Group versus population level demographics: An analysis of comparability using long term data on wild white‐faced capuchin monkeys (Cebus capucinus imitator)

Primates have long been used as indicator species for assessing overall ecosystem health. However, area‐wide census methods are time consuming, costly, and not always feasible under many field conditions. Therefore, it is important to establish whether monitoring a subset of a population accurately reflects demographic changes occurring in the population at large. Over the past 35 years, we have conducted 15 area‐wide censuses in Sector Santa Rosa, Costa Rica. These efforts have revealed important trends in population growth patterns of capuchin monkeys following the protection and subsequent regeneration of native forests. During this same period, we have also intensively studied a subset of the capuchin groups. Comparing these two datasets, we investigate whether the population structures of the closely monitored groups are reliable indicators of area‐wide demographic patterns. We compare the overall group size and the individual age/sex class compositions of study groups and nonstudy groups (i.e., those contacted during area‐wide censuses only). Our study groups contained more individuals overall with a larger proportion of infants, and there were indications that the proportion of adult and subadult males was lower. These differences can be ascribed either to sampling errors or real differences attributable to human presence and/or better habitat quality for the study groups. No other sex/age classes differed, and major demographic changes were simultaneously evident in both study and nonstudy groups. This study suggests that the Santa Rosa capuchin population is similarly impacted by large‐scale ecological patterns observable within our study groups.     

Using palaeolimnological and limnological data to reconstruct the recent history of European lake ecosystems: introduction

1. As future climate change is expected to have a major impact on freshwater lake ecosystems, it is important to assess the extent to which changes taking place in freshwater lakes can be attributed to the degree of climate change that has already taken place. 2. To address this issue, it is necessary to examine evidence spanning many decades by combining long‐term observational data sets and palaeolimnological records. 3. Here, we introduce a series of case studies of seven European lakes for which both long‐term data sets and sediment records are available. Most of the sites have been affected by eutrophication and are now in recovery. 4. The studies attempt to disentangle the effects of climate change from those of nutrient pollution and conclude that nutrient pollution is still the dominant factor controlling the trophic state of lakes. 5. At most sites, however, there is also evidence of climate influence related in some cases to natural variability in the climate system, and in others to the trend to higher temperatures over recent decades attributed to anthropogenic warming. 6. More generally and despite some problems, the studies indicate the value of combining limnological and palaeolimnological records in reconstructing lake history and in disentangling the changing role of different pressures on lake ecosystems.     

Pockets of resistance: Response of arid‐land fish communities to climate,hydrology, and wildfire

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Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths

High‐throughput sequencing is a powerful tool, but suffers biases and errors that must be accounted for to prevent false biological conclusions. Such errors include batch effects; technical errors only present in subsets of data due to procedural changes within a study. If overlooked and multiple batches of data are combined, spurious biological signals can arise, particularly if batches of data are correlated with biological variables. Batch effects can be minimized through randomization of sample groups across batches. However, in long‐term or multiyear studies where data are added incrementally, full randomization is impossible, and batch effects may be a common feature. Here, we present a case study where false signals of selection were detected due to a batch effect in a multiyear study of Alpine ibex (Capra ibex). The batch effect arose because sequencing read length changed over the course of the project and populations were added incrementally to the study, resulting in nonrandom distributions of populations across read lengths. The differences in read length caused small misalignments in a subset of the data, leading to false variant alleles and thus false SNPs. Pronounced allele frequency differences between populations arose at these SNPs because of the correlation between read length and population. This created highly statistically significant, but biologically spurious, signals of selection and false associations between allele frequencies and the environment. We highlight the risk of batch effects and discuss strategies to reduce the impacts of batch effects in multiyear high‐throughput sequencing studies.     

