Evaluation of genetic homeostasis in animals at different stages of ontogenesis in the environment

Modern methods of genetic homeostasis assessment in animals are described in the present article. The single gel-electrophoresis test (Comet Assay), micronuclei test, chromosome aberration frequency, and sister chromatid exchanges are reviewed in detail. The questions of test-sensitivity of given methods and principles or their application for genetic homeostasis assessment in wild populations of animals are considered.     

A chi-square goodness-of-fit analysis of dependent resource selection data

The chi2 goodness-of-fit test is commonly used for testing if animals use resources in proportion to availability. This method assumes independence of resource selection among animals. In reality, this assumption is violated if animals display antisocial or gregarious behavior. Data from a study of sharp-tailed grouse in eastern Washington suggested some dependency among observations. Realizing that this dependency can have a great influence on inference for resource selection data, we develop a technique to incorporate information on dependent observations through a simple adjustment of the usual goodness-of-fit statistic. We also demonstrate how confidence intervals on proportional use may be modified for dependent observations. Simulation is used to compare our method to other methods.     

Sifaka positional behavior: ontogenetic and quantitative genetic approaches

In many primate species, hands and feet are large relative to neonatal body weight, and they subsequently exhibit negative allometric growth during ontogeny. Here, data are presented showing that this pattern holds for a wild population of lemur, Verreaux's sifaka (Propithecus verreauxi verreauxi). Using morphometric data collected on this population, it is shown that younger animals possess relatively large hands and feet. This ontogenetic pattern suggests a simple behavioral test: do juvenile animals with their larger, almost adult‐sized hands and feet locomote on similarly sized substrates as adult animals? Using locomotor bout sampling, this question was tested by collecting positional behavior data on this population. Results from this test find no differences in locomotor behaviors or substrate use between yearlings and adult animals. To place these results in a broader evolutionary context, heritabilities and selection gradients of hands, feet, and other limb elements for animals in this population were estimated. Among limb elements, heritabilities range from 0.16–0.44, with the foot having the lowest value. Positive directional selection acts most strongly on the foot (directional selection gradient = 0.119). The low heritability and positive selection coefficient indicate that selection has acted, and continues to act, on foot size in young animals. These results are interpreted within a functional context with respect to the development of locomotor coordination: larger feet enable young animals to use “adult‐sized” substrates when they move through their habitat. It is suggested that the widespread pattern of negative allometry of the extremities in sifaka and other primates is maintained by selection, and does not simply reflect a primitive developmental pathway that has no adaptive basis. Am J Phys Anthropol 131:261–271, 2006. © 2006 Wiley‐Liss, Inc.     

SEQUENTIAL FEMALE ASSESSMENT DRIVES COMPLEX SEXUAL SELECTION ON BOWER SHAPE IN A CICHLID FISH

In many animals, sexual selection on male traits results from female mate choice decisions made during a sequence of courtship behaviors. We use a bower‐building cichlid fish, Nyassachromis cf. microcephalus, to show how applying standard selection analysis to data on sequential female assessment provides new insights into sexual selection by mate choice. We first show that the cumulative selection differentials confirm previous results suggesting female choice favors males holding large volcano‐shaped sand bowers. The sequential assessment analysis reveals these cumulative differentials are the result of selection acting on different bower dimensions during the courtship sequence; females choose to follow males courting from tall bowers, but choose to engage in premating circling with males holding bowers with large diameter platforms. The approach we present extends standard selection analysis by partitioning the variances of increasingly accurate estimates of male reproductive fitness and is applicable to systems in which sequential female assessment drives sexual selection on male traits.     

Use of field data in pig genomic selection schemes: a simulation study

The aim of this study was to test how genetic gain for a trait not measured on the nucleus animals could be obtained within a genomic selection pig breeding scheme. Stochastic simulation of a pig breeding program including a breeding nucleus, a multiplier to produce and disseminate semen and a production tier where phenotypes were recorded was performed to test (1) the effect of obtaining phenotypic records from offspring of nucleus animals, (2) the effect of genotyping production animals with records for the purpose of including them in a genomic selection reference population or (3) to combine the two approaches. None of the tested strategies affected genetic gain if the trait under investigation had a low economic value of only 10% of the total breeding goal. When the relative economic weight was increased to 30%, a combination of the methods was most effective. Obtaining records from offspring of already genotyped nucleus animals had more impact on genetic gain than to genotype more distant relatives with phenotypes to update the reference population. When records cannot be obtained from offspring of nucleus animals, genotyping of production animals could be considered for traits with high economic importance.     

