STATISTICAL ANALYSIS OF HETEROZYGOSITY DATA: INDEPENDENT SAMPLE COMPARISONS

The distribution of mean heterozygosities under an infinite allele model with constant mutation rate was examined through simulation studies. It was found that, although the variance of the distribution decreases with increasing numbers of loci examined as expected, the shape of the distribution may remain skewed or bimodal. The distribution becomes symmetrical for increasing mean heterozygosity levels and numbers of loci. As a result, parametric statistical tests may not be valid for making comparisons among populations or species. Independent sample t-tests were examined in detail to determine the frequency of rejection of the null hypothesis when pairs of samples are drawn from populations with the same mean heterozygosity. Differing numbers of loci and levels of mean heterozygosity were examined. For mean heterozygosity levels above 7.5%, t-tests provide the proper rejection rate, with as few as five loci. When mean heterozygosity is as low as 2.5%, the t-test is conservative even when 40 loci are examined in each population. Independent sample t-tests were then examined for their power to detect true differences between populations as the degree of difference and number of loci vary. Although large differences can be found with high certainty, differences on the order of 5% heterozygosity may require that large numbers of loci (>40) be examined in order to be 80% or more certain of detecting them. In addition, it is emphasized that, for small numbers of loci (<25), the statistical detection of differences of interesting magnitude requires that relatively rare sampling events occur and that much larger differences be observed among the samples than exist for the population means. Two reasons exist for the lack of sensitivity of the test procedures. First, when mean heterozygosity levels are low, the non-normality of the sample means is perhaps most important. Second, even when mean heterozygosity levels are high or when sample sizes are large enough so sample means are approximately normally distributed, the intrinsically high interlocus variance of heterozygosity estimates makes the tests insensitive to the presence of heterozygosity differences that might be biologically meaningful. Finally, the implications of the results of this study are discussed with regard to observed low levels of correlation between heterozygosity and other explanatory variables.     

Further analysis of mandibular molar crown and cusp areas in Pliocene and early Pleistocene hominids

Crown and cusp areas of mandibular molars were measured and analyzed on a sample of 249 specimens attributed to Australopithecus afarensis, A. africanus, A. (Paranthropus) robustus, A. (P.) boisei, and early Homo. In addition to intertaxon comparisons, we compared data that had been collected independently by two of the authors using methods that differ slightly in technique of measurement. Interobserver differences were evaluated by the t-test of paired comparisons, method error statistic, percent differences, and principal component analysis. Results suggest that between-technique error of measurement of overall crown area is small. Error estimates for individual cusp area measurements were of larger relative magnitude. However, these were not sufficient to detract from the conclusions derived from comparative analyses. Our results are in general agreement with previous assessments of early hominid dental size. Crown areas of A. africanus, however, exhibit a mosaic pattern, with M1 similar in size to that of A. afarensis and early Homo, and M2 and M3 similar in size to that of A. robustus. Intertaxon comparisons of relative cusp area were undertaken by univariate statistics and principal component analysis. These analyses revealed that while A. (P.) robustus and A. (P.) boisei both possess mandibular molars with cusp proportions significantly different from the ‘non-robust’ taxa, these differences are substantially greater in A. (P.) boisei. © 1994 Wiley-Liss, Inc.     

Inter- and intra-specific differences in filtering activities between two unionids, Anodonta woodiana and Unio douglasiae, in ambient eutrophic lake waters

