The rise and fall of the adaptive landscape?

The discussion of the adaptive landscape in the philosophical literature appears to be divided along the following lines. On the one hand, some claim that the adaptive landscape is either “uninterpretable” or incoherent. On the other hand, some argue that the adaptive landscape has been an important heuristic, or tool in the service of explaining, as well as proposing and testing hypotheses about evolutionary change. This paper attempts to reconcile these two views.

The rise and fall of surgery for the “floating” kidney

The latter half of the nineteenth century produced a remarkable expansion of surgical practice. Although most of these new techniques and concepts were soundly based, others, such as the movable or floating kidney, were later ridiculed and discredited.In Glasgow Royal Infirmary during the 48 years from 1880, when movable kidney was first mentioned in the annual reports of the hospital, to 1928 472 patients (89% female) were diagnosed as suffering from the condition. Nearly half of them (216) underwent operation and the operative mortality was low. In the first decade of this century an average of 18 cases a year were admitted to the wards of the infirmary. From 1915 to 1920 the number of cases dropped, as did the proportion undergoing operation, but in the 1920s the numbers increased again.In common with other ineffective treatments for imaginary diseases, operations for the movable kidney simply faded away in Britain in the 1930s.     

The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?

It is a basis of darwinian evolution that the microevolutionary mechanisms that can be studied in the present are sufficient to account for macroevolution. However, this idea needs to be tested explicitly, as highlighted here by the example of the superceding of dinosaurs and pterosaurs by birds and placental mammals that occurred near the Cretaceous/Tertiary boundary approximately 65 million years ago. A major problem for testing the sufficiency of microevolutionary processes is that independent ideas (such as the existence of an extraterrestrial impact, and the extinction of dinosaurs) were linked without the evidence for each idea being evaluated separately. Here, we suggest and discuss five testable models for the times and divergences of modern mammals and birds. Determination of the model that best represents these events will enable the role of microevolutionary mechanisms to be evaluated. The question of the sufficiency of microevolutionary processes for macroevolution is solvable, and available evidence supports an important role for biological processes in the initial decline of dinosaurs and pterosaurs.     

Can mangroves keep pace with contemporary sea level rise? A global data review

Coastal vegetated wetlands such as mangrove forests provide multiple ecosystem services, though are potentially threatened by contemporary accelerated sea level rise (SLR), in addition to other immediate threats such as agriculture and coastal development. Several studies have revealed that mangroves are able to adapt to, and keep pace with local relative SLR through vertical surface elevation change (SEC), however data are lacking, with often only surface accretion rate (SAR) data available. We systematically review published studies of SEC and SAR from globally distributed monitoring sites using meta-analysis, and compare them with the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5) SLR scenarios. Hydro-geomorphic setting plays an important role, with basin mangroves potentially less vulnerable to SLR through land building processes. We find that SAR in both basin and fringe mangroves can cope with low SLR scenario (RCP 2.6) throughout the 100 years projection period. However, SAR can only keep pace with high SLR scenario (RCP 8.5) up to year 2070 and 2055 in basin and fringe mangrove settings respectively. These were associated with potential sediment accumulation of 41 cm and 29 cm respectively from the baseline. Mangrove degradation promoted lowering trends of SEC, while mangrove management such as rehabilitation practice stimulated positive trends of SEC. Mangrove ecosystems may be vulnerable to contemporary SLR in small island locations such as the Caribbean, East Africa and parts of the Indo-Pacific that are dominated by fringe mangroves and where SEC cannot keep pace with both low and high IPCC AR5 SLR scenarios. A global expansion of current mangrove surface elevation monitoring effort is urgently needed in order to better assess the vulnerability of mangroves, and the factors affecting their resiliency in the face of rising sea levels.     

The enigma of the rise of angiosperms: can we untie the knot?

