An evaluation of the miles method of ageing using the Tepe Hissar dental sample.

The Miles system of ageing, based upon analysis of the rate of molar wear, was evaluated using the available dental sample from Tepe Hissar, Iran. The independently estimated ages for the mandibles and maxillae of the same individuals were found to be highly correlated (r = 0.87, p less than 0.001). Ages of a subsample of the dentitions were compared with skeletal ages for the same individuals estimated from pubic symphyseal faces and found to be significantly correlated (r = 0.82, p less than 0.005) with no significant differences in the mean ages. Although a complete evaluation of the Miles method would require its testing on a controlled population, the available dental sample from Tepe Hissar provided evidence of the reliability and validity of the Miles method of ageing archeological populations on the basis of dental wear. Due to selective retention of burial remains, the available skeletal sample from Tepe Hissar I-III is not representative of the human populations of the site and can not be used to generate meaningful demographic statistics.     

Generalizing Double and Triple Sampling for Repeated Surveys and Partial Verification

Population composition is often estimated by double sampling in which the value of a covariate is noted on each of a large number of randomly selected units and the value of the covariate and the exact class to which the unit belongs is noted for a smaller sample. The cross‐classified sample can be used to estimate the classification rates and these, in turn, can be used in conjunction with the estimated distribution of the covariate to obtain an improved estimate of the population composition over that obtained by direct observation of the identity of the individuals in a small sample. There are two approaches to this problem characterized by the way in which the classification rates are defined. The simplest approach uses estimates of the probability P(i | j) that the unit is actually in class i given that the covariate is in class j. The more complicated approach uses estimates of the probability Pi | j) that the covariate falls in class j given that the unit is actually in class i. The latter approach involves estimating more parameters than the former but avoids the necessity for the two samples to be drawn from the same population. We show the two approaches can be combined when there are multiple surveys. For example, one might conduct a disease survey for several years; in each year the accurate and/or error‐prone techniques may be applied to samples. The sensitivities and specificities of the error‐prone test are assumed constant across surveys. Generalizations allow for more than one error‐prone classifier and partial verification (estimation of misclassification rates by application of the accurate technique to fixed subsamples from each error‐prone category). The general approach is illustrated by considering a repeated survey for malaria.     

The effect of reference sample composition and size on dental age interval estimates

Objectives

Validation studies in juvenile dental age estimation primarily focus on point estimates while interval performance for reference samples of different ancestry group compositions has received minimal attention. We tested the effect of reference sample size and composition by sex and ancestry group on age interval estimates.

Materials and Methods

The dataset consisted of Moorrees et al. dental scores from panoramic radiographs of 3334 London children of Bangladeshi and European ancestry and 2–23 years of age. Model stability was assessed using standard error of mean age-at-transition for univariate cumulative probit and sample size, group mixing (sex or ancestry), and staging system as factors. Age estimation performance was tested using molar reference samples of four sizes, stratified by year of age, sex, and ancestry. Age estimates were performed using Bayesian multivariate cumulative probit with 5-fold cross-validation.

Results

Standard error increased with decreasing sample size but showed no effect from mixing by sex or ancestry. Estimating ages using a reference and target sample of different sex reduced success rate significantly. The same test by ancestry groups had a lesser effect. Small sample size (n < 20/year of age) negatively affected most performance metrics.

Discussion

We found that reference sample size, followed by sex, primarily drove age estimation performance. Combining reference samples by ancestry produced equivalent or better estimates of age by all metrics than using a single-demographic reference of smaller size. We further proposed that population specificity is an alternative hypothesis of intergroup difference that has been erroneously treated as a null.     

Further Results in Estimating the Classification Error in Discriminance Analysis

Basing on the approach by McLachlan (1977) a procedure for the conditional and common error estimation of the classification error in discriminance analysis is described for k ≧ 2 classes. As a rapid procedure for large sample sizes and feature numbers, a modification of the resubstitution method is proposed being favourable with respect to computing time. Both methods provide useful estimations for the probability of misclassification. In calculating the weighting function w, deviations from preconditions known from the MANOVA such as the skewness, the truncation or the inequality of the covariance matrices, hardly play any role; it appears that only a variation of the sample sizes of the classes substantially influences the weighting functions. The error rates of the tested error estimation methods likewise in effect depend on the sample sizes of the classes. Violations of the mentioned preconditions in the form described above result in different variations of the error estimates, depending on these sample sizes. A comparison between error estimation and allocation relative to a simulated population demonstrates the goodness of the used error estimation procedures.     

