Efficiency of indirect selection at selection equilibrium

Summary Efficiency of indirect selection compared with that of direct selection to increase the mean value of some trait has been usually studied by considering a single generation of indirect and direct responses to selection only. However, under continued selection, genetic variances and covariances, and therefore expected genetic responses, change each generation due to linkage disequilibrium. With directional and truncation selection, genetic parameters asymptote to limiting values after several generations. The efficiency of indirect selection is examined in this limiting situation. The ratio of correlated response to direct response for the trait to improve in the limit is compared with the ratio after the first generation of selection. For all initial parameter values for which indirect selection is more efficient than direct selection, relative efficiency of indirect selection is smaller in the limit than in the first generation. For some parameter values, indirect selection is more efficient than direct selection in the first generation, but less efficient in the limit. Expressions for minimum values of the initial genetic correlation and heritability of the alternative trait required for indirect selection to be preferred in the limit are derived. These values are higher when limiting responses are used instead of single generation responses. The loss in relative efficiency of indirect selection from changes in genetic parameters due to selection should be taken into account when applications of indirect selection are considered.     

Agricultural food subsidies, migratory connectivity and large-scale disturbance in arctic coastal systems: a case study

An allochthonous input can modify trophic relationships, byproviding an external resource that is normally limiting withina system. The subsidy may not only elicit a growth responseof the primary producers via a bottom-up effect, but it alsomay lead to runaway herbivore growth in the absence of increasedpredation. If the consumer is migratory and predation is similarlydampened in the alternative system, the increased numbers mayproduce a top-down cascade of direct and indirect effects onan ecosystem that may be a great distance from the source ofthe subsidy. In an extreme case, it can lead to a catastrophicshift in ecosystem functioning as a result of biotic exploitationthat produces an alternative stable state. The loss of resilienceis particularly sensitive to herbivore density which can resultin two different outcomes to the vegetation on which the consumerfeeds. Over-compensatory growth of above-ground biomass givesway to sward destruction and near irreversible changes in soilproperties as density of a herbivore increases. A striking temporalasymmetry exists between a reduction in the consumer populationand recovery of damaged vegetation and degraded soils.     

Beyond the browse line: complex cascade effects mediated by white‐tailed deer

In many ecosystems, browsing of large mammals can affect plant species compositions. However, much less is known about potential above‐ and below‐ground trophic interactions of large browsing mammals. This study focused on the direct and indirect effects of browsing on trophic and abiotic interactions within forest ecosystems. To quantify above‐ and below‐ground cascade effects, white‐tailed deer have been excluded for over 18 years from three 4‐ha plots, which were paired with same sized deer access plots. Our results demonstrate complex direct and indirect cascade effects on forest food webs. Deer exclusion directly altered woody species composition and significantly increased shrub and sapling density. Above‐ground cascade effects include greater leaf litter accumulation and higher arthropod density and biomass within the exclosures. Below‐ground indirect effects include significant decrease in soil nutrients, and higher arbuscular mycorrhizal fungal inoculum potential in the exclosures. Because ecosystems have finite resource availability, high deer density may imbalance the system by redirecting resources toward maintaining deer biomass at the expense of multiple trophic levels throughout the forest community. Both complex bottom up and top down trophic cascade effects demonstrated largely unidirectional negative responses suggesting that high deer density has reduced the biodiversity of the forest community.     

Effect of selection on genetic parameters of correlated traits

Summary Changes in genetic parameters of correlated traits due to the buildup of linkage (gametic phase) disequilibrium from repeated truncation selection on a single trait are studied. After several generations of selection, an equilibrium is approached where there are no further changes in genetic parameters and limiting values are reached. Formulae are derived under an infinitesimal model for these limiting values of genetic variances and covariances, heritabilities, and genetic correlations between traits directly and indirectly selected. Changes from generation zero to the limit in all these parameters become greater as heritability of the trait under direct selection increases and, to a lesser extent, as intensity of selection increases. Change in heritability of a trait under indirect selection also increases as the absolute value of the correlation between the trait under indirect and the trait under direct selection increases. The change is maximum when the initial value of heritability is close to 0.5 and insignificant when the initital value is close to zero or one. Change in the genetic correlation between the trait under direct selection and the trait under indirect selection is maximum when its initial value is close to ±0.6 and insignificant when its initial value is close to zero or ±1. Heritability of the trait indirectly selected and genetic correlation between that trait and the trait directly selected always decrease in absolute value, whereas genetic correlation between two traits indirectly selected can either decrease or increase in absolute value. It is suggested that use be made of formulae at selection equilibrium in the prediction of correlated responses after several generations of selection.     