Multiple hypotheses have been put forward to explain the rise of angiosperms to ecological dominance following the Cretaceous. A unified scheme incorporating all these theories appears to be an inextricable knot of relationships, processes and plant traits. Here, we revisit these hypotheses, categorising them within frameworks based on plant carbon economy, resistance to climatic stresses, nutrient economy, biotic interactions and diversification. We maintain that the enigma remains unresolved partly because our current state of knowledge is a result of the fragmentary nature of palaeodata. This lack of palaeodata limits our ability to draw firm conclusions. Nonetheless, based on consistent results, some inferences may be drawn. Our results indicate that a complex multidriver hypothesis may be more suitable than any single‐driver theory. We contend that plant carbon economy and diversification may have played an important role during the early stages of gymnosperms replacement by angiosperms in fertile tropical sites. Plant tolerance to climatic stresses, plant nutrition, biotic interactions and diversification may have played a role in later stages of angiosperm expansion within temperate and harsh environments. The angiosperm knot remains partly tied, but to unravel it entirely will only be feasible if new discoveries are made by scientific communities.     

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq).We applied ChIP-seq to map the chromosomal binding sites for two ISWI-containing nucleosome remodeling factors, ACF and RSF, in Drosophila embryos. Employing several polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF-1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters.Further validation included controls using chromatin of mutant embryos that do not express ACF1 or RSF-1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and appear as ‘Phantom Peaks’. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin.Mining the modENCODE ChIP-seq profiles identifies potential Phantom Peaks in many profiles of epigenetic regulators. These profiles and other ChIP-seq data featuring prominent Phantom Peaks must be validated with chromatin from cells in which the protein of interest has been depleted.     

Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of Panamá

Molecular and geological evidence indicates that the emergence of the Isthmus of Panamá influenced the historical biogeography of the Neotropics in a complex, staggered manner dating back at least 9 Myr bp. To assess the influence of Isthmus formation on the biogeography of the harlequin beetle-riding pseudoscorpion, Cordylochernes scorpioides, we analysed mitochondrial COI sequence data from 71 individuals from 13 locations in Panamá and northern South America. Parsimony and likelihood-based phylogenies identified deep divergence between South American and Panamanian clades. In contrast to low haplotype diversity in South America, the Panamanian Cordylochernes clade is comprised of three highly divergent lineages: one clade consisting predominantly of individuals from central Panamá (PAN A), and two sister clades (PAN B1 and PAN B2) of western Panamanian pseudoscorpions. Breeding experiments demonstrated a strictly maternal mode of inheritance, indicating that our analyses were not confounded by nuclear-mitochondrial pseudogenes. Haplotype diversity is striking in western Atlantic Panamá, where all three Panamanian clades can occur in a single host tree. This sympatry points to the existence of a cryptic species hybrid zone in western Panamá, a conclusion supported by interclade crosses and coalescence-based migration rates. Molecular clock estimates yield a divergence time of approximately 3 Myr between the central and western Panamanian clades. Taken together, these results are consistent with a recent model in which a transitory proto-Isthmus enabled an early wave of colonization out of South America at the close of the Miocene, followed by sea level rise, inundation of the terrestrial corridor and then a second wave of colonization that occurred when the Isthmus was completed approximately 3 Myr bp.     

Periodontitis and Alzheimer’s disease: oral systemic link still on the rise?

doi: 10.1111/j.1741‐2358.2012.00660.x Periodontitis and Alzheimer’s disease: Oral systemic link still on the rise? Over the past few years, there has been a rapid rise in the older segments of the world population, which has brought along with it a major health concern: dementia. Alzheimer’s disease, considered to be the most common cause of dementia, has become a prospect feared by the elderly. Inflammation of the brain is strongly implicated in Alzheimer’s disease which could be enhanced by systemic inflammation. Periodontitis being a chronic inflammatory condition, which can cause systemic inflammation, the question is whether chronic periodontitis can initiate or hasten the rate of progression of Alzheimer’s disease in susceptible individuals. In this article, the authors outline the proposed oral systemic link between periodontitis and Alzheimer’s disease.     