The adequacy of aging techniques in vertebrates for rapid estimation of population mortality rates from age distributions

As a key parameter in population dynamics, mortality rates are frequently estimated using mark–recapture data, which requires extensive, long‐term data sets. As a potential rapid alternative, we can measure variables correlated to age, allowing the compilation of population age distributions, from which mortality rates can be derived. However, most studies employing such techniques have ignored their inherent inaccuracy and have thereby failed to provide reliable mortality estimates. In this study, we present a general statistical model linking birth rate, mortality rate, and population age distributions. We next assessed the reliability and data needs (i.e., sample size) for estimating mortality rate of eight different aging techniques. The results revealed that for half of the aging techniques, correlations with age varied considerably, translating into highly variable accuracies when used to estimate mortality rate from age distributions. Telomere length is generally not sufficiently correlated to age to provide reliable mortality rate estimates. DNA methylation, signal‐joint T‐cell recombination excision circle (sjTREC), and racemization are generally more promising techniques to ultimately estimate mortality rate, if a sufficiently high sample size is available. Otolith ring counts, otolithometry, and age‐length keys in fish, and skeletochronology in reptiles, mammals, and amphibians, outperformed all other aging techniques and generated relatively accurate mortality rate estimation with a sample size that can be feasibly obtained. Provided the method chosen is minimizing and estimating the error in age estimation, it is possible to accurately estimate mortality rates from age distributions. The method therewith has the potential to estimate a critical, population dynamic parameter to inform conservation efforts within a limited time frame as opposed to mark–recapture analyses.     

An elusive paleodemography? A comparison of two methods for estimating the adult age distribution of deaths at late Classic Copan,Honduras

Comparison of different adult age estimation methods on the same skeletal sample with unknown ages could forward paleodemographic inference, while researchers sort out various controversies. The original aging method for the auricular surface (Lovejoy et al., 1985a) assigned an age estimation based on several separate characteristics. Researchers have found this original method hard to apply. It is usually forgotten that before assigning an age, there was a seriation, an ordering of all available individuals from youngest to oldest. Thus, age estimation reflected the place of an individual within its sample. A recent article (Buckberry and Chamberlain, 2002) proposed a revised method that scores theses various characteristics into age stages, which can then be used with a Bayesian method to estimate an adult age distribution for the sample. Both methods were applied to the adult auricular surfaces of a Pre-Columbian Maya skeletal population from Copan, Honduras and resulted in age distributions with significant numbers of older adults. However, contrary to the usual paleodemographic distribution, one Bayesian estimation based on uniform prior probabilities yielded a population with 57% of the ages at death over 65, while another based on a high mortality life table still had 12% of the individuals aged over 75 years. The seriation method yielded an age distribution more similar to that known from preindustrial historical situations, without excessive longevity of adults. Paleodemography must still wrestle with its elusive goal of accurate adult age estimation from skeletons, a necessary base for demographic study of past populations.     

A method for estimating penetrance of pathogenic mutations in a mitochondrial genome

Variation in the manifestation age is typical of many mitochondrial diseases. The estimation of penetrance of pathogenic mutations causing such diseases is usually conducted on samples of individuals whose age exceeds the maximum age of the disease manifestation. In the case of rare diseases, samples of sufficient size sometimes cannot be formed. In this study, we propose a method for estimating penetrance involving individuals of any age. The efficiency of the method is demonstrated using Leber hereditary optic neuropathy as an example. It is shown that the method provides an unbiased estimate of penetrance and considerably reduces the error of this estimate in comparison with a sample including individuals whose age exceeds the maximum age of disease manifestation.     

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as "noise" or "error") within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms.     

