Statistical strategy for stereospecific hydrogen NMR assignments: Validation procedures for the floating prochirality method

Summary We examine the statistical and other considerations which determine the validity and reproducibility of stereospecific hydrogen NMR assignments obtained by the floating prochirality method. In this method, the assignment of a prochiral configuration of hydrogens at selected centers is allowed to float during the structure refinement, and the distribution of prochiral orientations in highly refined structures is subjected to statistical analysis. The underlying statistical basis for this approach is examined and potential limitations of current approaches are identified. As an example, approximately 1300 distance constraints obtained from NOESY spectra of oxidized horse cytochrome c have been used to examine several computational strategies. Repeated calculations were done by several different methods on both the whole molecule (104 residues plus heme) and on a 23-residue fragment containing two helices, a turn, and flanking residues. The results show that, even with NOE constraints alone, one third of the centers may be reproducibly assigned, provided appropriate precautions are taken. These precautions include adjustments for multiple statistical comparisons and characterization of statistical interactions between prochiral centers. The analysis demonstrates that inadequately constrained systems, such as fragments from a larger molecule, may produce misleading results, raising concerns about methods which rely solely on intraresidue and sequential interresidue contraints. A mathematical model describing interactions among prochiral centers is described and validated, and protocols for assignment and statistical validation are presented.     

Diversity of palmar pattern ridge counts in Iranian populations

We analyzed bilateral palmar prints of 3,158 individuals from 13 Iranian populations of diverse origins for palmar pattern ridge counts. Right palms did not show greater counts than the left in the majority of the populations studied. Highly significant interpopulational variation was observed for most palmar areas of both males and females. Dendrograms of males and combined sexes showed a good fit with the ethnohistoric background of the populations studied. The results thus demonstrate variation in the palmar pattern ridge counts of populations of diverse origins and may be used as a good measure of population distance.     

Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities

Summary A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways. Derivatives of the NOE intensities with respect to the dihedral angles are analytically calculated, and efficiently evaluated with the use of a filter technique for identifying the dominant terms of these derivatives. This new method was implemented in the distance geometry program DIANA. As an initial test, we refined 30 rigid distorted helical structures, using a simulated data set of NOE distance constraints for a rigid standard -helix. The final root-mean-square deviations of the refined structures relative to the standard helix were less than 0.1 Å, and the R-factors dropped from values between 7% and 32% to values of less than 0.5% in all cases, which compares favorably with the results from distance geometry calculations. In particular, because spin diffusion was not explicitly considered in the evaluation of exact¹H–¹H distances corresponding to the simulated NOE intensities, a group of nearly identical distance geometry structures was obtained which had about 0.5 Å root-mean-square deviation from the standard -helix. Further test calculations using an experimental NOE data set recorded for the protein trypsin inhibitor K showed that the complete relaxation matrix refinement procedure in the DIANA program is functional also with systems of practical interest.Abbreviations RMSD root-mean-square deviation - NOE nuclear Overhauser enhancement - NOESY 2-dimensional nuclear Overhauser enhancement spectroscopy - CPU central processing unit     

On the stochastic model for estimation of mutational distance between homologous proteins

Summary A set of simple equations is derived which gives the relationship between the observed amino acid differences per 100 codons and the evolutionary distance per 100 codons using Holmquist's stochastic model of molecular evolution.Contribution No. 910 from the National Institute of Genetics, Mishima, Shizuoka-ken 411 Japan.     

Feral donkey Equus asinus populations on the Karpaz peninsula, Cyprus

Numerous researchers have documented the adverse effects of feral donkeys Equus asinus introduced to semi-arid ecosystems. With the release of feral donkeys and potential increasing populations in natural habitats in northern Cyprus, there is concern for negative impacts on vegetation and native species. In the north of the island, there has been only one published study of feral donkey populations, and population estimators were relatively subjective. We estimated feral donkey populations on the Karpaz Peninsula using line transect surveys and quantitative distance sampling estimators. We stratified the sampling by using 11 sample units within the study area. We evaluated potential biases associated with habitat, topography, and perpendicular distance from the transect line and found that these variables did not bias donkey detections during our surveys. Using program DISTANCE, we found that a hazard rate cosine model was the best model that described our distance data based on model selection criterion (Akaikes Information Criteria adjusted for small sample bias). Estimated effective strip width was 280.19 m and detection probability was 0.47 with this model. Estimated donkey density was 6.7 donkeys/km², and estimated total abundance was 800 donkeys for the entire 132.5 km² study area. Of 95 donkey groups detected: 16% were detected in agricultural habitats with flat topography, 9% were detected in agricultural habitats with sloped topography, 24% were detected in shrub/forest habitats with flat topography, and 51% were detected in shrub/forest habitats with sloped topography. Of 102 behavioral observations recorded (multiple behaviors were detected in groups), frequencies of behaviors were 1% bedded, 70% standing, 22% grazing, 6% moving, and 2% other. Our estimated donkey population density in the Karpaz Peninsula was >2 times densities reported in arid regions of the United States and Australia, but slightly lower than earlier density estimates reported for the Karpaz region. These estimates of feral donkey populations in the Karpaz Peninsula provide a quantitative baseline from which to make population management decisions.     