Inter-specific and intra-specific differences in the filtering activities of two unionid bivalves, Unio douglasiae and Anodonta woodiana, which thrive in small agricultural canals, were compared using a flow-through chamber system of ambient eutrophic lake water. The mean filtration rates (FRs) of these two species, size-matched for similar shell length, were not significantly different (t-test, t = 0.024, P = 0.981), whereas there were significant differences in the FRs between mussels of different ages (t-test, t = 5.137, P = 0.001), different densities (t-test, t = 8.297, P < 0.0001), and different currents (t-test, t = 3.898, P = 0.005). The FRs of A. woodiana increased significantly more with higher temperatures in younger mussels (P < 0.01, maximum FR = 0.352 ± 0.157 L/h at 13.5–20.4 °C) than in adults. However, the mortality of the mussels was comparatively higher in younger mussels due to a low tolerance to ammonia. Correlation coefficients and PCA results collectively indicate that the two dominant unionid mussels in the canal had a strong relationship with the seston level in the lake (turbidity, suspended solids and chlorophyll-a), resulting in a higher FR, pseudo-faeces production, and ammonia tolerance and a lower mortality. In addition, the validation of the biomanipulation used in the mussel-controlled system is discussed in an effort to improve the water quality of eutrophic lakes and streams and the conservation of the benthic mussel community.     

Robustness of Statistical Tests in the Two-Sample Location Problem

A simulation study was performed to compare three statistical tests with respect to their performances in the two-sample location problem for contaminated normal distributions. The three tests were: the t-test, the rank-transformed t-test, and the Wilcoxon rank-sum test. The results showed the t-test to be inferior to the other two tests.     

Sample Sizes for Comparisons of k Treatments with a Control Based on Different Definitions of the Power

The determination of sample sizes for the comparison of k treatments against a control by means of the test of Dunnett (1955, 1964) as well as by means of the multiple t-test will be considered. The power in multiple comparisons can be defined in different ways, see Hochberg and Tamhane (1987). We will derive formulas for the per-pair power, the any-pair power and the all-pairs power for both one- and two-sided comparisons. Tables will be provided that allow sample sizes to be determined for preassigned values of the power.     

Phenotypic plasticity in age and size at maturity and its effects on the integrated phenotypic expressions of life history traits of Cardamine flexuosa (Cruciferae)

We analyzed variation in phenotypic plasticity of life history traits between two Cardamine flexuosa populations based on differences in plasticity of age and size at maturity. C. flexuosa (Cruciferae) is a facultative, vernalization-sensitive, long-day annual, and its phenology and the phenotypic expressions of many life history traits are largely controlled by photoperiod and vernalization in natural populations. We used plants from two populations which differed in their responses to chilling and photoperiod treatments. The timing of developmental processes was changed by controlling temperature and photoperiod regimes in growth chambers. Plasticity in size at maturity was analyzed as changes in a growth trajectory using two parameters, age at maturity (Δt) and growth rate (k). Both traits showed plasticity, but differences between the populations were found mostly for Δt. Distinctive differences in size at maturity of individuals in the two populations were mainly due to different amounts of plasticity in Δt. Variations in plasticity of nine other life history traits and their associations to age and size at maturity were also analyzed. Variation for eight of the traits can be described, at least in part, as a function of age and size at maturity for both populations, and most of the variation in the total number of seeds was explained by age and size at maturity. Only age at maturity had any effect on changes in resource allocation. The nine life history traits were integrated through associated character expressions with age and size at maturity. Changes in the association between a trait and age and/or size at maturity were rather conservative compared to changes in the plasticity of a trait between the two populations. Associations with age and size at maturity are mostly explicable in terms of inherent relationships in the developmental processes, and they may limit the ecological range expansion and the adaptive evolution of plasticity in C. flexuosa. The negative correlation between reproductive allocation and age at maturity can be a cost of delaying maturation in C. flexuosa.     

Nucleotide variation at the dopa decarboxylase (<Emphasis Type="Italic">Ddc</Emphasis>) gene in natural populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.     

