The taxonomic implications of cranial shape variation in Homo erectus

The taxonomic status of Homo erectus sensu lato has been a source of debate since the early 1980s, when a series of publications suggested that the early African fossils may represent a separate species, H. ergaster. To gain further resolution regarding this debate, 3D geometric morphometric data were used to quantify overall shape variation in the cranial vault within H. erectus using a new metric, the sum of squared pairwise Procrustes distances (SSD). Bootstrapping methods were used to compare the H. erectus SSD to a broad range of human and nonhuman primate samples in order to ascertain whether variation in H. erectus most clearly resembles that seen in one or more species. The reference taxa included relevant phylogenetic, ecological, and temporal analogs including humans, apes, and both extant and extinct papionin monkeys. The mean cranial shapes of different temporogeographic subsets of H. erectus fossils were then tested for significance using exact randomization tests and compared to the distances between regional groups of modern humans and subspecies/species of the ape and papionin monkey taxa. To gauge the influence of sexual dimorphism on levels of variation, comparisons were also made between the mean cranial shapes of single-sex samples for the reference taxa. Results indicate that variation in H. erectus is most comparable to single species of papionin monkeys and the genus Pan, which included two species. However, H. erectus encompasses a limited range of variation given its extensive geographic and temporal range, leading to the conclusion that only one species should be recognized. In addition, there are significant differences between the African/Georgian and Asian H. erectus samples, but not between H. ergaster (Georgia+Africa, excluding OH 9 and Daka) and H. erectus sensu stricto. This finding is in line with expectations for intraspecific variation in a long-lived species with a wide, but probably discontinuous, geographic distribution.     

A Study of Log-Logistic Model in Survival Analysis

In survival analysis when the mortality reaches a peak after some finite period and then slowly declines, it is appropriate to use a model which has a nonmonotonic failure rate. In this paper we study the log-logistic model whose failure rate exhibits the above behavior and its mean residual life behaves in the reverse fashion. The maximum likelihood estimation of the parameters is examined and it is proved analytically that unique maximum likelihood estimates exist for the parameters. A lung cancer data set is analyzed. Confidence intervals for the parameters as well as for the critical points of the failure rate and mean residual life functions are obtained for the high performance status (PS) and low PS subgroups, where the term performance status is a measure of general medical status.     

Experimental analysis of variance for DNA hybridization: II. Precision

Using DNAs from the Virginia opossum (Didelphis virginiana), we estimated the variance components for two classes of replicate hybrids: different drivers matched to the same tracer and different homoduplexes made from tracers matched to identical drivers. A nested analysis of variance (ANOVA) was used to partition total variance among four levels: Individuals, extracts, preparations, and different aliquots from the same preparation. The variance contributed by these levels depended on the kind of hybrid replicate (driver or tracer) and on the index of thermal stability (T_mode, T_m, T₅₀H, or Normalized Percentage Hybridization). For replicate drivers, significant variance contributions were made by (1) individuals to T_m, (2) extracts to T_mode and NPH but not T_m, and (3) different preparations to NPH. The composite T₅₀H measure calculated from both T_m and NPH revealed effects from both constituent indices. For replicate tracers, preparation error was the single most consistent effect across all indices, followed by extract effects for those indices that incorporated a measure of percent hybridization (T₅₀H NPH). Total variance of the four indices was qualitatively similar for both drivers and tracers: T_mode ranked lowest, followed in order by T_m, T₅₀H, and NPH, with the variance of NPH being as much as 100 times greater than for T_mode. These results provide guidelines for the design of experiments to generate DNA hybridization-based phylogenies and to assess their robustness with bootstrapping. Replicate drivers for a distance matrix based on T_m should use different individuals, whereas one based on T_mode could minimally use different extracts from the same individual. Thus, T_mode may be the index of choice for DNA hybridization experiments when material, time, and money are limited.Correspondence to: R. Bleiweiss     

The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus

Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much controversy and speculation. Here we present the first cDNAs of nuclear protein genes from red algae: Those encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from Chondrus crispus. A phylogenetic analysis including GAPDH gene sequences from a number of eukaryotic taxa, cyanobacteria, and purple bacteria suggests that chloroplasts and rhodoplasts together form a monophyletic group of cyanobacterial descent and that rhodophytes separated from chlorophytes at about the same time as animals and fungi. The composite GAPDH tree further demonstrates that chloroplast and cytosolic GAPDH genes are closely related to their homologs in cyanobacteria and purple bacteria, respectively, the presumptive ancestors of chloroplasts and mitochondria, thereby firmly establishing the endosymbiotic origin of these nuclear genes and their fixation in eukaryotic cells before the rhodophyte/chlorophyte separation. The present data are in conflict with phylogenetic inferences based on plastid-encoded rbcL sequences supporting a polyphyletic origin of rhodoplasts and chloroplasts. Comparison of rbcL to GAPDH phylogenies suggests that rbcL trees may be misleading because they are composed of branches representing ancient duplicated (paralogous) genes. Correspondence to: R. Cerff     

