Microsatellite variability and genetic distances.

We analyze the within- and between-population dynamics of the distribution of the number of repeats at multiple microsatellite DNA loci subject to stepwise mutation. Analytical expressions for moments up to the fourth order within a locus and the variance of between-locus variance at mutation-drift equilibrium have been obtained. These statistics may be used to test the appropriateness of the one-step mutation model and to detect between-locus variation in the mutation rate. Published data are compatible with the one-step mutation model, although they do not reject the two-step model. Using both multinomial sampling and diffusion approximations for the analysis of the genetic distance introduced by Goldstein et al. [Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727], we show that this distance follows a chi 2 distribution with degrees of freedom equal to the number of loci when there is no variation in mutation rates among the loci. In the presence of such variation, the variance of the distance is obtained. We conclude that the number of microsatellite loci required for the construction of phylogenetic trees with reliable branch lengths may be several hundred. Also, mutations that change repeat scores by several units, even though extremely rare, may dramatically influence estimates of population parameters.

Protocols for listing threatened species can forecast extinction

Risk-ranking protocols are used widely to classify the conservation status of the world's species. Here we report on the first empirical assessment of their reliability by using a retrospective study of 18 pairs of bird and mammal species (one species extinct and the other extant) with eight different assessors. The performance of individual assessors varied substantially, but performance was improved by incorporating uncertainty in parameter estimates and consensus among the assessors. When this was done, the ranks from the protocols were consistent with the extinction outcome in 70-80% of pairs and there were mismatches in only 10-20% of cases. This performance was similar to the subjective judgements of the assessors after they had estimated the range and population parameters required by the protocols, and better than any single parameter. When used to inform subjective judgement, the protocols therefore offer a means of reducing unpredictable biases that may be associated with expert input and have the advantage of making the logic behind assessments explicit. We conclude that the protocols are useful for forecasting extinctions, although they are prone to some errors that have implications for conservation. Some level of error is to be expected, however, given the influence of chance on extinction. The performance of risk assessment protocols may be improved by providing training in the application of the protocols, incorporating uncertainty in parameter estimates and using consensus among multiple assessors, including some who are experts in the application of the protocols. Continued testing and refinement of the protocols may help to provide better absolute estimates of risk, particularly by re-evaluating how the protocols accommodate missing data.

Slowing down a pine invasion despite uncertainty in demography and dispersal

1. Management decisions regarding invasive plants often have to be made quickly and in the face of fragmentary knowledge of their population dynamics. However, recommendations are commonly made on the basis of only a restricted set of parameters. Without addressing uncertainty and variability in model parameters we risk ineffective management, resulting in wasted resources and an escalating problem if early chances to control spread are missed. 2. Using available data for Pinus nigra in ungrazed and grazed grassland and shrubland in New Zealand, we parameterized a stage-structured spread model to calculate invasion wave speed, population growth rate and their sensitivities and elasticities to population parameters. Uncertainty distributions of parameters were used with the model to generate confidence intervals (CI) about the model predictions. 3. Ungrazed grassland environments were most vulnerable to invasion and the highest elasticities and sensitivities of invasion speed were to long-distance dispersal parameters. However, there was overlap between the elasticity and sensitivity CI on juvenile survival, seedling establishment and long-distance dispersal parameters, indicating overlap in their effects on invasion speed. 4. While elasticity of invasion speed to long-distance dispersal was highest in shrubland environments, there was overlap with the CI of elasticity to juvenile survival. In shrubland invasion speed was most sensitive to the probability of establishment, especially when establishment was low. In the grazed environment elasticity and sensitivity of invasion speed to the severity of grazing were consistently highest. Management recommendations based on elasticities and sensitivities depend on the vulnerability of the habitat. 5. Synthesis and applications. Despite considerable uncertainty in demography and dispersal, robust management recommendations emerged from the model. Proportional or absolute reductions in long-distance dispersal, juvenile survival and seedling establishment parameters have the potential to reduce wave speed substantially. Plantations of wind-dispersed invasive conifers should not be sited on exposed sites vulnerable to long-distance dispersal events, and trees in these sites should be removed. Invasion speed can also be reduced by removing seedlings, establishing competitive shrubs and grazing. Incorporating uncertainty into the modelling process increases our confidence in the wide applicability of the management strategies recommended here.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05–7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

