Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.     

Isotope evidence for the intensive use of marine foods by Late Upper Palaeolithic humans

We report here on direct evidence for the intensive consumption of marine foods by anatomically modern humans at approximately 12,000 years ago. We undertook isotopic analysis of bone collagen from three humans, dating to the late Palaeolithic, from the site of Kendrick's Cave in North Wales, UK. The isotopic measurements of their bone collagen indicated that ca. 30% of their dietary protein was from marine sources, which we interpret as likely being high trophic level marine organisms such as marine mammals. This indicates that towards the end of the Pleistocene modern humans were pursuing a hunting strategy that incorporated both marine and terrestrial mammals. This is the first occurrence of the intensive use of marine resources, specifically marine mammals, that becomes even more pronounced in the subsequent Mesolithic period.     

Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism

The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.     

A new chronostratigraphic framework for the Upper Palaeolithic of Riparo Mochi (Italy)

The rockshelter of Mochi, on the Ligurian coast of Italy, is often used as a reference point in the formation of hypotheses concerning the arrival of the Aurigancian in Mediterranean Europe. Yet, the site is poorly known. Here, we describe the stratigraphic sequence based on new field observations and present 15 radiocarbon determinations from the Middle Palaeolithic (late Mousterian) and Early Upper Palaeolithic (Aurignacian and Gravettian) levels. The majority of dates were produced on humanly modified material, specifically marine shell beads, which comprise some of the oldest directly-dated personal ornaments in Europe. The radiocarbon results are incorporated into a Bayesian statistical model to build a new chronological framework for this key Palaeolithic site. A tentative correlation of the stratigraphy to palaeoclimatic records is also attempted.     

山顶洞人与现代华北人头骨非测量性特征比较及中国更新世晚期人类演化的一些问题

山顶洞人化石是迄今在东亚地区发现的数量最为丰富、保存状态最为完好的更新世晚期人类化石。多年来,山顶洞人作为东亚地区更新世晚期人类的代表,在研究东亚地区现代蒙古人种及美洲印第安人起源方面发挥着重要作用。随着对现代人起源与演化研究的深入,学术界对更新世晚期人类演化及现代人群形成过程的许多细节及演化机制予以了越来越多的注意,提出了现代人群出现时间及现代人群分化时间的概念。一些研究对山顶洞人的演化程度及其在东亚地区现代人群形成上的作用也提出了不同看法。为了深入探讨这些问题,本文对12项颅骨非测量特征在山顶洞人与现代中国人的表现情况进行了对比研究。发现有8项特征在山顶洞人与现代中国人之间具有不同的表现,作者认为山顶洞人在颅骨特征表现上较现代中国人具有更多的原始性。在此基础上,作者就更新世晚期人群内部变异、现代人群特征标准等问题进行了讨论。     

Strontium isotope evidence for migration in late Pleistocene Rangifer: implications for Neanderthal hunting strategies at the Middle Palaeolithic site of Jonzac, France

In order to understand the behaviours and subsistence choices of Palaeolithic hunter-gatherers, it is essential to understand the behavioural ecology of their prey. Here, we present strontium isotope data from sequentially-sampled enamel from three reindeer (Rangifer tarandus ssp.) and a single bison (Bison cf. priscus) from the late Middle Palaeolithic site of Jonzac (Chez-Pinaud), France. The results are used to investigate the ranging and migratory behaviours of these important prey species. We found that the bison had isotope values most consistent with a local range, while the three reindeer had values indicating a seasonal migration pattern. Due to the similarity of the patterning of two of the three reindeer and in conjunction with zooarchaeological results, we suggest that they may have been from the same herd, were likely killed around the same point during their seasonal round and may therefore be the product of a single hunting event or a small number of successive hunting events. The isotope analyses complement the zooarchaeological data and have allowed greater insight into the palaeoecology of these species, the palaeoenvironment, and Neanderthal site use and hunting strategies.     

The Anthropology of Modern Human Teeth: Dental Morphology and Its Variation in Recent Human Populations

The Anthropology of Modern Human Teeth: Dental Morphology and Its Variation in Recent Human Populations. G. Richard Scott and Christy G. Turner 11. New York: Cambridge University Press, 1997.382 pp.     

Separation of Populations of Human Lymphocytes by Freezing and Thawing

ATTEMPTS to provide a physical separation of functional populations of lymphocytes have exploited a wide variety of cellular characteristics^1–12. Work with other cell types has shown that different cells have different susceptibilities to damage during freezing and thawing^13–18 which suggested that this stress could possibly be used as a selectively damaging procedure. Functional lymphocytes can be recovered after freezing^19–23 and possible differences in the survival of populations of small lymphocytes frozen over a range of cooling rates in the presence of various concentrations of dimethylsulphoxide (DMSO) were investigated. Differential survival after thawing was assessed by stimulation with specific and non-specific stimulants using a microplate culture technique. Separation could only be achieved, however, by stimulating a sub-population of lymphocytes before freezing. Variation of the cooling conditions could be used either to damage or to protect the resulting activated cells in comparison with the unstimulated small lymphocytes.     