Predator cue and prey density interactively influence indirect effects on Basal resources in intertidal oyster reefs

Predators can influence prey abundance and traits by direct consumption, as well as by non-consumptive effects of visual, olfactory, or tactile cues. The strength of these non-consumptive effects (NCEs) can be influenced by a variety of factors, including predator foraging mode, temporal variation in predator cues, and the density of competing prey. Testing the relative importance of these factors for determining NCEs is critical to our understanding of predator-prey interactions in a variety of settings. We addressed this knowledge gap by conducting two mesocosm experiments in a tri-trophic intertidal oyster reef food web. More specifically, we tested how a predatory fish (hardhead catfish, Ariopsis felis) directly influenced their prey (mud crabs, Panopeus spp.) and indirectly affected basal resources (juvenile oysters, Crassostrea virginica), as well as whether these direct and indirect effects changed across a density gradient of competing prey. Per capita crab foraging rates were inversely influenced by crab density, but they were not affected by water-borne predator cues. As a result, direct consumptive effects on prey foraging rates were stronger than non-consumptive effects. In contrast, predator cue and crab density interactively influenced indirect predator effects on oyster mortality in two experiments, with trait-mediated and density-mediated effects of similar magnitude operating to enhance oyster abundance. Consistent differences between a variable predator cue environment and other predator cue treatments (no cue and constant cue) suggests that an understanding of the natural risk environment experienced by prey is critical to testing and interpreting trait-mediated indirect interactions. Further, the prey response to the risk environment may be highly dependent on prey density, particularly in prey populations with strong intra-specific interactions.     

Female mating decisions: maximizing fitness?

Sexual selection theory assumes that maximizing fitness is the ultimate goal in every mating decision. Fitness can be maximized directly by increasing the number of offspring (direct benefits) or indirectly by maximizing offspring's lifetime reproductive success (indirect benefits). Whereas there is considerable evidence in the literature for the influence of mating decisions on direct benefits, indirect benefits have been more elusive. Here, we review the variables that influence mating decisions made by females of freshwater fish and how these affect their fitness directly, as well as indirectly. Females enhance their fitness by matching their mating decisions to current environmental conditions, using a wide range of pre- and post-copulation mechanisms that enable them to maximize benefits from mating. Male sexual traits and courtship displays are signals used by females as a way of assessing male quality in terms of both direct and indirect benefits. Polyandry is very common among freshwater fish species, and indirect benefits have been hypothesized as drivers of its predominance. Despite intensive theoretical work, and multiple suggestions of the effects of indirect benefits, to date no study has been able to demonstrate experimentally the existence of indirect benefits in freshwater fish species. Additionally, most studies of direct benefits measure short-term benefits of mating decisions. In both cases, lifetime reproductive success is not assessed. Therefore, we are led to conclude that evidence as to whether female mating decisions result in direct and/or indirect benefits in freshwater fish species is still lacking. These results should be considered in light of the ongoing debate about the significance of indirect benefits in female mating decisions.     

Growth and surface binding of proteins byNeisseria meningitidis in normal human serum

The addition of normal human serum to a chemically defined medium stimulated the growth ofNeisseria meningitidis strain M1011 greatly. Both lag times and mean generation times were reduced. Growth in human serum alone was rapid but quickly became nutrientlimited. Iron was not a limiting factor for growth in human serum. One major limiting factor of serum was cysteine.N. meningitidis grown in serum also bound serum proteins, including transferrin and immunoglobulin, as demonstrated by direct and indirect fluorescent-antibody techniques.     