Phenotypic effect of mutations in evolving populations of RNA molecules

Background. The secondary structure of folded RNA sequences is a good model to map phenotype onto genotype, as represented by the RNA sequence. Computational studies of the evolution of ensembles of RNA molecules towards target secondary structures yield valuable clues to the mechanisms behind adaptation of complex populations. The relationship between the space of sequences and structures, the organization of RNA ensembles at mutation-selection equilibrium, the time of adaptation as a function of the population parameters, the presence of collective effects in quasispecies, or the optimal mutation rates to promote adaptation all are issues that can be explored within this framework. Results. We investigate the effect of microscopic mutations on the phenotype of RNA molecules during their in silico evolution and adaptation. We calculate the distribution of the effects of mutations on fitness, the relative fractions of beneficial and deleterious mutations and the corresponding selection coefficients for populations evolving under different mutation rates. Three different situations are explored: the mutation-selection equilibrium (optimized population) in three different fitness landscapes, the dynamics during adaptation towards a goal structure (adapting population), and the behavior under periodic population bottlenecks (perturbed population). Conclusions. The ratio between the number of beneficial and deleterious mutations experienced by a population of RNA sequences increases with the value of the mutation rate µ at which evolution proceeds. In contrast, the selective value of mutations remains almost constant, independent of µ, indicating that adaptation occurs through an increase in the amount of beneficial mutations, with little variations in the average effect they have on fitness. Statistical analyses of the distribution of fitness effects reveal that small effects, either beneficial or deleterious, are well described by a Pareto distribution. These results are robust under changes in the fitness landscape, remarkably when, in addition to selecting a target secondary structure, specific subsequences or low-energy folds are required. A population perturbed by bottlenecks behaves similarly to an adapting population, struggling to return to the optimized state. Whether it can survive in the long run or whether it goes extinct depends critically on the length of the time interval between bottlenecks. © 2010 Stich et al; licensee BioMed Central Ltd.

Morfometria, variação anual no peso e demografia do Tico-tico-rei-cinza (Lanio pileatus: thraupidae) em dois ambientes de caatinga no nordeste do Brasil

The caatinga is considered the only exclusively Brazilian biome, with a total area of 735.000km². It is estimated that about 59% of this area has already been removed and only 2% are protected in conservations units. The region is characteristic by strong seasonality and heterogeneity in their environments. This paper sets generate information on morphological and population patterns Lanio pilatus in two areas of caatinga of Estação Ecológica do Seridó (ESEC – Seridó), Serra Negra do Norte - RN. Data collection was performed in six phases between July 2012 and December 2014, covering the end of the dry and rainy seasons in the region. The captures were performed with nets and individuals captured were marked with metal rings and measured (weight, wing length, tail, tarsus, culmen and tip of the bill to nostril). Through these measures, we observed that only males of open area range in weight during the dry and rainy season, youngs were significantly lower for all parameters measured, and males were larger than females in three characteristics (weight, wing length and tail) in open area and only one (wing length) in the closed area. The population parameters were generated from the mark-capture-recapture technique by program MARK, using the techniques of robust design and CJS. The survival probability of detection and population estimates varied with time. Only individuals of open area fluctuated in their estimates during the study. Overall, the environment was a great mediator of results which increases the need for more studies on the life history of the species in the region.

