Interspecific patterns for egg and clutch sizes of African Bufonidae (Amphibia: Anura)

Little is known about reproductive trade-offs in African amphibians, but such data, particularly in the form of quantitative measurements, are a key for investigating life history evolution. Here we compile and analyze known data on African bufonids from published material and new data from preserved museum specimens, to investigate interspecific patterns of egg and clutch sizes variation. Our data is a composite of mixed sources, including ova data from dissected females and laid clutches from observations in the field. Our study shows that, as body size increases, clutch size increases but egg size decreases, and when correcting for body size, egg size is inversely correlated with clutch size. These parameter interactions however, are different for different reproductive modes. In free-swimming larval developing species, the same trends are recovered, but for lecithotrophic viviparous species no significant correlations could be recovered for clutch size and body size nor for the trade-off between clutch size and egg size, and egg size is positively related to body size. The egg size of Nimbaphrynoides occidentalis (Angel, 1943) is a clear outlier, which may be due to its matrotrophic viviparous reproduction. In addition, we observed no statistical difference between ova data collected from dissections and laid clutch data from field observations, which suggests that such a mixed dataset has utility in comparative analyses.     

Data Quality and the Comparative Method: The Case of Primate Group Size

The comparative method is frequently employed to study primate behavior and evolution. The method is used to infer adaptations, and considerable improvements have been made with respect to its implementation. Despite these advances, scant attention has been given to the nature of the data that are used in comparative analyses. This creates a potential problem as data are often compiled from studies conducted by multiple researchers, whose methods may differ, resulting in variation in data quality. In this article, we investigate the quality of data employed in studies of primate group size. Several issues concerning data quality arise when assembling data on group size. For example, data quality may be compromised if group sizes are estimated from censuses, unhabituated groups, or groups with unrecognized individuals. To mitigate these and other data quality issues, we gathered data from the literature on 23 monkeys and apes using well-defined and biologically relevant criteria for inclusion. We compare our results with those of eight published compilations of group size. Most studies did not provide details regarding the criteria for including data. We found that our group size values were uncorrelated or weakly correlated with those from three other studies and differed in a consistent fashion from those of one other study. Because conclusions derived from comparative analyses are only as accurate as the data that they use, future studies should provide details regarding data collection to ensure their reliability.     

Population bottlenecks and Pleistocene human evolution

We review the anatomical and archaeological evidence for anearly population bottleneck in humans and bracket the time whenit could have occurred. We outline the subsequent demographicchanges that the archaeological evidence of range expansionsand contractions address, and we examine how inbreeding effectivepopulation size provides an alternative view of past populationsize change. This addresses the question of other, more recent,population size bottlenecks, and we review nonrecombining andrecombining genetic systems that may reflect them. We examinehow these genetic data constrain the possibility of significantpopulation size bottlenecks (i.e., of sufficiently small sizeand/or long duration to minimize genetic variation in autosomaland haploid systems) at several different critical times inhuman history. Different constraints appear in nonrecombiningand recombining systems, and among the autosomal loci most areincompatible with any Pleistocene population size expansions.Microsatellite data seem to show Pleistocene population sizeexpansions, but in aggregate they are difficult to interpretbecause different microsatellite studies do not show the sameexpansion. The archaeological data are only compatible witha few of these analyses, most prominently with data from Aluelements, and we use these facts to question whether the viewof the past from analysis of inbreeding effective populationsize is valid. Finally, we examine the issue of whether inbreedingeffective population size provides any reasonable measure ofthe actual past size of the human species. We contend that ifthe evidence of a population size bottleneck early in the evolutionof our lineage is accepted, most genetic data either lack theresolution to address subsequent changes in the human populationor do not meet the assumptions required to do so validly. Itis our conclusion that, at the moment, genetic data cannot disprovea simple model of exponential population growth following abottleneck 2 MYA at the origin of our lineage and extendingthrough the Pleistocene. Archaeological and paleontologicaldata indicate that this model is too oversimplified to be anaccurate reflection of detailed population history, and thereforewe find that genetic data lack the resolution to validly reflectmany details of Pleistocene human population change. However,there is one detail that these data are sufficient to address.Both genetic and anthropological data are incompatible withthe hypothesis of a recent population size bottleneck. Suchan event would be expected to leave a significant mark acrossnumerous genetic loci and observable anatomical traits, butwhile some subsets of data are compatible with a recent populationsize bottleneck, there is no consistently expressed effect thatcan be found across the range where it should appear, and thisabsence disproves the hypothesis.     

