Does forest extent affect salamander survival? Evidence from a long‐term demographic study of a tropical newt

Forest loss has been associated with reduced survival in many vertebrates, and previous research on amphibians has mostly focused on effects at early life stages. Paramesotriton hongkongensis is a tropical newt that breeds in streams but spends up to 10 months per year in terrestrial habitats. Populations are threatened by habitat degradation and collection for the pet trade, but the cryptic terrestrial lifestyle of this newt has limited our understanding of its population ecology, which inhibits development of a species‐specific conservation plan. We conducted an eight‐year (2007–2014) mark–recapture study on four P. hongkongensis populations in Hong Kong and used these data to evaluate relationships between forest cover, body size, and rainfall on survival and to estimate population sizes. Hong Kong has been subjected to repeated historic territory‐wide deforestation, and thus, we wanted to determine whether there was a link between forest extent as a proxy of habitat quality and newt demography. Annual survival was positively associated with forest cover within core habitat of all populations and negatively related to body size. Mean annual survival (~60%) was similar to that of other stream‐dwelling amphibians, but varied among years and declined substantially in 2012–2013, perhaps due to illegal collection. Despite the link between forest extent and survival, population sizes declined at the most forested site by 40% and increased by 104% and 134% at two others. Forest protection and consequential secondary succession during recent decades in Hong Kong may have been responsible for persistence of P. hongkongensis populations.     

Does climate variability influence the demography of wild primates? Evidence from long‐term life‐history data in seven species

Earth's rapidly changing climate creates a growing need to understand how demographic processes in natural populations are affected by climate variability, particularly among organisms threatened by extinction. Long‐term, large‐scale, and cross‐taxon studies of vital rate variation in relation to climate variability can be particularly valuable because they can reveal environmental drivers that affect multiple species over extensive regions. Few such data exist for animals with slow life histories, particularly in the tropics, where climate variation over large‐scale space is asynchronous. As our closest relatives, nonhuman primates are especially valuable as a resource to understand the roles of climate variability and climate change in human evolutionary history. Here, we provide the first comprehensive investigation of vital rate variation in relation to climate variability among wild primates. We ask whether primates are sensitive to global changes that are universal (e.g., higher temperature, large‐scale climate oscillations) or whether they are more sensitive to global change effects that are local (e.g., more rain in some places), which would complicate predictions of how primates in general will respond to climate change. To address these questions, we use a database of long‐term life‐history data for natural populations of seven primate species that have been studied for 29–52 years to investigate associations between vital rate variation, local climate variability, and global climate oscillations. Associations between vital rates and climate variability varied among species and depended on the time windows considered, highlighting the importance of temporal scale in detection of such effects. We found strong climate signals in the fertility rates of three species. However, survival, which has a greater impact on population growth, was little affected by climate variability. Thus, we found evidence for demographic buffering of life histories, but also evidence of mechanisms by which climate change could affect the fates of wild primates.     

How reliable is the monitoring of permanent vegetation plots? A test with multiple observers

Questions: A multiple plot design was developed for permanent vegetation plots. How reliable are the different methods used in this design and which changes can we measure? Location: Alpine meadows (2430 m a.s.l.) in the Swiss Alps. Methods: Four inventories were obtained from 40 m² plots: four subplots (0.4 m²) with a list of species, two 10m transects with the point method (50 points on each), one subplot (4m²) with a list of species and visual cover estimates as a percentage and the complete plot (40 m²) with a list of species and visual estimates in classes. This design was tested by five to seven experienced botanists in three plots. Results: Whatever the sampling size, only 45‐63% of the species were seen by all the observers. However, the majority of the overlooked species had cover < 0.1%. Pairs of observers overlooked 10‐20% less species than single observers. The point method was the best method for cover estimate, but it took much longer than visual cover estimates, and 100 points allowed for the monitoring of only a very limited number of species. The visual estimate as a percentage was more precise than classes. Working in pairs did not improve the estimates, but one botanist repeating the survey is more reliable than a succession of different observers. Conclusion: Lists of species are insufficient for monitoring. It is necessary to add cover estimates to allow for subsequent interpretations in spite of the overlooked species. The choice of the method depends on the available resources: the point method is time consuming but gives precise data for a limited number of species, while visual estimates are quick but allow for recording only large changes in cover. Constant pairs of observers improve the reliability of the records.     

