Genetic parameters for endocrine and traditional fertility traits,hyperketonemia and milk yield in dairy cattle

High-yielding cows may suffer from negative energy balance during early lactation, which can lead to ketosis and delayed ability of returning to cyclicity after calving. Fast recovery after calving is essential when breeding for improved fertility. Traditionally used fertility traits, such as the interval from calving to first insemination (CFI), have low heritabilities and are highly influenced by management decisions. Herd Navigator™ management program samples and analyses milk progesterone and β-hydroxybutyrate (BHB) automatically during milking. In this study, the genetic parameters of endocrine fertility traits (measured from milk progesterone) and hyperketonemia (measured from milk BHB) in early lactation were evaluated and compared with traditional fertility traits (CFI, interval from calving to the last insemination and interval from first to last insemination) and the milk yield in red dairy cattle herds in Finland. Data included observations from 14 farms from 2014 to 2017. Data were analyzed with linear animal models using DMU software and analyses were done for first parity cows. Heritability estimates for traditional fertility traits were low and varied between 0.03 and 0.07. Estimated heritabilities for endocrine fertility traits (interval from calving to the first heat (CFH) and commencement of luteal activity (C-LA)) were higher than for traditional fertility traits (0.19 to 0.33). Five slightly different hyperketonemia traits divided into two or three classes were studied. Linear model heritability estimates for hyperketonemia traits were low, however, when the threshold model was used for binary traits the estimates became slightly higher (0.07 to 0.15). Genetic correlation between CFH and C-LA for first parity cows was high (0.97) as expected since traits are quite similar. Moderate genetic correlations (0.47 to 0.52) were found between the endocrine fertility traits and early lactation milk yield. Results suggest that the data on endocrine fertility traits measured by automatic systems is a promising tool for improving fertility, specifically when more data is available. For hyperketonemia traits, dividing values into three classes instead of two seemed to work better. Based on the current study and previous studies, where higher heritabilities have been found for milk BHB traits than for clinical ketosis, milk BHB traits are a promising indicator trait for resistance to ketosis and should be studied more. It is important that this kind of data from automatic devices is made available to recording and breeding organizations in the future.     

A nonparametric method of estimation of the population size in capture–recapture experiments

A recent method for estimating a lower bound of the population size in capture–recapture samples is studied. Specifically, some asymptotic properties, such as strong consistency and asymptotic normality, are provided. The introduced estimator is based on the empirical probability generating function (pgf) of the observed data, and it is consistent for count distributions having a log-convex pgf (-class). This is a large family that includes mixed and compound Poisson distributions, and their independent sums and finite mixtures as well. The finite-sample performance of the lower bound estimator is assessed via simulation showing a better behavior than some close competitors. Several examples of application are also analyzed and discussed.     

Induced abortion ratio in modern Sweden falls with age,but rises again before menopause

A woman's reproductive value decreases over her reproductive life span and it is therefore predicted that the likelihood of termination of investment in a child decreases with increasing age. An eventual increase in termination ratio in the oldest age groups, as is often found in abortion statistics, could depend on older women on average having larger families rather than on age per se. We used data on abortions and births in Sweden during 1994 to investigate how abortion ratio is related to age and parity of women. We found that age-specific abortion ratio is U-shaped (i.e. that it is highest for the youngest and for the oldest age groups) in each parity class from zero to four children but that age-dependence breaks down in higher parity classes (5, ≥6). Thus, for each of the parity classes 0–4, the incidence of abortion decreases with age up to a point, but increases again as women approach menopause. This late increase in induced abortion ratio seems to depend on age per se. The data indicate that abortion ratio is an inverse function of fertility, and that investment in new reproduction gradually decreases as a woman approaches menopause. Assuming grandmothering as an important driving force in human life history evolution, such a pattern might indicate that the transition from behavioural investment in one's own children to one's grandchildren is a gradual process similar to the decline in ovarian function.     