Demographic consequences of changing body size in a terrestrial salamander

Changes in climate can alter individual body size, and the resulting shifts in reproduction and survival are expected to impact population dynamics and viability. However, appropriate methods to account for size‐dependent demographic changes are needed, especially in understudied yet threatened groups such as amphibians. We investigated individual‐ and population‐level demographic effects of changes in body size for a terrestrial salamander using capture–mark–recapture data. For our analysis, we implemented an integral projection model parameterized with capture–recapture likelihood estimates from a Bayesian framework. Our study combines survival and growth data from a single dataset to quantify the influence of size on survival while including different sources of uncertainty around these parameters, demonstrating how selective forces can be studied in populations with limited data and incomplete recaptures. We found a strong dependency of the population growth rate on changes in individual size, mediated by potential changes in selection on mean body size and on maximum body size. Our approach of simultaneous parameter estimation can be extended across taxa to identify eco‐evolutionary mechanisms acting on size‐specific vital rates, and thus shaping population dynamics and viability.     

The energetic equivalence rule rejected because of a potentially common sampling error: evidence from carabid beetles

Abundance data from pitfall traps are widely used to estimate the relationship between beetle body size and abundance. Such data probably overestimate densities of large bodied species and may overestimate slopes of size‐abundance relationships. Here, we test this idea by comparing size‐abundance patterns found using data from pitfall trapping with those found with data from a quantitative method of estimating abundance, quadrat sampling. We use data from a total of 47 communities. As expected, slopes of size‐abundance relationships are significantly more positive when estimated using data from pitfall traps compared to when using quadrat sampling data. This was seen when looking across different communities, within communities sampled by both methods and when focusing on the set of species found by both methods within a community. These results were also generally found regardless of method of analysis, which were done using regression with species values as independent data points and using the independent contrast method, and with slopes estimated using ordinary least square regression or the structural relation. Most important, slopes of size‐abundance relationships based on data from pitfall traps were on average significantly more positive than ?0.75 on log–log scales, and thus inconsistent with the energetic equivalence rule. Slopes based on quadrat sampling, on the other hand, were on average not significantly different from ?0.75. The rejection of the energetic equivalence rule based on data from pitfall traps here is therefore a sampling artefact. Similar problems may apply to abundance data from virtually all insect trapping methods, and should make us consider re‐examining many of the size‐abundance patterns documented so far. As a large proportion of all animal species are insects, and traps are widely used to estimate abundance, this is a potentially important problem for our general understanding of the relationship between species body size and abundance.     

Accounting for variability in sample size estimation with applications to nonadherence and estimation of variance and effect size

We consider sample size calculations for testing differences in means between two samples and allowing for different variances in the two groups. Typically, the power functions depend on the sample size and a set of parameters assumed known, and the sample size needed to obtain a prespecified power is calculated. Here, we account for two sources of variability: we allow the sample size in the power function to be a stochastic variable, and we consider estimating the parameters from preliminary data. An example of the first source of variability is nonadherence (noncompliance). We assume that the proportion of subjects who will adhere to their treatment regimen is not known before the study, but that the proportion is a stochastic variable with a known distribution. Under this assumption, we develop simple closed form sample size calculations based on asymptotic normality. The second source of variability is in parameter estimates that are estimated from prior data. For example, we account for variability in estimating the variance of the normal response from existing data which are assumed to have the same variance as the study for which we are calculating the sample size. We show that we can account for the variability of the variance estimate by simply using a slightly larger nominal power in the usual sample size calculation, which we call the calibrated power. We show that the calculation of the calibrated power depends only on the sample size of the existing data, and we give a table of calibrated power by sample size. Further, we consider the calculation of the sample size in the rarer situation where we account for the variability in estimating the standardized effect size from some existing data. This latter situation, as well as several of the previous ones, is motivated by sample size calculations for a Phase II trial of a malaria vaccine candidate.     