Comparing short protein substructures by a method based on backbone torsion angles

An efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes Δt, the root mean square difference in ? and ψ torsion angles over a small number of amino acids (typically 3–5). Using this algorithm, large number of protein substrates comparisons were feasible. The parameter Δt was sensitive to variations in local protein conformation, and it correlates with Δr, the root mean square deviation in atomic coordinates. Values for Δt were obtained that define similarity thresholds, which determine whether two substructure are considered structurally similar. To set a lower bound on the similarity threshold, we estimated the component of Δt due to measurement noise fromcomparisons of independently refined coordinates of the same protein. A sample distribution of Δt from nonhomologous protein comparisons identified an upper bound on the similarity threshold, one that refrains from incorporating large numbers of nonmatching comparisons large numbers of nonmatching comparisons. Unlike methods based on Cα atoms alone, Δt was sensitive to rotations in the peptide plane, shown to occur in several proteins. Comparisons of homologus proteins by Δt showed that the active site torsion angles are highly conserved. The Δt method was applied to the α-chain of human hemoglobin, where it readily demonstrated the local differences in the structures of different ligation states.     

Mating system parameters and population genetic structure in pioneer populations of Prosopis velutina (Leguminosae)

This study describes the genetic structure and provides estimates of mating system parameters in three natural populations of Prosopis velutina Woot. in southeastern Arizona. F statistics derived from isozyme data revealed the presence of both interpopulation and intrapopulation genetic differentiation. This population structure is discussed in relation to the ecological history of these populations that invaded the grasslands sites from adjacent riparian areas within the last 90 years, and possible modes of seed dispersal. The multilocus estimation program MLT of Ritland (Journal of Heredity 8: 235–237, 1990) was used to provide estimates of t_s, t_m, and the fixation index (F) of the maternal parents. Average estimates of t_s ranged from 0.591 to 0.912. Estimates of t_m ranged from 0.609 to 1.004, and averaged 0.758. The difference between t_m and t_s, which provides a measure of biparental inbreeding, averaged 0.058. This last result, together with significant heterogeneity found in pollen allele frequencies, suggests that a family structure has developed in the populations. A negative F value for one of the populations suggests selection against homozygotes between the seedling stage and maturity.     

DEVELOPMENTAL STABILITY IN LEAVES OF CLARKIA TEMBLORIENSIS (ONAGRACEAE) AS RELATED TO POPULATION OUTCROSSING RATES AND HETEROZYGOSITY

Four natural populations of Clarkia tembloriensis, whose levels of heterozygosity and rates of outcrossing were previously found to be correlated, are examined for developmental instability in their leaves. From the northern end of the species range, we compare a predominantly selfing population (t? = 0.26) with a more outcrossed population (t? = 0.84), which is genetically similar. From the southern end of the range, we compare a highly selfing population (t? = 0.03) with a more outcrossed population (t? = 0.58). We measured developmental stability in the populations using two measures of within-plant variation in leaf length as well as calculations of fluctuating asymmetry (FA) for several leaf traits. Growth-chamber experiments show that selfing populations are significantly more variable in leaf length than more outcrossed populations. Developmental instability can contribute to this difference in population-level variance. Plants from more homozygous populations tend to have greater within-plant variance over developmentally comparable nodes than plants from more heterozygous populations, but the difference is not significant. At the upper nodes of the plant, mature leaf length declines steadily with plant age, allowing for a regression of leaf length on node. On average, the plants from more homozygous populations showed higher variance about the regression (MSE) and lower R² values, suggesting that the decline in leaf length with plant age is less stable in plants from selfing populations than in plants from outcrossing populations. Fluctuating asymmetry (FA) was calculated for four traits within single leaves at up to five nodes per plant. At the early nodes of the plant where leaf arrangement is opposite, FA was also calculated for the same traits between opposite leaves at a node. Fluctuating asymmetry is significantly greater in the southern selfing population than in the neighboring outcrossed population. Northern populations do not differ in FA. Fluctuating asymmetry can vary significantly between nodes. The FA values of different leaf traits were not correlated. We show that developmental stability can be measured in plants using FA and within-plant variance. Our data suggest that large differences in breeding system are associated with differences in stability, with more inbred populations being the least stable.     