Ornamental plumage coloration and condition are dependent on age in eastern bluebirds Sialia sialis

Male eastern bluebirds Sialia sialis have striking ultraviolet (UV)-blue coloration on their heads, backs, rumps, wings, and tails and bold chestnut coloration on their breasts. These colored areas are ornaments that correlate with pairing date and reproductive effort, and thus probably influence the choice of mates by females. Such ornaments are expected to increase in color with age and body condition. We investigated the effects of age on body condition and the UV-blue and chestnut coloration of males over four years using both cross-sectional (comparing age classes) and longitudinal analyses (following individuals as they age). We found that both the body condition index and brightness of UV-blue rump coloration increased with age, while UV-blue tail plumage coloration increased between yearling and older males, and the chestnut breast coloration decreased in the oldest age class. The proximate mechanisms whereby individuals reliably signal age via rump brightness and tail coloration are probably different. Contour feathers, including rump feathers, are molted at approximately the same time in all age classes and are likely subject to the same production costs in all age classes. In contrast, the molt schedule of the tail and wing feathers differs between individuals of yearling and older age classes, with yearlings retaining wing and tail feathers for several months longer than adults. The relationship between tail color and age was probably, in part, a consequence of yearlings expressing tails that have increased feather wear and accumulation of dirt. In general, UV-blue coloration increased with age while chestnut plumage decreased with age, indicating that older individuals may tradeoff investing energy in structural and melanin ornaments. By assessing overall plumage coloration, female eastern bluebirds could estimate age class when choosing mates.     

An explicit approach to evolutionarily stable dispersal strategies: no cost of dispersal

The evolution of dispersal is examined by looking at evolutionarily stable strategies (ESS) for dispersal parameters in discrete time multisite models without any cost of dispersal. ESS are investigated analytically, based on explicit results on sensitivity analysis of matrix models. The basic model considers an arbitrary number of sites and a single age class. An ESS for dispersal parameters is obtained when the spatial reproductive values, calculated at the density-dependent population equilibrium, are equal across sites. From this basic formulation, one derives equivalently that all local populations should be at equilibrium in the absence of migration, and that dispersal between sites should be balanced, i.e., the numbers of individuals arriving to and leaving a site are equal. These results are then generalized to a model with several age classes. Equal age-specific reproductive values do not however imply balanced dispersal in this case. Our results generalize to any number of sites and age classes those available ?M. Doebeli, Dispersal and dynamics, Theoret. Popul. 47 (1995) 82 for two sites and one age class.     

A general procedure for predicting rates of inbreeding in populations undergoing mass selection

Predictions of rates of inbreeding (DeltaF), based on the concept of long-term genetic contributions assuming the infinitesimal model, are developed for populations with discrete or overlapping generations undergoing mass selection. Phenotypes of individuals are assumed to be recorded prior to reproductive age and to remain constant over time. The prediction method accounts for inheritance of selective advantage both within and between age classes and for changing selection intensities with age. Terms corresponding to previous methods that assume constant selection intensity with age are identified. Predictions are accurate (relative errors < or =8%), except for cases with extreme selection intensities in females in combination with high heritability. With overlapping generations DeltaF reaches a maximum when parents are equally distributed over age classes, which is mainly due to selection of the same individuals in consecutive years. DeltaF/year decreases much more slowly compared to DeltaF/generation as the number of younger individuals increases, whereas the decrease is more similar as the number of older individuals increases. The minimum DeltaF (per year or per generation) is obtained when most parents were in the later age classes, which is mainly due to an increased number of parents per generation. With overlapping generations, the relationship between heritability and DeltaF is dependent on the age structure of the population.     