Effects of plot size on the ordination of vegetation samples

Questions: Do ordination patterns differ when based on vegetation samples recorded in plots of different size? If so, how large is the effect of plot size relative to the effects of data set heterogeneity and of using presence/absence or cover‐abundance data? Can we combine plots of different size in a single ordination? Methods: Two homogeneous and two heterogeneous data sets were sampled in Czech forests and grasslands. Cover‐abundances of plant species were recorded in series of five or six nested quadrats of increasing size (forest 49‐961 m2; grassland 1‐49 m²). Separate ordinations were computed for plots of each size for each data set, using either species presences/absences or cover‐abundances recorded on an ordinal scale. Ordination patterns were compared with Procrustean analysis. Also, ordinations of data sets jointly containing plots of different size were calculated; effects of plot size were evaluated using a Monte Carlo test in constrained ordination. Results: The results were consistent between forest and grassland data sets. In homogeneous data sets, the effect of presence/absence vs. cover‐abundance was similar to, or larger than, the effect of plot size; for presence/absence data the differences between ordinations of differently sized plots were smaller than for cover‐abundance data. In heterogeneous data sets, the effect of plot size was larger than the effect of presence‐absence vs. cover‐abundance. The plots of smaller size (= 100 m2 in forests, = 4 m² in grasslands) yielded the most deviating ordination patterns. Joint ordinations of differently sized plots mostly did not yield patterns that would be artifacts of different plot size, except for plots from the homogeneous data sets that differed in size by a factor of four or higher. Conclusions: Variation in plot size does influence ordination patterns. Smaller plots tend to produce less stable ordination patterns, especially in data sets with low ß‐diversity and species cover‐abundances. Data sets containing samples from plots of different sizes can be used for ordination if they represent vegetation with large ß‐diversity. However, if data sets are homogeneous, i.e. with low ß‐diversity, the differences in plot sizes should not be very large, in order to avoid the danger of plot size differences distorting the real vegetation differentiation in ordination patterns.     

Increase of tooth size in prehistoric coastal Peru, 10,000 B.P.-1,000 B.P.

Teeth increase in size during a 9,000-year period in an archaeologically derived, radiocarbon dated sample of skeletons from a geographically restricted area of coastal Peru. Although cultural change is extensive, including the transition to food production and pottery making, teeth do not reduce as predicted under these conditions by Brace's Probable Mutation Effect. Since most of the dental literature dealing with size change of teeth focuses upon dental reduction, hypotheses explaining why teeth increase through time are not well developed. No obvious selective forces explaining size increase are apparent in the present data. Attrition decreases through time. The increase in tooth size in this collection may be a function of overall cranialfacial size increase, which (pending further data) may be related to a general body size increase.     

Female gigantism in a New Guinea population of the spider Nephila maculata

In many arthropods, female clutch size is positively correlated with female size but the benefits of increased size are presumed to be counterbalanced by the mortality risks incurred through delayed maturation. The orb-weaving spiders of the genus Nephila are characterized in part by large female size, and among species female size declines with increasing latitude, suggesting that one important mortality risk associated with delayed female maturation is the end of the growing season. The best-studied species inhabit strongly seasonal habitats. To explore the hypothesis that female size is limited by season length, I collected data concerning size-dependent growth and development rates, prey capture success, predation risk, and female fecundity from a population of N. maculata inhabiting a nearly aseasonal habitat. Comparisons of these data with observations from another N. maculata population and from congeners inhabiting more seasonal sites support the hypothesis that female size in this genus may be limited primarily by seasons length. Combined with recent phylogenetic evidence that male size is an ancestral characteristic, these results indicate that sexual size dimorphism in this group has evolved due to fitness advantages of delayed female maturation.     

Dynamic relationships between body size,species richness,abundance, and energy use in a shallow marine epibenthic faunal community

We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species‐averaged values with individual‐based estimates which allow species to potentially occupy multiple size classes. For individual‐based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species‐based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual‐based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species‐based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic equivalence.     

Field sampling is biased against small-ranged species of high conservation value: a case study on the sphingid moths of East Africa

The range size of species co-occurring in local assemblages is a pivotal variable in assessments of a site’s conservation value. Assemblages featuring many small-ranged species are given more priority than assemblages consisting mainly of wide-ranging species. However, the assembly of relevant information can be challenging and local range size distributions of tropical invertebrates are rarely available for conservation planning. We present such data for sphingid moths in East Africa, a highly diverse region of high conservation value. We compare geographic range size distributions based on field samples with predictions from modelled range map data. Using this system as a case study, we provide evidence for a systematic sampling bias when inferring average local range sizes from field data. Unseen species (i.e., species present but missed in local sampling) are often those with small ranges (hence, of high conservation value). Using an elevational gradient, we illustrate how this bias can lead to false, counterintuitive assessments of environmental effects on local range size distributions. Furthermore, with particular reference to sphingid moths in the study region, we show that current protected areas appear unrelated to the spatial distribution of species richness or average geographic range sizes at a local scale. We discuss the need to treat field sampled data with caution and in concert with other data sources such as probabilistic models.     

