How do primates affect seed germination? A meta‐analysis of gut passage effects on neotropical plants

Biotic seed dispersal is a key process maintaining biodiversity in tropical forests where most trees produce vertebrate‐dispersed seeds. Existing meta‐analyses suggest an overall positive effect of vertebrate gut passage on seed germination, but no significant effects for non‐flying mammals. However, previous meta‐analyses combined rodents (seed predators) and primates (seed dispersers) into the non‐flying mammals category, which may confound specific effects of each group on seed germination. However positive effects of monkeys on germination had previously been found in some studies. Here we disentangle the role of Neotropical primates as contributors to seed dispersal in tropical forests by running a meta‐analysis to determine the overall magnitude of gut passage effects on seed germination percentage and mean time to germination. We also compare effect sizes as a function of different feeding guilds, gut complexities, and seed size. Our results show a strong, positive effect of primates on seed germination percentage and on the number of days to first germination. Strictly frugivorous monkeys, the group most threatened by extinction, showed the highest dispersal quality, increasing germination percentage by 75%. Primates that include insects in their diets had no average effect on germination percentage or time. Gut passage had different outcomes on seeds with different sizes; both large and small seeds showed similar increases in germination percentages after gut passage, but only large seeds germinated faster than control seeds after gut passage. Our results show a relevant role for primates in providing high seed dispersal quality and as drivers of forest regeneration. The combined effects of defaunation and forest fragmentation may result in decreased regeneration of trees, which has the potential to affect negatively both forest structure and ecosystem processes. Finally, we provide general guidelines for standardizing research on seed dispersal by primates. Synthesis Consuming fleshy fruits and dispersing seeds is the main ecological service provided by vertebrates to plants. Vertebrate increases seed germination due to treatment given during digestive system passage. Previous meta‐analyses suggest an overall positive effect of vertebrate gut passage on germination, but no insights are available on its variation among different functional groups of mammals. Our analyses indicated that gut passage by Neotropical primates increased seed germination. Strict frugivores, the ones most threatened by extinction, were the most efficient. Our results show a relevant role for primates in providing high seed dispersal quality and as drivers of forest regeneration, which can be meaningful for conservation in a community scale.     

How does elevated ozone impact soybean? A meta‐analysis of photosynthesis,growth and yield

Surface ozone concentrations ([O₃]) during the growing season in much of the northern temperate zone reach mean peak daily concentrations of 60 p.p.b. Concentrations are predicted to continue to rise over much of the globe during the next 50 years. Although these low levels of ozone may not induce visible symptoms on most vegetation, they can result in substantial losses of production and reproductive output. Establishing the vulnerability of vegetation to rising background ozone is complicated by marked differences in findings between individual studies. Ozone effects are influenced by exposure dynamics, nutrient and moisture conditions, and the species and cultivars that are investigated. Meta‐analytic techniques provide an objective means to quantitatively summarize treatment responses. Soybean has been the subject of many studies of ozone effects. It is both the most widely planted dicotyledonous crop and a model for other C₃ annual plants. Meta‐analytic techniques were used to quantitatively summarize the response of soybean to an average, chronic ozone exposure of 70 p.p.b., from 53 peer‐reviewed studies. At maturity, the average shoot biomass was decreased 34% and seed yield was 24% lower. Even in studies where [O₃] was < 60 p.p.b., there was a significant decrease in biomass and seed production. At low [O₃], decreased production corresponded to a decrease in leaf photosynthesis, but in higher [O₃] the larger loss in production was associated with decreases in both leaf photosynthesis and leaf area. The impact of ozone increased with developmental stage, with little effect on vegetative growth and the greatest effect evident at completion of seed filling. Other stress treatments, including UV‐B and drought, did not alter the ozone response. Elevated carbon dioxide significantly decreased ozone‐induced losses, which may be explained by a significant decrease in stomatal conductance.     

How does the magnitude of genetic variation affect ecological and reproductive character displacement?

