Do we know enough? A scientific and ethical analysis of the basis for genetic-based personalized nutrition

This article discusses the prospects and limitations of the scientific basis for offering personalized nutrition advice based upon individual genetic information. Two divergent scientific positions are presented, with an ethical comment. The crucial question is whether the current knowledge base is sufficiently strong for taking an ethically responsible decision to offer personalized nutrition advice based upon gene–diet–health interaction. According to the first position, the evidence base for translating the outcomes of nutrigenomics research into personalized nutritional advice is as yet immature. There is also limited evidence that genotype-based dietary advice will motivate appropriate behavior changes. Filling the gaps in our knowledge will require larger and better randomized controlled trials. According to the second position, personalized nutrition must be evaluated in relation to generally accepted standard dietary advice—partly derived from epidemiological observations and usually not proven by clinical trials. With personalized nutrition, we cannot demand stronger evidence. In several specific cases of gene–diet interaction, it may be more beneficial for individuals with specific genotypes to follow personalized advice rather than general dietary recommendations. The ethical comment, finally, considers the ethical aspects of deciding how to proceed in the face of such uncertainty. Two approaches for an ethically responsible way forward are proposed. Arguing from a precautionary approach, it is suggested that personalized dietary advice should be offered only when there is strong scientific evidence for health effects, followed by stepwise evaluation of unforeseen behavioral and psychological effects. Arguing from theoretical and applied ethics as well as psychology, it is also suggested that personalized advice should avoid paternalism and instead focus on supporting the autonomous choice of each person.     

Habitat fragmentation and large-scale conservation: what do we know for sure?

We review the ecological effects of habitat fragmentation, comparing the theoretical approaches that have been taken to understanding it with the existing evidence from empirical studies. Theory has emphasized the spatial aspects of fragmentation and the role of dispersal among patches, and has generated interesting predictions such as a nonlinear relationship between the amount of remaining habitat and the probability of species persistence. However, while the few available large-scale empirical studies of fragmentation all tend to show that it has major effects, these documented effects tend to be relatively simple ones such as the degradation of habitat quality within fragments. There is good reason to be cautious of any claim that corridors or the spatial configuration of remaining habitat can compensate for the overall loss of habitat.
This is an invited Minireview on the occasion of the 50th anniversary of the Nordic Ecological Society Oikos.     

Plantations of exotic tree species in Britain: irrelevant for biodiversity or novel habitat for native species?

Novel or emergent ecosystems arising from human action present both threats and opportunities for biodiversity. It has been suggested that exotic species can “facilitate” or “inhibit” native biodiversity through habitat modification. In Britain, there is a discussion over the contribution to biodiversity of plantations of exotic conifer species as these are commonly thought to have little relevancy as a habitat for native biodiversity. To address this we compared the species richness of a range of different taxonomic groups (lichens, bryophytes, fungi, vascular plants, invertebrates and songbirds) in exotic and native forest stands of differing structural stages in northern and southern Britain. In terms of overall native species-richness there was no significant difference between the exotic and the native stands. In the north, six species groups showed higher values in the exotic Sitka spruce (Picea sitchensis) stands with the remaining six showing higher values in the native Scots pine (Pinus sylvestris) stands. Most notably, lichen species richness was much lower in the exotic stands compared to the native stands, whereas bryophyte and fungal species richness was proportionately higher in the exotic stands. In the south, five species groups (all invertebrate taxa) showed higher species richness in exotic Norway spruce (Picea abies) stands compared to native oak (Quercus robur) stands. Five species groups had higher species-richness in the oak stands, in particular lichens and fungi. It is concluded that emergent ecosystems of exotic conifer species are not irrelevant to biodiversity. Where already well-established they can provide habitat for native species particularly if native woodland is scarce and biodiversity restoration is an immediate priority.     

Do we know enough about controlling sediment to mitigate damage to stream ecosystems?

Stream and river ecosystems have suffered extensive degradation, and billions are expended annually on restoration efforts. However, few of these projects are monitored, and restoration effectiveness is often unknown. Consequently, there is a poor scientific foundation for restoration designs. Since many stream restoration efforts are at least partially targeted at controlling erosion of channel banks and beds, the effects of a large-scale, long-term stream erosion control effort in six Mississippi watersheds was assessed using 10–16 years of suspended sediment and water discharge records. Flow-adjusted suspended sediment concentrations showed no trends in five of the watersheds and a slight downward trend in one watershed, which was treated with small reservoirs as well as bed and bank erosion protection. Results indicate the inability of orthodox stream management structures (weirs and bank protection) to reduce watershed sediment yield and the need for a stronger scientific basis for stream restoration.     