A Bayesian Latent Variable Mixture Model for Longitudinal Fetal Growth

Summary Fetal growth restriction is a leading cause of perinatal morbidity and mortality that could be reduced if high‐risk infants are identified early in pregnancy. We propose a Bayesian model for aggregating 18 longitudinal ultrasound measurements of fetal size and blood flow into three underlying, continuous latent factors. Our procedure is more flexible than typical latent variable methods in that we relax the normality assumptions by allowing the latent factors to follow finite mixture distributions. Using mixture distributions also permits us to cluster individuals with similar observed characteristics and identify latent classes of subjects who are more likely to be growth or blood flow restricted during pregnancy. We also use our latent variable mixture distribution model to identify a clinically meaningful latent class of subjects with low birth weight and early gestational age. We then examine the association of latent classes of intrauterine growth restriction with latent classes of birth outcomes as well as observed maternal covariates including fetal gender and maternal race, parity, body mass index, and height. Our methods identified a latent class of subjects who have increased blood flow restriction and below average intrauterine size during pregnancy. These subjects were more likely to be growth restricted at birth than a class of individuals with typical size and blood flow.     

A generalized model of social and biological contagion

We present a model of contagion that unifies and generalizes existing models of the spread of social influences and microorganismal infections. Our model incorporates individual memory of exposure to a contagious entity (e.g. a rumor or disease), variable magnitudes of exposure (dose sizes), and heterogeneity in the susceptibility of individuals. Through analysis and simulation, we examine in detail the case where individuals may recover from an infection and then immediately become susceptible again (analogous to the so-called SIS model). We identify three basic classes of contagion models which we call epidemic threshold, vanishing critical mass, and critical mass classes, where each class of models corresponds to different strategies for prevention or facilitation. We find that the conditions for a particular contagion model to belong to one of the these three classes depend only on memory length and the probabilities of being infected by one and two exposures, respectively. These parameters are in principle measurable for real contagious influences or entities, thus yielding empirical implications for our model. We also study the case where individuals attain permanent immunity once recovered, finding that epidemics inevitably die out but may be surprisingly persistent when individuals possess memory.     

Factors affecting the errors in the estimation of evolutionary distances between sequences

Phylogenetic methods that use matrices of pairwise distances between sequences (e.g., neighbor joining) will only give accurate results when the initial estimates of the pairwise distances are accurate. For many different models of sequence evolution, analytical formulae are known that give estimates of the distance between two sequences as a function of the observed numbers of substitutions of various classes. These are often of a form that we call "log transform formulae". Errors in these distance estimates become larger as the time t since divergence of the two sequences increases. For long times, the log transform formulae can sometimes give divergent distance estimates when applied to finite sequences. We show that these errors become significant when t approximately 1/2 |lambda(max)|(-1) logN, where lambda(max) is the eigenvalue of the substitution rate matrix with the largest absolute value and N is the sequence length. Various likelihood-based methods have been proposed to estimate the values of parameters in rate matrices. If rate matrix parameters are known with reasonable accuracy, it is possible to use the maximum likelihood method to estimate evolutionary distances while keeping the rate parameters fixed. We show that errors in distances estimated in this way only become significant when t approximately 1/2 |lambda(1)|(-1) logN, where lambda(1) is the eigenvalue of the substitution rate matrix with the smallest nonzero absolute value. The accuracy of likelihood-based distance estimates is therefore much higher than those based on log transform formulae, particularly in cases where there is a large range of timescales involved in the rate matrix (e.g., when the ratio of transition to transversion rates is large). We discuss several practical ways of estimating the rate matrix parameters before distance calculation and hence of increasing the accuracy of distance estimates.     

A model‐based approach to characterize individual inbreeding at both global and local genomic scales

Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated with respect to an arbitrary base population consisting of ancestors that are assumed unrelated. We herein propose a model‐based approach to estimate and characterize individual inbreeding at both global and local genomic scales by assuming the individual genome is a mosaic of homozygous‐by‐descent (HBD) and non‐HBD segments. The HBD segments may originate from ancestors tracing back to different periods in the past defining distinct age‐related classes. The lengths of the HBD segments are exponentially distributed with class‐specific parameters reflecting that inbreeding of older origin generates on average shorter stretches of observed homozygous markers. The model is implemented in a hidden Markov model framework that uses marker allele frequencies, genetic distances, genotyping error rates and the sequences of observed genotypes. Note that genotyping errors, low‐fold sequencing or genotype‐by‐sequencing data are easily accommodated under this framework. Based on simulations under the inference model, we show that the genomewide inbreeding coefficients and the parameters of the model are accurately estimated. In addition, when several inbreeding classes are simulated, the model captures them if their ages are sufficiently different. Complementary analyses, either on data sets simulated under more realistic models or on human, dog and sheep real data, illustrate the range of applications of the approach and how it can reveal recent demographic histories among populations (e.g., very recent bottlenecks or founder effects). The method also allows to clearly identify individuals resulting from extreme consanguineous matings.     

The measurement of the characteristics of natural selection

A new index for the intensity of natural selection is proposed. This index is designed to measure the strength of the selection process itself rather than the effect of the process operating on a particular population for a particular period of time. However a new index for the effect of selection is also proposed.The indices can be used when the population being acted on is divided into classes with all the individuals in a class having the same susceptibility to the selection process. The fitting of susceptibility functions is discussed for cases where the division into classes is based upon the values of a quantitative variable.     

Demographic analysis from summaries of an age-structured population

Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.     

Measuring changes in physical size and predicting weight of sows during gestation

Changes in physical body size during gestation were monitored using 529 sets of sow measurements. All sows were from the same herd and production system with a range in parity from 1 to 8. Sows were individually weighed, P2 backfat thickness was determined by ultrasound and morphometric measurements of body size were taken five times during gestation: day 0 (at service), day 25, day 50, day 80 and day 110. The morphometric measurements included sow height (from floor to last rib at the midline, from floor to ventral surface and from floor to hip), heart girth, depth of last rib, length (from snout to tail and from anterior scapula to tail) and width (at ham, at last rib and at shoulder). Regression analyses were used to model the relationship between day of gestation or parity number and morphometric measurements of body size. Regression equations were also developed to estimate sow weight from physical measurements, day of gestation and parity. As expected, sow dimensions, in general, increased as pregnancy progressed and also with increasing parity number. The relationships between day of gestation and body dimensions were described by linear and quadratic regression models, which had a range of adjusted R2 values up to 0.99. Similar relationships to parity number had a range of R2 values between 0.51 and 0.96. Sow depth, which can be used as an estimate of the width of the sow when lying, equalled the maximum width of the gestation stall (650 mm) at day 103 of gestation. However, by day 40 of gestation, predicted mean sow depth (570 mm) equalled the width at the rear of the crate. The implication of this is that after day 40 of gestation, the average sow was too wide for the rear of the crate when lying in a recumbent position. On day 110 of gestation, 95% of the mean sow body depths would be accommodated in stalls that were 674 mm wide; however, the range in body sizes with increasing parity number suggests the use of more than one stall width would be appropriate. Sow weight could be estimated with an adjusted R2 value of 0.81 and with a residual standard deviation (r.s.d.) of 16.5 kg using heart girth alone, or more accurately using a model with parity, day of gestation, P2 backfat depth and heart girth as the parameters (R2 = 0.89, r.s.d. 12.4 kg).     

Biophysical basis for three distinct dynamical mechanisms of action potential initiation