The importance of selection at the level of the pair over 25 years in a natural population of birds

Knowledge of the pattern of selection in natural populations is fundamental for our understanding of the evolutionary process. Selection at higher levels has gained considerable theoretical support in recent years, and one possible level of selection is the breeding pair where fitness is a function of the pair and cannot be reduced to single individuals. We analyzed the importance of pair‐level selection over 25 years in a natural population of the collared flycatcher. Pair‐level selection was significant in five and probably in another 9 years. The relative importance of pair‐level selection varied over years and can have stronger or the same strength as directional selection. This means that selection can act on the combination of the breeding pair in addition to selection on each individual separately. Overall, the conservative estimates obtained here show that this is a potentially important form of selection.     

Extreme heterogeneity of population response to climatic variation and the limits of prediction

Certain general facets of biotic response to climate change, such as shifts in phenology and geographic distribution, are well characterized; however, it is not clear whether the observed similarity of responses across taxa will extend to variation in other population‐level processes. We examined population response to climatic variation using long‐term incidence data (collected over 42 years) encompassing 149 butterfly species and considerable habitat diversity (10 sites along an elevational gradient from sea level to over 2,700 m in California). Population responses were characterized by extreme heterogeneity that was not attributable to differences in species composition among sites. These results indicate that habitat heterogeneity might be a buffer against climate change and highlight important questions about mechanisms maintaining interpopulation differences in responses to weather. Despite overall heterogeneity of response, population dynamics were accurately predicted by our model for many species at each site. However, the overall correlation between observed and predicted incidence in a cross validation analysis was moderate (Pearson's r = 0.23, SE 0.01), and 97% of observed data fell within the predicted 95% credible intervals. Prediction was most successful for more abundant species as well as for sites with lower annual turnover. Population‐level heterogeneity in response to climate variation and the limits of our predictive power highlight the challenges for a future of increasing climatic variability.     

Increased tree densities in South African savannas: >50 years of data suggests CO2 as a driver

For the past century, woody plants have increased in grasslands and savannas worldwide. Woody encroachment may significantly alter ecosystem functioning including fire regimes, herbivore carrying capacity, biodiversity and carbon storage capacity. Traditionally, increases in woody cover and density have been ascribed to changes in the disturbance regime (fire and herbivores) or rainfall. Increased atmospheric CO₂ concentrations may also contribute, by increasing growth rates of trees relative to grasses. This hypothesis is still heavily debated because usually potential CO₂ effects are confounded by changes in land use (disturbance regime). Here we analyse changes in woody density in fire experiments at three sites in South African savannas where the disturbance regime (fire and herbivores) was kept constant for 30 and 50 years. If global drivers had significant effects on woody plants, we would expect significant increases in tree densities and biomass over time under the constant disturbance regime. Woody density remained constant in a semiarid savanna but tripled in a mesic savanna between the 1970s and 1990s. At the third site, a semiarid savanna near the southern limits of the biome, tree density doubled from the mid 1990s to 2010. Interpretation of the causes is confounded by population recovery after clearing, but aerial photograph analysis on adjacent non‐cleared areas showed an accompanying 48% increase in woody cover. Increased CO₂ concentrations are consistent with increased woody density while other global drivers (rainfall) remained constant over the duration of the experiments. The absence of a response in one semiarid savanna could be explained by a smaller carbon sink capacity of the dominant species, which would therefore benefit less from increased CO₂. Understanding how savannas and grasslands respond to increased CO₂ and identifying the causes of woody encroachment are essential for the successful management of these systems.     

Elevation‐dependent responses of tree mast seeding to climate change over 45 years

