasticity and selection is the organizing principle of evolution. Both are interdependent. The feedback between output and input signals inextricably intertwines both stochasticity and natural selection, and the individual- and population-levels of selection. Sexual reproduction with its generation of pre-selected variation is the paradigmatic bet-hedging enterprise and its evolutionary success is the selective signature of stochastic environments.Sexual reproduction is the proof of concept that (epi)genetic variation is no accidental occurrence but a highly regulated process and environmental stochasticity is its evolutionary “raison d’être”.Evolutionary biology is plaqued by a multitude of controversies (e.g. concerning the level of selection issue and sociobiology. Almost miraculously, these controversies can be resolved by the cybernetic model of evolution and its implications.
... Saltwater crocodile (Crocodylus porosus) farming is a rapidly evolving agricultural practice and in order to keep up with the industry expansion their will need to be corresponding improvements in productivity and efficiency. Although much of the crocodile production in Australia currently relies on the wild harvesting of eggs, future genetic improvement of desirable phenotypes (Isberg et al., 2003(Isberg et al., , 2005a(Isberg et al., , 2005b(Isberg et al., , 2006a(Isberg et al., , 2006b and the ultimate environmental sustainability of industry are likely to be best managed through "on farm" captive breeding and egg production; it is within this context, that we propose the development of technology leading towards the establishment of artificial insemination in the crocodile. Althouse (2007) has defined artificial insemination as the process of mechanically and unnaturally depositing semen into the female reproductive tract with the goal of achieving conception, highlighting the drivers that lead to the implementation of this practice in a range of animal industries. ...
... Although still an emerging livestock industry, the Australian crocodile industry, following the lead of other livestock industries, has recently developed a comprehensive genetic improvement program[22]. Research efforts have thus far focused on genetic and phenotypic parameter estimation for selection objectives and selection criteria required for multitrait index selection[22][23][24][25][26]. However, this type of animal selection occurs with little or no knowledge of what is occurring at the DNA level. ...
Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary.
A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1).
We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear.This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers placed on this genetic map have been evaluated in up to 18 other extant species of crocodilian, this map will be of intrinsic value to comparative mapping efforts aimed at understanding genome content and organization among crocodilians, as well as the molecular evolution of reptilian and other amniote genomes. As researchers continue to work towards elucidation of the crocodilian genome, this first generation map lays the groundwork for more detailed mapping investigations, as well as providing a valuable scaffold for future genome sequence assembly.
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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Dispersal heterogeneity is increasingly being observed in ecological populations and has long been suspected as an explanation for observations of non-Gaussian dispersal. Recent empirical and theoretical studies have begun to confirm this. Using an integro-difference model, we allow an individual's diffusivity to be drawn from a trait distribution and derive a general relationship between the dispersal kernel's moments and those of the underlying heterogeneous trait distribution. We show that dispersal heterogeneity causes dispersal kernels to appear leptokurtic, increases the population's spread rate, and lowers the critical reproductive rate required for persistence in the face of advection. Wavespeed has been shown previously to be determined largely by the form of the dispersal kernel tail. We qualify this by showing that when reproduction is low, the precise shape of the tail is less important than the first few dispersal moments such as variance and kurtosis. If the reproductive rate is large, a dispersal kernel's asymptotic tail has a greater influence over wavespeed, implying that estimating the prevalence of traits which correlate with long-range dispersal is critical. The presence of multiple dispersal behaviors has previously been characterized in terms of long-range versus short-range dispersal, and it has been found that rare long-range dispersal essentially determines wavespeed. We discuss this finding and place it within a general context of dispersal heterogeneity showing that the dispersal behavior with the highest average dispersal distance does not always determine wavespeed.
