Male and Female Reproductive Success in <Emphasis Type="Italic">Macaca sylvanus</Emphasis> in Gibraltar: No Evidence for Rank Dependence

The relationship between social rank and reproductive success is one of the key questions for understanding differences in primate social group structures. We determined the paternity of 18 infants in a social group of Barbary macaques (Macaca sylvanus) born over a period of 6 yr in the provisioned, free-ranging colony in Gibraltar. We successfully used 13 pairs of primers of variable microsatellite loci to amplify DNA from blood and hair samples and applied the computer programs CERVUS 2.0 and KINSHIP 1.3 to assign paternity to 13 candidate males. We collected data for 19 females that had given birth to 66 infants over a period of 7 yr. We used paternity analyses and female birth records to test the hypothesis that social rank is correlated with reproductive success. Results showed that numbers of paternities and maternities were equally distributed among all reproducing individuals in the social group regardless of rank. Subadult males reproduced as often as adult males. High-ranking females did not start to reproduce earlier than low-ranking females. Interestingly, there was a tendency toward a positive correlation between the ranks of mothers and the ranks of the corresponding fathers. It might be concluded either that a correlation between social rank and reproductive success is generally absent in Barbary macaques or that artificially favorable environmental conditions in Gibraltar preclude any correlation between social rank and reproductive success.     

An intrinsic rank test for k independent samples

Considerations on the sensitivity of the KRUSKAL-WALLIS Analysis of Variance by Ranks suggest an alternative method that is less sensitive to spurious interchange of ranks and tied ranks yet offers sufficient power. The Intrinsic Rank Test for k Independent Samples is proposed in this sense as an alternative method to the KRUSKAL- WALLIS test. The Intrinsic Rank Test is based on rank information, but the criterion ranks (intrinsic ranks) are not directly derïved from the observations, but rather indirectly, by means of a further transformation, from the ordinal ranks assigned in the usual manner. The incidence of the intrinsic ranks upon the k samples is then used to calculate a X²-like test statistic, which is readily evaluated with the Gamma distribution.     

The Nonparametric Behrens‐Fisher Problem: Asymptotic Theory and a Small‐Sample Approximation

A generalization of the Behrens‐Fisher problem for two samples is examined in a nonparametric model. It is not assumed that the underlying distribution functions are continuous so that data with arbitrary ties can be handled. A rank test is considered where the asymptotic variance is estimated consistently by using the ranks over all observations as well as the ranks within each sample. The consistency of the estimator is derived in the appendix. For small samples (n₁, n₂ ≥ 10), a simple approximation by a central t‐distribution is suggested where the degrees of freedom are taken from the Satterthwaite‐Smith‐Welch approximation in the parametric Behrens‐Fisher problem. It is demonstrated by means of a simulation study that the Wilcoxon‐Mann‐Whitney‐test may be conservative or liberal depending on the ratio of the sample sizes and the variances of the underlying distribution functions. For the suggested approximation, however, it turns out that the nominal level is maintained rather accurately. The suggested nonparametric procedure is applied to a data set from a clinical trial. Moreover, a confidence interval for the nonparametric treatment effect is given.     

A Generalized Intrinsic Rank Test for k Independent Samples

The original intrinsic rank test is generalized in that the sizes of the k samples may now be arbitrary, and the number of intrinsic rank intervals need not equal the number of samples. Furthermore, the size of these intervals can be made variable, subject only to relatively mild constraints. These generalizations permit the formulation and testing of more specific hypotheses concerning the commonality of the sample distributions. A generalized intrinsic rank function is used to transform the usual ordinal ranks, obtained from the combined samples, into intrinsic ranks. Original sample identity and intrinsic ranks are then cross-tabulated and evaluated as 2-way contingency table.     