Commentary: Do we have a consistent terminology for species diversity? The fallacy of true diversity

There is no single best index that can be used to answer all questions about species diversity. Entropy-based diversity indices, including Hill’s indices, cannot account for geographical and phylogenetic structure. While a single diversity index arises if we impose several constraints—most notably that gamma diversity be completely decomposed into alpha and beta diversity—there are many ecological questions regarding species diversity for which it is counterproductive, requiring decomposability. Non-decomposable components of gamma diversity may quantify important intrinsic ecological properties, such as resilience or nestedness.     

Do forest-dwelling plant species disperse along landscape corridors?

Woody corridors in fragmented landscapes have been proposed as alternative habitats for forest plants, but the great variation in species-specific responses blurs the overall assessment. The aim of this study was to estimate the dispersal success of forest-dwelling plants from a stand into and along an attached woody corridor, and to explain the observed patterns from the point of view of species’ dispersal traits and corridor properties. We sampled 47 forest–corridor transects in the agricultural landscapes of southeastern Estonia. Regionally common forest-dwelling species (observed in at least 10 % of seed-source forests) were classified on the basis of their ecological response profile—forest-restricted species (F-type) and forest-dwelling generalists (G-type). Species richness and the proportion of F-type species decreased sharply from the seed-source forest core to the forest edge and to the first 10–15 m of the corridor, while G-type species richness remained constant throughout the transect. Corridor structure had a species-specific effect—F species were promoted by old (≥50 years) and wide (≥10 m) corridors, while G species were supported by young and narrow corridors with ditch-related soil disturbances. Moderate shade (canopy cover <75 %) was optimal for all forest-dwelling species. Large dispersule weight, and not seed weight, dispersal vector or Ellenberg’s indicator values, was the trait that differentiated F species from G species. We conclude that most woody corridors are only dispersal stepping-stone habitats for habitat generalist species, and not for specialists. Only century old corridors can relieve the dispersal limitation of forest-restricted species.     

Enhancing gardens as habitats for plant-associated invertebrates: should we plant native or exotic species?

Domestic gardens, typically consisting of a mixture of native and non-native plants, support biodiversity. The relative value of these native and non-native plants for invertebrates is largely unknown. To address this a replicated field experiment with plots planted with one of three assemblages of non-invasive perennial and shrubby garden plants (treatments), based on plant origin [UK native, near-native (Northern Hemisphere) and Exotic (Southern Hemisphere)] was established. Over 4 years the invertebrates were recorded by Vortis suction sampler and amount of plant material measured. The abundance of above ground plant-inhabiting invertebrates increased with canopy cover and was higher on the native treatment. For several functional groups including herbivores and some predatory groups the near-native plants supported only marginally fewer individuals compared to native plots, with exotic plants being less favoured. The experiment demonstrated that gardens and other cultivated ornamental plantings support a wide range of plant-inhabiting invertebrates from primary functional groups regardless of the plants’ origin and the more plant matter (canopy cover) available the greater the abundance. Greater abundance of invertebrates will be supported by gardens and cultivated planting schemes with plantings biased towards native and near-native plants and that provide dense vegetation cover. However, exotic plants should not be dismissed as these are inhabited by some invertebrates.     

Do species evenness and plant density influence the magnitude of selection and complementarity effects in annual plant species mixtures?

Abstract Plant species richness influences primary productivity via mechanisms that (1) favour species with particular traits (selection effect) and (2) promote niche differentiation between species (complementarity). Influences of species evenness, plant density and other properties of plant communities on productivity are poorly defined, but may depend on whether selection or complementarity prevails in species mixtures. We predicted that selection effects are insensitive to species evenness but increase with plant density, and that the converse is true for complementarity. To test predictions, we grew three species of annuals in monocultures and in three‐species mixtures in which evenness of established plants was varied at each of three plant densities in a cultivated field in Texas, USA. Above‐ground biomass was smaller in mixtures than expected from monocultures because of negative ‘complementarity’ and a negative selection effect. Neither selection nor complementarity varied with species evenness, but selection effects increased at the greatest plant density as predicted.     

Do we know the absolute values of intracellular free calcium concentration?

More than 20 years ago, it was shown that the addition of EGTA increases the affinity of the plasma membrane Ca2+ pump for Ca2+ by an order of magnitude. The left-hand shift of Ca2+-dependencies in the presence of EGTA has been also documented in studies of the sarcoplasmic reticulum Ca2+ pump, mitochondrial Ca2+-transporter as well as Ca2+-binding by calmodulin and troponin C. These data allow us to hypothesise that this effect is caused by an admixture of di- and trivalent cations possessing high affinity for EGTA and interacting with Ca2+-transporting and binding proteins. Here, we propose that polyvalent cations affect the estimation of absolute values of free intracellular Ca2+ concentration. Indeed, EGTA sharply increases the apparent affinity of the fluorescent Ca2+ indicators quin-2 and fluo-3 for Ca2+. The impact of polyvalent cations on Ca2+ measurement was further confirmed by the study showing the high sensitivity of Ca2+-induced fluo-3 fluorescence to Mn2+, Fe2+, Cu2+, and Co2+ seen in the absence of EGTA.     