We use seed count data from a New Zealand mono‐specific mountain beech forest to test for decadal trends in seed production along an elevation gradient in relation to changes in climate. Seedfall was collected (1965 to 2009) from seed trays located on transect lines at fixed elevations along an elevation gradient (1020 to 1370 m). We counted the number of seeds in the catch of each tray, for each year, and determined the number of viable seeds. Climate variables were obtained from a nearby (<2 km) climate station (914‐m elevation). Variables were the sum or mean of daily measurements, using periods within each year known to correlate with subsequent interannual variation in seed production. To determine trends in mean seed production, at each elevation, and climate variables, we used generalized least squares (GLS) regression. We demonstrate a trend of increasing total and viable seed production, particularly at higher elevations, which emerged from marked interannual variation. Significant changes in four seasonal climate variables had GLS regression coefficients consistent with predictions of increased seed production. These variables subsumed the effect of year in GLS regressions with a greater influence on seed production with increasing elevation. Regression models enforce a view that the sequence of climate variables was additive in their influence on seed production throughout a reproductive cycle spanning more than 2 years and including three summers. Models with the most support always included summer precipitation as the earliest variable in the sequence followed by summer maximum daily temperatures. We interpret this as reflecting precipitation driven increases in soil nutrient availability enhancing seed production at higher elevations rather than the direct effects of climate, stand development or rising atmospheric CO₂ partial pressures. Greater sensitivity of tree seeding at higher elevations to changes in climate reveals how ecosystem responses to climate change will be spatially variable.     

The temporal response to drought in a Mediterranean evergreen tree: comparing a regional precipitation gradient and a throughfall exclusion experiment

Like many midlatitude ecosystems, Mediterranean forests will suffer longer and more intense droughts with the ongoing climate change. The responses to drought in long‐lived trees differ depending on the time scale considered, and short‐term responses are currently better understood than longer term acclimation. We assessed the temporal changes in trees facing a chronic reduction in water availability by comparing leaf‐scale physiological traits, branch‐scale hydraulic traits, and stand‐scale biomass partitioning in the evergreen Quercus ilex across a regional precipitation gradient (long‐term changes) and in a partial throughfall exclusion experiment (TEE, medium term changes). At the leaf scale, gas exchange, mass per unit area and nitrogen concentration showed homeostatic responses to drought as they did not change among the sites of the precipitation gradient or in the experimental treatments of the TEE. A similar homeostatic response was observed for the xylem vulnerability to cavitation at the branch scale. In contrast, the ratio of leaf area over sapwood area (LA/SA) in young branches exhibited a transient response to drought because it decreased in response to the TEE the first 4 years of treatment, but did not change among the sites of the gradient. At the stand scale, leaf area index (LAI) decreased, and the ratios of stem SA to LAI and of fine root area to LAI both increased in trees subjected to throughfall exclusion and from the wettest to the driest site of the gradient. Taken together, these results suggest that acclimation to chronic drought in long‐lived Q. ilex is mediated by changes in hydraulic allometry that shift progressively from low (branch) to high (stand) organizational levels, and act to maintain the leaf water potential within the range of xylem hydraulic function and leaf photosynthetic assimilation.     

Long‐Term Weight Development in Women: A 15‐Year Follow‐up of the Effects of Pregnancy

Objective: The aim of this study was to evaluate how well prepregnancy BMI, gestational weight gain, and postpartum weight retention predict retention of weight 15 years later among parous women. Research Methods and Procedures: The Stockholm Pregnancy and Women's Nutrition (SPAWN) study is a long‐term follow‐up study of women who delivered children in 1984 to 1985 (n = 2342). The participants initially filled out questionnaires about their eating and exercise habits, social circumstances, etc. before, during, and at 1 year after pregnancy. Anthropometric data were also sampled. Fifteen years later, these women were invited to take part in the follow‐up study. Anthropometric measurements were collected, and similar questions were asked. Five hundred sixty‐three women participated in the SPAWN 15‐year follow‐up study. The sample was divided into groups to examine three presumably critical time periods: 1) overweight and normal weight before pregnancy; 2) low, intermediate, and high weight gainers during pregnancy; and 3) low, intermediate, and high weight retainers at 1 year after pregnancy. Results: The overweight women did not gain more weight during pregnancy or retain more weight at 1 year follow‐up. High weight gainers during pregnancy retained more weight at the 1‐year and the 15‐year follow‐ups. High weight retainers had gained more during pregnancy and retained it at the 15‐year follow‐up. Fifty‐six percent of the high weight gainers during pregnancy ended up in the high weight retainers group. Discussion: Women who are overweight before pregnancy do not have a higher risk of postpartum weight retention than normal weight women. Thus, it is not necessarily the initially overweight woman who should be the target or focus of weight control programs during or after pregnancy. Both high weight gainers and high weight retainers had higher BMI at the 15‐year follow‐up, although only 56% of the high weight gainers during pregnancy were also classified as high weight retainers at the 1‐year follow‐up. Weight retention at the end of the postpartum year predicts future overweight 15 years later.     