The Matched Pairs Problem with Exponential Variates

Two classes of tests for the hypothesis of bivariate symmetry are studied. For paired exponential survival times (t_1j, t_2j), the classes of tests are those based on t_1j-t_2j and those based on log t_1j–log t_2j. For each class the sign, signed ranks, t and likelihood ratio tests are compared via Pitman's criterion of asymptotic relative efficiency (ARE). For tests based on t_1j — t_2j, it is found that: (1) the efficacy of the paired t depends on the coefficient of variation (CV) of the pair means, (2) the signed rank test has the same ARE to the sign test as for the usual location problem. For tests based on log t_1j — log t_2j, the ARE comparisons reduce to the well-known results for the one-sample location problem for samples from a logistic density. Hence, the signed rank test is asymptotically efficient. Furthermore, analyses based on log t_1j — log t_2j are not complicated by the underlying pairing mechanism.     

On an Unbiased Variance Estimator for the WILCOXON-MANN-WHITNEY-Statistic Based on Ranks

For some applications of the WILCOXON-MANN-WHITNEY-statistic its variance has to be estimated. So e.g. for the test of POTTHOFF (1963) to detect differences in medians of two symmetric distributions as well as for the computation of approximate, confidence bounds for the probability P(X₁ ≥ X₂), cf. GOVINDARAJULU (1968). In the present paper an easy to compute variance estimator is proposed which as only information uses the ranks of the data with the additional property that it is unbiased for the finite variance. Because of its invariance under any monotone transformation of the data its applicability is not confined to quantitative data. The estimator may be applied to ordinal data just as well. Some properties are discussed and a numerical example is given.     

Effect of a Treatment with Naphthaleneacetic Acid on the Arrangement of Lateral Roots in Onion (Allium cepa L): General Pattern and Coordination between Ranks

Lateral roots in Allium cepa arise in longitudinal rows opposite the protoxylem poles of adventitious roots. The number, spacing within ranks and positional relationship to laterals in different ranks were analysed in control roots and those treated with an auxin (α-naphthaleneacetic acid). Treatment increased numbers of laterals per rank and distributed the more evenly in all ranks. Laterals of control roots were concentrated in two neighbouring ranks. Auxin-treated roots showed a more regular distribution of laterals between ranks and close spacing of laterals along each rank. Comparisons with theoretical random distributions suggest a dispersed spacing model for lateral root arrangement with mutual repulsion between successive lateral roots within each rank both in control and auxintreated roots. On the other hand, there is some interaction between laterals in different ranks in 0.1 mM NAA-treated roots.     

MAX-rank: a simple and robust genome-wide scan for case-control association studies

In genome-wide association studies (GWAS), single-marker analysis is usually employed to identify the most significant single nucleotide polymorphisms (SNPs). The trend test has been proposed for analysis of case-control association. Three trend tests, optimal for the recessive, additive and dominant models respectively, are available. When the underlying genetic model is unknown, the maximum of the three trend test results (MAX) has been shown to be robust against genetic model misspecification. Since the asymptotic distribution of MAX depends on the allele frequency of the SNP, using the P-value of MAX for ranking may be different from using the MAX statistic. Calculating the P-value of MAX for 300,000 (300 K) or more SNPs is computationally intensive and the software and program to obtain the P-value of MAX are not widely available. On the other hand, the MAX statistic is very easy to calculate without complex computer programs. Thus, we study whether or not one could use the MAX statistic instead of its P-value to rank SNPs in GWAS. The approaches using the MAX and its P-value to rank SNPs are referred to as MAX-rank and P-rank. By applying MAX-rank and P-rank to simulated and four real datasets from GWAS, we found the ranks of SNPs with true association are very similar using both approaches. Thus, we recommend to use MAX-rank for genome-wide scans. After the top-ranked SNPs are identified, their P-values based on MAX can be calculated and compared with the significance level. The work of Q. Li was partially supported by the Knowledge Innovation Program of the Chinese Academy of Sciences, No. 30465W0 and 30475V0. The research of Z Li was partially sponsored by NIH grant EY014478.     