Scorpion β-toxin interference with NaV channel voltage sensor gives rise to excitatory and depressant modes

Scorpion β toxins, peptides of ～70 residues, specifically target voltage-gated sodium (Na(V)) channels to cause use-dependent subthreshold channel openings via a voltage-sensor trapping mechanism. This excitatory action is often overlaid by a not yet understood depressant mode in which Na(V) channel activity is inhibited. Here, we analyzed these two modes of gating modification by β-toxin Tz1 from Tityus zulianus on heterologously expressed Na(V)1.4 and Na(V)1.5 channels using the whole cell patch-clamp method. Tz1 facilitated the opening of Na(V)1.4 in a use-dependent manner and inhibited channel opening with a reversed use dependence. In contrast, the opening of Na(V)1.5 was exclusively inhibited without noticeable use dependence. Using chimeras of Na(V)1.4 and Na(V)1.5 channels, we demonstrated that gating modification by Tz1 depends on the specific structure of the voltage sensor in domain 2. Although residue G658 in Na(V)1.4 promotes the use-dependent transitions between Tz1 modification phenotypes, the equivalent residue in Na(V)1.5, N803, abolishes them. Gating charge neutralizations in the Na(V)1.4 domain 2 voltage sensor identified arginine residues at positions 663 and 669 as crucial for the outward and inward movement of this sensor, respectively. Our data support a model in which Tz1 can stabilize two conformations of the domain 2 voltage sensor: a preactivated outward position leading to Na(V) channels that open at subthreshold potentials, and a deactivated inward position preventing channels from opening. The results are best explained by a two-state voltage-sensor trapping model in that bound scorpion β toxin slows the activation as well as the deactivation kinetics of the voltage sensor in domain 2.     

Does more mean less? The value of information for conservation planning under sea level rise

Many studies have explored the benefits of adopting more sophisticated modelling techniques or spatial data in terms of our ability to accurately predict ecosystem responses to global change. However, we currently know little about whether the improved predictions will actually lead to better conservation outcomes once the costs of gaining improved models or data are accounted for. This severely limits our ability to make strategic decisions for adaptation to global pressures, particularly in landscapes subject to dynamic change such as the coastal zone. In such landscapes, the global phenomenon of sea level rise is a critical consideration for preserving biodiversity. Here, we address this issue in the context of making decisions about where to locate a reserve system to preserve coastal biodiversity with a limited budget. Specifically, we determined the cost‐effectiveness of investing in high‐resolution elevation data and process‐based models for predicting wetland shifts in a coastal region of South East Queensland, Australia. We evaluated the resulting priority areas for reserve selection to quantify the cost‐effectiveness of investment in better quantifying biological and physical processes. We show that, in this case, it is considerably more cost effective to use a process‐based model and high‐resolution elevation data, even if this requires a substantial proportion of the project budget to be expended (up to 99% in one instance). The less accurate model and data set failed to identify areas of high conservation value, reducing the cost‐effectiveness of the resultant conservation plan. This suggests that when developing conservation plans in areas where sea level rise threatens biodiversity, investing in high‐resolution elevation data and process‐based models to predict shifts in coastal ecosystems may be highly cost effective. A future research priority is to determine how this cost‐effectiveness varies among different regions across the globe.     

Othenio Abel (1875–1946): the rise and decline of paleobiology in German paleontology

Othenio Abel is widely acclaimed as the founder of paleobiology; of the journal Palaeobiologica and of the Paleobiological Society in Vienna. His National–Socialist sympathies, which he shared with fellow paleobiologist Henry Fairfield Osborn from the American Museum of Natural History, resulted in his forced retirement from the University of Vienna in 1934. Abel secured subsequent employment at the University of Göttingen, later sought help from Nazi officials to create his own institute in Salzburg. A leader amongst German paleontologists, Abel supported efforts of the Deutsche Palaeontologische Gesellschaft to align paleobiology with Nazi ideology (‘National–Socialism is politically applied biology’) to secure more support for the discipline. Abel's paleobiology was neo-Lamarckian in nature, based on a ‘reaction theory’ of adaptation. Abel attempted to unify paleontology with biology under a universal law of nature – the Law of Biological Inertia – that itself was anchored in classical physics.     

