Emerging infectious disease: what are the relative roles of ecology and evolution?

The increasing threat of infectious diseases in humans has renewed interest in factors leading to the emergence of new diseases and the re-emergence of familiar diseases. Examples of seemingly novel diseases currently spreading in human populations include HIV, dengue hemorrhagic fever and Lyme disease; drug-resistant forms of well-known diseases such as tuberculosis are also increasing. The problem of disease emergence also extends to other animal and plant populations. In most current epidemics, ecological factors (e.g. migration, climate, agricultural practices) play a more significant role in disease emergence than evolutionary changes in pathogens or hosts. Evolutionary biologists and ecologists have much to offer to the development of strategies for the control of emerging diseases.     

Do evolution and ecology need the Gaia hypothesis?

Gaia theory, which describes the life-environment system of the Earth as stable and self-regulating, has remained at the fringes of mainstream biological science owing to its historically inadequate definition and apparent incompatibility with individual-level natural selection. The key issue is whether and why the biosphere might tend towards stability and self-regulation. We review the various ways in which these issues have been addressed by evolutionary and ecological theory, and relate these to 'Gaia theory'. We then ask how this theory extends the perspectives offered by these disciplines, and how it might be tested by novel modelling approaches and laboratory experiments using emergent technologies.     

How labile are the egg‐laying preferences of seed beetles?

Abstract.  1. Previous studies have produced conflicting results with respect to the genetic lability of host preference in the seed beetle Callosobruchus maculatus .
2. In this study, replicate lines of an Asian population were kept on an ancestral host (mung bean) or switched to a novel host (cowpea). After 40+ generations, lines were assayed for host preference (in choice tests) and host acceptance (under no-choice conditions), and were compared to African lines chronically associated with cowpea.
3. Host preference diverged in the expected direction. When presented a mixture of cowpeas and mung beans, females from the cowpea lines laid a greater fraction of their eggs on cowpea than did females from the mung bean lines. Preference for cowpea was nearly as strong in the cowpea lines as it was in the cowpea-adapted African lines.
4. In contrast, the experimental host shift did not affect long-term host acceptance. African females laid more eggs if given cowpeas than if given mung beans, but realised fecundities in the cowpea and mung bean lines were similar on the two hosts. Females from all lines laid more eggs if they were reared on cowpea than on mung bean, but rearing host had no effect on either relative host acceptance or host preference.
5. Comparisons with earlier studies suggest that the lability of host preference varies among beetle populations, which precludes generalisation at the species level. Because lines were maintained under no-choice conditions, modification of host preference probably occurred via a lower acceptance threshold for the novel host, without a concomitant change in the long-term acceptance of the ancestral host.     

What moves us? How mobility and movement are at the center of human evolution

Movement is central to the survival of all free‐living organisms. Consequently, movement and what anthropologists often refer to as mobility, which is the sum of small‐scale movements tracked across larger geographic and temporal scales, are key targets of selection. Movement and mobility also underpin many of the key features that make us human and that allowed our lineage to adapt to changing environments across the globe. The most obvious example is the evolution of humans' singular mode of locomotion. Bipedalism is arguably the most important derived anatomical trait of the hominin lineage. The mechanisms and circumstances that gave rise to this novel mode of movement remain subjects of intense research.     

How FAIR are plant sciences in the twenty-first century? The pressing need for reproducibility in plant ecology and evolution

The need for open, reproducible science is of growing concern in the twenty-first century, with multiple initiatives like the widely supported FAIR principles advocating for data to be Findable, Accessible, Interoperable and Reusable. Plant ecological and evolutionary studies are not exempt from the need to ensure that the data upon which their findings are based are accessible and allow for replication in accordance with the FAIR principles. However, it is common that the collection and curation of herbarium specimens, a foundational aspect of studies involving plants, is neglected by authors. Without publicly available specimens, huge numbers of studies that rely on the field identification of plants are fundamentally not reproducible. We argue that the collection and public availability of herbarium specimens is not only good botanical practice but is also fundamental in ensuring that plant ecological and evolutionary studies are replicable, and thus scientifically sound. Data repositories that adhere to the FAIR principles must make sure that the original data are traceable to and re-examinable at their empirical source. In order to secure replicability, and adherence to the FAIR principles, substantial changes need to be brought about to restore the practice of collecting and curating specimens, to educate students of their importance, and to properly fund the herbaria which house them.     

How many fish populations in Finland are affected by acid precipitation?

Synopsis The number of fish populations affected or lost from small lakes in southern and central Finland due to acid precipitation is estimated. Tolerance limits (pH and labile aluminum) of common fish species were obtained from a fish status survey of 80 lakes. These tolerance values were used to estimate the proportion of affected lakes from the water chemistry data of 783 statistically selected lakes. The proportion of anthropogenically acidified lakes was estimated by calculating pre-acidification pH and aluminum concentrations of the lakes, using a steady-state model based on water chemistry. The number of fish populations for which acidification has affected growth or population structure was estimated at between 2200 and 4400. Out of these, the number of fish populations that have disappeared due to acid precipitation would be about 1000–2000. Almost 60% of the affected or lost populations are roach, Rutilus rutilus, the most sensitive of the common fish species in small lakes in southern and central Finland. Less than 15% of the damaged population is European perch, Perca fluviatilis, the most common species. This is due to the substantially higher tolerance of perch to acidified water in comparison with roach.     

How optimal are the binding energetics of barnase and barstar?