Assessing putative interlocus sexual conflict in Drosophila melanogaster using experimental evolution

The theoretical foundation of sexually antagonistic coevolution is that females suffer a net fitness cost through their interactions with males. The empirical prediction is that direct costs to female lifetime fecundity will exceed indirect benefits despite a possible increase in the genetic quality of offspring. Although direct costs of males have been repeatedly shown, to date no study has comprehensively tested whether females are compensated for this direct harm through indirect benefits. Here we use experimental evolution to show that a mutation giving Drosophila melanogaster females nearly complete resistance to the direct costs of male courtship and remating, but which also excluded almost all indirect benefits, is strongly favoured by selection. We estimated the selection coefficient favouring the resistance allele to be +20%. These results demonstrate that any indirect benefits that females accrued were not sufficient to counter-balance the direct costs of males, and reinforce a large body of past studies by verifying interlocus sexual conflict in this model system.     

Subcellular Metabolite Levels in Spinach Leaves : Regulation of Sucrose Synthesis during Diurnal Alterations in Photosynthetic Partitioning

The alterations of subcellular metabolite levels during the day in spinach leaves have been investigated using nonaqueous density gradient centrifugation to separate chloroplasts, cytosol, and vacuole. The results provide direct evidence for the role of sucrose phosphate synthase and cytosolic fructose 1,6-bisphosphatase in regulating sucrose synthesis in leaves and also show that the phosphate translocator is kinetically limiting in vivo.     

Direct effects of tillage on the activity density of ground beetle (Coleoptera: Carabidae) weed seed predators

Ground beetles are well known as beneficial organisms in agroecosystems, contributing to the predation of a wide range of animal pests and weed seeds. Tillage has generally been shown to have a negative effect on ground beetles, but it is not known whether this is because of direct mortality or the result of indirect losses resulting from dispersal caused by habitat deterioration. In 2005, field experiments measured direct, tillage-induced mortality, of four carabid weed seed predators, Harpalus rufipes DeGeer, Agonum muelleri Herbst, Anisodactylus merula Germar, and Amara cupreolata Putzeys, and one arthropod predator, Pterostichus melanarius Illiger, common to agroecosystems in the northeastern United States. Three tillage treatments (moldboard plow, chisel plow, and rotary tillage) were compared with undisturbed controls at two sites (Stillwater and Presque Isle) and at two dates (July and August) in Maine. Carabid activity density after disturbance was measured using fenced pitfall traps installed immediately after tillage to remove any effects of dispersal. Rotary tillage and moldboard plowing reduced weed seed predator activity density 52 and 54%, respectively. Carabid activity density after chisel plowing was similar to the undisturbed control. This trend was true for each of the weed seed predator species studied. However, activity density of the arthropod predator P. melanarius was reduced by all tillage types, indicating a greater sensitivity to tillage than the four weed seed predator species. These results confirm the need to consider both direct and indirect effects of management in studies of invertebrate seed predators.     

Natural Direct and Indirect Effects on the Exposed: Effect Decomposition under Weaker Assumptions

Summary We define natural direct and indirect effects on the exposed. We show that these allow for effect decomposition under weaker identification conditions than population natural direct and indirect effects. When no confounders of the mediator‐outcome association are affected by the exposure, identification is possible under essentially the same conditions as for controlled direct effects. Otherwise, identification is still possible with additional knowledge on a nonidentifiable selection‐bias function which measures the dependence of the mediator effect on the observed exposure within confounder levels, and which evaluates to zero in a large class of realistic data‐generating mechanisms. We argue that natural direct and indirect effects on the exposed are of intrinsic interest in various applications. We moreover show that they coincide with the corresponding population natural direct and indirect effects when the exposure is randomly assigned. In such settings, our results are thus also of relevance for assessing population natural direct and indirect effects in the presence of exposure‐induced mediator‐outcome confounding, which existing methodology has not been able to address.     

Role of cell attachment in leaching of chalcopyrite mineral by Thiobacillus ferrooxidans

Summary Experiments on the leaching of copper from chalcopyrite mineral by the bacterium Thiobacillus ferrooxidans show that, in the presence of adequate amounts of sulphide, iron-grown bacteria preferentially oxidise sulphur in the ore (through direct attachment) rather than ferrous sulphate in solution. At 20% pulp density, the leaching initially takes place by a predominantly direct mechanism. The cell density in the liquid phase increases, but the Fe²⁺ is not oxidised. However, in the later stages when less solid substrate is available and the cell density becomes very high, the bacteria start oxidising Fe²⁺ in the liquid phase, thus contributing to the indirect mechanism of leaching. Contrary to expectations, the rate of leaching increased with increasing particle size in spite of the decreasing specific surface area. This has been found to be due to increasing attachment efficiency with increase in particle size. Offprint requests to: R. Kumar     