Spatial dynamics in model plant communities: what do we really know?

A variety of models have shown that spatial dynamics and small-scale endogenous heterogeneity (e.g., forest gaps or local resource depletion zones) can change the rate and outcome of competition in communities of plants or other sessile organisms. However, the theory appears complicated and hard to connect to real systems. We synthesize results from three different kinds of models: interacting particle systems, moment equations for spatial point processes, and metapopulation or patch models. Studies using all three frameworks agree that spatial dynamics need not enhance coexistence nor slow down dynamics; their effects depend on the underlying competitive interactions in the community. When similar species would coexist in a nonspatial habitat, endogenous spatial structure inhibits coexistence and slows dynamics. When a dominant species disperses poorly and the weaker species has higher fecundity or better dispersal, competition-colonization trade-offs enhance coexistence. Even when species have equal dispersal and per-generation fecundity, spatial successional niches where the weaker and faster-growing species can rapidly exploit ephemeral local resources can enhance coexistence. When interspecific competition is strong, spatial dynamics reduce founder control at large scales and short dispersal becomes advantageous. We describe a series of empirical tests to detect and distinguish among the suggested scenarios.     

Practical tool for landscape planning? An empirical investigation of network based models of habitat fragmentation

This study presents a graph-theoretical modelling approach using daily movements and habitat demands of different target bird species in an urban context to assess: 1) habitable land cover types, 2) threshold distances between patches of habitat, 3) the required minimum accessible habitat areas and 4) the effects of barriers and stepping stones. The modelling approach is tested using empirical data from field surveys in the urban area of Stockholm, Sweden.
The results show that groups of small habitat patches can house the same species as larger contiguous patches as long as they are perceived as functionally connected by the inhabitant organisms. Furthermore, we found that binary habitat/non-habitat representations of the landscape could roughly explain the variation in species occurrence, as long as habitat was properly defined. However, the explanatory power of the landscape models increased when features of matrix heterogeneity such as stepping stones and barriers were accounted for.
Synthesis and application: in a world where forest ecosystems are becoming increasingly fragmented there is an urgent need to find comprehensive and scientifically relevant methods for managing and planning ecosystems. This study shows that: 1) groups of well placed small habitat patches can, together, be sufficient to attract birds in intensively developed areas, 2) the presented modelling approach can help identify such groups of patches, 3) matrix heterogeneity should preferably be accounted for, and 4) proper assessments of habitable land cover types are important. Finally, we argue that the modelling approach applied here may substantially improve landscape management and planning at scales ranging from whole landscapes down to neighbourhoods.     

Do vegetation patch spatial patterns disrupt the spatial organization of plant species?

The mechanisms that structure plant diversity and generate long-range correlated spatial patterns have important implications for the conservation of fragmented landscapes. The ability to disperse and persist influences a plant species’ capacity for spatial organization, which can play a critical role in structuring plant diversity in metacommunities. This study examined the spatial patterns of species diversity within a network of patches in Cabo de Gata Natural Park, southeastern Spain. The objectives were to understand how the spatial heterogeneity of species composition (beta diversity) varies in a structured landscape, and how the long-range spatial autocorrelation of plant species is affected by the spatial configuration of patches.The mechanisms underlying the spatial distribution of plants acted at two scales. Between patches, spatial variation in species distributions was greater than that expected based on spatial randomization, which indicated that movement among patches was restricted. Within patches, diffusion processes reduced spatial variability in species distributions, and the effect was more prominent in large patches. Small patch size negatively influenced the long-range spatial autocorrelation of characteristic species, whereas inter-patch distance had a stronger effect on species frequency than it had on the disruption of spatial organized patterns.The long-range spatial autocorrelation was evaluated based on the dispersal abilities of the species. Among the 106 species evaluated, 39% of the woody species, 17% of the forbs, and 12% of the grasses exhibited disrupted long-range spatial autocorrelation where patches were small. The species that are more vulnerable to the effects of fragmentation tended to be those that have restricted dispersal, such as those that have short-range dispersal (atelechoric), e.g., Phlomis purpurea, Cistus albidus, Teucrium pseudochamaepytis, Brachypodium retusum, and the ballistic species, Genista spartioides. Helianthemum almeriense is another vulnerable species that has actively restricted dispersal (antitelechory), which is common in arid regions. Wind dispersers such as Launaea lanifera were less vulnerable to the effects of fragmentation. Long-distance dispersers whose persistence depends on facilitative interactions with other individuals, e.g., allogamous species such as Thymus hyemalis, Ballota hirsuta, and Anthyllis cytisoides, exhibit disrupted long-range spatial autocorrelation when patch size is reduced.     