Life history of the common pandora, Pagellus erythrinus (Linnaeus, 1758) (Actinopterygii: Sparidae) from southern Portugal

The common pandora, Pagellus erythrinus, is a commercially important seabream for coastal fisheries in the north and central eastern Atlantic. Age, growth and reproductive aspects of the southern Portuguese population were estimated by analysing 386 specimens ranging in total length (TL) from 12.0 to 44.8 cm. Ages were estimated by counting growth bands on otoliths and verified by marginal increment analysis, with specimens ranging in age from 1 to 21 years. The von Bertalanffy growth function was selected as the most adequate model to fit this species' growth, with the estimated parameters being L-inf = 47.14 cm TL, k = 0.084 year(-1) and t(0) = - 4.42 year. The gonads were analyzed macroscopically over a one-year period and the reproductive spawning season found to occur from March to July. The length at first maturity for males occurs at 17.58 cm TL and 1.15 years while females mature at slightly smaller sizes (17.29 cm TL) and younger ages (1.04 years). The results presented in this study are important for comparing this population's parameters with those of other populations of the same species occurring in other areas, as well as for future studies, for assessing eventual changes in population parameters over time.

Gravitational waves as dark sirens: an astrophysical and cosmological analysis

Despite the success of the ΛCDM model in describing the Universe, a possible tension between early- and late-Universe cosmological measurements is calling for new independent cosmological probes. Amongst the most promising ones, gravitational waves (GWs) can provide a self-calibrated measurement of the luminosity distance. However, to obtain cosmological constraints, additional information is needed to break the degeneracy between parameters in the gravitational waveform. In this thesis, we exploit the latest LIGO-Virgo-KAGRA Gravitational Wave Transient Catalog (GWTC-3) of GW sources to constrain the background cosmological parameters together with the astrophysical properties of Binary Black Holes (BBHs), using information from their mass distribution. We expand the public code MGCosmoPop, previously used for the application of this technique, by implementing a state-of-the-art model for the mass distribution, needed to account for the presence of non-trivial features, i.e. a truncated power law with two additional Gaussian peaks, referred to as Multipeak. We then analyse GWTC-3 comparing this model with simpler and more commonly adopted ones, both in the case of fixed and varying cosmology, and assess their goodness-of-fit with different model selection criteria, and their constraining power on the cosmological and population parameters. We also start to explore different sampling methods, namely Markov Chain Monte Carlo and Nested Sampling, comparing their performances and evaluating the advantages of both. We find concurring evidence that the Multipeak model is favoured by the data, in line with previous results, and show that this conclusion is robust to the variation of the cosmological parameters. We find a constraint on the Hubble constant of H0 = 61.10+38.65−22.43 km/s/Mpc (68% C.L.), which shows the potential of this method in providing independent constraints on cosmological parameters. The results obtained in this work have been included in [1].

Reference Values For High-density Lipoprotein Particle Size And Volume By Dynamic Light Scattering In A Brazilian Population Sample And Their Relationships With Metabolic Parameters.

Current data indicate that the size of high-density lipoprotein (HDL) may be considered an important marker for cardiovascular disease risk. We established reference values of mean HDL size and volume in an asymptomatic representative Brazilian population sample (n=590) and their associations with metabolic parameters by gender. Size and volume were determined in HDL isolated from plasma by polyethyleneglycol precipitation of apoB-containing lipoproteins and measured using the dynamic light scattering (DLS) technique. Although the gender and age distributions agreed with other studies, the mean HDL size reference value was slightly lower than in some other populations. Both HDL size and volume were influenced by gender and varied according to age. HDL size was associated with age and HDL-C (total population); non- white ethnicity and CETP inversely (females); HDL-C and PLTP mass (males). On the other hand, HDL volume was determined only by HDL-C (total population and in both genders) and by PLTP mass (males). The reference values for mean HDL size and volume using the DLS technique were established in an asymptomatic and representative Brazilian population sample, as well as their related metabolic factors. HDL-C was a major determinant of HDL size and volume, which were differently modulated in females and in males.