While previous studies on character displacement tended to focus on trait divergence and convergence as a result of long-term evolution, recent studies suggest that character displacement can be a special case of evolutionary rescue, where rapid evolution prevents species extinction by weakening interspecific competition. Here we analyzed a simple model to examine how the magnitude of genetic variation affects evolutionary rescue via ecological and reproductive character displacement that weakens interspecific competition in exploitation of shared resources (i.e., resource competition) and in the mating process caused by incomplete species recognition (i.e., reproductive interference), respectively. We found that slow trait divergence due to small genetic variance results in species extinction in reproductive character displacement but not in ecological character displacement. This is because one species becomes rare in slow character displacement, and this causes deterministic extinction due to minority disadvantage of reproductive interference. On the other hand, there is no deterministic extinction in the process of ecological character displacement. Furthermore, species extinction becomes less likely in the case of positive covariance between ecological and reproductive traits as divergence of the ecological trait (e.g., root depths) increases the divergence speed of the reproductive trait (e.g., flower colors) and vice versa. It will be interesting to compare intraspecific genetic (co)variance of ecological and reproductive traits in future studies for understanding how ecological and reproductive character displacement occur without extinction.     

Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations?

Accurately estimating genetic variance components is important for studying evolution in the wild. Empirical work on domesticated and wild outbred populations suggests that dominance genetic variance represents a substantial part of genetic variance, and theoretical work predicts that ignoring dominance can inflate estimates of additive genetic variance. Whether this issue is pervasive in natural systems is unknown, because we lack estimates of dominance variance in wild populations obtained in situ. Here, we estimate dominance and additive genetic variance, maternal variance, and other sources of nongenetic variance in eight traits measured in over 9000 wild nestlings linked through a genetically resolved pedigree. We find that dominance variance, when estimable, does not statistically differ from zero and represents a modest amount (2-36%) of genetic variance. Simulations show that (1) inferences of all variance components for an average trait are unbiased; (2) the power to detect dominance variance is low; (3) ignoring dominance can mildly inflate additive genetic variance and heritability estimates but such inflation becomes substantial when maternal effects are also ignored. These findings hence suggest that dominance is a small source of phenotypic variance in the wild and highlight the importance of proper model construction for accurately estimating evolutionary potential.     

What explains variation in the impacts of exotic plant invasions on the nitrogen cycle? A meta‐analysis

Exotic plant invasions can notably alter the nitrogen (N) cycle of ecosystems. However, there is large variation in the magnitude and direction of their impact that remains unexplained. We present a structured meta‐analysis of 100 papers, covering 113 invasive plant species with 345 cases of invasion across the globe and reporting impacts on N cycle‐related metrics. We aim to explain heterogeneity of impacts by considering methodological aspects, properties of the invaded site and phylogenetic and functional characteristics of the invaders and the natives. Overall, plant invasions increased N pools and accelerated fluxes, even when excluding N‐fixing invaders. The impact on N pools depended mainly on functional differences and was greater when the invasive plants and the natives differed in N‐fixation ability, plant height and plant/leaf habit. Furthermore, the impact on N fluxes was related mainly to climate, being greater under warm and moist conditions. Our findings show that more functionally distant invaders occurring in mild climates are causing the strongest alterations to the N cycle.     

How does competition affect the transmission of information?

The use of social information is a prerequisite to the evolution of culture. In humans, social learning allows individuals to aggregate adaptive information and increase the complexity of technology at a level unparalleled in the animal kingdom. However, the potential to use social information is related to the availability of this type of information. Although most cultural evolution experiments assume that social learners are free to use social information, there are many examples of information withholding, particularly in ethnographic studies. In this experiment, we used a computer-based cultural game in which players were faced with a complex task and had the possibility to trade a specific part of their knowledge within their groups. The dynamics of information transmission were studied when competition was within- or exclusively between-groups. Our results show that between-group competition improved the transmission of information, increasing the amount and the quality of information. Further, informational access costs did not prevent social learners from performing better than individual learners, even when between-group competition was absent. Interestingly, between-group competition did not entirely eliminate access costs and did not improve the performance of players as compared with within-group competition. These results suggest that the field of cultural evolution would benefit from a better understanding of the factors that underlie the production and the sharing of information.     

How does mutation affect the distribution of phenotypes?