Semen collected from 10 saltwater crocodiles (Crocodylus porosus) was used to investigate sperm in vitro manipulation and preservation. Preliminary studies revealed that phosphate buffered saline (PBS) without Ca2 +, Mg2 + and egg yolk (EY) was a suitable extender for studies of sperm physiology. Spermatozoa diluted in PBS showed no change in survival [% motility (M), rate of sperm movement (R) and % plasma membrane integrity (PI)] when diluted over a range of 1:1 to 1:16. Except for a small decline in PI, there was no change in sperm survival when semen diluted without EY was cooled rapidly to and rewarmed from 0 °C. The addition of EY (0, 5, 10 and 20% v/v) had no beneficial effect on sperm survival when incubated in PBS for 1 h at 30 °C or after 24 h storage at 4 °C. Whilst crocodile spermatozoa exposed to a range of anisotonic media and then returned to solutions of 390 mosM kg− 1 retained their M from 220 to 390 mosM kg− 1, PI remained high in hypotonic media (25–280 mosM kg −1); spermatozoa showed an increase (P < 0.05) in the incidence of flagellar coiling (FC) with increasing hypotonic conditions. The adverse effect of anisotonic conditions on sperm M and FC recovered somewhat when sperm were returned to the 390 mosM kg −1 media, but not to pre-treatment levels. Exposure of crocodile spermatozoa to respective concentrations of 0.68 M, 1.35 M and 2.7 M glycerol, dimethylsulphoxide (DMSO), and dimethylacetamide (DMA) after 2 h storage at 4 °C (equilibration) resulted in a reduction in M, but no change in PI. Sperm cryopreserved in the same cryoprotectant media within 0.25 mL straws at − 6 °C/min in a programmable freezer and thawed at 37 °C for 1 min showed a major decline (P < 0.05) of M but there was moderate protection of PI (DMA 2.7 M — 17.7 ± 4.4; DMSO 2.7 M — 22.7 ± 1.4 and glycerol 2.7 M — 25.7 ± 6.4). Sperm thawed and immediately washed to remove the cryoprotectant showed an improvement (P < 0.05) in PI but not M. Future studies of crocodile sperm preservation should explore the apparent disjunction between low levels of M and the high tolerance of the plasma membrane to anisotonic conditions and cryoprotectant toxicity.
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.
Among-individual variation in vital parameters such as birth and death rates that is unrelated to age, stage, sex, or environmental fluctuations is referred to as demo-graphic heterogeneity. This kind of heterogeneity is preva-lent in ecological populations, but is almost always left out of models. Demographic heterogeneity has been shown to affect demographic stochasticity in small populations and to increase growth rates for density-independent popula-tions. The latter is due to "cohort selection," where the most frail individuals die out first, lowering the cohort's average mortality as it ages. The importance of cohort selection to population dynamics has only recently been recognized. We use a continuous time model with density dependence, based on the logistic equation, to study the effects of demographic heterogeneity in mortality and reproduction. Reproductive heterogeneity is introduced in three ways: parent fertility, offspring viability, and parent-offspring correlation. We find that both the low-density growth rate and the equilib-rium population size increase as the magnitude of mortality heterogeneity increases or as parent-offspring phenotypic correlation increases. Population dynamics are affected by complex interactions among the different types of hetero-geneity, and trade-off scenarios are examined which can sometimes reverse the effect of increased heterogeneity. We show that there are a number of different homogeneous ap-proximations to heterogeneous models, but all fail to capture important parts of the dynamics of the full model.
The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome-wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex-specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib-pair analysis to take advantage of our full-sib pedigree structure, together with a half-sib analysis to account for, and take advantage of, the large difference in sex-specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non-avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.
The first evidence of genetic linkage and sex-specific recombination in the order Crocodylia is reported. This study was conducted using a resource pedigree of saltwater crocodiles consisting of 16 known-breeding pairs (32 adults) and 101 juveniles. A total of 21 microsatellite loci were available for analysis. Ten of the 21 loci showed linkage with 4 linkage groups: 3 pairwise (Cj131/Cj127, CUD68/Cj101, and Cj107/Cp10) and 1 four-locus (Cj122, CUD78, Cj16, and Cj104) being found. Linkage analysis on the 21 loci revealed evidence of sex-specific differences in recombination rates. All 5 nonzero interlocus intervals were longer in females than in males, with the 4-loci linkage group 3-fold longer in females than in males (41.63 cM and 14.1 cM, respectively). This is the first report of sex-specific recombination rates in a species that exhibits temperature-dependent sex determination.
Abstract The survival of about eight generations of a large strain of laying hens was analysed separating the rearing period (RP) from the production period (PP), after hens were housed. For RP (respectively PP), 97.8% (resp., 94.1% ) of the 109 160 (resp., 100 665) female records were censored after 106 days (resp., 313 days) on the average. A Cox proportional hazards model stratified by flock (= season) and including a hatch-within-flock (HWF) fixed effect seemed to reasonably fit the RP data. For PP, this model could be further simplified to a non-stratified Weibull model. The extension of these models to sire-dam frailty (mixed) models permitted the estimation of the sire genetic variances at 0.261 ± 0.026 and 0.088 ± 0.010 for RP and PP, respectively. Heritabilities on the log scale were equal to 0.48 and 0.19. Non-additive genetic effects could not be detected. Selection was simulated by evaluating all sires and dams, after excluding all records from the last generation. Then, actual parents of this last generation were distributed into four groups according to their own pedigree index. Raw survivor curves of the progeny of extreme parental groups substantially differed (e.g., by 1.7% at 300 days for PP), suggesting that selection based on solutions from the frailty models could be efficient, despite the very large proportion of censored records.