Multivariate Association and Dimension Reduction: A Generalization of Canonical Correlation Analysis

Summary In this article, we propose a new generalized index to recover relationships between two sets of random vectors by finding the vector projections that minimize an L ₂ distance between each projected vector and an unknown function of the other. The unknown functions are estimated using the Nadaraya–Watson smoother. Extensions to multiple sets and groups of multiple sets are also discussed, and a bootstrap procedure is developed to detect the number of significant relationships. All the proposed methods are assessed through extensive simulations and real data analyses. In particular, for environmental data from Los Angeles County, we apply our multiple‐set methodology to study relationships between mortality, weather, and pollutants vectors. Here, we detect existence of both linear and nonlinear relationships between the dimension‐reduced vectors, which are then used to build nonlinear time‐series regression models for the dimension‐reduced mortality vector. These findings also illustrate potential use of our method in many other applications. A comprehensive assessment of our methodologies along with their theoretical properties are given in a Web Appendix.     

Nonparametric One‐way Analysis of Variance of Replicated Bivariate Spatial Point Patterns

A common problem in neuropathological studies is to assess the spatial patterning of cells on tissue sections and to compare spatial patterning between disorder groups. For a single cell type, the cell positions constitute a univariate point process and interest focuses on the degree of spatial aggregation. For two different cell types, the cell positions constitute a bivariate point process and the degree of spatial interaction between the cell types is of interest. We discuss the problem of analysing univariate and bivariate spatial point patterns in the one‐way design where cell patterns have been obtained for groups of subjects. A bootstrapping procedure to perform a nonparametric one‐way analysis of variance of the spatial aggregation of a univariate point process has been suggested by Diggle, Lange and Bene? (1991). We extend their replication‐based approach to allow the comparison of the spatial interaction of two cell types between groups, to include planned comparisons (contrasts) and to assess whole groups against complete spatial randomness and spatial independence. We also accommodate several replicate tissue sections per subject. An advantage of our approach is that it can be applied when processes are not stationary, a common problem in brain tissue sections since neurons are arranged in cortical layers. We illustrate our methods by applying them to a neuropathological study to investigate abnormalities in the functional relationship between neurons and astrocytes in HIV associated dementia. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Plant neighbour diversity

Abstract. Neighbour diversity is the diversity of other plant species contacting a reference species. The expected value and confidence intervals of neighbour diversity assuming random contacts can be found using bootstrapping. In general, frequent species have higher expected neighbour diversities with narrow confidence intervals than infrequent species. In fixed sand dunes dominated by lichens and bryophytes most species have lower than expected neighbour diversity. However, the fixed sand dunes seem to be a mixture of two patch types, with the species in lichen-rich patches having higher diversities than the species in bryophyte-rich patches. In hay pastures, nearly all species have lower than expected neighbour diversities. The more frequent the species is, the less is its expected neighbour diversity. This implies that its frequent species are selective as to their neighbours, and so they drive a biological formation of spatial pattern.     

Visual data analysis and decision support methods for non-deterministic LCA

Principal components analysis coupled with non-parametric bootstrapping is introduced with an example as a powerful tool to help visualise, analyse and decide on comparative or single non-deterministic LCI/LCIA results. Decision support is provided by adding non-parametric bootstrapping (NPB) to the GA1A plane, which is a special case of principle comments analysis (PCA) built around the Promethée multicriteria decision aid model. In addition to an easy to analyse visual presentation of otherwise complex and cluttered numerical results, PCA with NPB is equally at ease will all data uncertainty formats used to date in LCA.     

The Leinster and Cobbold indices improve inferences about microbial diversity

An increasing number of ecological studies compare the diversity of microbial taxa along environmental gradients or between imposed treatments. Estimates are often based on analysis-of-variance of taxon-richness inferred from pyrosequencing data. We conducted a reanalysis of three 454-pyrosequencing studies on arbuscular-mycorrhizal-fungal diversity to evaluate the suitability of using the Leinster and Cobbold diversity-indices (LCdis) to assess diversity. We expected that the potential of LCdis to consider phylogenic relationships could resolve problems arising from ambiguous species-delineation in microbial-systems. Our reanalysis showed that comparisons between studies differing considerably in sequencing depth may be risky. Moreover, we show that LCdis not only reproduce the results of analyses of variance but can also resolve issues connected to variation in sequence read number, while additionally representing a less conservative metric of diversity than analysis-of-variance of taxa-richness. Based on these results we advocate the use of inclusive diversity indices in ecological studies targeting microbial communities.     

Estimating the Power of the Gehan Test

A bootstrap method suggested by COLLINGS and HAMILTON (1988) to estimate the power of the two-sample Wilcoxon test is adapted to use for estimating the power of the Gehan test. A Monte Carlo simulation study is done to determine how well the method works in this case.