Making red squirrels more visible: the use of baited visual counts to monitor populations

Understanding changes in the distribution and abundance of the red squirrel Sciurus vulgaris in Europe, as a result of the spread of the introduced North American grey squirrel Sciurus carolinensis, is vital to planning and implementing red squirrel conservation measures. We studied the effectiveness of a variation on a common method of monitoring squirrels, standardised visual counts that made use of a diffuse baiting approach to increase their detectability. Significantly more sightings of squirrels occurred on baited than on unbaited visual transect lines in trials with the assistance of volunteers, and we recommend the use of baits in future studies.     

Half a century of succession in a temperate oakwood: from species‐rich community to mesic forest

Aim Lowland woodlands in Europe went through dramatic changes in management in the past century. This article investigates the influence of two key factors, abandonment of coppicing and increased pressure of ungulates, in thermophilous oakwoods. We focused on three interconnected topics: (1) Has the assumed successional trend lead to impoverishment of the vegetation assemblages? (2) Has it resulted in vegetation homogenization? (3) Are the thermophilous oakwoods loosing their original character? Location Czech Republic, Central Europe. Methods The vegetation in 46 semi‐permanent plots was recorded three times: firstly, shortly after the abandonment of coppicing (1953) and then, after four to six decades of secondary succession and strong game impact (1992 and 2006). Overall trends and changes in species spectra were analysed. Results There is a marked successional shift towards species‐poorer communities growing in cooler, moister and nutrient‐richer conditions. The change was significantly different in parts affected and unaffected by high numbers of ungulates yet only for herbs, not the woody species. However, observed change in species composition was not accompanied by significant homogenization process that is the general process reported from elsewhere. A sharp decline in plant species typical for thermophilous woodland communities and in endangered species indicates that the original character of the woodland has been gradually lost. Main conclusions Thermophilous oakwoods have been largely replaced by mesic forests. Lowland oakwoods in continental parts of Europe historically depended on active management, which kept the understorey conditions light and warm. Successional processes in the 20th century caused a critical loss of species diversity at various spatial levels. However, artificially high numbers of ungulates, which otherwise have a negative impact, probably held up succession, so that the changes may still be reversible.     

Changes in the timing of hay cutting in Germany do not keep pace with climate warming

A unique long‐term phenological data set of over 110 000 records of 1st cutting dates for haymaking across Germany, spanning the years 1951–2011 was examined. In addition, we analyzed a long‐term data set in the beginning of flowering of meadow foxtail (Alopecurus pratensis) covering the last 20 years. We tested whether hay‐cutting dates (based on a human decision when to cut) showed trends, temperature relationships and spatial distribution similar to the development of this grassland species, and if these trends could be related to climate change. The timing of 1st hay cut was strongly influenced (P < 0.001) by altitude, latitude and longitude, revealing in particular an east‐west gradient. Over the past 60 years, there have been changes in the timing of hay cutting, with the majority of German federal states having significant (P < 0.05) advances of approximately 1 day per decade. Overall, the response to mean March–May temperature was highly significant (?2.87 days °C^?1; P < 0.001). However, in the last 20 years, no federal state experienced a significant advance and two were even significantly delayed. The temperature response in this post‐1991 period became less or non‐significant for most of the federal states. We suggest that differences in agricultural land use and unequal uptakes of Agri‐Environment Schemes (AES, which encourage later cutting) were likely to be responsible for the regional differences, while the general increase in AES appears to have confounded the overall trend in hay cutting in the last 20 years. Trends over time and responses to temperature were small relative to those associated with the phenology of meadow foxtail. The advance in phenology of this species is greater than the advance in hay cutting, implying that hay cutting may not be keeping pace with a changing climate, which may have a positive effect on grassland ecology.     