A finite-population revenue management model and a risk-ratio procedure for the joint estimation of population size and parameters

Many dynamic revenue management models divide the sale period into a finite number of periods T and assume, invoking a fine-enough grid of time, that each period sees at most one booking request. These Poisson-type assumptions restrict the variability of the demand in the model, but researchers and practitioners were willing to overlook this for the benefit of tractability of the models. In this paper, we criticize this model from another angle. Estimating the discrete finite-period model poses problems of indeterminacy and non-robustness: Arbitrarily fixing T leads to arbitrary control values and on the other hand estimating T from data adds an additional layer of indeterminacy. To counter this, we first propose an alternate finite-population model that avoids this problem of fixing T and allows a wider range of demand distributions, while retaining the useful marginal-value properties of the finite-period model. The finite-population model still requires jointly estimating market size and the parameters of the customer purchase model without observing no-purchases. Estimation of market-size when no-purchases are unobservable has rarely been attempted in the marketing or revenue management literature. Indeed, we point out that it is akin to the classical statistical problem of estimating the parameters of a binomial distribution with unknown population size and success probability, and hence likely to be challenging. However, when the purchase probabilities are given by a functional form such as a multinomial-logit model, we propose an estimation heuristic that exploits the specification of the functional form, the variety of the offer sets in a typical RM setting, and qualitative knowledge of arrival rates. Finally we perform simulations to show that the estimator is very promising in obtaining unbiased estimates of population size and the model parameters.

Gait and foot clearance parameters obtained using shoe-worn inertial sensors in a large-population sample of older adults

In order to distinguish dysfunctional gait; clinicians require a measure of reference gait parameters for each population. This study provided normative values for widely used parameters in more than 1400 able-bodied adults over the age of 65. We also measured the foot clearance parameters (i.e., height of the foot above ground during swing phase) that are crucial to understand the complex relationship between gait and falls as well as obstacle negotiation strategies. We used a shoe-worn inertial sensor on each foot and previously validated algorithms to extract the gait parameters during 20 m walking trials in a corridor at a self-selected pace. We investigated the difference of the gait parameters between male and female participants by considering the effect of age and height factors. Besides; we examined the inter-relation of the clearance parameters with the gait speed. The sample size and breadth of gait parameters provided in this study offer a unique reference resource for the researchers.

Mating system parameters in a high density population of andirobas in the Amazon forest

The objective of this work was to estimate the mating system parameters of a andiroba (Carapa guianensis) population using microsatellite markers and the mixed and correlated mating models. Twelve open‑pollinated progeny arrays of 15 individuals were sampled in an area with C. guianensis estimated density of 25.7 trees per hectare. Overall, the species has a mixed reproductive system, with a predominance of outcrossing. The multilocus outcrossing rate (t m = 0.862) was significantly lower than the unity, indicating that self‑pollination occurred. The rate of biparental inbreeding was substantial (t m ‑ t s = 0.134) and significantly different from zero. The correlation of selfing within progenies was high (r s = 0.635), indicating variation in the individual outcrossing rate. Consistent with this result, the estimate of the individual outcrossing rate ranged from 0.598 to 0.978. The multilocus correlation of paternity was low (r p(m) = 0.081), but significantly different from zero, suggesting that the progenies contain full‑sibs. The coancestry within progenies (Θ = 0.185) was higher and the variance effective size (Ne(v) = 2.7) was lower than expected for true half‑sib progenies (Θ = 0.125; Ne(v) = 4). These results suggest that, in order to maintain a minimum effective size of 150 individuals for breeding, genetic conservation, and environmental reforestation programs, seeds from at least 56 trees must be collected.

5C.09: Heritability of renal function parameters and electrolyte levels in the Swiss population