Transduction of graded synaptic input into trains of all-or-none action potentials (spikes) is a crucial step in neural coding. Hodgkin identified three classes of neurons with qualitatively different analog-to-digital transduction properties. Despite widespread use of this classification scheme, a generalizable explanation of its biophysical basis has not been described. We recorded from spinal sensory neurons representing each class and reproduced their transduction properties in a minimal model. With phase plane and bifurcation analysis, each class of excitability was shown to derive from distinct spike initiating dynamics. Excitability could be converted between all three classes by varying single parameters; moreover, several parameters, when varied one at a time, had functionally equivalent effects on excitability. From this, we conclude that the spike-initiating dynamics associated with each of Hodgkin's classes represent different outcomes in a nonlinear competition between oppositely directed, kinetically mismatched currents. Class 1 excitability occurs through a saddle node on invariant circle bifurcation when net current at perithreshold potentials is inward (depolarizing) at steady state. Class 2 excitability occurs through a Hopf bifurcation when, despite net current being outward (hyperpolarizing) at steady state, spike initiation occurs because inward current activates faster than outward current. Class 3 excitability occurs through a quasi-separatrix crossing when fast-activating inward current overpowers slow-activating outward current during a stimulus transient, although slow-activating outward current dominates during constant stimulation. Experiments confirmed that different classes of spinal lamina I neurons express the subthreshold currents predicted by our simulations and, further, that those currents are necessary for the excitability in each cell class. Thus, our results demonstrate that all three classes of excitability arise from a continuum in the direction and magnitude of subthreshold currents. Through detailed analysis of the spike-initiating process, we have explained a fundamental link between biophysical properties and qualitative differences in how neurons encode sensory input.     

Development in the Usage and Comprehension of Greeting Calls in a Free‐Ranging Group of Japanese Macaques (Macaca fuscata)

The main objective of this study is to clarify the developmental process involved in both the usage of greeting calls and the response to greeting calls by Japanese macaques. These greeting calls facilitate affiliative interactions by communicating benign intent. Specifically, individuals frequently emit greeting calls when interacting with less‐predictable individuals. Here, we examined whether the targets at which greeting calls are directed, along with associated behavioral responses, differed among the age classes, by conducting a cross‐sectional observation of females aged 0–5 yr and their mothers. We found that infant females showed a weak tendency to emit greeting calls at no specific receivers, unlike that by older females. Adult females emitted greeting calls more frequently when approaching unrelated females than related females. In contrast, young adult or juvenile females exhibited no significant difference in the proportion of the calls with related and unrelated conspecifics. Adult and young adult females were more likely to respond affiliatively to other individuals that approached using greeting calls compared with silent approaches, whereas juveniles did not exhibit different responses to the two types of approaches. This study showed that the target‐specific usage and affiliative response to greeting calls emerge with changes in the developmental stage. Furthermore, the fact that even young adults did not use greeting calls as adults indicates that the usage of greeting calls is modified in conjunction with the expansion of social relationships.     

Bayesian Semiparametric Frailty Selection in Multivariate Event Time Data

Biomedical studies often collect multivariate event time data from multiple clusters (either subjects or groups) within each of which event times for individuals are correlated and the correlation may vary in different classes. In such survival analyses, heterogeneity among clusters for shared and specific classes can be accommodated by incorporating parametric frailty terms into the model. In this article, we propose a Bayesian approach to relax the parametric distribution assumption for shared and specific‐class frailties by using a Dirichlet process prior while also allowing for the uncertainty of heterogeneity for different classes. Multiple cluster‐specific frailty selections rely on variable selection‐type mixture priors by applying mixtures of point masses at zero and inverse gamma distributions to the variance of log frailties. This selection allows frailties with zero variance to effectively drop out of the model. A reparameterization of log‐frailty terms is performed to reduce the potential bias of fixed effects due to variation of the random distribution and dependence among the parameters resulting in easy interpretation and faster Markov chain Monte Carlo convergence. Simulated data examples and an application to a lung cancer clinical trial are used for illustration.     

Prostaglandin-induced enhancement of the in vitro anamnestic response.

The ability of various prostaglandins (PGs) to affect the in vitro anamnestic immune response of keyhole limpet hemocyanin (KLH)-primed rabbit popliteal lymph node cells was investigated. Of the four PGs studied (PGA1, PGE2 and PGF2alpha), PGE1 was found to have a stimulatory effect, whereas PGA1, PGE2 and pgf2alpha were ineffective in stimulating or inhibiting the in vitro anamnestic response. Under the conditions studied, a 3.5-fold increase in antibody production was obtained in PGE1-treated, KLH-stimulated cultures. Maximum enhancement was obtained when 0.2 mug of PGE1 were added at the time of culture initiation and were allowed to remain in contact with the lymph node cells for 24 hours.     