LOW FREQUENCY OF t HAPLOTYPES IN NATURAL POPULATIONS OF HOUSE MICE (MUS MUSCULUS DOMESTICUS)

t haplotypes are a naturally occurring, autosomal, meiotic-drive system found on chromosome 17 of the house mouse. They show non-Mendelian transmission from heterozygous +/t males, such that 90% or more of the male's offspring inherit the t-bearing chromosome. Although they are expected to become rapidly fixed, surveys of natural populations typically report low overall frequencies of only ~15–25% +/t heterozygotes. Generally, such studies of t haplotypes in wild populations have sampled only small numbers of individuals due to the need to genotype mice by breeding, thus we have conducted a large survey of wild mice, Mus musculus domesticus, using DNA markers to examine the frequency and distribution of t haplotypes in natural populations. The overall frequency of +/t heterozygotes from our entire sample was 0.062, which is much lower than all previous estimates of t haplotype frequency. t haplotypes were patchily distributed and rare, and were present in only 46% of the populations we sampled. There were no significant sex-specific differences in the frequency of t haplotypes. Our data suggest that the frequency of +/t heterozygotes in independent populations varies with respect to population size and stability: t haplotypes were at low frequency in all large, relatively persistent populations, whereas they were at more variable, and often higher, frequencies in small, temporally unstable populations. The extinction and recolonization of many of the smaller populations may contribute to the greater variation in t haplotype frequency observed, and small populations may be important reservoirs of t haplotypes in the wild. The highest frequencies of t haplotypes were obtained from populations with semilethal, or complementing lethal, t haplotypes, where t/t homozygous mice were present.     

Gender determination by body weight and linear measurements in American and Chilean flamingos,previously surgically sexed: Within-sex comparison to greater flamingo measurements

Gender was determined by laparoscopic visualization of the gonads for 38 adult American flamingos (Phoenicopterus ruber ruber L.) and 36 adult Chilean flamingos (P. chilensis L.). Concomitant body weight (kg) and linear measurements (mm) of the culmen (bill), tarsus (tarsometatarsus), middle toe, and wing were taken. Statistical comparisons of body weight and linear measurements for male vs. female were made for each species. Also, the same-sex statistical comparisons were made between these two species, and between each of these two species and with data for greater flamingos (P. r. roseas L.) from a previous publication. As previously published for greater flamingos, an overlap between sexes existed in all measurements with males on average larger than females for both American and Chilean flamingos. However, Students' t-test indicated a significant sexual difference for all measurements between males and females of each species except for culmen length in Chilean flamingos. Students' t-test also indicated a significant difference when species were compared (Chilean vs. greater, and American vs. Chilean) and subspecies (American vs. greater) were compared for most of the 5 measurements. Thus, despite limitations imposed by between-sex overlap, weights and linear measurements, especially tarsus, middle toe, and wing length, appear to be useful in determining an individual's gender when species or subspecies identification is considered.     

Population transcriptomics: insights from <Emphasis Type="Italic">Drosophila simulans,</Emphasis><Emphasis Type="Italic">Drosophila sechellia</Emphasis> and their hybrids

Sequence differentiation has been widely studied between populations and species, whereas interest in expression divergence is relatively recent. Using microarrays, we compared four geographically distinct populations of Drosophila simulans and a population of Drosophila sechellia, and interspecific hybrids. We observed few differences between populations, suggesting a slight population structure in D. simulans. This structure was observed in direct population comparisons, as well as in interspecific comparisons (hybrids vs. parents, D. sechellia vs. D. simulans). Expression variance is higher in the French and Zimbabwean populations than in the populations from the ancestral range of D. simulans (Kenya and Seychelles). This suggests a large scale phenomenon of decanalization following the invasion of a new environment. Comparing D. simulans and D. sechellia, we revealed 304 consistently differentially expressed genes, with striking overrepresentation of genes of the cytochrome P450 family, which could be related to their role in detoxification as well as in hormone regulation. We also revealed differences in genes involved in Juvenile hormone and Dopamine differentiation. We finally observed very few differentially expressed genes between hybrids and parental populations, with an overrepresentation of X-linked genes.     