Application of a stability statistic to international maize yield trials

Summary Genotype x environment (GE) interaction encountered in experiments complicates genotype selection and varietal recommendation. The integration of yield and stability of genotypes into a single parameter may make selection and recommendation easier. Kang developed a rank-sum method that allows selection for both yield and the stability variance statistics ( _i ² or s _i ² ) of Shukla. The objective of this research was to compare the rank-sum selection method to selection based on yield alone in five international maize (Zea mays L.) yield trials. Ranks were assigned for yield (the highest mean yield received a rank of 1) and for _i ² and s _i ² (the lowest value received a rank of 1). The yield and _i ² ranks and/or the yield and s _i ² ranks for each genotype were summed. Each trial contained two reference entries (REs). Yield rank or rank-sum of each genotype was compared to yield rank or rank-sum of the best RE (BRE). GE interaction was significant for all trials. Heterogeneity in the GE interaction due to the linear effect of a covariate (differences in fertility and/or cultural practices) was significant in Trials 1, 2, and 5. Overall, in all trials, 29 genotypes were selected on the basis of yield alone. On the basis of _i ² and yield rank-sum, 32 genotypes were identified, with 11 being lower yielding than the 29 yield-based selections. On the basis of s _i ² and yield rank-sum, 31 genotypes were selected, with 11 being lower yielding than the yield-bases selections. Obviously, yield is sacrificed when the rank-sum method is used in the selection process. However, selection based on yield alone may not be adequate when GE interaction is significant because of testing in diverse environments.     

Inbreeding and endogamy in Tatarstan

The random inbreeding (F _st) and local inbreeding (a) values have been calculated for populations of the district and rural municipality ranks of 16 and 13 raions (administrative districts) of Tatarstan, Russia, respectively. The correlations between all inbreeding values are positive and vary from 0.38 to 0.80. The endogamy index has been calculated for populations of the district rank; it varies from 0.45 in Pestrechinskii raion to 0.74 in Aktanyshskii raion. Cartographic extrapolation of the endogamy indices has been performed.     

Linnean ranks,temporal banding,and time‐clipping: why not slaughter the sacred cow?

In a recent study, Avise & Liu (2011) (Biological Journal of the Linnean Society 102: 707–714) presented evidence indicating that Linnean ranks are not temporally standardized (i.e. taxa of the same rank differ greatly in age). This is one more argument that ranks veil rather than convey biological comparability. The authors also discuss recent suggestions as to how these shortcomings should be overcome, in particular temporal banding (by which the same rank is assigned to taxa of the same geological age) and time‐clipping (adding a code to each taxon denoting the geological episode when it originated). In this short comment, it is argued that both temporal banding and time‐clipping may be deleterious in taxonomic practice and that the abandonment of the Linnean ranks is long overdue. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 732–734.     

Changes of dominance rank,age, and tenure of wild Japanese macaque males in the Kinkazan a troop during seven years

Male age-rank and tenure-rank relationships were studied for seven years in unprovisioned Japanese macaque (Macaca fuscata fuscata) troop on Kinkazan Island, Japan. Males whose estimated ages were between 15 and 19 yr old monopolized the highest ranks, while older males whose estimated ages were ≥ 20 yr old tended to decline in rank, resulting in a humped age-rank curve. The ranks of males tended to rise as their tenure in the troop increased. The departure of higher-ranking males was the social mechanism for changes in rank, suggesting that the disappearance of higher-ranking males plays an important role in determining rank dominance.     

The subgeneric nomenclature for the herbaceous-stemmed Smilax species (Smilacaceae) of North America

The several names and ranks given to the North American group ofSmilax with biovulate locules together with both herbaceous and nonprickly stems are listed chronologically and discussed nomenclaturally. It is concluded that this group of approximately nine species should be known at the generic rank asNemexia Raf. or at the rank of subgenus asSmilax subgenusLuiste Raf. or at section rank asSmilax sectionNemexia (Raf.) A. DC.     