Hypothesis Testing of Inclusion of the Tolerance Interval for the Assessment of Food Safety

In the testing of food quality and safety, we contrast the contents of the newly proposed food (genetically modified food) against those of conventional foods. Because the contents vary largely between crop varieties and production environments, we propose a two-sample test of substantial equivalence that examines the inclusion of the tolerance intervals of the two populations, the population of the contents of the proposed food, which we call the target population, and the population of the contents of the conventional food, which we call the reference population. Rejection of the test hypothesis guarantees that the contents of the proposed foods essentially do not include outliers in the population of the contents of the conventional food. The existing tolerance interval (TI₀) is constructed to have at least a pre-specified level of the coverage probability. Here, we newly introduce the complementary tolerance interval (TI₁) that is guaranteed to have at most a pre-specified level of the coverage probability. By applying TI₀ and TI₁ to the samples from the target population and the reference population respectively, we construct a test statistic for testing inclusion of the two tolerance intervals. To examine the performance of the testing procedure, we conducted a simulation that reflects the effects of gene and environment, and residual from a crop experiment. As a case study, we applied the hypothesis testing to test if the distribution of the protein content of rice in Kyushu area is included in the distribution of the protein content in the other areas in Japan.     

Testing Equivalence Simultaneously for Location and Dispersion of two Normally Distributed Populations

In clinical trials with an active control usually therapeutical equivalence of a new treatment is investigated by looking at a location parameter of the distributions of the primary efficacy variable. But even if the location parameters are close to each other existing differences in variability may be connected with different risks for under or over treatment in an individual patient. Assuming normally distributed responses a multiple test procedure applying two shifted one-sided t-tests for the mean and accordingly two one-sided F-tests for the variances is proposed. Equivalence in location and variability is established if all four tests lead to a rejection at the (one-sided) level α. A conservative procedure “correcting” the t-tests for heteroscedasticity is derived. The choice of a design in terms of the global level α, the global power, the relevant deviations in the population means and variances, as well as the sample size is outlined. Numerical calculations of the actual level and power for the proposed designs show, that for balanced sample sizes the classical uncorrected one-sided t-tests can be used safely without exaggerating the global type I error probability. Finally an example is given.     

Conferences and symposia sponsored by the Aquatic Ecosystem Health and Management Society

Conferences and symposia sponsored by the Aquatic Ecosystem Health and Management Society     

Differentiation of Closely Related and Distant Human Populations by Multilocus DNA Fingerprinting

Using multilocus DNA fingerprinting with phage M13 DNA as a probe, we have investigated a heterogeneous group of four human populations from Eastern Europe and Northeastern Asia. These populations belong to two language families: Indo-European (Eastern Slavonic branch: Russians, Belarussians) and Altaian (Turkic branch: Yakuts). The experimental results were treated by different statistical techniques: cluster analysis, multidimensional scaling, and multiple correspondence analysis. Coefficients of genetic differentiation were estimated using similarity indices and heterozygosities. The results of our study demonstrated similarity of Belarussian populations and significant differences between the group of Slavonic populations and Yakuts.     

Phonetic Ability and Related Anatomy of the Newborn and Adult Human, Neanderthal Man, and the Chimpanzee

The sounds of human speech make human language a rapid medium of communication through a process of speech encoding. The presence of sounds like the vowels [a], [i], and [u] makes this process possible. The supralaryngeal vocal tracts of newborn Homo sapiens and chimpanzee are similar and resemble the reconstructed vocal tract of the fossil La Chapelle-aux-Saints Neanderthal man. Vocal tract area functions that were directed toward making best possible approximations to the human vowels [a], [i], and [u], as well as certain consonantal configurations, were modeled by means of a computer program. The lack of these vowels in the phonetic repertories of these creatures, who lack a supralaryngeal pharyngeal region like that of adult Homo sapiens, may be concomitant with the absence of speech encoding and a consequently linguistic ability inferior to modern man.     

Use of the Multinomial Dirichlet Model for Analysis of Subdivided Genetic Populations

The distribution found by compounding the multinomial distribution with the Dirichlet distribution has been suggested as a basis for the estimation of parameters in subdivided populations, in particular of the "correlation between genotypes" within subpopulations. It is shown that the estimators deriving from these procedures perform poorly when the data are generated by the classical Wright drift model of subdivided populations. This conclusion suggests that the compound distribution estimation approach does not provide a good estimation procedure for real populations which are reasonably described by the Wright model.     

Use of Yeast Populations Fractionated by Zonal Centrifugation to Study the Cell Cycle

Zonal centrifugation in a sucrose density gradient was used to separate yeast cells primarily by size and thus by age in the cell cycle. This approach provides an alternative to synchronous growth for examining the properties of cells at different stages in the cell cycle.