Does long‐distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro‐forest landscape

Tropical trees often display long‐distance pollen dispersal, even in highly fragmented landscapes. Understanding how patterns of spatial isolation influence pollen dispersal and interact with background patterns of fine‐scale spatial genetic structure (FSGS) is critical for evaluating the genetic consequences of habitat fragmentation. In the endangered tropical timber tree Dysoxylum malabaricum (Meliaceae), we apply eleven microsatellite markers with paternity and parentage analysis to directly estimate historic gene flow and contemporary pollen dispersal across a large area (216 km²) in a highly fragmented agro‐forest landscape. A comparison of genetic diversity and genetic structure in adult and juvenile life stages indicates an increase in differentiation and FSGS over time. Paternity analysis and parentage analysis demonstrate high genetic connectivity across the landscape by pollen dispersal. A comparison between mother trees in forest patches with low and high densities of adult trees shows that the frequency of short‐distance mating increases, as does average kinship among mates in low‐density stands. This indicates that there are potentially negative genetic consequences of low population density associated with forest fragmentation. Single isolated trees, in contrast, frequently receive heterogeneous pollen from distances exceeding 5 km. We discuss the processes leading to the observed patterns of pollen dispersal and the implications of this for conservation management of D. malabaricum and tropical trees more generally.     

Does a long‐term shift in Wood Stork diet foreshadow adaptability to human‐induced rapid environmental change?

To preserve biodiversity, identifying at‐risk populations and developing conservation plans to mitigate the effects of human‐induced rapid environmental change (HIREC) are essential. Changes in diet, especially for food‐limited species, can aid in detecting populations being impacted by HIREC, and characterizing the quality, abundance, and temporal and spatial consistency of newly consumed food items may provide insight concerning the likelihood of a species persisting in a changing environment. We used Wood Storks (Mycteria americana) nesting in the Florida Everglades as a model system to study the possible effects of HIREC on a food‐limited population. We compared the diets of Wood Storks in 2013 and 2014 with those reported during the 1970s before major anthropogenic activities affected the Everglades system and prey availability. Wood Storks in our study consumed more large‐bodied sunfish species (Lepomis spp.), fewer native marsh fishes, and more non‐native fish species than during the 1970s. Large sunfish and non‐native fish are relatively rare in the drying pools of Everglades marshes where storks traditionally forage, suggesting that Wood Storks may be using novel foraging habitats such as created wetlands (i.e., canals and stormwater ponds). Although created wetlands have long hydroperiods conducive to maintaining large‐bodied fishes and could provide alternative foraging habitat when prey availability is reduced in natural marshes, additional studies are needed to determine the extent to which these wetlands are used by Wood Storks and, importantly, the quality of prey items potentially available to foraging Wood Storks in created wetlands.     

What is the risk‐benefit ratio of long‐term antipsychotic treatment in people with schizophrenia?

The long‐term benefit‐to‐risk ratio of sustained antipsychotic treatment for schizophrenia has recently been questioned. In this paper, we critically examine the literature on the long‐term efficacy and effectiveness of this treatment. We also review the evidence on the undesired effects, the impact on physical morbidity and mortality, as well as the neurobiological correlates of chronic exposure to antipsychotics. Finally, we summarize factors that affect the risk‐benefit ratio. There is consistent evidence supporting the efficacy of antipsychotics in the short term and mid term following stabilization of acute psychotic symptoms. There is insufficient evidence supporting the notion that this effect changes in the long term. Most, but not all, of the long‐term cohort studies find a decrease in efficacy during chronic treatment with antipsychotics. However, these results are inconclusive, given the extensive risk of bias, including increasing non‐adherence. On the other hand, long‐term studies based on national registries, which have lower risk of bias, find an advantage in terms of effectiveness during sustained antipsychotic treatment. Sustained antipsychotic treatment has been also consistently associated with lower mortality in people with schizophrenia compared to no antipsychotic treatment. Nevertheless, chronic antipsychotic use is associated with metabolic disturbance and tardive dyskinesia. The latter is the clearest undesired clinical consequence of brain functioning as a potential result of chronic antipsychotic exposure, likely from dopaminergic hypersensitivity, without otherwise clear evidence of other irreversible neurobiological changes. Adjunctive psychosocial interventions seem critical for achieving recovery. However, overall, the current literature does not support the safe reduction of antipsychotic dosages by 50% or more in stabilized individuals receiving adjunctive psychosocial interventions. In conclusion, the critical appraisal of the literature indicates that, although chronic antipsychotic use can be associated with undesirable neurologic and metabolic side effects, the evidence supporting its long‐term efficacy and effectiveness, including impact on life expectancy, outweighs the evidence against this practice, overall indicating a favorable benefit‐to‐risk ratio. However, the finding that a minority of individuals diagnosed initially with schizophrenia appear to be relapse free for long periods, despite absence of sustained antipsychotic treatment, calls for further research on patient‐level predictors of positive outcomes in people with an initial psychotic presentation.     

