Phylogenetic plant community structure along elevation is lineage specific

The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage‐specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co‐occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.     

A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows

We developed a method for studying the synchrony of behaviour based on calculations of overdispersion of a binomial process. The lying behaviour of cows was investigated under two different housing units inside the same barn. The first unit housed 30 cows undergoing conventional milking and the second unit housed 27 cows undergoing automatic milking. The lying behaviour of the cows was observed over 3 weeks in 12 periods of 6 h each. Every 5 min, we counted the number of cows lying down in the cubicles. As external cues, like feeding and conventional milking, can promote synchrony in dairy cows, we expected that cows conventionally milked would show more behavioural synchrony than automatically milked cows. Cows lied down synchronously in both units (overdispersion 1.67, P < 0.01). Lying synchrony tended to be slightly bigger in automatically than in conventionally milked cows (overdispersion 1.76 v. 1.58, P = 0.09), although the proportion of cows lying down was on average greater in conventionally than in automatically milked cows (60.7% v. 45.6%). This suggests that synchronized lying behaviour in cows is a constant phenomenon that depends on social facilitation rather than on external cues. The overdispersion index appears to be a useful tool for studying the synchrony of animal behaviour when observations are made at the group level.     

Evaluating Dependence Among Mule Deer Siblings in Fetal and Neonatal Survival Analyses

Abstract: The assumption of independent sample units is potentially violated in survival analyses where siblings comprise a high proportion of the sample. Violation of the independence assumption causes sample data to be overdispersed relative to a binomial model, which leads to underestimates of sampling variances. A variance inflation factor, c, is therefore required to obtain appropriate estimates of variances. We evaluated overdispersion in fetal and neonatal mule deer (Odocoileus hemionus) datasets where more than half of the sample units were comprised of siblings. We developed a likelihood function for estimating fetal survival when the fates of some fetuses are unknown, and we used several variations of the binomial model to estimate neonatal survival. We compared theoretical variance estimates obtained from these analyses with empirical variance estimates obtained from data-bootstrap analyses to estimate the overdispersion parameter, c. Our estimates of c for fetal survival ranged from 0.678 to 1.118, which indicate little to no evidence of overdispersion. For neonatal survival, 3 different models indicated that ĉ ranged from 1.1 to 1.4 and averaged 1.24–1.26, providing evidence of limited overdispersion (i.e., limited sibling dependence). Our results indicate that fates of sibling mule deer fetuses and neonates may often be independent even though they have the same dam. Predation tends to act independently on sibling neonates because of dam-neonate behavioral adaptations. The effect of maternal characteristics on sibling fate dependence is less straightforward and may vary by circumstance. We recommend that future neonatal survival studies incorporate additional sampling intensity to accommodate modest overdispersion (i.e., ĉ = 1.25), which would facilitate a corresponding ĉ adjustment in a model selection analysis using quasi-likelihood without a reduction in power. Our computational approach could be used to evaluate sample unit dependence in other studies where fates of individually marked siblings are monitored.     

Density dependence and the spread of anthelmintic resistance

Variation in the strength of selection pressures acting upon different subpopulations may cause density-dependent regulatory processes to act differentially on particular genotypes and may influence the rate of selection of adaptive traits. Using host-helminth parasite systems as examples, we investigate the impact of different positive and negative density dependence on the potential spread of anthelmintic resistance. Following chemotherapy, the negative density-dependent processes restricting parasite population growth will be relaxed, increasing the genetic contribution of resistant parasites to the next generation. Simple deterministic models of directly transmitted nematodes that merge population dynamics and genetics show that the frequency of drug-resistant alleles may increase faster in species whose population size is down-regulated by density-dependent parasite fecundity than in species with density-dependent establishment or parasite mortality. A genetically structured population dynamics model of an indirectly transmitted nematode is used to highlight how population regulation will influence the resistance allele frequency in different parasite lifestages. Results indicate that surveys aimed at monitoring the evolution of drug resistance should consider carefully which life stage to sample, and the time following treatment samples should be collected. Anthelmintic resistance offers a good opportunity to apply fundamental evolutionary and ecological principles to the management of a potentially crucial public health problem.     

One‐Sided Test to Assess Correlation in Linear Logistic Models using Estimating Equations

A score‐type test is proposed for testing the hypothesis of independent binary random variables against positive correlation in linear logistic models with sparse data and cluster specific covariates. The test is developed for univariate and multivariate one‐sided alternatives. The main advantage of using score test is that it requires estimation of the model only under the null hypothesis, that in this case corresponds to the binomial maximum likelihood fit. The score‐type test is developed from a class of estimating equations with block‐diagonal structure in which the coefficients of the linear logistic model are estimated simultaneously with the correlation. The simplicity of the score test is illustrated in two particular examples.     

A Comparison of Regression Models for Small Counts

ABSTRACT Count data with means <2 are often assumed to follow a Poisson distribution. However, in many cases these kinds of data, such as number of young fledged, are more appropriately considered to be multinomial observations due to naturally occurring upper truncation of the distribution. We evaluated the performance of several versions of multinomial regression, plus Poisson and normal regression, for analysis of count data with means <2 through Monte Carlo simulations. Simulated data mimicked observed counts of number of young fledged (0, 1, 2, or 3) by California spotted owls (Strix occidentalis occidentalis). We considered size and power of tests to detect differences among 10 levels of a categorical predictor, as well as tests for trends across 10-year periods. We found regular regression and analysis of variance procedures based on a normal distribution to perform satisfactorily in all cases we considered, whereas failure rate of multinomial procedures was often excessively high, and the Poisson model demonstrated inappropriate test size for data where the variance/mean ratio was <1 or >1.2. Thus, managers can use simple statistical methods with which they are likely already familiar to analyze the kinds of count data we described here.     

Does predation result in adult sex ratio skew in a sexually dimorphic insect genus?

Theory proposes that sexually dimorphic, polygynous species are at particularly high risk of sex-biased predation, because conspicuous males are more often preyed upon compared to females. We tested the effects of predation on population sex ratio in a highly sexually dimorphic insect genus (Hemideina). In addition, introduction of a suite of novel mammalian predators to New Zealand during the last 800 years is likely to have modified selection pressures on native tree weta. We predicted that the balance between natural and sexual selection would be disrupted by the new predator species. We expected to see a sex ratio skew resulting from higher mortality in males with expensive secondary sexual weaponry; combat occurs outside refuge cavities between male tree weta. We took a meta-analytic approach using generalized linear mixed models to compare sex ratio variation in 58 populations for six of the seven species in Hemideina. We investigated adult sex ratio across these populations to determine how much variation in sex ratio can be attributed to sex-biased predation in populations with either low or high number of invasive mammalian predators. Surprisingly, we did not detect any significant deviation from 1 : 1 parity for adult sex ratio and found little difference between populations or species. We conclude that there is little evidence of sex-biased predation by either native or mammalian predators and observed sex ratio skew in individual populations of tree weta is probably an artefact of sampling error. We argue that sex-biased predation may be less prevalent in sexually dimorphic species than previously suspected and emphasize the usefulness of a meta-analytic approach to robustly analyse disparate and heterogeneous data.