Mixture models for estimating the size of a closed population when capture rates vary among individuals

We develop a parameterization of the beta-binomial mixture that provides sensible inferences about the size of a closed population when probabilities of capture or detection vary among individuals. Three classes of mixture models (beta-binomial, logistic-normal, and latent-class) are fitted to recaptures of snowshoe hares for estimating abundance and to counts of bird species for estimating species richness. In both sets of data, rates of detection appear to vary more among individuals (animals or species) than among sampling occasions or locations. The estimates of population size and species richness are sensitive to model-specific assumptions about the latent distribution of individual rates of detection. We demonstrate using simulation experiments that conventional diagnostics for assessing model adequacy, such as deviance, cannot be relied on for selecting classes of mixture models that produce valid inferences about population size. Prior knowledge about sources of individual heterogeneity in detection rates, if available, should be used to help select among classes of mixture models that are to be used for inference.     

Anthropogenic harvesting pressure and changes in life history: insights from a rocky intertidal limpet

The importance of large breeding individuals for maintaining the health of marine fish and invertebrate populations has long been recognized. Unfortunately, decades of human harvesting that preferentially remove larger individuals have led to drastic reductions in body sizes of many of these species. Such size-selective harvesting is particularly worrisome for sequentially hermaphroditic species where the larger size classes are composed primarily of one sex. Whether these species can maintain stable sex ratios under sustained harvesting pressure depends on the level of plasticity of their life-history traits. Here, we show that populations of a marine limpet (Lottia gigantea) can adjust a fundamental aspect of their life history (the timing of sex change) when subjected to size-selective harvesting. As predicted by theoretical models, individuals from harvested populations change sex at smaller sizes and grow at slower rates compared to individuals from protected populations. In addition, the relative size at which the change from male to female occurs remains constant (~0.75; size at sex change/maximum size) across populations, regardless of harvesting pressure. Our results show that population-level demographic and life-history data, in conjunction with existing theory, can be sufficient to predict the responses of sequential hermaphrodites to harvesting pressure. Furthermore, they suggest such species can potentially adapt to size-selective harvesting.     

Effect of parity on bone mineral density in female rhesus macaques from Cayo Santiago

This cross-sectional study investigates the relationship between parity, bone mineral density, and spontaneous osteopenia/osteoporosis in a large skeletal population of female rhesus macaques (Macaca mulatta) from the free-ranging colony of Cayo Santiago, Puerto Rico. The sample consists of 119 mature female monkeys aged 4.0-22.2 years at time of death. The data consist of measurements of bone mineral content (BMC) and bone mineral density (BMD), obtained from dual-energy X-ray absorptiometry (DEXA) of the last lumbar vertebra. After controlling for age, there is a significant increase in BMD of the spine with increasing parity (P = 0.0006), up to a parity of 7 offspring. Thus, high parity initially has a positive effect on BMD in female rhesus monkeys, but this positive effect disappears with parities that are greater than 7 offspring. After controlling for parity, however, age has a negative (P = 0.015) effect on BMD, beginning several years after the attainment of peak BMD (age 9.5 years). Thus, it appears that parity initially mitigates the effects of aging, but the positive effect of parity on BMD is eventually overwhelmed by the aging process. Mean BMC and BMD values are higher in parous females compared to nulliparous females in the same age range. Similarly, females with low parity have significantly lower mean BMD values than do age-matched high-parity controls, and the frequency of osteopenia and osteoporosis is greater in low-parity females. Forty-three percent (43%) of the osteopenic/osteoporotic females in the sample are members of the low-parity group, even though it composes only 13% (16/119) of the entire sample. This study demonstrates that the free-ranging female rhesus monkeys from Cayo Santiago are a good nonhuman primate model for the study of bone mineral density, parity, osteopenia, and osteoporosis.