Regulation of the plant plasma membrane H+-ATPase by its C-terminal domain: what do we know for sure?

The plant plasma membrane H⁺-ATPase is kept at a low activity level by its C-terminal domain, the inhibitory function of which is thought to be mediated by two regions (region I and II) interacting with cytoplasmic domains essential for the catalytic cycle. The activity of the enzyme is well known to be regulated by 14-3-3 proteins, the association of which requires phosphorylation of the penultimate H⁺-ATPase residue, but can be abolished by phosphorylation of residues close-by. The current knowledge about H⁺-ATPase regulation is briefly summed up here, combined with data that query some of the above statements. Expression of various C-terminal deletion constructs of PMA2, a H⁺-ATPase isoform from Nicotiana plumbaginifolia, in yeast indicates that three regions, which do not correspond to regions I or II, contribute to autoinhibition. Their individual and combined action can be abolished by (mimicking) phosphorylation of three threonine residues located within or close to these regions. With respect to the wild-type PMA2, mimicking phosphorylation of two of these residues increases enzyme activity. However, constitutive activation of wild-type PMA2 requires 14-3-3 association. Altogether, the data suggest that regulation of the plant H⁺-ATPase occurs in progressive steps, mediated by several protein kinases and phosphatases, thus allowing gradual as well as fine-tuned adjustment of its activity. Moreover, mating-based split ubiquitin assays indicate a complex interplay between the C-terminal domain and the rest of the enzyme. Notably, their tight contact does not seem to be the cause of the inactive state of the enzyme.     

Restoration of beech forest for saproxylic beetles—effects of habitat fragmentation and substrate density on species diversity and distribution

The influence of spatial location and density of beech snags on species diversity and distribution patterns of saproxylic beetles was studied in a 2,400 ha forest landscape in southern Sweden. Complete snag surveys were combined with a beetle survey using small window traps directly attached to the beech snags. The density of beech snags ≥30 cm dbh varied between one and seven snags per ha within the study area, corresponding to 1.1–5.1 m³/ha. A total of 2,610 specimens of 180 saproxylic beetles species were trapped, of which 19 species were red-listed. Within the study area, the number of red-listed and formerly red-listed species was highest around traps in old-growth stands, intermediate in managed stands contiguous with old-growth and lowest in managed stands isolated from old-growth by a two km-wide zone without beech forest. Logistic regressions revealed negative relationships between distance to old-growth forest and occurrence of eleven species, among them six red-listed or formerly red-listed species. The number of non red-listed species was not correlated with isolation from old-growth forest. The number of red-listed species also increased with snag density within 200–300 m around the traps. Our results suggest that red-listed species generally have a lower dispersal capacity than other saproxylic beetles. We conclude that retention of dead wood close to existing populations is more beneficial for red-listed species than an even distribution of snags across the forest landscape.     

Do host alternating aphids know which plant they are on?

Abstract.

• 1 To determine whether an aphid is ‘aware’ of which plant it is on, clones of a host alternating aphid, Cavariella aegopodii Scop., reared on its primary (Salix) or secondary (Daucus) host, were subjected to autumnal conditions.
• 2 Old clones produced males and egg laying females when exposed to autumnal conditions on the primary host but autumnal migrants and males when on the secondary host.
• 3 Unlike some other host alternating aphids, Cavariella did not have to spend a period on the secondary host or go through the spring migrant stage before producing sexuals.
• 4 The adaptive significance of a host alternating aphid being ‘aware’ of which host plant it is on is discussed in the light of these results.

     

The relative of species pools in determining plant species richness: an alternative explanation of species coexistence?

Explanations of the pattern of species have traditionally relied on small-scale, local processes occurring in ecological time. Differences in species richness have associated with different mechanisms avoiding competition, such as spatiotemporal heterogeneity (weaker competitors may find a more favourable place or time) or environmental stress (competition is assumed to be less intensive under difficult conditions). More recently, large-scale process have been taken into account, raising such questions as: which plant species may potentially grow in a certain community? Are evolutionary processes and species dispersal responsible for the differences between communities? The species-pool theory attempts to answer these general questions, and information about species pools is needed for the design of experiments where the number of species in a community is manipulated.