自然环境下影响扬子鳄繁殖的环境因子

生态因子对生物的生长、发育、生殖和分布有着直接和间接的影响.在1998～2005年对扬子鳄繁殖研究中心内自然环境下鳄卵及其繁殖地环境因子进行调查,包括窝卵数、产卵时间、出壳时间、孵化期内温度、湿度的变化情况、雏鳄孵出后的存活数量以及巢区的植被盖度.调查发现天气状况直接影响母鳄产卵时间、卵的孵化质量与雏鳄的出壳数量.盖度相对大于0.5的窝巢中多数卵基本能正常发育,盖度小于0.5的窝巢中可能只有少数几枚卵发育正常.     

Explaining productivity-diversity relationships in plants

Relationships between productivity and diversity in plant communities have been widely documented. Unimodal productivity-diversity relationships are most common along natural productivity gradients, and fertilization generally reduces diversity. Five distinct hypotheses invoke changes in competition to explain why diversity should decline from intermediate to high productivity. Because experiments measuring the effects of competition on diversity are rare, four of the five hypotheses have not been directly tested, but each hypothesis makes unique predictions that allow for indirect tests. The indirect evidence is often conflicting, and while none of the hypotheses can be rejected, only the dynamic equilibrium hypothesis is consistently supported. A new hypothesis, however, is supported by indirect evidence and may help to explain the variation in the shape of productivity-diversity relationships, as well as the most common patterns. Diversity may be high in environments that promote size symmetric competition, where soil resources limit growth and are homogeneously distributed within the soil volume explored by individual plants. Conversely, diversity may be low in environments that promote size asymmetric competition, where light is limiting, or where soil resources are limiting and are patchily distributed within rooting zones.     

微藻光合作用制氢——能源危机的最终出路?

微藻光合作用制氢是解决能源短缺问题的有效途径.本文介绍了微藻光合作用制氢的机理,包括蓝藻固氮酶和可逆氢酶产氢以及绿藻可逆氢酶产氢的机理.在分析光合制氢限制因素的基础上,指出筛选和构建高效放氢藻株是制氢的有效途径.然后介绍了“直接生物光解”、固氮酶放氢和“间接生物光解”等制氢方式.利用绿藻“间接生物光解”水制氢是一种最有发展潜力的制氢方式.本文最后展望了微藻光合制氢的前景.     

Inhibition of the gelation of extracellular and intracellular hemoglobin S by selective acetylation with methyl acetyl phosphate

Methyl acetyl phosphate binds to the 2,3-diphosphoglycerate (2,3-DPG) binding site of hemoglobin and selectively acetylates three amino groups at or near that site. The subsequent binding of 2,3-DPG is thus impeded. When intact sickle cells are exposed to methyl acetyl phosphate, their abnormally high density under anaerobic conditions is reduced to the density range of oxygenated, nonsickling erythrocytes. This change is probably due to a combination of direct and indirect effects induced by the specific acetylation. The direct effect is on the solubility of deoxyhemoglobin S, which is increased from 17 g/dL for unmodified hemoglobin S to 22 g/dL for acetylated hemoglobin S at pH 6.8. Acetylated hemoglobin S does not gel at pH 7.4, up to a concentration of 32 g/dL. The indirect effect could be due to the decreased binding of 2,3-DPG to deoxyhemoglobin S within the sickle erythrocyte, thus hindering the conversion of oxyhemoglobin S to the gelling form, deoxyhemoglobin S.     

Context-dependent effects of ranaviral infection on northern leopard frog life history traits