Mixture and nonmixture cure fraction models assuming discrete lifetimes: Application to a pelvic sarcoma dataset

Different cure fraction models have been used in the analysis of lifetime data in presence of cured patients. This paper considers mixture and nonmixture models based on discrete Weibull distribution to model recurrent event data in presence of a cure fraction. The novelty of this study is the use of a discrete lifetime distribution in place of usual existing continuous lifetime distributions for lifetime data in presence of cured fraction, censored data, and covariates. In the verification of the fit of the proposed model it is proposed the use of randomized quantile residuals. An extensive simulation study is considered to evaluate the properties of the estimates of the parameters related to the proposed model. As an illustration of the proposed methodology, it is considered an application considering a medical dataset related to lifetimes in a retrospective cohort study conducted by Puchner et al. (2017) that consists of 147 consecutive cases with surgical treatment of a sarcoma of the pelvis between the years of 1980 and 2012.     

Combining limnological and palaeolimnological data to disentangle the effects of nutrient pollution and climate change on lake ecosystems: problems and potential

1. As long‐term observational lake records continue to lengthen, the historical overlap with lake sediment records grows, providing increasing opportunities for placing the contemporary ecological status of lakes in a temporal perspective. 2. Comparisons between long‐term data sets and sediment records, however, require lake sediments to be accurately dated and for sediment accumulation rates to be sufficiently rapid to allow precise matching with observational data. 3. The critical role of the sediment record in this context is its value in tracking the changing impact of human activity on a lake from a pre‐disturbance reference through to the present day. 4. Here, we use data from a range of lakes across Europe presented as case studies in this Special Section. The seven sites considered all possess both long‐term observational records and high‐quality sediment records. Our objective is to assess whether recent climate change is having an impact on their trophic status and in particular whether that impact can be disentangled from the changes associated with nutrient pollution. 5. The palaeo‐data show clear evidence for the beginning of nutrient pollution varying from the mid‐nineteenth century at Loch Leven to the early and middle twentieth century at other sites. The monitoring data show different degrees of recovery when judged against the palaeo‐reference. 6. The reason for limited recovery is attributed to continuing high nutrient concentrations related to an increase in diffuse nutrient loading or to internal P recycling, but there is some evidence that climate change may be playing a role in offsetting recovery at some sites. If this is the case, then lake ecosystems suffering from eutrophication may not necessarily return to their pre‐eutrophication reference status despite the measures that have been taken to reduce external nutrient loading. 7. The extent to which future warming might further limit such recovery can be evaluated only by continued monitoring combined with the use of palaeo‐records that set the pre‐eutrophication reference.     

Damped long‐term host–parasite Red Queen coevolutionary dynamics: a reflection of dilution effects?

An increase in biological diversity leads to a greater stability of ecosystem properties. For host–parasite interactions, this is illustrated by the ‘dilution effect’: a negative correlation between host biodiversity and disease risk. We show that a similar mechanism might stabilise host–parasite dynamics at a lower level of diversity, i.e. at the level of genetic diversity within host species. A long‐term time shift experiment, based on a historical reconstruction of a Daphnia–parasite coevolution, reveals infectivity cycles with more stable amplitude in experienced than in naive hosts. Coevolutionary models incorporating an increase in host allelic diversity over time explain the detected asymmetry. The accumulation of resistance alleles creates an opportunity for the host to stabilise Red Queen dynamics. It leads to a larger arsenal enhancing the host performance in its coevolution with the parasite in which ‘it takes all the running both antagonists can do to keep in the same place’.     