The potential for mutational processes to influence patterns of neutral or adaptive phenotypic evolution is not well understood. If mutations are directionally biased, shifting trait means in a particular direction, or if mutation generates more variance in some directions of multivariate trait space than others, mutation itself might be a source of bias in phenotypic evolution. Here, we use mutagenesis to investigate the affect of mutation on trait mean and (co)variances in zebrafish, Danio rerio. Mutation altered the relationship between age and both prolonged swimming speed and body shape. These observations suggest that mutational effects on ontogeny or aging have the potential to generate variance across the phenome. Mutations had a far greater effect in males than females, although whether this is a reflection of sex‐specific ontogeny or aging remains to be determined. In males, mutations generated positive covariance between swimming speed, size, and body shape suggesting the potential for mutation to affect the evolutionary covariation of these traits. Overall, our observations suggest that mutation does not generate equal variance in all directions of phenotypic space or in each sex, and that pervasive variation in ontogeny or aging within a cohort could affect the variation available to evolution.     

How does pollination mutualism affect the evolution of prior self‐fertilization? A model

The mode of pollination is often neglected regarding the evolution of selfing. Yet the distribution of mating systems seems to depend on the mode of pollination, and pollinators are likely to interfere with selfing evolution, since they can cause strong selective pressures on floral traits. Most selfing species reduce their investment in reproduction, and display smaller flowers, with less nectar and scents (referred to as selfing syndrome). We model the evolution of prior selfing when it affects both the demography of plants and pollinators and the investment of plants in pollination. Including the selfing syndrome in the model allows to predict several outcomes: plants can evolve either toward complete outcrossing, complete selfing, or to a stable mixed‐mating system, even when inbreeding depression is high. We predict that the evolution to high prior selfing could lead to evolutionary suicides, highlighting the importance of merging demography and evolution in models. The consequence of the selfing syndrome on plant–pollinator interactions could be a widespread mechanism driving the evolution of selfing in animal‐pollinated taxa.     

How does variance in fertility change over the demographic transition?

Most work on the human fertility transition has focused on declines in mean fertility. However, understanding changes in the variance of reproductive outcomes can be equally important for evolutionary questions about the heritability of fertility, individual determinants of fertility and changing patterns of reproductive skew. Here, we document how variance in completed fertility among women (45–49 years) differs across 200 surveys in 72 low- to middle-income countries where fertility transitions are currently in progress at various stages. Nearly all (91%) of samples exhibit variance consistent with a Poisson process of fertility, which places systematic, and often severe, theoretical upper bounds on the proportion of variance that can be attributed to individual differences. In contrast to the pattern of total variance, these upper bounds increase from high- to mid-fertility samples, then decline again as samples move from mid to low fertility. Notably, the lowest fertility samples often deviate from a Poisson process. This suggests that as populations move to low fertility their reproduction shifts from a rate-based process to a focus on an ideal number of children. We discuss the implications of these findings for predicting completed fertility from individual-level variables.     

How does climate warming affect plant‐pollinator interactions?

Climate warming affects the phenology, local abundance and large-scale distribution of plants and pollinators. Despite this, there is still limited knowledge of how elevated temperatures affect plant-pollinator mutualisms and how changed availability of mutualistic partners influences the persistence of interacting species. Here we review the evidence of climate warming effects on plants and pollinators and discuss how their interactions may be affected by increased temperatures. The onset of flowering in plants and first appearance dates of pollinators in several cases appear to advance linearly in response to recent temperature increases. Phenological responses to climate warming may therefore occur at parallel magnitudes in plants and pollinators, although considerable variation in responses across species should be expected. Despite the overall similarities in responses, a few studies have shown that climate warming may generate temporal mismatches among the mutualistic partners. Mismatches in pollination interactions are still rarely explored and their demographic consequences are largely unknown. Studies on multi-species plant-pollinator assemblages indicate that the overall structure of pollination networks probably are robust against perturbations caused by climate warming. We suggest potential ways of studying warming-caused mismatches and their consequences for plant-pollinator interactions, and highlight the strengths and limitations of such approaches.     

Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta‐analysis

Meta-analysis is increasingly used in ecology and evolutionary biology. Yet, in these fields this technique has an important limitation: phylogenetic non-independence exists among taxa, violating the statistical assumptions underlying traditional meta-analytic models. Recently, meta-analytical techniques incorporating phylogenetic information have been developed to address this issue. However, no syntheses have evaluated how often including phylogenetic information changes meta-analytic results. To address this gap, we built phylogenies for and re-analysed 30 published meta-analyses, comparing results for traditional vs. phylogenetic approaches and assessing which characteristics of phylogenies best explained changes in meta-analytic results and relative model fit. Accounting for phylogeny significantly changed estimates of the overall pooled effect size in 47% of datasets for fixed-effects analyses and 7% of datasets for random-effects analyses. Accounting for phylogeny also changed whether those effect sizes were significantly different from zero in 23 and 40% of our datasets (for fixed- and random-effects models, respectively). Across datasets, decreases in pooled effect size magnitudes after incorporating phylogenetic information were associated with larger phylogenies and those with stronger phylogenetic signal. We conclude that incorporating phylogenetic information in ecological meta-analyses is important, and we provide practical recommendations for doing so.     

Salt tolerance in Lycopersicon species. V. Does genetic variability at quantitative trait loci affect their analysis?

 Salt tolerance was studied comparatively in three families derived from crosses between Lycopersicon esculentum Mill. and two related wild species [two accessions of Lycopersicon pimpinellifolium (Jusl.) Mill. and one accession of Lycopersicon chesmannii f.minor (Hook.f.) Mull.] by means of QTL analysis of fruit yield and earliness under conditions of salinity. From six polymorphic genomic regions involved in salt tolerance, three contained segregant salt-tolerant QTLs for the three families; two were found only in both families derived from L.pimpinellifolium; and one, involved in fruit number, was detected only in one of the L.pimpinellifolium families. Some differences regarding the effects of the wild alleles at orthologous QTLs were found. These effects were always negative in the L. chesmannii family. Comparing both L. pimpinellifolium families, the “wild” alleles at two out of nine common QTLs for fruit number and weight had effects with opposite directions, and the mode of gene action was clearly different at five of them. QTL analysis of earliness revealed the largest genotypic differences among families. Most drastic differences were found for the epistatic interactions in which all genomic regions containing QTLs were involved. These interactions between unlinked genes increased the range of variation of means, mainly upwards, as compared with genotypes at individual QTLs. Only one (affecting fruit weight) out of 27 interactions was detected in both L.pimpinellifolium families. Heterotic effects found for salt tolerance in one of the families can be explained by the presence of overdominant (or pseudo-overdominant) and dominant gene effects at QTLs controlling final fruit yield under conditions of salinity. Allelic variation at salt-tolerant QTLs exists, changing the additive and, mainly, the non-additive components of the genotypic value. Consequently, it may negatively affect the general applicability (or efficiency) of marker-assisted selection to improve salt tolerance in other segregant populations where QTLs were not studied. The use of more informative co-dominant markers, like microsatelites, might overcome these problems. Received: 5 August 1996/Accepted: 25 October 1996     

How do genetic correlations affect species range shifts in a changing environment?

Species may be able to respond to changing environments by a combination of adaptation and migration. We study how adaptation affects range shifts when it involves multiple quantitative traits evolving in response to local selection pressures and gene flow. All traits develop clines shifting in space, some of which may be in a direction opposite to univariate predictions, and the species tracks its environmental optimum with a constant lag. We provide analytical expressions for the local density and average trait values. A species can sustain faster environmental shifts, develop a wider range and greater local adaptation when spatial environmental variation is low (generating low migration load) and multitrait adaptive potential is high. These conditions are favoured when nonlinear (stabilising) selection is weak in the phenotypic direction of the change in optimum, and genetic variation is high in the phenotypic direction of the selection gradient.     

How does poaching affect the size of national parks?

A variety of human activities have detrimental impacts on populations of species the park is designed to protect. These impacts range from direct hunting for trophy or subsistence needs, through vehicular collisions, to the direct loss of habitat due to forestry and agricultural activity. These impacts reduce the effective size of the parks and require changes in management policy that deal both with the direct cause of the problem and the underlying social conflicts that the presence of parks can place on humans in the surrounding communities. Recent studies from the Serengeti illustrate that increases in anti-poaching patrols increase the risk of poacher detection and lead to dramatic declines in levels of poaching. The economic arguments that support investment in anti-poaching patrols, rather than increased sentences for poachers who are caught, can be generalized to examine the costs and benefits of other changes in natural resource management that arise when attempting to manage the impact of anthropogenic activities in and around national parks.     