Does menopausal transition really influence mental health? Findings from the prospective long‐term Zurich study

In the prospective long‐term Zurich study, we re‐examined the hypothesized association between mental health problems in women and the transition through menopausal stages. One hundred sixty‐eight women from a population‐based Swiss community cohort were prospectively followed up from age 21 to 50. At age 50, the occurrence of hot flushes/night sweats and sleep disturbances was significantly more frequent in peri‐ and post‐menopausal women. Irritability/nervousness was increased only in peri‐menopausal women, but that association was accounted for by neuroticism trait scores at age 30. Transitions to peri‐ or post‐menopause were not related to changes in either the prevalence rates of DSM major depressive episode or anxiety disorders, or the course of psychopathological syndromes as assessed by the Symptom Checklist 90 ‐ Revised. The null associations held when adjusting for duration of reproductive period or age at menopause. Preceding mental health problems between ages 21 and 41, increased neuroticism trait scores at age 30, and concurrent psychosocial distress were significantly related to mental health problems occurring between ages 41 and 50. Depending upon the cut‐off point that was chosen, the arbitrary dichotomization of a continuous depression outcome produced spurious associations with the menopausal transition. We conclude that mental health problems between ages 41 and 50 are probably not directly related to the menopausal transition, and that previously reported associations could be false positives due to inadequate dichotomizations, reporting bias, undisclosed multiple adjustments or overfitting.     

Exploring lake ecosystems: hierarchy responses to long‐term change?

Shifts in climate regime have provoked substantial trophic‐ and species‐dependent changes within ecosystems. With growing concerns of present global warming, we examined potential lake ecosystem responses, natural hierarchy responses (i.e. immediate responses at lower system levels as opposed to delayed responses at higher system levels), and possible shifts among abiotic (physics, nutrients) and biotic (phytoplankton, zooplankton) system components. Specifically, we analyzed decadal data collected from Müggelsee, a lake in Berlin, Germany, for climate‐induced abiotic and biotic changes, their timing and type, and classified them as abrupt permanent, gradual permanent, abrupt temporary, or monotonic. We further categorized variable changes as a function of system hierarchy, including lake physics (ice, temperature, stratification), nutrients (phosphorus, nitrogen, silicate), plankton, and levels of integration (i.e. species, taxonomic groups, and total plankton). Contrary to current theory, data suggest abrupt responses did not occur in a hierarchy‐dependent manner, nor was a clear pattern observed among functional system‐based categories. Abrupt permanent changes were the most prominent response pattern observed, suggesting they may be driven by large‐scale climatic oscillations and by surpassed thresholds, as noted in previous case studies. Gradual changes coincided with affected abiotic parameters spanning an expansive time range; for example, climatic effects in spring preceded changes in nutrient limitation. Variables displaying no long‐term changes pointed to compensation processes caused by, e.g., simultaneously acting forces of warming trends and climate‐independent changes in trophic state. Nevertheless, the complexity of response patterns at the single system level manifested clear chronological regime shifts in abiotic and biotic parameters in spring and, to a lesser extent, in summer. With regard to projected global warming, the majority of currently unaffected system levels may face impending thermal thresholds, achievement of which would result in an accelerated shift in ecosystem state.     

Dynamics in Central European near‐natural Abies‐Fagus forests: Does the mosaic‐cycle approach provide an appropriate model?