The extracellular ribonuclease barnase and its intracellular inhibitor barstar bind fast and with high affinity. Although extensive experimental and theoretical studies have been carried out on this system, it is unclear what the relative importance of different contributions to the high affinity is and whether binding can be improved through point mutations. In this work, we first applied Poisson-Boltzmann electrostatic calculations to 65 barnase-barstar complexes with mutations in both barnase and barstar. The continuum electrostatic calculations with a van der Waals surface dielectric boundary definition result in the electrostatic interaction free energy providing the dominant contribution favoring barnase-barstar binding. The results show that the computed electrostatic binding free energy can be improved through mutations at W44/barstar and E73/barnase. Furthermore, the determinants of binding affinity were quantified by applying COMparative BINding Energy (COMBINE) analysis to derive quantitative structure-activity relationships (QSARs) for the 65 complexes. The COMBINE QSAR model highlights approximately 20 interfacial residue pairs as responsible for most of the differences in binding affinity between the mutant complexes, mainly due to electrostatic interactions. Based on the COMBINE model, together with Brownian dynamics simulations to compute diffusional association rate constants, several mutants were designed to have higher binding affinities than the wild-type proteins.     

Are species' responses to global change predicted by past niche evolution?

Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here, we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and 2000 are available, along with a species-level phylogeny and data on climatic, habitat and trophic niches. We found that species'' proneness to demographic decline is associated with slow evolution of the habitat niche in the past, in addition to certain current-day life-history and ecological traits. A similar result was found at a higher taxonomic level, where families prone to decline have had a history of slower evolution of climatic and habitat niches. Our results support the view that niche conservatism can prevent some species from coping with environmental change. Thus, linking patterns of past niche evolution and contemporary species dynamics for large species samples may provide insights into how niche evolution may rescue certain lineages in the face of global change.     

Dormancy and germination: How does the crop seed decide?

Whether seeds germinate or maintain dormancy is decided upon through very intricate physiological processes. Correct timing of these processes is most important for the plants life cycle. If moist conditions are encountered, a low dormancy level causes pre‐harvest sprouting in various crop species, such as wheat, corn and rice, this decreases crop yield and negatively impacts downstream industrial processing. In contrast, a deep level of seed dormancy prevents normal germination even under favourable conditions, resulting in a low emergence rate during agricultural production. Therefore, an optimal seed dormancy level is valuable for modern mechanised agricultural systems. Over the past several years, numerous studies have demonstrated that diverse endogenous and environmental factors regulate the balance between dormancy and germination, such as light, temperature, water status and bacteria in soil, and phytohormones such as ABA (abscisic acid) and GA (gibberellic acid). In this updated review, we highlight recent advances regarding the molecular mechanisms underlying regulation of seed dormancy and germination processes, including the external environmental and internal hormonal cues, and primarily focusing on the staple crop species. Furthermore, future challenges and research directions for developing a full understanding of crop seed dormancy and germination are also discussed.     

Is nitrification affected by the diameter and other properties of soil aggregates?

Nitrification was measured in fractions of chernozemic rendzina and lessivē soil differing in aggregate size. In both soils the maximum rates occurred in aggregates between 1 and 3 mm in diameter. The effects of structural and other properties (particle composition, pore-size distribution, surface area, organic C and total N content, ratio of air volume to water volume in aggregates) proved to be insignificant except for the nitrification rate in the lessivē soil, which positively correlated with the fraction of particles between 20 and 50 μm in diameter.     

How much are stranding records affected by variation in reporting rates? A case study of small delphinids in the Bay of Biscay

Marine vertebrate strandings offer an opportunistic sampling scheme that can provide abundant data over long periods. Because the stranding process involves biological, physical and sociological parameters, confounding complicates the interpretation of results. The statistical analysis of these data relies on generalized linear or additive models in order to infer long-term trends, but does not easily account for drift or variation in reporting rates. Here, we capitalized on county-level (administrative) variation following the passing of a law for compulsory reporting of stranded marine mammals in France to investigate how variation in reporting rates may affect the observed trend in stranded small delphinids in the Bay of Biscay. Using a time-series spanning more than 30 years across eight administrative counties, we built variance partitioning models for the analysis of count data. We discussed the choice of an appropriate likelihood to conclude the Negative Binomial useful and interpretable in the context of small delphinid strandings. We expanded the model with a recent methodology to detect structural breaks in the time series, focusing on overdispersion. We performed statistical robustness checks with respect to variations in reporting rates and discuss their causal interpretation in the context of observational data. Stranding frequencies increased on average 7-fold over 30 years. We conclude that reporting rates to the French stranding network have been stable since the early 1990s, and the average 3-fold increase in stranded small delphinids observed in the Bay of Biscay since 1990 is due to other factors, including bycatch. Codes and data are available to replicate the analysis to other national stranding networks.     

What can whole genome expression data tell us about the ecology and evolution of personality?

Consistent individual differences in behaviour, aka personality, pose several evolutionary questions. For example, it is difficult to explain within-individual consistency in behaviour because behavioural plasticity is often advantageous. In addition, selection erodes heritable behavioural variation that is related to fitness, therefore we wish to know the mechanisms that can maintain between-individual variation in behaviour. In this paper, we argue that whole genome expression data can reveal new insights into the proximate mechanisms underlying personality, as well as its evolutionary consequences. After introducing the basics of whole genome expression analysis, we show how whole genome expression data can be used to understand whether behaviours in different contexts are affected by the same molecular mechanisms. We suggest strategies for using the power of genomics to understand what maintains behavioural variation, to study the evolution of behavioural correlations and to compare personality traits across diverse organisms.