Eight years of ant‐exclusion from citrus canopies: effects on the arthropod assemblage and on fruit yield

• 1 Ants are important generalist predators in most terrestrial ecosystems. However, because many ant species are also hemipteran mutualists, their role in agriculture has generally been considered to be negative for plants.
• 2 In the present study, we report an experiment in ant‐exclusion from tree canopies in an organic citrus grove with two main objectives: (i) to examine whether the absence of ants increased the abundance of some beneficial arthropods and reduced the attack of some pests such as aphids and (ii) to examine whether ant‐exclusion increased the fruit yield of citrus trees.
• 3 The exclusion of ants from tree canopies had positive effects on the arthropod assemblage and on fruit yield. However, the 8‐year duration of the experiment can be divided into two periods with contrasting results. In the first period, the arthropod assemblage was only slightly affected, except for a greater density of aphids in ant‐excluded trees; in addition, fruit yield was higher in ant‐excluded trees than in the control ones. In the second period, ant‐exclusion increased the abundance of most arthropod groups, although the previous positive effect on fruit yield was no longer observed.
• 4 There are two main conclusions of the present study. First, from an applied perspective, ant‐exclusion from tree canopies is not a sound management alternative in citrus plantations in the Mediterranean. Second, the 8‐year duration of the experiment highlighted the importance of long‐term experiments in community ecology and biological control because the effects observed in the first 4 years of the experiment were very different from what occurred subsequently.

     

Long‐Term Dynamics of Microbial Biofilm Communities of the River Rhine with Special References to Ciliates

The aim of this study was to quantify and qualify seasonal changes of all important components of a microbial biofilm community. We explored the development of the biofilm community structure on submerged glass slides for 15 months including all organisms from bacteria to macro‐invertebrates. Besides bacteria, heterotrophic flagellates were the most abundant biofilm component followed by ciliates, meiofauna organisms and algae. Most important were sessile choanoflagellates, peritrichous ciliates and some crustaceans. Ciliates and macrofauna were the most important components with regard to the total biovolume. The biofilm architecture was strongly influenced by extracellular structures produced by protozoans and macro‐invertebrates. Alterations within the biofilm community were mainly due to changes in abundances rather than in the composition except for heterotrophic flagellates and macro‐invertebrates. Biofilm organisms were dominated by planktivorous organisms exerting a strong grazing impact on the plankton organisms in this large river. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Phenological overlap of interacting species in a changing climate: an assessment of available approaches

Concern regarding the biological effects of climate change has led to a recent surge in research to understand the consequences of phenological change for species interactions. This rapidly expanding research program is centered on three lines of inquiry: (1) how the phenological overlap of interacting species is changing, (2) why the phenological overlap of interacting species is changing, and (3) how the phenological overlap of interacting species will change under future climate scenarios. We synthesize the widely disparate approaches currently being used to investigate these questions: (1) interpretation of long‐term phenological data, (2) field observations, (3) experimental manipulations, (4) simulations and nonmechanistic models, and (5) mechanistic models. We present a conceptual framework for selecting approaches that are best matched to the question of interest. We weigh the merits and limitations of each approach, survey the recent literature from diverse systems to quantify their use, and characterize the types of interactions being studied by each of them. We highlight the value of combining approaches and the importance of long‐term data for establishing a baseline of phenological synchrony. Future work that scales up from pairwise species interactions to communities and ecosystems, emphasizing the use of predictive approaches, will be particularly valuable for reaching a broader understanding of the complex effects of climate change on the phenological overlap of interacting species. It will also be important to study a broader range of interactions: to date, most of the research on climate‐induced phenological shifts has focused on terrestrial pairwise resource–consumer interactions, especially those between plants and insects.     

A panel of microsatellite markers to detect and monitor demographic bottlenecks in the riverine dragonfly Orthetrum coerulescens F.

Odonates (dragonflies and damselflies) are important indicators for monitoring anthropogenic impacts on freshwater ecosystems. We developed a panel of microsatellite loci for the keeled skimmer Orthetrum coerulescens, a libellulid dragonfly inhabiting small streams. By using two different isolation techniques, nine microsatellite loci have been isolated. Screening of 209 individuals resulted in an overall number of 88 alleles, ranging from three to 19 alleles per locus. The observed heterozygosity ranged from 0.37 to 0.83. One locus showed significant deviation from Hardy–Weinberg equilibrium.