A Method for Estimating Penetrance of Pathogenic Mutations in a Mitochondrial Genome

Variation in the age of onset is typical of many mitochondrial diseases. The estimation of penetrance of deleterious mtDNA mutations causing such diseases is usually conducted on samples of individuals whose age exceeds the maximum age of the disease manifestation. In the case of rare diseases, samples of sufficient size sometimes cannot be formed. In this study, we propose a method for estimating penetrance involving individuals of any age. The efficiency of the method is demonstrated using Leber hereditary optic neuropathy as an example. It is shown that the method provides an unbiased estimate of penetrance and considerably reduces the error of this estimate in comparison with a sample including individuals whose age exceeds the maximum age of disease manifestation.     

Calibrating Recruitment Estimates for Mourning Doves From Harvest Age Ratios

ABSTRACT We examined results from the first national-scale effort to estimate mourning dove (Zenaida macroura) age ratios and developed a simple, efficient, and generalizable methodology for calibrating estimates. Our method predicted age classes of unknown-age wings based on backward projection of molt distributions from fall harvest collections to preseason banding. We estimated 1) the proportion of late-molt individuals in each age class, and 2) the molt rates of juvenile and adult birds. Monte Carlo simulations demonstrated our estimator was minimally biased. We estimated model parameters using 96,811 wings collected from hunters and 42,189 birds banded during preseason from 68 collection blocks in 22 states during the 2005–2007 hunting seasons. We also used estimates to derive a correction factor, based on latitude and longitude of samples, which can be applied to future surveys. We estimated differential vulnerability of age classes to harvest using data from banded birds and applied that to harvest age ratios to estimate population age ratios. Average, uncorrected age ratio of known-age wings for states that allow hunting was 2.25 (SD 0.85) juveniles:adult, and average, corrected ratio was 1.91 (SD 0.68), as determined from harvest age ratios from an independent sample of 41,084 wings collected from random hunters in 2007 and 2008. We used an independent estimate of differential vulnerability to adjust corrected harvest age ratios and estimated the average population age ratio as 1.45 (SD 0.52), a direct measure of recruitment rates. Average annual recruitment rates were highest east of the Mississippi River and in the northwestern United States, with lower rates between. Our results demonstrate a robust methodology for calibrating recruitment estimates for mourning doves and represent the first large-scale estimates of recruitment for the species. Our methods can be used by managers to correct future harvest survey data to generate recruitment estimates for use in formulating harvest management strategies.     

Variation in occlusal dental wear of two Chalcolithic populations in the southern Levant

Occlusal wear rate and wear plane in two Chalcolithic ( approximately 6500-5500 BP) samples from the southern Levant were compared, using paired first and second mandibular molars. Though food staples in both societies were derived from agro-pastoralism, they were located in distinct environmental regions: Wadi (W.) Makkukh in the Judean desert, and Peqi'in in the Upper Galilee. Accordingly, it was predicted that variation in wear should occur due to their location in distinct environments. Jaw size and tooth size were measured to estimate the possible impact of these variables on wear scores. Molar occlusal surfaces were divided into four quadrants, and wear scores were recorded for each quadrant. Principal axis analysis was then performed between total wear scores of paired, adjacent first and second molars to assess wear rates. Principal axis analysis was also used to analyze the change in occlusal wear plane in each sample by comparing between-buccal-cusps wear scores of the first molar with lingual wear scores of the second molar. The results indicate that the occlusal wear plane was similar in both samples but that wear tended to be more rapid in W. Makkukh. Since both samples were similar in jaw/tooth size, it is argued that the results reflect less refined food-processing methods as well as the unintentional ingestion of sand by individuals interred in the Judean desert.     

A correlation of tooth wear and age among modern Igloolik eskimos.

The level of molar wear can be estimated reliably by measuring the cusp height. A correlation between age and the level of molar wear, expressed by a normalizing index (TWI) of cusp height, was found to exist in a sample of modern Igloolik Northwest Territories Eskimos. Not only was it possible to derive linear regression models to test the degree of correlation in the sample of 46 female and 39 male maxillary casts of Igloolik Eskimos, but the models were capable of accurately predicting the age of natives of the neighboring Hall Beach community. Sexual dimorphism in molar wear, perhaps attributable to differential bruxism, was demonstrated for the Igloolik sample. Based on the combined estimate of slopes for each maxillary molar pair for females and males, it was discovered that the male maxillary molars are worn approximately 30% more rapidly than female maxillary molars.     