OBJECTIVE: Electrolytes handling by the kidney is essential for volume and blood pressure (BP) homeostasis but their distribution and heritability are not well described. We estimated the heritability of kidney function as well as of serum and urine concentrations, renal clearances and fractional excretions for sodium, chloride, potassium, calcium, phosphate and magnesium in a Swiss population-based study. DESIGN AND METHOD: Nuclear families were randomly selected from the general population in Switzerland. We estimated glomerular filtration rate (eGFR) using the CKD-EPI and MDRD equations. Urine was collected separately during day and night over 24-hour. We used the ASSOC program (S.A.G.E.) to estimate narrow sense heritability, including as covariates in the model: age, sex, body mass index and study center. RESULTS: The 1128 participants (537 men and 591 women from 273 families), had mean (sd) age of 47.4(17.5) years, body mass index of 25.0 (4.5) kg/m2 and CKD-EPI of 98.0(18.5) mL/min/1.73 m2. Heritability estimates (SE) were 46.0% (0.06), 48.0% (0.06) and 18.0% (0.06) for CKD-EPI, MDRD and 24-hour creatinine clearance (P < 0.05), respectively. Heritability [SE] of serum concentration was highest for calcium (37%[0.06]) and lowest for sodium (13%[0.05]). Heritabilities [SE] of 24-h urine concentrations and excretions, and of fractional excretions were highest for calcium (51%[0.06], 44%[0.06] and 51%[0.06], respectively) and lowest for potassium (11%[0.05], 10%[0.05] and 16%[0.06], respectively). All results were statistically different from zero.(Figure is included in full-text article.) CONCLUSIONS: : Serum and urine levels, urinary excretions and renal handling of electrolytes, particularly calcium, are heritable in the general adult population. Identifying genetic variants involved in electrolytes homeostasis may provide useful insight into the pathophysiological mechanisms involved in common chronic diseases such as kidney diseases, hypertension and diabetes.

Reference range of uterine artery Doppler parameters between the 11th and 14th pregnancy weeks in a population sample from Northeast Brazil

PURPOSE: To establish reference values for the first trimester uterine artery resistance index (UtA-RI) and pulsatility index (UtA-PI) in healthy singleton pregnant women from Northeast Brazil. METHODS: A prospective observational cohort study including 409 consecutive singleton pregnancies undergoing routine early ultrasound screening at 11 - 14 weeks of gestation was performed. The patients responded to a questionnaire to assess maternal epidemiological characteristics. The left and right UtA-PI and UtA-RI were examined by color and pulsed Doppler by transabdominal technique and the mean UtA-PI, mean UtA-RI and the presence of bilateral protodiastolic notching were recorded. Quartile regression was used to estimate reference values. RESULTS: The mean±standard deviation UtA-RI and UtA-PI were 0.7±0.1 and 1.5±0.5, respectively. When segregated for gestation age, mean UtA-PI was 1.6±0.5 at 11 weeks, 1.5±0.6 at 12 weeks, 1.4±0.4 at 13 weeks and 1.3±0.4 at 14 weeks' gestation and mean UtA-RI was 0.7±0.1 at 11 weeks, 0.7±0.1 at 12 weeks, 0.6±0.1 at 13 weeks and 0.6±0.1 at 14 weeks' gestation. Uterine artery bilateral notch was present in 261 (63.8%) patients. We observed that the 5th and 95th percentiles of the UtA-PI and UtA-RI uterine arteries were 0.7 and 2.3 and, 0.5 and 0.8, respectively. CONCLUSION: Normal reference range of uterine artery Doppler in healthy singleton pregnancies from Northeast Brazil was established. The 95th percentile of UtA-PI and UtA-RI values may serve as a cut-off for future prediction of pregnancy complications studies (i.e., pre-eclampsia) in Northeast Brazil.

Estimates of genetic and phenotypic parameters in a segregant population of rice irrigated by continuous flooding

Estimates of genetic and phenotypic parameters were obtained by using data from families of a recurrent selection program in rice. An experiment using population CNA-IRAT 4ME/1/1 was conducted at two locations (Lambari and Cambuquira) in the State of Minas Gerais, Brazil. At Lambari, families S0:2 and S0:3 were assessed during crop seasons 1992/1993 and 1993/1994, respectively. In the Cambuquira trial, only S0:3 families were tested in 1993/1994. The experimental design was a 10 x 10 lattice with three replications. The following traits were assessed: grain yield (GY), mean number of days to flowering (FL), plant height (PH), and the incidence of neck blast (NB) caused by Pyricularia grisea and grain staining (GS) caused by Drechslera oryzae. This population proved to be promising for recurrent selection, as it had high average yield and genetic variability. Heritability estimates obtained using variance components were generally greater than estimates of realized heritability, and heritability obtained by parent-offspring regression