In proportional hazards models, the hazard of an animal λ(t), ie, its probability of dying or being culled at time t given it is alive prior to t, is described as λ(t) = λ0(t)e(w'e) where λ0(t) is a 'baseline' hazard function and e(w'B) represents the effect of covariates w on culling rate. A distribution can be attached to elements S(q) in θ, identifying, for example, genetic effects and leading to mixed survival models, also called 'frailty' models. To estimate the parameters τ of the distribution of frailty terms, a Bayesian analysis is proposed. Inferences are drawn from the marginal posterior density π(τ) which can be derived from the joint posterior density via Laplacian integration, a powerful technique related to saddlepoint approximations. The validity of this technique is shown here on simulated examples by comparing the resulting approximate π(τ) to the one obtained by algebraic integration. This exact calculation is feasible in very specific cases only, whereas the saddlepoint approximation can be applied to situations where λ0(t) is arbitrary (Cox models) or parametric (eg, Weibull), where the frailty terms are correlated through a known relationship matrix, or in more general models with stratification and/or time-dependent covariates. The influence of the censoring rate and the data structure is also illustrated.
Records of mortality during the first year of life of 8,642 lambs from a composite population at the U.S. Meat Animal Research Center were studied using survival and logistic analyses. The traditional logistic approach analyzes the binary response of whether or not a lamb survived until a particular time point, thus disregarding information on the actual age at death. Survival analysis offers an alternative way to study mortality, wherein the response variable studied is the precise age at death while accounting for possible record censoring. Lamb mortality was studied across five periods based on management practices: birth to weaning, birth to 120 d of age, birth to 365 d of age, weaning to 365 d of age, and 120 to 365 d of age. Explanatory variables included in the models were sex, type of birth, age of dam, and whether or not a lamb was raised in a nursery. The survival analysis was implemented using Weibull and Cox proportional hazards models with sire as random effect. The logistic approach evaluated sire, animal, and maternal effects models. Lambs culled during any period were treated as censored in the survival analyses and were assumed alive in the logistic analyses. Similar estimates of the explanatory variables were obtained from the survival and logistic analyses, but the survival analyses had lower standard errors than the logistic analyses, suggesting a slight superiority of the former approach. Heritability estimates were generally consistent across all periods ranging from 0.15 to 0.21 in the Weibull model, 0.12 to 0.20 in the Cox model, 0.08 to 0.11 in the logistic sire model, 0.04 to 0.05 in the logistic animal model, and 0.03 to 0.07 in the maternal effects logistic model. Maternal effects were important in the early stages of lamb life, but the maternal heritability was less than 0.07 in all the stages studied with a negative correlation (-0.86 to -0.61) between direct and maternal effects. The estimates of additive genetic variance indicate that the use of survival analysis estimates in breeding schemes could allow for effective selection against mortality, thereby improving sheep productivity, welfare, and profitability.
Variation in piglets weaned per sow per year is the main factor explaining differences in income between piglet producers. This parameter is the result of prolificacy of sows and survival rate of piglets. Data on 54500 piglets born between 1988 and 1994 at four nucleus breeding units of a pig breeding organization were used in an analysis of piglet survival. Animals were from two different dam lines. Piglet survival until weaning was considered and management was aimed at weaning at 28 days of age. Variance and covariance components were obtained using mixed models which included direct genetic and maternal genetic effects. In addition, the model included sex, breed, parity and herd-year-season as fixed effect, birth weight as covariable and sow as permanent environmental effect. Bayesian analysis, implemented using Gibbs sampling, was used to estimate the effects and parameters. Heritability of direct and maternal genetic effects was 0.11 (±0.01) and 0.09 (±0.01), respectively, in the full model. Genetic correlation between direct and maternal genetic effects was —0.56 (±0.06). Consequences of excluding maternal genetic effects or permanent environmental effects were studied. Based on the presented results it is concluded that simultaneous selection on maternal and direct genetic merit offers the opportunity to increase piglet survival.
Amongst all fully formed piglets at the end of gestation, piglet survival until weaning (PS) is on average 81%. Selection for fast lean growth and increased litter size tends to decrease piglet survivability. Estimated heritabilities for PS and its component traits are generally low, on average around 0.04. Despite this, selection for improved survival is possible since the genetic variance for the trait is substantial. Genetic analyses indicated significant genetic correlations between PS on one side and litter size, gestation length, within-litter variation in birth weight, feed intake, gain, and backfat on the other. Genetic correlation of PS with birth weight, however, was low. Selection on birth weight as an indirect way to improve PS is doubtful. Genetic differences between piglets in survivability will be reflected in differences in body composition rather than in differences in birth weight. Experimental work on litters with high versus low genetic merit for PS, results of various selection experiments and experimental work with Meishan pigs support these findings.