Application of the anatomical method to estimate the maximum adult stature and the age‐at‐death stature

This study focuses on the age adjustment of statures estimated with the anatomical method. The research material includes 127 individuals from the Terry Collection. The cadaveric stature (CSTA)–skeletal height (SKH) ratios indicate that stature loss with age commences before SKH reduction. Testing three equations to estimate CSTA at the age at death and CSTA corrected to maximum stature from SKH indicates that the age correction of stature should reflect the pattern of age‐related stature loss to minimize estimation error. An equation that includes a continuous and linear age correction through the entire adult age range [Eq. (1)] results in curvilinear stature estimation error. This curvilinear stature estimation error can be largely avoided by applying a second linear equation [Eq. (2)] to only individuals older than 40 years. Our third equation [Eq. (3)], based on younger individuals who have not lost stature, can be used to estimate maximum stature. This equation can also be applied to individuals of unknown or highly uncertain age, because it provides reasonably accurate estimates until about 60/70 years at least for males. Am J Phys Anthropol 152:96–106, 2013. © 2013 Wiley Periodicals, Inc.     

Incorporating harvest rates into the sex-age-kill model for white-tailed deer

Although monitoring population trends is an essential component of game species management, wildlife managers rarely have complete counts of abundance. Often, they rely on population models to monitor population trends. As imperfect representations of real-world populations, models must be rigorously evaluated to be applied appropriately. Previous research has evaluated population models for white-tailed deer (Odocoileus virginianus); however, the precision and reliability of these models when tested against empirical measures of variability and bias largely is untested. We were able to statistically evaluate the Pennsylvania sex-age-kill (PASAK) population model using realistic error measured using data from 1,131 radiocollared white-tailed deer in Pennsylvania from 2002 to 2008. We used these data and harvest data (number killed, age-sex structure, etc.) to estimate precision of abundance estimates, identify the most efficient harvest data collection with respect to precision of parameter estimates, and evaluate PASAK model robustness to violation of assumptions. Median coefficient of variation (CV) estimates by Wildlife Management Unit, 13.2% in the most recent year, were slightly above benchmarks recommended for managing game species populations. Doubling reporting rates by hunters or doubling the number of deer checked by personnel in the field reduced median CVs to recommended levels. The PASAK model was robust to errors in estimates for adult male harvest rates but was sensitive to errors in subadult male harvest rates, especially in populations with lower harvest rates. In particular, an error in subadult (1.5-yr-old) male harvest rates resulted in the opposite error in subadult male, adult female, and juvenile population estimates. Also, evidence of a greater harvest probability for subadult female deer when compared with adult (≥2.5-yr-old) female deer resulted in a 9.5% underestimate of the population using the PASAK model. Because obtaining appropriate sample sizes, by management unit, to estimate harvest rate parameters each year may be too expensive, assumptions of constant annual harvest rates may be necessary. However, if changes in harvest regulations or hunter behavior influence subadult male harvest rates, the PASAK model could provide an unreliable index to population changes. © 2012 The Wildlife Society.     

New insights into estimating the age of old Scots pine from increment cores with stem rot

Trunk inner rot is a common phenomenon in some old-growth pine dominated forests, making it impossible to determine tree age by counting annual rings. We compared the efficiency of five methods to estimate the age of hollow pine trees (Pinus sylvestris L.). Our main aims were to select the best-performing method and to test whether the age of the tree or the proportion of rot influences the accuracy of estimation. We used full increment cores (reaching the pith or within 1 cm of it) from 100 trees (54–562 years old) collected in northern Sweden and simulated rotten centres of three different sizes in order to test the methods. The lowest error rates were obtained when less than a third of the sample was missing (down to 5.0 % error rate), and by using a method based on the growth pattern of a set of healthy trees. Using linear extrapolation of the mean radial growth led to large overestimates (up to three times the number of absent rings) with error rates up to 27.3 %. We also found that the performance of all methods was reduced in cores from older trees. Our main conclusion is that non-linear methods should be preferred for age estimation of hollow pines. We also argue that more precision in the age estimation could be gained already in the field by collecting multiple cores from rotten trees or by developing alternative coring methods.     