The end of "naive reductionism": rise of systems biology or renaissance of physiology?

Systems biology is an emerging discipline focused on tackling the enormous intellectual and technical challenges associated with translating genome sequence into a comprehensive understanding of how organisms are built and run. Physiology and systems biology share the goal of understanding the integrated function of complex, multicomponent biological systems ranging from interacting proteins that carry out specific tasks to whole organisms. Despite this common ground, physiology as an academic discipline runs the real risk of fading into the background and being superseded organizationally and administratively by systems biology. My goal in this article is to discuss briefly the cornerstones of modern systems biology, specifically functional genomics, nonmammalian model organisms and computational biology, and to emphasize the need to embrace them as essential components of 21st-century physiology departments and research and teaching programs.     

Are Ca2+ channels in neutrophils activated by a rise in cytosolic free Ca2+?

It was recently suggested that the opening of neutrophil plasma membrane Ca2+ channels by chemotactic agents is mediated by a rise in free cytosolic Ca2+ concentration ([Ca2+]i). This hypothesis was tested in human cells monitoring [Ca2+]i with the indicator indo-1. In cells loaded with the Ca2+-chelating agent bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetate, transmembrane Ca2+ uptake could be stimulated by formyl-methionyl-leucyl-phenylalanine (fMLP) even when [Ca2+]i was at or below the resting level. In contrast, simply elevating [Ca2+]i in unstimulated cells failed to increase transmembrane uptake. It was concluded either that Ca2+ uptake across the plasma membrane is activated directly by the formation of the chemotactic factor-receptor complex or, more likely, that a transduction mechanism distinct from changes in [Ca2+]i is involved.     

Adaptation to sea level rise: does local adaptation influence the demography of coastal fish populations?

This study compared the growth of two western mosquitofish Gambusia affinis populations that were previously demonstrated to have genetic adaptations that increased survival under lethal salinity exposures. The objective was to evaluate how genetic adaptations to lethal salinity stress affect population demography when exposed to sublethal salinity stress. Results indicate that chronic salinity exposure had a generally negative impact on population size, but fish originating from one of the two populations established with fish from a brackish site exhibited an increase in population size. Saltwater intrusion seems to result in reduced population size for most populations. Some populations inhabiting more saline sites, however, may develop localized adaptations, mitigating the consequences of increased salinity on population productivity.     

Is a rise in intracellular concentration of free calcium necessary or sufficient for stimulated cytoskeletal-associated actin?

The addition of the calcium ionophore A23187 to rabbit neutrophils increases the amount of actin associated with the cytoskeleton regardless of the presence or absence of calcium in the incubation medium. In the presence of extracellular calcium, the effect of A23187 is biphasic with respect to concentration. The action of the ionophore is rapid, transient, and is inhibited by pertussis toxin, hyperosmolarity, and quinacrine. On the other hand, the addition of pertussis toxin or hyperosmolarity has small if any, effect on the rise in intracellular calcium produced by A23187. While quinacrine does not affect the fMet-Leu-Phe-induced increase in cytoskeletal actin and the polyphosphoinositide turnover, its addition inhibits completely the stimulated increase in Ca-influx produced by the same stimulus. The results presented here suggest that a rise in the intracellular concentration of free calcium is neither necessary nor sufficient for the stimulated increase in cytoskeletal-associated actin. A possible relationship between the lipid remodeling stimulated by chemoattractants and the increased cytoskeletal actin is discussed.     