Question: The mosaic‐cycle concept of forest dynamics dominates in Central Europe. According to this concept intermediate‐scale disturbances only accelerate the forest break‐up under existing cycles of forest development. Is such an approach correct, or should new developmental cycles be elaborated for intermediate‐scale disturbances? Location: Near‐natural Abies alba ‐ Fagus sylvatica forests in the ?wiétokrzyski National Park in Central Poland. In these forests intermediate‐scale disturbances occurred between 1970 and 1990. Methods: Data were collected twice in areas surrounding 212 permanent sample points (in 1994 and 2004). Two increment cores were taken from 259 sample Abies trees. The effect of intermediate‐scale disturbances on radial increment of Abies was assessed. Probabilities of stand transition during a 10‐year period between individual stages and phases of development of the mixed forest were calculated. The development stages and phases were arranged into hypothetical succession series of successive changes. Results: In 1994 70 stands and in 2004, 47 stands representing stages and phases containing the older generation formed by trees > 100–150 years were found. Also, in 1994 142 and in 2004, 165 stands representing stages and phases containing the younger generations only, formed by trees < 100‐150 years, were recorded. Stages and phases containing only younger generations do not occur in the existing forest development cycle which does not consider the influence of intermediate‐scale disturbances separately. Two developmental cycles, which take into account the presence of the older generation and the younger generations only (under conditions of the occurrence of intermediate‐scale disturbances), are proposed. Conclusion: The mosaic‐cycle concept of forest dynamics can be used to analyse the dynamics of Central European near‐natural mixed‐species forests, but new developmental cycles should be elaborated for intermediate‐scale disturbances.     

Do photosynthetic limitations of evergreen Quercus ilex leaves change with long‐term increased drought severity?

Seasonal drought can severely impact leaf photosynthetic capacity. This is particularly important for Mediterranean forests, where precipitation is expected to decrease as a consequence of climate change. Impacts of increased drought on the photosynthetic capacity of the evergreen Quercus ilex were studied for two years in a mature forest submitted to long‐term throughfall exclusion. Gas exchange and chlorophyll fluorescence were measured on two successive leaf cohorts in a control and a dry plot. Exclusion significantly reduced leaf water potential in the dry treatment. In both treatments, light‐saturated net assimilation rate (A_max), stomatal conductance (g_s), maximum carboxylation rate (V_cmax), maximum rate of electron transport (J_max), mesophyll conductance to CO₂ (g_m) and nitrogen investment in photosynthesis decreased markedly with soil water limitation during summer. The relationships between leaf photosynthetic parameters and leaf water potential remained identical in the two treatments. Leaf and canopy acclimation to progressive, long‐term drought occurred through changes in leaf area index, leaf mass per area and leaf chemical composition, but not through modifications of physiological parameters.     

Genomic‐scale comparison of sequence‐ and structure‐based methods of function prediction: Does structure provide additional insight?

A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.     

Is long‐term protection useful for the regeneration of disturbed plant communities in dry areas?

In dry areas, natural plant communities are mainly affected by climatic stress and human disturbances – overgrazing, ploughing and biomass harvesting – that accelerate their degradation. Management techniques, including creation of national parks (fencing), are needed to conserve natural resources/biodiversity. The long‐term effects of protection on the plant communities should be monitored. This study assessed the results of long‐term protection on the composition and diversity of the natural plant communities of Sidi Toui National Park (southern Tunisia) using the point‐quadrat method and ecological indicators of the ecosystem structure. Comparison of these indicators for the period 1990–2011 inside (fenced) and outside (disturbed) the Park showed that regeneration of natural vegetation increased during the first decade of the fencing period (1990–2001), but declined during the period (2008–2011). After a long period of fencing, plant tufts were bigger and aged, and the ecosystem dynamics decreased. In the absence of animal activities, the hardpan at the soil surface impedes seedling emergence. This suggests that long‐term fencing is not recommended for conserving floral diversity in dryland ecosystems. To ensure and maintain the regeneration of these ecosystems, fencing periods alternating with controlled grazing (by introducing wild herbivores) are recommended.     