To identify causes of mortality in young captive crocodiles, detailed necropsy and laboratory examination was done on 54 (30 Crocodylus porosus, 22 C. novaeguineae, 2 of unrecorded species). Although multiple infections often confounded interpretation it was concluded that the major infectious diseases, of approximately equal importance, were coccidiosis, bacterial septicaemia with Gram-negative organisms, and metazoan parasitism including ascariasis and pentastomiasis. A range of other lesions and agents was recognised, including keratitis, enteritis of unknown aetiology, non-suppurative encephalitis, traumatic peritonitis and trematodes located in renal tubules, gut and blood vessels. Some crocodiles in poor condition had only mild lesions associated with metazoan parasites and the cause of death or illness could not be clearly determined, although it was considered likely that adaptation failure was a contributing factor.
SUMMARY To investigate husbandry-disease associations in farmed crocodiles 7 farms in Queensland and the Northern Territory were visited and details of past and present farm design and husbandry practices were recorded. In addition pathological examination of 300 (mostly young) crocodiles was carried out (85 necropsied, one biopsied and 214 examined retrospectively).
Mortality rate and occurrence of disease, especially opportunistic infections with bacteria and fungi, were highest during winter months and in farms located at greater latitudes. A difference in the presence and prevalence of disease between the initial establishment phase of Northern Territory crocodile farms (1984–87) and currently (1988–91) was apparent; parasitic infections are now relatively infrequent and bacterial septicaemias and mycoses less common as a result of some provision of artificial heating for juveniles.
Gross and microscopic changes observed in visceral and periarticular gout, bacterial hepatitis/septicaemia, deep and superficial mycosis, pentastomiasis and other parasitic infections are described.
The survival of about eight generations of a large strain of laying hens was analysed separating the rearing period (RP) from the production period (PP), after hens were housed. For RP (respectively PP), 97.8% (resp., 94.1% ) of the 109,160 (resp., 100,665) female records were censored after 106 days (resp., 313 days) on the average. A Cox proportional hazards model stratified by flock (= season) and including a hatch-within-flock (HWF) fixed effect seemed to reasonably fit the RP data. For PP, this model could be further simplified to a non-stratified Weibull model. The extension of these models to sire-dam frailty (mixed) models permitted the estimation of the sire genetic variances at 0.261 +/- 0.026 and 0.088 +/- 0.010 for RP and PP, respectively. Heritabilities on the log scale were equal to 0.48 and 0.19. Non-additive genetic effects could not be detected. Selection was simulated by evaluating all sires and dams, after excluding all records from the last generation. Then, actual parents of this last generation were distributed into four groups according to their own pedigree index. Raw survivor curves of the progeny of extreme parental groups substantially differed (e.g., by 1.7% at 300 days for PP), suggesting that selection based on solutions from the frailty models could be efficient, despite the very large proportion of censored records.
Crocodile morphometric (head, snout-vent and total length) measurements were recorded at three stages during the production chain: hatching, inventory [average age (+/-SE) is 265.1 +/- 0.4 days] and slaughter (average age is 1037.8 +/- 0.4 days). Crocodile skins are used for the manufacture of exclusive leather products, with the most common-sized skin sold having 35-45 cm in belly width. One of the breeding objectives for inclusion into a multitrait genetic improvement programme for saltwater crocodiles is the time taken for a juvenile to reach this size or age at slaughter. A multivariate restricted maximum likelihood analysis provided (co)variance components for estimating the first published genetic parameter estimates for these traits. Heritability (+/-SE) estimates for the traits hatchling snout-vent length, inventory head length and age at slaughter were 0.60 (0.15), 0.59 (0.12) and 0.40 (0.10) respectively. There were strong negative genetic (-0.81 +/- 0.08) and phenotypic (-0.82 +/- 0.02) correlations between age at slaughter and inventory head length.
Repeatability and phenotypic correlations were estimated for saltwater crocodile reproductive traits. No pedigree information was available to estimate heritability or genetic correlations, because the majority of breeder animals on farms were wild-caught. Moreover, as the age of the female breeders could not be accounted for, egg-size measurements were used as proxies. The reproductive traits investigated were clutch size (total number of eggs laid), number of viable eggs, number of eggs that produced a live, healthy hatchling, hatchability, average snout-vent length of the hatchlings and time of nesting. A second data set was also created comprising binary data of whether or not the female nested. Repeatability estimates ranged from 0.24 to 0.68 for the measurable traits, with phenotypic correlations ranging from -0.15 to 0.86. Repeatability for whether a female nested or not was 0.58 on the underlying scale. Correlations could not be estimated between the measurement and binary traits because of confounding. These estimates are the first published for crocodilian reproduction traits.
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