Standardization of an indirect PTA-ELISA for detection ofFusarium spp. in infected grains

Plant pathogenic fungi of the genusFusarium cause agriculturally important diseases of small grain cereals and maize. Especially the contamination of grains with the mycotoxin deoxynivalenol (DON) is harmful for animals and humans. For quantification of the severity ofFusarium head blight (FHB) in resistance evaluation and selection of cereals a fast, economical and reliable method is essential. Immunological methods appear to be particularly suitable for such an assessment. The results demonstrate that a selected antiserum was appropriate for the detection ofFusarium-exoantigens (ExoAg) in cereal grains by an indirect ELISA-format, although a discrimination between variousFusarium-species was not possible. The polyclonal antibody detection system was optimized for different parameters and a standard test protocol was elaborated. Presented at the 26^th Mykotoxin-Workshop in Herrsching, Germany, May 17–19, 2004     

Evaluating the self‐domestication hypothesis of human evolution

“Self‐domestication” has been invoked to understand important aspects of human evolution, integrating physiological, behavioral, and morphological information in a novel way. It proposes that selection for reduced aggression on animals undergoing domestication provides a model for selection favoring prosocial behaviors in humans and for a set of seemingly independent features, which arose as a result of developmental correlation. We review the history of the idea and examine patterns of domestication. A lack of empirical studies on evolutionary rates and variation thwarts meaningful comparison with domestication. The neural crest hypothesis for domestication has great explanatory power but it is difficult to test. We suggest a scenario in which the morphological byproducts of domestication can act as an honest signal of reduced xenophobia. Future studies should test if alternative explanations for the features deemed to result from self‐domestication are mutually exclusive and generate data to test predictions of these hypotheses.     

Copying and sexual selection

Recent studies of a variety of polygynously mating animals indicate that females do not always choose mates independently, but instead may copy the choices of others. Copying could serve either to increase the accuracy of mate assessment or to reduce its costs. It is also likely to affect the intensity of sexual selection.     

Behaviour as a tool in the assessment of animal welfare

A central issue in animal welfare research is how to assess the welfare state of animals objectively and scientifically. I argue that this issue can be approached by asking two key questions: 1) is the animal physically healthy and 2) does the animal have what it wants? Behaviour is used to answer both of these questions. In the assessment of physical health, it can be used for clinical and pre-clinical diagnosis. In the assessment of what animals want, it has a major role through choice and preference testing. It is particularly important that applied ethologists develop methods for assessing welfare in situ--in the places where concern for animal welfare is greatest such as on farms and in zoos.     

Principles and methods of occupational psychophysiological selection of deep-water divers]

A complex of methods is suggested for professional psychophysiological selection of deep divers: the count of signals under time deficit conditions, simple and complex coordination of analyzers function, tepping test, the study of attention concentration using the Ivanov-Smolensky tables and finding of numbers with switching. This complex together with assessment of number range by deviation method allows making correct prediction during selection of specialists with high probability equal to 0.9. The efficiency of professional selection increases due to the reliable correlation between the results of psychophysiological research and predisposition to development of decompressive disease.     

Statistical Evaluation of Toxicological Experimental Design for Bayesian Model Averaged Benchmark Dose Estimation with Dichotomous Data

A method is presented to statistically evaluate toxicity study design for dose– response assessment aimed at minimizing the uncertainty in resulting Benchmark dose (BMD) estimates. Although the BMD method has been accepted as a valuable tool for risk assessment, the traditional no observed adverse effect level (NOAEL)/lowest observed adverse effective level (LOAEL) approach is still the principal basis for toxicological study design. To develop similar protocols for experimental design for BMD estimation, methods are needed that account for variability in experimental outcomes, and uncertainty in dose–response model selection and model parameter estimates. Based on Bayesian model averaging (BMA) BMD estimation, this study focuses on identifying the study design criteria that can reduce the uncertainty in BMA BMD estimates by using a Monte Carlo pre-posterior analysis on BMA BMD predictions. The results suggest that (1) as more animals are tested there is less uncertainty in BMD estimates; (2) one relatively high dose is needed and other doses can then be appropriately spread over the resulting dose scale; (3) placing different numbers of animals in different dose groups has very limited influence on improving BMD estimation; and (4) when the total number of animals is fixed, using more (but smaller) dose groups is a preferred strategy.     

The pleiotropic effect of selection for behavior on coat color in grey rats (Rattus norvegicus)

The effects of selection for a type of behavior relative to humans (tame and aggressive) on the intensity of coat color in agouti rats with the AAHH genotype were studied. Animals that were not under selection for behavior (wild animals) were used as the control. Morphometric analysis of the hair parameters that influence the intensity of coat color demonstrated that, on the one hand, polymorphism in the main coat color exists in the population of wild agouti rats, that is, both light and dark agouti animals exist. On the other hand, it was demonstrated that selection for a type of behavior in rats is accompanied by selection of animals that differ in the intensity of the main genetically identical coat color. Dark-colored animals are more prevelent among the aggressive animals, while light-colored animals prevail among tame animals. The association of the effects of selection for behavior with the modification of coat color is probably caused by the presence of common neurohormonal mechanisms for the regulation of these processes.     

Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection

The objective of this study was to quantify the accuracy achievable from imputing genotypes from a commercially available low-density marker panel (2730 single nucleotide polymorphisms (SNPs) following edits) to a commercially available higher density marker panel (51 602 SNPs following edits) in Holstein-Friesian cattle using Beagle, a freely available software package. A population of 764 Holstein-Friesian animals born since 2006 were used as the test group to quantify the accuracy of imputation, all of which had genotypes for the high-density panel; only SNPs on the low-density panel were retained with the remaining SNPs to be imputed. The reference population for imputation consisted of 4732 animals born before 2006 also with genotypes on the higher density marker panel. The concordance between the actual and imputed genotypes in the test group of animals did not vary across chromosomes and was on average 95%; the concordance between actual and imputed alleles was, on average, 97% across all SNPs. Genomic predictions were undertaken across a range of production and functional traits for the 764 test group animals using either their real or imputed genotypes. Little or no mean difference in the genomic predictions was evident when comparing direct genomic values (DGVs) using real or imputed genotypes. The average correlation between the DGVs estimated using the real or imputed genotypes for the 15 traits included in the Irish total merit index was 0.97 (range of 0.92 to 0.99), indicating good concordance between proofs from real or imputed genotypes. Results show that a commercially available high-density marker panel can be imputed from a commercially available lower density marker panel, which will also have a lower cost, thereby facilitating a reduction in the cost of genomic selection. Increased available numbers of genotyped and phenotyped animals also has implications for increasing the accuracy of genomic prediction in the entire population and thus genetic gain using genomic selection.     

The evolution of animal genitalia: distinguishing between hypotheses by single species studies

Rapid evolution of genitalia is one of the most general patterns of morphological diversification in animals. Despite its generality, the causes of this evolutionary trend remain obscure. Several alternative hypotheses have been suggested to account for the evolution of genitalia (notably the lock-and-key, pleiotropism, and sexual selection hypotheses). Here, I argue that thorough intraspecific studies are the key to gaining insight into the patterns and processes of genitalic evolution. Critical assumptions and predictions that may be used to distinguish between the different hypotheses are identified and discussed. However, current knowledge of selection on genitalia, or even of the degree of phenotypic and genotypic variability of genital morphology, is highly limited, allowing only a very tentative assessment of the various hypotheses. In-depth single species studies of current patterns and processes of selection on genitalia are badly needed, and a single species research program is briefly outlined.     

Assessment of Optimal Selected Prognostic Factors

The identification and assessment of prognostic factors is one of the major tasks in clinical research. The assessment of one single prognostic factor can be done by recently established methods for using optimal cutpoints. Here, we suggest a method to consider an optimal selected prognostic factor from a set of prognostic factors of interest. This can be viewed as a variable selection method and is the underlying decision problem at each node of various tree building algorithms. We propose to use maximally selected statistics where the selection is defined over the set of prognostic factors and over all cutpoints in each prognostic factor. We demonstrate that it is feasible to compute the approximate null distribution. We illustrate the new variable selection test with data of the German Breast Cancer Study Group and of a small study on patients with diffuse large B‐cell lymphoma. Using the null distribution for a p‐value adjusted regression trees algorithm, we adjust for the number of variables analysed at each node as well. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Evolution of brain region volumes during artificial selection for relative brain size

The vertebrate brain shows an extremely conserved layout across taxa. Still, the relative sizes of separate brain regions vary markedly between species. One interesting pattern is that larger brains seem associated with increased relative sizes only of certain brain regions, for instance telencephalon and cerebellum. Till now, the evolutionary association between separate brain regions and overall brain size is based on comparative evidence and remains experimentally untested. Here, we test the evolutionary response of brain regions to directional selection on brain size in guppies (Poecilia reticulata) selected for large and small relative brain size. In these animals, artificial selection led to a fast response in relative brain size, while body size remained unchanged. We use microcomputer tomography to investigate how the volumes of 11 main brain regions respond to selection for larger versus smaller brains. We found no differences in relative brain region volumes between large‐ and small‐brained animals and only minor sex‐specific variation. Also, selection did not change allometric scaling between brain and brain region sizes. Our results suggest that brain regions respond similarly to strong directional selection on relative brain size, which indicates that brain anatomy variation in contemporary species most likely stem from direct selection on key regions.     