Affinities between contemporary and skeletal Jewish and non-Jewish groups based on tooth morphology

Samples from five Jewish and six non-Jewish populations were compared in terms of the frequencies of 19 dental morphological variables. All but one of the samples came from Europe, North Africa, or the Middle East. Nine were from contemporary populations, and two were skeletal. Of the skeletal groups, one was Jewish, excavated on Mount Zion, Jerusalem, and dated at around 3,000 years old; and the other non-Jewish, excavated on the east coast of Australia, and dated at between 1,000 and 200 years old. Assessment of affinity between the different groups was based on smallest space analysis and cluster analysis. The results demonstrated relative proximity of the Jewish groups (with one exception), despite the fact that they came from a wide geographical area. In particular, the sample from Mount Zion showed greater affinity with three of the four living Jewish populations than with most non-Jewish groups. The skeletal Australian sample formed a cluster of its own, distinct from all the other groups. For six of the groups, the relationships based on tooth morphology showed good correspondence with known relationships based on single locus polymorphisms. The similarity of the Jewish groups to each other in terms of both tooth morphology and single locus polymorphisms was of special interest, since differences in other morphological and anthropometric characteristics, thought to be the result of selection, are known to exist between the Jewish populations.     

Empirical comparison of distance equations using discrete traits

The use of the Grewal-Smith statistic in measuring biological distance among skeletal population samples has been questioned since it was first applied to human populations. Recently, in an attempt to stabilize the variance of the Grewal-Smith statistic for use with non-metric analysis, Sjøvold ('73) and Green and Suchey ('76) have introduced corrections and alternative transformations which may enhance the meaning of biological distance among population samples. Their recommendations improve the statistics for specific variable ranges; i.e., small sample size and low trait frequencies. Thirteen equations representing Grewal-Smith, Freeman-Tukey, Anscombe, and Bartlett transformations and/or corrections, were compared using rank order correlation statistics on actual biological distances generated by real population data as presented in existing literature. Results from testing these actual distance models show little variation between equations based on the populational data sets used. Based on these findings, the distance model resulting from the Grewal-Smith statistic is not inferior to the more sophisticated models, although the latter may be superior by allowing specific improvements for small sample size and/or low trait frequencies.     

Predation by vertebrates and invertebrates on the seeds of five canopy tree species of an Amazonian forest

We studied the pre-germination loss of seeds to invertebrate and vertebrate seed predators of 5 species of Amazonian trees (Astrocaryum macrocalyx—Palmae; Bertholletia excelsa—Lecithydaceae; Calatola venezuelana—Icacinaceae; Dipteryx micrantha—Leguminosae (Papilionoidae); Hymenaea courbaril-Leguminosae (Caesalpinoidae)). These five species were selected from a large tree flora on several criteria. All possess large (3–10 cm) well-protected seeds that might plausibly be attractive to mammalian seed predators. The reproductive biology of three of the species, or close congeners, had been studied elsewhere in the Neotropics (Astrocaryum, Dipteryx, Hymenaea); one is important to the economy of southeastern Peru (Bertholletia); and one, despite large and apparently edible seeds, appeared to suffer no pre-germination loss to predators (Calatola). We conducted the research in mature forests in the Manu National Park of southeastern Peru where mammal densities are unperturbed by human activities. Densities of adult trees of the five species in our area range from very high (>30 per ha: Astrocaryum) to very low (1 per ha: Hymenaea).Loss of seeds to all causes, and to mammalian seed predators in particular, was determined for seeds placed in 2-square meter mammal exclosures and in open controls located at 10 m (near) and 50 m (far) from a large mature individual of the target species (with minor variations in the design for Astrocaryum and Calatola). The exclosures were of two types: impermeable—designed to exclude all mammals, but not invertebrate seed predators, and semipermeable—designed to admit small (<500 g), but not large mammals. Experimental and control plots were stocked with apparently viable seeds during the dry-wet transition period (October–November) and scored one year later.A significant distance effect (higher predation near vs far from a large conspecific adult) was found in only one of the species (Astrocaryum), the only one to be attacked with high frequency by invertebrate seed predators. The absence of any detectable distance effect attributable to mammals suggests that mammals, over the course of a year, thoroughly search the forest floor for seeds. Invertebrates may thus be responsible for most pre-germination distance (density) effects. With respect to the treatments, we found three qualitatively distinct results: seeds of three species (Astrocaryum, Bertholletia, Dipteryx) were significantly protected by the impermeable, but not semipermeable exclosures, implicating small mammals in seed loss; the seeds of one species (Hymenaea) were significantly protected by exclosures of both types, implicating large mammals; and the seeds of one species (Calatola) exhibited 100% survival, whether or not protected by exclosures.The importance of large mammals as seed predators is generally underestimated in these experiments because semipermeable exclosures may serve as foraging reserves for small mammals. Finally, we noted no relationship between the intensity of mammalian seed predation (as suggested by the survival of unprotected seeds) and the abundance of adults of the five species in the environment. The diversity of results obtained for the five species reveals that large-seeded tropical trees may display a wide range of demographic patterns, and points to the likely importance of post-germination bottlenecks in the population biology of many species, even those that may experience severe pre-germination seed loss.     

Spatial pattern changes of grazing cattle population I

A cattle population presents three spatial patterns according to their behaviour. These patterns are as follows: the random spatial pattern which occurs when the cattle move during grazing (feeding), the aggregated spatial pattern which occurs when they rest, and the regular or quasi-regular spatial pattern which occurs when they separate into two or more subgroups. In this study, these three states of behaviour were represented by a mathematical model, and a method to test the pattern statistically was derived.