Can community structure track sea‐level rise? Stress and competitive controls in tidal wetlands

Climate change impacts, such as accelerated sea‐level rise, will affect stress gradients, yet impacts on competition/stress tolerance trade‐offs and shifts in distributions are unclear. Ecosystems with strong stress gradients, such as estuaries, allow for space‐for‐time substitutions of stress factors and can give insight into future climate‐related shifts in both resource and nonresource stresses. We tested the stress gradient hypothesis and examined the effect of increased inundation stress and biotic interactions on growth and survival of two congeneric wetland sedges, Schoenoplectus acutus and Schoenoplectus americanus. We simulated sea‐level rise across existing marsh elevations and those not currently found to reflect potential future sea‐level rise conditions in two tidal wetlands differing in salinity. Plants were grown individually and together at five tidal elevations, the lowest simulating an 80‐cm increase in sea level, and harvested to assess differences in biomass after one growing season. Inundation time, salinity, sulfides, and redox potential were measured concurrently. As predicted, increasing inundation reduced biomass of the species commonly found at higher marsh elevations, with little effect on the species found along channel margins. The presence of neighbors reduced total biomass of both species, particularly at the highest elevation; facilitation did not occur at any elevation. Contrary to predictions, we documented the competitive superiority of the stress tolerator under increased inundation, which was not predicted by the stress gradient hypothesis. Multifactor manipulation experiments addressing plant response to accelerated climate change are integral to creating a more realistic, valuable, and needed assessment of potential ecosystem response. Our results point to the important and unpredicted synergies between physical stressors, which are predicted to increase in intensity with climate change, and competitive forces on biomass as stresses increase.     

Three years of insecticide resistance monitoring in Anopheles gambiae in Burkina Faso: resistance on the rise?

ABSTRACT: Background and methods A longitudinal Anopheles gambiae s.l. insecticide-resistance monitoring programme was established in four sentinel sites in Burkina Faso. For three years, between 2008 and 2010, WHO diagnostic dose assays were used to measure the prevalence of resistance to all the major classes of insecticides at the beginning and end of the malaria transmission season. Species identification and genotyping for target site mutations was also performed and the sporozoite rate in adults determined. RESULTS: At the onset of the study, resistance to DDT and pyrethroids was already prevalent in An. gambiae s.l. from the south-west of the country but mosquitoes from the two sites in central Burkina Faso were largely susceptible. Within three years, DDT and permethrin resistance was established in all four sites. Carbamate and organophosphate resistance remains relatively rare and largely confined to the south-western areas although a small number of bendiocarb survivors were found in all sites by the final round of monitoring. The ace-1R target site resistance allele was present in all localities and its frequency exceeded 20% in 2010 in two of the sites. The frequency of the 1014 F kdr mutation increased throughout the three years and by 2010, the frequency of 1014 F in all sites combined was 0.02 in Anopheles arabiensis, 0.56 in An. gambiae M form and 0.96 in An. gambiae S form. This frequency did not differ significantly between the sites. The 1014 S kdr allele was only found in An. arabiensis but its frequency increased significantly throughout the study (P = 0.0003) and in 2010 the 1014 S allele frequency was 0.08 in An. arabiensis. Maximum sporozoite rates (12%) were observed in Soumousso in 2009 and the difference between sites is significant for each year. CONCLUSION: Pyrethroid and DDT resistance is now established in An. gambiae s.l. throughout Burkina Faso. Results from diagnostic dose assays are highly variable within and between rounds of testing, and hence it is important that resistance monitoring is carried out on more than one occasion before decisions on insecticide procurement for vector control are made. The presence of 1014 S in An. gambiae s.l., in addition to 1014 F, is not unexpected given the recent report of 1014 S in Benin but highlights the importance of monitoring for both mutations throughout the continent. Future research must now focus on the impact that this resistance is having on malaria control in Burkina Faso.