Landscape and oceanic barriers shape dispersal and population structure in the island nematode Pristionchus pacificus

In this study evolutionary host plant patterns at ranks from order to species were analysed using spatial evolutionary and ecological vicariance analysis (SEEVA), based on a multigene phylogeny of 45 ascomycete fungal species. The objective was to understand speciation events and host associations in Ophiognomonia (Gnomoniaceae). Species of this genus are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on plants in the families of Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae, and Sapindaceae. A second objective was to determine whether speciation events are influenced by host conservatism, host specialization, or host switching at different taxonomic host ranks. Host differences between sister clades were interpreted using the divergence index (D) from the SEEVA analysis, ranging from 0 for no divergence to 1 for maximum possible divergence. Several fungal subclades showed clear patterns of host order/family conservatism (D = 1.00) for hosts in Betulaceae, Fagaceae, Juglandaceae, and Rosaceae. Clear trends of host specialization at host genus and species ranks (D = 1.00) were suggested within these host families. Independent host jumps were observed for two species at the family rank and three at the order rank. As a result of this study, host specificity and specialization is hypothesized as a mechanism that can strongly contribute to speciation patterns in fungal pathogens. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 1–16.     

BRANCHING PATTERN IN ONION ADVENTITIOUS ROOTS

The pattern of topographic distribution of lateral roots (LRs) along the adventitious root of Allium cepa L. was studied in relation to the adventitious root vascular system. In the onion LRs arise in vertical files opposite the protoxylem poles, thus forming protoxylem-based ranks of LRs along the mother root. Two protoxylem-based ranks are shown to support large numbers of LRs, whereas the remaining ranks are considerably less prolific. Within each rank short distances between longitudinal neighbor LRs are uncommon. The results suggest that the developing LR influences the location of subsequent LRs forming in the same protoxylem-based rank. The frequency with which longitudinal neighbor LRs formed in adjacent protoxylem-based ranks was significantly high, whereas their appearance in the same rank or in nonadjacent ranks was more restricted. Similarly, the existence of nonrandom clumps of LRs could be demonstrated at certain levels of the adventitious root. The possible effects of interaction between protoxylem-based ranks of LRs as well as likely agents operating from the parent root vascular system are discussed insofar as they represent factors favoring the clumping of LRs.     

Trying to See Red Through Stickleback Photoreceptors: Functional Substitution of Receptor Sensitivities

A key to understanding animal behavior is knowledge of the sensory information animals extract from their environment. For visually motivated tasks, the information animals obtain through their eyes is often assumed to be essentially the same as that perceived by humans. However, known differences in structure and processing among the visual systems of different animals clearly indicate that the world seen by each is different. A well‐characterized difference between human and other animal visual systems is the number of types and spectral sensitivities of their photoreceptors. We are developing a technique, functional substitution, that exploits knowledge of these differences to portray for human subjects, colors as they would appear through the photoreceptors of another animal. In a specific application, we ask human subjects to rank hues of male threespine stickleback (Gasterosteus aculeatus) throats viewed through stickleback photopigments. We compare these ranks to ranks of the same throat hues viewed through normal human photoreceptors. We find essentially no difference between the two sets of rankings. This suggests that any differences in human and stickleback rankings of such hues would result from differences in post‐receptoral neural processing. Using a previously developed model of stickleback neural processing, we established another ranking of the hues which was again essentially the same as the rankings produced by the human subjects. A growing literature indicates that stickleback do rank such hues in the evaluation of males as potential mates or threats. Although our results do not demonstrate that humans and stickleback use the same mechanisms to assess color, our experiments significantly failed to show that stickleback and human rankings of throat hues should be different. Nevertheless, a comparison of all these rankings to ranks derived from subjective color scoring by human observers suggests that color scoring may utilize other cues and should thus be used cautiously.     

Testosterone and Linear Social Dominance Status in Captive Male Dabbling Ducks in Winter