An ex vivo readout for evaluation of dendritic cell-induced autologous cytotoxic T lymphocyte responses against esophageal cancer

Esophageal cancer is a highly malignant disease that despite surgery and adjuvant therapies has an extremely poor outcome. Dendritic cell (DC) immunotherapy as a novel promising strategy could be an alternative for treating this malignancy. Effective DC-mediated immune responses can be achieved by raising cytotoxic T lymphocyte (CTL) response against multiple antigens through loading DCs with total tumor RNA. However, the efficacy of this strategy first needs to be evaluated in a pre-clinical setting. The aim of the study was to set up an ex vivo autologous human readout assay for assessing the effects of DC-mediated cytotoxic responses, using total tumor RNA as an antigen load. Biopsy specimens of seven esophageal cancer patients were used to establish primary cultures of normal and cancer cells and to obtain autologous RNA for loading DCs. Mature DCs loaded with either normal or tumor RNA were obtained and subsequently used to raise various lymphocytes populations. Apoptosis levels of the autologous cultures were measured before and after incubating the cultures with the different lymphocytes populations. The mean apoptosis levels in the tumor cell cultures, induced by lymphocytes instructed by DCs loaded with tumor RNA, significantly increased with 15.6% ±2.9 SEM (range 3.4–24.5%, t-test, P < 0.05). Incubation of the normal cultures with the lymphocytes populations showed a mean non-significant increase in apoptosis of 0.4% ±3.4 SEM (range −13.9 to 9.8%, t-test, P = 0.7). Here, we introduce a practical, patient-specific autologous readout assay for pre-clinical testing of DC-mediated cytotoxic responses. Additionally, we demonstrated that the use of autologous tumor RNA as a strategy for raising cytotoxic responses against multiple tumor antigens could be effective for treating esophageal cancer. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On the WILCOXON-MANN-WHITNEY-Test as Nonparametric Analogue and Extension of t-Test

In the present paper some basic aspects of the WILCOXON -MANN -WHITNEY -test under various assumptions concerning the underlying distributions are studied. Starting with a formal analogy to Student's t-test its specific sensibility is worked out and the connexion to the problem of testing differences in location is discussed in detail as well as to the model with ordered alternatives. Further a counter example is given showing that the common verbal formulation the WILCOXON -MANN -WHITNEY -test being a test on ‘differences in distribution’ in general is misleading. As an example of an extended application of the WILCOXON -MANN -WHITNEY -statistic the test of POTT-HOFF (1963) on differences in medians of symmetric distributions is treated together with a discussion on suitable variance estimators to guarantee appropriate asymptotic distribution.     

Mutant allele frequencies in domestic cat populations on the Spanish Mediterranean coast,and their genetic distances from other European and North African cat populations

New genetic profiles of domestic cat populations were studied in different parts of the Spanish Mediterranean coast. The t ^b frequency is the most outstanding differentiated factor between the populations analyzed. The low t ^b frequencies found in Barcelona and other Catalan localities are the most important characteristic of these populations and, probably, find an explanation in the extraordinarily high historical and commercial relationships between Barcelona and the Eastern Mediterranean (Greece, especially) during the 14th and 15th centuries. In other Spanish Mediterranean littoral cities the t ^b frequencies reach higher values and are more similar to those found in other Western European cat populations. Significant differences found in certain allelic frequencies (Orange and Blotched) caused by the urban-rural effect are discovered between Barcelona and two nearby rural cat populations.     