Are long‐term widespread avian body size changes related to food availability? A test using contemporaneous changes in carotenoid‐based color

Recent changes in global climate have been linked with changes in animal body size. While declines in body size are commonly explained as an adaptive thermoregulatory response to climate warming, many species do not decline in size, and alternative explanations for size change exist. One possibility is that temporal changes in animal body size are driven by changes in environmental productivity and food availability. This hypothesis is difficult to test due to the lack of suitable estimates that go back in time. Here, we use an alternative, indirect, approach and assess whether continent‐wide changes over the previous 100 years in body size in 15 species of Australian birds are associated with changes in their yellow carotenoid‐based plumage coloration. This type of coloration is strongly affected by food availability because birds cannot synthesize carotenoids and need to ingest them, and because color expression depends on general body condition. We found significant continent‐wide intraspecific temporal changes in body size (wing length) and yellow carotenoid‐based color (plumage reflectance) for half the species. Direction and magnitude of changes were highly variable among species. Meta‐analysis indicated that neither body size nor yellow plumage color showed a consistent temporal trend and that changes in color were not correlated with changes in size over the past 100 years. We conclude that our data provide no evidence that broad‐scale variation in food availability is a general explanation for continent‐wide changes in body size in this group of species. The interspecific variability in temporal changes in size as well as color suggests that it might be unlikely that a single factor drives these changes, and more detailed studies of museum specimens and long‐term field studies are required to disentangle the processes involved.     

Why are leaf‐cutting ants more common in early secondary forests than in old‐growth tropical forests? An evaluation of the palatable forage hypothesis

I evaluated the hypothesis that leaf‐cutting ants are more common in early successional forests than in old‐growth forests because pioneer species, which dominate in early successional habitats, appear more susceptible to leafcutters than shade‐tolerant species, which dominate primary forests (palatable forage hypothesis). The relative importance of pioneer and shade‐tolerant species as plant resources for leaf‐cutting ant colonies was evaluated (1) by literature review of leaf‐cutting ants’ diet, and (2) experimentally, using field assays to determine leafcutter's selectivity. Pioneer species were harvested three times more frequently than shade‐tolerant species and made up the largest component of the diet in all the studies reviewed. The amount harvested was not correlated with the plant species abundance. In addition, leaves from pioneer plants were selected eight times more than leaves from shade‐tolerant species in the field assays. These results support the palatable forage hypothesis. Leafcutters probably select pioneer leaves because of their low level of chemical defenses and high nutrient content. The high availability of pioneer species in early successional forest probably decreases the cost to locate palatable resources. Therefore, early successional habitats support more ant colonies than old‐growth forests. On the other hand, the effective defense mechanisms of mature plant species and the high dispersion of palatable plants could explain the low density of leaf‐cutting ant colonies in old‐growth forests. The palatable forage hypothesis is compared with other hypotheses that explain leaf‐cutting ant density. The preference of foundress queens for forest clearings, the dependence of small colonies on herbs, and the importance of pioneer plant species for mature colonies (palatable forage hypothesis) can be considered complementary, because they focus on different stages of the colony's life history. Consequently, the availability of pioneer plants appears to be one of the most influential factors determining mature leaf‐cutting ant nest densities in Neotropical forests.     

Why do some small islands lack vegetation? Evidence from long‐term introduction experiments

Classic island biogeography theory predicts that very small islands, near the extreme lower end of the species–area relationship, should support very few species. At times no species may be present, however, due to randomness in the immigration–extinction dynamics. Alternatively, a lack of vegetation on very small islands may indicate that such islands do not contain the appropriate habitat for the establishment or long‐term survival of plants, or that disturbances are too frequent or intense. These potential mechanisms were evaluated in the central Exumas, Bahamas, where surveys of 117 small islands revealed that over a third of the islands supported no terrestrial plant life. Area and exposure were significant predictors of whether a small island was vegetated or not in multiple logistic regressions. No islands naturally devoid of vegetation were colonized over a 17‐yr period, and only two naturally vegetated islands lost all vegetation. Experimental introductions of two species –Sesuvium portulacastrum and Borrichia arborescens– revealed that a number of islands naturally lacking vegetation were able to sustain introduced populations over the long term (up to 15 yr). Drought and hurricanes appeared to have reduced the establishment success and possibly long‐term survival of the introductions, although some populations survived four major hurricanes. Turnover rates of both introduced species were often an order of magnitude higher on the experimental introduction islands than on other islands in the archipelago. It appears many of the islands in this system that naturally lack vegetation may be physically capable of supporting terrestrial plant life, yet have no plants primarily due to barriers to colonization.