Dominance hierarchies play an important role in avoidance and/or solving conflicts in gregarious species. In dabbling ducks (Anas species), dominance allows for feeding‐site monopolization in winter quarters where resources are generally limited. In addition, male social rank should theoretically favour access to mates. Dominance rank can be associated with morphological traits, and is often correlated with aggressiveness, a behavioural trait generally related to high testosterone levels. In this study, we investigated the existence of a winter group structure based on dominance relationships and tested for a linear hierarchy, in three species of captive male dabbling ducks (mallard Anas platyrhynchos, pintail A. acuta and wigeon A. penelope). We then analysed the relationship between dominance ranks, morphological parameters and testosterone levels measured in early (Oct.) and mid‐winter (Dec./Jan.). We found that the three male groups of the three species exhibited a linear hierarchy. Testosterone levels differed during winter and between species. Morphologic measurements, body mass and body condition were not correlated with individual dominance ranks, whereas dominant males had higher testosterone levels than subordinates. The slopes of the relationships were similar between species and winter period, but the y‐intercepts differed between species and between early and mid‐winter phases. The linear hierarchy found in the three species indicates that dominance relationships strongly structure dabbling duck groups in winter. Lack of correlation between rank and morphological characters, but correlation of rank with testosterone levels suggests that social rank is more dependent on behavioural traits such as aggressive behaviour. The differences between species and winter periods are discussed in relation to migration and wintering phenology.     

Rank Tests for Complete Block Designs

In this article a general univariate K-sample rank test for complete block designs with proportional cell frequencies is derived. It is shown that the test statistic has under H₀ and for arbitrary scores asymptotically a X²-distribution with K — 1 degrees of freedom. Special cases of this test are the Kruskal-Wallis test and the Friedman test. The test is compared with the Benard-van-Elteren test, the Mack-Skillings test and a test proposed by Downton. Finally the application of the test is illustrated by two examples.     

Changes to feeding and dominance ranks following the introduction of novel feeds to African catfish

The effect of changing feeds on individual feed intake and feeding and dominance ranks in groups of African catfish Clarias gariepinus was investigated. Following feeding on a commercial feed groups (n = 3) of six African catfish were either fed fish meal (FM42) or maize gluten (MG35) based feeds for 5 days before being switched to the other feed for 5 days. Energy intake was significantly lower on FM42 than on MG35, dry matter intake and protein intake were significantly lower on FM42 than on commercial feed and this occurred whether FM42 was fed first or second. There were no significant differences between intake of MG35 and commercial feed. Thus, the action of changing the feed on its own did not affect feed intake since the decrease was shown to be feed‐specific to FM42. Six types of agonistic behaviours were identified and used to assign dominance rank. There were no correlations between dominance and feeding ranks. This was due to non‐linear hierarchies with one dominant fish in each group. Feeding ranks were more stable when feeding MG35 than FM42. Feeding rank stability (Kendall's coefficient of concordance) was significant in five out of six groups fed MG35 (compared with three out of six fed FM42). Feeding rank stability was higher in five out of the six groups when they were fed MG35 than when the same group was fed FM42. The experiment provided evidence that the introduction of a novel feed can, but does not necessarily, alter feed intake and that feed can influence the stability of feeding ranks.     

Intertroop Transfer and Dominance Rank Structure of Nonnatal Male Japanese Macaques in Yakushima, Japan

We examined the interaction between intertroop transfer and male dominance ranks in a wild population of Japanese macaques (Macaca fuscata yakui) in Yakushima using data collected over 15 years. Intertroop transfer tended to maintain a linear, stable, and age-graded dominance rank order among nonnatal males irrespective of variation in troop size or composition. All males that joined a troop at the top of the rank order were prime adults. Among males joining at lower ranks, entry at the most subordinate position in the hierarchy was common. Males joining at lower ranks tended to join troops in which all other resident males were the same age or older. Adult males tended to join troops with few or no males. Young males tended to join troops with many resident males, and in which a relatively large proportion of males was other young ones. Intertroop transfer was responsible for most rank changes of resident males. The most common cause of males rising in rank was the emigration or death of a higher-ranking male. Males fell in rank most frequently as a result of a new male joining the troop at the top of the hierarchy. Rank reversals among resident males were rare. The cumulative effects of male transfers produce sociodemographic variation within a troop over time and sociodemographic diversity among troops in a local population. A key feature of intertroop diversity is that larger troops have a significantly greater proportion of young males than smaller troops. This diversity also creates the potential for intertroop variation in the severity of male competition and provides a range of options for transferring males.