Maternal effects on offspring size and number in mosquitofish,Gambusia holbrooki

Given a trade-off between offspring size and number, all mothers are predicted to produce the same optimal-sized offspring in a given environment. In many species, however, larger and/or older mothers produce bigger offspring. There are several hypotheses to explain this but they lack strong empirical support. In organisms with indeterminate growth, there is the additional problem that maternal size and age are positively correlated, so what are their relative roles in determining offspring size? To investigate this, we measured the natural relationship between maternal and offspring size in a wild population of Gambusia holbrooki (eastern mosquitofish), and experimentally disentangled the effects of maternal age and size on offspring size in the laboratory. In combination, our data indicate that the relationship between maternal and offspring size is nonlinear. Small mothers seem to produce larger than average offspring due to integer effects associated with very small broods. For extremely large mothers, which were only sampled in our wild data, these larger than average offspring may result from greater maternal resources or age effects. However, maternal age had no effect on offspring size or number in the laboratory experiment. Our results highlight the importance of sampling the full size–range of mothers when investigating maternal effects on offspring size. They also point to the difficulty of experimentally manipulating maternal size, because any change in size is invariably associated with a change in at least one factor affecting growth (be it temperature, food availability, or density) that might also have an indirect effect on offspring size.     

Robust covariate-adjusted log-rank statistics and corresponding sample size formula for recurrent events data

Summary .   Recurrent events data are frequently encountered in clinical trials. This article develops robust covariate-adjusted log-rank statistics applied to recurrent events data with arbitrary numbers of events under independent censoring and the corresponding sample size formula. The proposed log-rank tests are robust with respect to different data-generating processes and are adjusted for predictive covariates. It reduces to the Kong and Slud (1997, Biometrika 84, 847–862) setting in the case of a single event. The sample size formula is derived based on the asymptotic normality of the covariate-adjusted log-rank statistics under certain local alternatives and a working model for baseline covariates in the recurrent event data context. When the effect size is small and the baseline covariates do not contain significant information about event times, it reduces to the same form as that of Schoenfeld (1983, Biometrics 39, 499–503) for cases of a single event or independent event times within a subject. We carry out simulations to study the control of type I error and the comparison of powers between several methods in finite samples. The proposed sample size formula is illustrated using data from an rhDNase study.     

Estimating the global distribution of field size using crowdsourcing

There is an increasing evidence that smallholder farms contribute substantially to food production globally, yet spatially explicit data on agricultural field sizes are currently lacking. Automated field size delineation using remote sensing or the estimation of average farm size at subnational level using census data are two approaches that have been used. However, both have limitations, for example, automatic field size delineation using remote sensing has not yet been implemented at a global scale while the spatial resolution is very coarse when using census data. This paper demonstrates a unique approach to quantifying and mapping agricultural field size globally using crowdsourcing. A campaign was run in June 2017, where participants were asked to visually interpret very high resolution satellite imagery from Google Maps and Bing using the Geo‐Wiki application. During the campaign, participants collected field size data for 130 K unique locations around the globe. Using this sample, we have produced the most accurate global field size map to date and estimated the percentage of different field sizes, ranging from very small to very large, in agricultural areas at global, continental, and national levels. The results show that smallholder farms occupy up to 40% of agricultural areas globally, which means that, potentially, there are many more smallholder farms in comparison with the two different current global estimates of 12% and 24%. The global field size map and the crowdsourced data set are openly available and can be used for integrated assessment modeling, comparative studies of agricultural dynamics across different contexts, for training and validation of remote sensing field size delineation, and potential contributions to the Sustainable Development Goal of Ending hunger, achieve food security and improved nutrition and promote sustainable agriculture.     

Sensitivity of landscape measurements to changing grain size for fine-scale design and management

Landscape pattern quantities are affected by issues of scale, namely extent and resolution. The grain size (resolution) of fine-resolution geographic information system (GIS) data for two highly fragmented landscapes in USA and Italy were altered to evaluate the effect of grain size changes on landscape pattern metrics and cost-surface model outputs. Beginning with 3 m resolution data and resampling the data to 300 m resolution, we applied pattern metrics and cost-surface models (available in GIS software) and evaluated the types of behaviors in resulting quantities. Results showed that some pattern metrics are robust to changes in grain size (such as area, cohesion, interspersion and juxtaposition metrics), while others exhibit staircase-like or erratic responses. Compared to previous studies, we identified behavioral responses that differ from grain-size changes at coarser resolutions. Cost-surface models demonstrated robust or consistent responses to grain size changes in most cases. For both types of pattern measurement, however, we found that behaviors could differ contextually; that is, there could be different types of behaviors for different landscapes, classifications, or grain sizes. Results indicate that comparing spatial data collected at different scales (such as historical data to more recent, high-resolution sensed data) is complicated by different types of responses to changes in grain size. This may limit the applicability of tools for the measurement of landscape change over time if landscapes are represented by differently scaled data.     