Histologic examination of age of the First African Baptist Church adults

This study applies a recently formulated method of histologic estimation of age at death to samples of anterior femoral cortex taken from adult skeletons from the First African Baptist Church cemetery and compares the results with macroscopic age estimates made by J.L. Angel and J.O. Kelley. Of the 65 samples taken, 44 were sufficiently well preserved to produce readable thin sections, although most were so fragile that they had to be embedded before sectioning. In most cases the histologic ages agreed with the macroscopic age estimations within the standard error of the estimate of the histologic method. Most cases of disagreement could be attributed to poor preservation. Despite differences between individual gross and microscopic age estimates, the two methods proved to be significantly correlated and produced the same overall demographic picture of a population whose female members were likely to die at earlier ages than the males.     

Changes in articular eminence morphology with dental function

Measurements of mandibular fossa depth and slope of the articular eminence were obtained for human skeletal samples chosen to represent a wide spectrum of subsistence strategies and oral function: hunter-gatherers (Eskimos, Australians), American Indians dependent to a variable extent on maize agriculture, and early twentieth century American whites and blacks. In the Eskimo and Australian samples, a generalized and steady increase in fossa depth and slope was observed with increasing functional age (tooth wear) through wear level 5 (of 8), followed by a levelling off or slight decrease in fossa depth in later wear levels on the anterior teeth and a sharp decrease in fossa depth in later wear levels on the molars. Although much less consistent due in part to extensive and early molar loss, patterns of variation in the remaining samples were characterized overall by a decrease in fossa depth and slope with increasing wear, especially on the molars. Further, in those samples with high incidences of posterior tooth loss, fossa depth was routinely less and the eminence more gently sloped in subsamples having experienced molar loss than in subsamples retaining all their molars. These data provide evidence that the temporomandibular joint (TMJ) undergoes continuous morphological alteration throughout adult life, and that these alterations are probably mediated by dental function. Moreover, they suggest that differences in patterning of such alterations may exist among human groups with contrasting patterns of tooth use.     

DEVELOPMENT AND APPLICATION OF A MASS-ESTIMATION METHOD FOR WEDDELL SEALS

Traditional methods of acquiring mass data limit the ability to collect large samples from across populations of some pinnipeds, or to sample without great disturbance to the animals. In order to collect substantial samples of mass data from the Weddell seal (Leptonychotes weddellii) population in Erebus Bay, Antarctica, we developed the equipment and methods for estimating the mass of Weddell seals using digital photographs. Resulting regression models predict the mass of adult female seals to within ±13.8% of estimated mass, and ±25.9% of estimated mass for pups. We show the protocols developed are repeatable and efficient enough to be applied to a large number of animals in a relatively short period of time and may be useful for studies of other marine mammals. We caution that prediction intervals exist around mass estimates and must be accounted for when estimates are applied to biological questions. In a limited application of the method, differences in mass transfer between experienced and inexperienced maternal females and their pups were detected when prediction error variance around mass estimates was explicitly included. Similar mass‐estimation methods may therefore be useful in consideration of biological questions requiring large samples of mass previously unattainable.     

Relationship of Tooth Wear to Chronological Age among Indigenous Amazon Populations

In indigenous populations, age can be estimated based on family structure and physical examination. However, the accuracy of such methods is questionable. The aim of this cross-sectional study was to evaluate occlusal tooth wear related to estimated age in the remote indigenous populations of the Xingu River, Amazon. Two hundred and twenty three semi-isolated indigenous subjects with permanent dentition from the Arara (n = 117), Xicrin-Kayapó (n = 60) and Assurini (n = 46) villages were examined. The control group consisted of 40 non-indigenous individuals living in an urban area in the Amazon basin (Belem). A modified tooth wear index was applied and then associated with chronological age by linear regression analysis. A strong association was found between tooth wear and chronological age in the indigenous populations (p <0.001). Tooth wear measurements were able to explain 86% of the variation in the ages of the Arara sample, 70% of the Xicrin-Kaiapó sample and 65% of the Assurini sample. In the urban control sample, only 12% of ages could be determined by tooth wear. These findings suggest that tooth wear is a poor estimator of chronological age in the urban population; however, it has a strong association with age for the more remote indigenous populations. Consequently, these findings suggest that a simple tooth wear evaluation method, as described and applied in this study, can be used to provide a straightforward and efficient means to assist in age determination of newly contacted indigenous groups.