Evolutionary Diversification of Continuous Traits: Phylogenetic Tests and Application to Seed Size in the California Flora

Evolutionary diversification of a phenotypic trait reflects the tempo and mode of trait evolution, as well as the phylogenetic topology and branch lengths. Comparisons of trait variance between sister groups provide a powerful approach to test for differences in rates of diversification, controlling for differences in clade age. We used simulation analyses under constant rate Brownian motion to develop phylogenetically based F-tests of the ratio of trait variances between sister groups. Random phylogenies were used for a generalized evolutionary null model, so that detailed internal phylogenies are not required, and both gradual and speciational models of evolution were considered. In general, phylogenetically structured tests were more conservative than corresponding parametric statistics (i.e., larger variance ratios are required to achieve significance). The only exception was for comparisons under a speciational evolutionary model when the group with higher variance has very low sample size (number of species). The methods were applied to a large data set on seed size for 1976 species of California flowering plants. Seven of 37 sister-group comparisons were significant for the phylogenetically structured tests (compared to 12 of 37 for the parametric F-test). Groups with higher diversification of seed size generally had a greater diversity of fruit types, life form, or life history as well. The F-test for trait variances provides a simple, phylogenetically structured approach to test for differences in rates of phenotypic diversification and could also provide a valuable tool in the study of adaptive radiations.     

Genetic diversity of Eucalyptus hybrids estimated by genomic and EST microsatellite markers

The knowledge of breeding impacts on the genetic diversity of hybrids of Eucalyptus is crucial to the exploration of genetic resources. We estimated genetic polymorphic parameters of 112 hybrids of Eucalyptus spp. using 10 genomic simple sequence repeats (SSR) markers and 10 expressed sequence tags (EST) microsatellite markers. According to Student’s t-test, there were no significant differences between genomic SSR and EST-SSR markers. Our results also revealed high polymorphism in the hybrids analyzed, indicating that both markers are appropriate for use in genetic breeding programs.     

The effects of selection,drift and genetic variation on life‐history trait divergence among insular populations of natterjack toad,Bufo calamita

Although loss of genetic variation is frequently assumed to be associated with loss of adaptive potential, only few studies have examined adaptation in populations with little genetic variation. On the Swedish west coast, the northern fringe populations of the natterjack toad Bufo calamita inhabit an atypical habitat consisting of offshore rock islands. There are strong among‐population differences in the amount of neutral genetic variation, making this system suitable for studies on mechanisms of trait divergence along a gradient of within‐population genetic variation. In this study, we examined the mechanisms of population divergence using Q_ST–F_ST comparisons and correlations between quantitative and neutral genetic variation. Our results suggest drift or weak stabilizing selection across the six populations included in this study, as indicated by low Q_ST–F_ST values, lack of significant population × temperature interactions and lack of significant differences among the islands in breeding pond size. The six populations included in this study differed in both neutral and quantitative genetic variation. Also, the correlations between neutral and quantitative genetic variation tended to be positive, however, the relatively small number of populations prevents any strong conclusions based on these correlations. Contrary to the majority of Q_ST–F_ST comparisons, our results suggest drift or weak stabilizing selection across the examined populations. Furthermore, the low heritability of fitness‐related traits may limit evolutionary responses in some of the populations.     

MATING SYSTEM IN NATURAL POPULATIONS OF JEFFREY PINE

The mating system and allozyme variation at 20 loci in three Klamath Mountains and two Sierra Nevada populations of Jeffrey pine (Pinus jeffreyi Grev. & Balf.) were investigated. On average, multilocus estimates of the proportion of viable progeny due to outcrossing (t_m) were high in all populations (mean t_m = 0.935, range 0.881 to 0.971). Despite differences in stand structure, t_m did not differ (P > 0.05) between the Klamath (mean t_m = 0.933) and Sierra Nevada (mean t_m = 0.937) populations. At all but one locus in one population and at two in another, genotype frequencies fit (P > 0.05) Hardy-Weinberg expectations. Mean estimates of observed heterozygosity in Klamath (0.182) and Sierra Nevada (0.327) populations were comparable to values reported for other conifers.