Many ways to be small: different environmental regulators of size generate distinct scaling relationships in Drosophila melanogaster

Static allometries, the scaling relationship between body and trait size, describe the shape of animals in a population or species, and are generated in response to variation in genetic or environmental regulators of size. In principle, allometries may vary with the different size regulators that generate them, which can be problematic since allometric differences are also used to infer patterns of selection on morphology. We test this hypothesis by examining the patterns of scaling in Drosophila melanogaster subjected to variation in three environmental regulators of size: nutrition, temperature and rearing density. Our data indicate that different environmental regulators of size do indeed generate different patterns of scaling. Consequently, flies that are ostensibly the same size may have very different body proportions. These data indicate that trait size is not simply a read-out of body size, but that different environmental factors may regulate body and trait size, and the relationship between the two, through different developmental mechanisms. It may therefore be difficult to infer selective pressures that shape scaling relationships in a wild population without first elucidating the environmental and genetic factors that generate size variation among members of the population.     

Statistical determination of diagnostic species for site groups of unequal size

Aim: Concentration of species occurrences in groups of classified sites can be quantified with statistical measures of fidelity, which can be used for the determination of diagnostic species. However, for most available measures fidelity depends on the number of sites within individual groups. As the classified data sets typically contain site groups of unequal size, such measures do not enable a comparison of numerical fidelity values of species between different site groups. We therefore propose a new method of measuring fidelity with presence/absence data after equalization of the size of the site groups. We compare the properties of this new method with other measures of statistical fidelity, in particular with the Dufrêne‐Legendre Indicator Value (IndVal) index. Methods: The size of site groups in the data set is equalized, while relative frequencies of species occurrence within and outside of these groups are kept constant. Then fidelity is calculated using the phi coefficient of association. Results: Fidelity values after equalization are independent of site group size, but their numerical values vary independently of the statistical significance of fidelity. By changing the size of the target site group relative to the size of the entire data set, the fidelity measure can be made more sensitive to either common or rare species. We show that there are two modifications of the IndVal index for presence/absence data, one of which is also independent of the size of site groups. Conclusion: The phi coefficient applied to site groups of equalized size has advantages over other statistical measures of fidelity based on presence/absence data. Its properties are close to an intuitive understanding of fidelity and diagnostic species in vegetation science. Statistical significance can be checked by calculation of another fidelity measure that is a function of statistical significance, or by direct calculation of the probability of observed species concentrations by Fisher's exact test. An advantage of the new method over IndVal is its ability to distinguish between positive and negative fidelity. One can also weight the relative importance of common and rare species by changing the equalized size of the site groups.     

Seed size selection in heteromyids

Summary The general conclusion of this paper is that heteromyids do not select seed sizes on the basis of their body size. My conclusion comes from the analysis of new data from central New Mexico, analysis of data in the literature on food habits of heteromyids, and a reanalysis of Brown and Lieberman (1973) and Brown (1975). All of these sources agree that no seed size selection exists.Although no pattern of simple seed size selection was found, interesting differences were noticed among species. First, the tendency to husk appears to be related to the size of the rodent. Second, large heteromyids may depend on fruiting heads made up of small seeds. This may or may not have significance to the coexistece of heteromyid communities. At present, insufficient data are available to make conclusions along these lines.Intuitively satisfying hypotheses, such as seed size allocation by heteromyids, are normally very hard to lay to rest. It is my hope that this paper demonstrates the weight of evidece is against seed size allocation in heteromyids. Those who wish to maintain this hypothesis, or reveal that it or related hypotheses have anything to do with heteromyid coexistence, must now produce data to support their position.     

Winter territoriality in migrant Black Redstarts Phoenicurus ochrurus in the Mediterranean area

The nest predation hypothesis predicts that clutch size should be inversely related to the risk of nest predation. In this paper we analyse data on nest predation, clutch size and fledgling production in 128 Jackdaw nests in order to test if clutches are larger in the safer sites. The predation rate was positively correlated with the minimum nest-entrance dimensions (predation is greater in nests with large entrances). Clutch size was not related to the risk of nest predation, and our data do not therefore support the nest predation hypothesis.