Pathogens have important effects on host life-history traits, but the magnitude of these effects is often strongly context-dependent. The outcome of an interaction between a host and an infectious agent is often associated with the level of stress experienced by the host. Ranavirus causes disease and mortality in amphibian populations in various locations around the world, but most known cases of ranaviral infection have occurred in North America and the United Kingdom. While Ranavirus virulence has been investigated, the outcome of Ranavirus infection has seldom been related to the host environment. In a factorial experiment, we exposed Northern leopard frog (Lithobates pipiens, formerly Rana pipiens) tadpoles to different concentrations of Ranavirus and investigated the effect of host density on certain life-history traits, namely survival, growth rate, developmental stage and number of days from virus exposure to death. Our results suggest a prominent role of density in driving the direction of the interaction between L. pipiens tadpoles and Ranavirus. We showed that increasing animal holding density is detrimental for host fitness as mortality rate is higher, day of death earlier, development longer and growth rate significantly lower in high-density tanks. We observed a linear increase of detrimental effects when Ranavirus doses increased in low-density conditions, with control tadpoles having a significantly higher overall relative fitness. However, this pattern was no longer observed in high-density conditions, where the effects of increasing Ranavirus dose were limited. Infected and control animals fitness were consequently similar. We speculate that the host may eventually diverts the energy required for a metabolic/immune response triggered by the infection (i.e., direct costs of the infection) to better cope with the increase in environmental "stress" associated with high density (i.e., indirect benefits of the infection). Our results illustrate how the net fitness of organisms may be shaped by ecological context and emphasize the necessity of examining the direct/indirect costs and benefits balance to fully understand host-pathogen interactions.     

First- and second-order sociality determine survival and reproduction in cooperative cichlids

Cooperative breeders serve as a model to study the evolution of cooperation, where costs and benefits of helping are typically scrutinized at the level of group membership. However, cooperation is often observed in multi-level social organizations involving interactions among individuals at various levels. Here, we argue that a full understanding of the adaptive value of cooperation and the evolution of complex social organization requires identifying the effect of different levels of social organization on direct and indirect fitness components. Our long-term field data show that in the cooperatively breeding, colonial cichlid fish Neolamprologus pulcher, both large group size and high colony density significantly raised group persistence. Neither group size nor density affected survival at the individual level, but they had interactive effects on reproductive output; large group size raised productivity when local population density was low, whereas in contrast, small groups were more productive at high densities. Fitness estimates of individually marked fish revealed indirect fitness benefits associated with staying in large groups. Inclusive fitness, however, was not significantly affected by group size, because the direct fitness component was not increased in larger groups. Together, our findings highlight that the reproductive output of groups may be affected in opposite directions by different levels of sociality, and that complex forms of sociality and costly cooperation may evolve in the absence of large indirect fitness benefits and the influence of kin selection.     

Disentangling controls on animal abundance: Prey availability,thermal habitat,and microhabitat structure

The question of what controls animal abundance has always been fundamental to ecology, but given rapid environmental change, understanding the drivers and mechanisms governing abundance is more important than ever. Here, we determine how multidimensional environments and niches interact to determine population abundance along a tropical habitat gradient. Focusing on the endemic lizard Anolis bicaorum on the island of Utila (Honduras), we evaluate direct and indirect effects of three interacting niche axes on abundance: thermal habitat quality, structural habitat quality, and prey availability. We measured A. bicaorum abundance across a series of thirteen plots and used N‐mixture models and path analysis to disentangle direct and indirect effects of these factors. Results showed that thermal habitat quality and prey biomass both had positive direct effects on anole abundance. However, thermal habitat quality also influenced prey biomass, leading to a strong indirect effect on abundance. Thermal habitat quality was primarily a function of canopy density, measured as leaf area index (LAI). Despite having little direct effect on abundance, LAI had a strong overall effect mediated by thermal quality and prey biomass. Our results demonstrate the role of multidimensional environments and niche interactions in determining animal abundance and highlight the need to consider interactions between thermal niches and trophic interactions to understand variation in abundance, rather than focusing solely on changes in the physical environment.     

Early successional mechanisms in the rocky intertidal: the rôle of direct and indirect interactions

Indirect interactions during succession have received relatively little attention compared with direct interactions. The direct and indirect interactions among barnacles, algae, and herbivores in a rocky intertidal boulder field were evaluated. A factorial experimental design manipulating barnacle and limpet densities on cleared plots was employed. Barnacle density and percent cover of alage were monitored fortnightly for 5 months. The removal of a fine algal mat by herbivores led to higher recruitment of barnacles. The herbivores also prevented the establishment of algae in the absence of barnacles. The barnacles provided a refuge from herbivores for the algae by inhibiting the grazing activities of the limpets. In the absence of herbivores, the barnacles did not have a detectable effect on the algae which grew in thick mats. Through direct and indirect interactions, both barnacles and herbivores may have negatively affected their own performance. This suggests that indirect interactions may be important ecologically, but they need not always feed back positively for a species or group of species.