Prediction of response with overlapping generations accounting for multistage selection

Summary A generalization of Hill's equations predicting response to selection is developed that accounts for multiple stage selection in either or both sexes. The method accounts for the flow of genes for animals selected at later stages. This allows for the use of genetic gains from later stages, which explains the reduction in variance due to previous selection. Genetic gains from different selection differentials in each reproductive pathway are incorporated into the equations. The asymptotic response to a single cycle of selection is shown to agree with classical selection theory.The method is applied to a dairy progeny testing scheme representative of an artificial insemination organization in the USA. Two models were compared: (1) the first model accounted for two-stage selection of males, the first stage being based on pedigree information and the second stage on both pedigree and progeny test information; and (2) the second model assumed single-stage male selection. Selection was based on milk volume, milk fat, and milk protein yields. The predicted asymptotic rates for a single cycle of selection were overestimated by 6% and the cumulative response to continuous selection over 20 years was overestimated by 8% by assuming singlestage male selection.Journal Paper No. J14146 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa; Project No. 1053     

Artificial Selection for Whole Animal Low Intrinsic Aerobic Capacity Co-Segregates with Hypoxia-Induced Cardiac Pump Failure

Oxygen metabolism is a strong predictor of the general health and fitness of an organism. In this study, we hypothesized that a divergence in intrinsic aerobic fitness would co-segregate with susceptibility for cardiovascular dysfunction. To test this hypothesis, cardiac function was assessed in rats specifically selected over nineteen generations for their low (LCR) and high (HCR) intrinsic aerobic running capacity. As an integrative marker of native aerobic capacity, run time to exhaustion between LCR and HCR rats had markedly diverged by 436% at generation nineteen of artificial selection. In vivo assessment of baseline cardiac function by echocardiography and catheter-based conductance micromanometry showed no marked difference in cardiac performance. However, when challenged by exposure to acute hypoxia, cardiac pump failure occurred significantly earlier in LCR rats compared to HCR animals. Acute cardiac decompensation in LCR rats was exclusively due to the development of intractable irregular ventricular contractions. Analysis of isolated cardiac myocytes showed significantly slower sarcomeric relaxation and delayed kinetics of calcium cycling in LCR myocytes compared to HCR myocytes. This study also revealed that artificial selection for low native aerobic capacity is a novel pathologic stimulus that results in myosin heavy chain isoform switching in the heart as shown by increased levels of β-MHC in LCR rats. Together, these results provide evidence that alterations in sub-cellular calcium handling and MHC isoform composition are associated with susceptibility to compensatory cardiac remodeling and hypoxia induced pump failure in animals with low intrinsic aerobic capacity.     

Woodland caribou habitat selection patterns in relation to predation risk and forage abundance depend on reproductive state

The ideal free distribution assumes that animals select habitats that are beneficial to their fitness. When the needs of dependent offspring differ from those of the parent, ideal habitat selection patterns could vary with the presence or absence of offspring. We test whether habitat selection depends on reproductive state due to top‐down or bottom‐up influences on the fitness of woodland caribou (Rangifer tarandus caribou), a threatened, wide‐ranging herbivore. We combined established methods of fitting resource and step selection functions derived from locations of collared animals in Ontario with newer techniques, including identifying calf status from video collar footage and seasonal habitat selection analysis through latent selection difference functions. We found that females with calves avoided predation risk and proximity to roads more strongly than females without calves within their seasonal ranges. At the local scale, females with calves avoided predation more strongly than females without calves. Females with calves increased predation avoidance but not selection for food availability upon calving, whereas females without calves increased selection for food availability across the same season. These behavioral responses suggest that habitat selection by woodland caribou is influenced by reproductive state, such that females with calves at heel use habitat selection to offset the increased vulnerability of their offspring to predation risk.     

Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection

The identification of the causative genetic variants in quantitative trait loci (QTL) influencing phenotypic traits is challenging, especially in crosses between outbred strains. We have previously identified several QTL influencing tameness and aggression in a cross between two lines of wild-derived, outbred rats (Rattus norvegicus) selected for their behavior towards humans. Here, we use targeted sequence capture and massively parallel sequencing of all genes in the strongest QTL in the founder animals of the cross. We identify many novel sequence variants, several of which are potentially functionally relevant. The QTL contains several regions where either the tame or the aggressive founders contain no sequence variation, and two regions where alternative haplotypes are fixed between the founders. A re-analysis of the QTL signal showed that the causative site is likely to be fixed among the tame founder animals, but that several causative alleles may segregate among the aggressive founder animals. Using a formal test for the detection of positive selection, we find 10 putative positively selected regions, some of which are close to genes known to influence behavior. Together, these results show that the QTL is probably not caused by a single selected site, but may instead represent the joint effects of several sites that were targets of polygenic selection.