How does Sec63 affect the conformation of Sec61 in yeast?

The Sec complex catalyzes the translocation of proteins of the secretory pathway into the endoplasmic reticulum and the integration of membrane proteins into the endoplasmic reticulum membrane. Some substrate peptides require the presence and involvement of accessory proteins such as Sec63. Recently, a structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins was determined by cryo-electron microscopy (cryo-EM). Here, we show by co-precipitation that the Sec61 channel subunit Sbh1 is not required for formation of stable Sec63-Sec61 contacts. Molecular dynamics simulations started from the cryo-EM conformation of Sec61 bound to Sec63 and of unbound Sec61 revealed how Sec63 affects the conformation of Sec61 lateral gate, plug, pore region and pore ring diameter via three intermolecular contact regions. Molecular docking of SRP-dependent vs. SRP-independent signal peptide chains into the Sec61 channel showed that the pore regions affected by presence/absence of Sec63 play a crucial role in positioning the signal anchors of SRP-dependent substrates nearby the lateral gate.     

How does the age of hoverfly females affect their reproduction?

In the present study, we observed the effect of age of Episyrphus balteatus DeGeer (Diptera, Syrphidae) females on their fecundity and fertility (number and percentage of fertile eggs). Eight newborn E. batteatus couples were placed in separated cages (30 cm x 30 cm x 60 cm) and the number of eggs laid and the egg viability were recorded daily during 45 days. E. balteatus females had a pre-oviposition period of 10 days before mating happened. The fecundity increased steadily from day 11 to day 16 with an average of 30 eggs a day. During the following days (from day 23 to day 45), we found that the optimal fecundity was observed every second day and that 70.47% of the eggs laid during the entire life of the females were fertile. We also found that the fertility decreased significantly when the females were older than 38 days. As result, the age of hoverfly females influence significantly on their reproduction, with suggesting that hoverfly females from 2 to 5 weeks old are important agents for biological control programs.     

How is sexual conflict over parental care resolved? A meta‐analysis

Biparental care of offspring is both a form of cooperation and a source of conflict. Parents face a trade‐off between current and future reproduction: caring less for the current brood allows individuals to maintain energy reserves and increase their chances of remating. How can selection maintain biparental care, given this temptation to defect? The answer lies in how parents respond to changes in each other’s effort. Game‐theoretical models predict that biparental care is evolutionarily stable when reduced care by one parent leads its partner to increase care, but not so much that it completely compensates for the lost input. Experiments designed to reveal responses to reduced partner effort have mainly focused on birds. We present a meta‐analysis of 54 such studies, and conclude that the mean response was indeed partial compensation. Males and females responded differently and this was in part mediated by the type of manipulation used.     

How does averaging affect protein structure comparison on the ensemble level?

Recent algorithmic advances and continual increase in computational power have made it possible to simulate protein folding and dynamics on the level of ensembles. Furthermore, analyzing protein structure by using ensemble representation is intrinsic to certain experimental techniques, such as nuclear magnetic resonance. This creates a problem of how to compare an ensemble of molecules with a given reference structure. Recently, we used distance-based root-mean-square deviation (dRMS) to compare the native structure of a protein with its unfolded-state ensemble. We showed that for small, mostly alpha-helical proteins, the mean unfolded-state Calpha-Calpha distance matrix is significantly more nativelike than the Calpha-Calpha matrices corresponding to the individual members of the unfolded ensemble. Here, we give a mathematical derivation that shows that, for any ensemble of structures, the dRMS deviation between the ensemble-averaged distance matrix and any given reference distance matrix is always less than or equal to the average dRMS deviation of the individual members of the ensemble from the same reference matrix. This holds regardless of the nature of the reference structure or the structural ensemble in question. In other words, averaging of distance matrices can only increase their level of similarity to a given reference matrix, relative to the individual matrices comprising the ensemble. Furthermore, we show that the above inequality holds in the case of Cartesian coordinate-based root-mean-square deviation as well. We discuss this in the context of our proposal that the average structure of the unfolded ensemble of small helical proteins is close to the native structure, and demonstrate that this finding goes beyond the above mathematical fact.