What’s wrong with the modern evolutionary synthesis? A critical reply to Welch (2017)

Welch (Biol Philos 32(2):263–279, 2017) has recently proposed two possible explanations for why the field of evolutionary biology is plagued by a steady stream of claims that it needs urgent reform. It is either seriously deficient and incapable of incorporating ideas that are new, relevant and plausible or it is not seriously deficient at all but is prone to attracting discontent and to the championing of ideas that are not very relevant, plausible and/or not really new. He argues for the second explanation. This paper presents a twofold critique of his analysis: firstly, the main calls for reform do not concern the field of evolutionary biology in general but rather, or more specifically, the modern evolutionary synthesis. Secondly, and most importantly, these calls are not only inspired by the factors, enumerated by Welch, but are also, and even primarily, motivated by four problematic characteristics of the modern synthesis. This point is illustrated through a short analysis of the latest reform challenge to the modern synthesis, the so-called extended evolutionary synthesis. We conclude with the suggestion that the modern synthesis should be amended, rather than replaced.     

Multiple Feedbacks Contribute to a Centennial Legacy of Reindeer on Tundra Vegetation

Historical contingency is the impact of past events, like the timing and order of species arrival, on community assembly, and can sometimes result in alternative stable states of ecological communities. Large herbivores, wild and domestic, can cause profound changes in the structure and functioning of plant communities and therefore probably influence historical contingency; however, little empirical data on the stability of such shifts or subsequent drivers of stability are available. We studied the centennial legacy of reindeer (Rangifer tarandus) pressure on arctic tundra vegetation by considering historical milking grounds (HMGs): graminoid- and forb-dominated patches amid shrub-dominated tundra, formed by historical Sami reindeer herding practices that ended approximately 100 years ago. Our results show that the core areas of all studied HMGs remained strikingly stable, being hardly invaded by surrounding shrubs. Soil nitrogen concentrations were comparable to heavily grazed areas. However, the HMGs are slowly being reinvaded by vegetative growth of shrubs at the edges, and the rate of ingrowth increased with higher mineral N availability. Furthermore, our data indicate that several biotic feedbacks contribute to the stability of the HMGs: increased nutrient turnover supporting herbaceous vegetation, strong interspecific competition preventing invasion and herbivore damage to invading shrubs. In particular, voles and lemmings appear to be important, selectively damaging shrubs in the HMGs. We concluded that HMGs provide clear evidence for historical contingency of herbivore effects in arctic ecosystems. We showed that several biotic feedbacks can contribute to subsequent vegetation stability, but their relative importance will vary in time and space.     

Identification of Potential MR-Derived Biomarkers for Tumor Tissue Response to 177Lu-Octreotate Therapy in an Animal Model of Small Intestine Neuroendocrine Tumor

Magnetic resonance (MR) methods enable noninvasive, regional tumor therapy response assessment, but associations between MR parameters, underlying biology, and therapeutic effects must be investigated. The aim of this study was to investigate response assessment efficacy and biological associations of MR parameters in a neuroendocrine tumor (NET) model subjected to radionuclide treatment. Twenty-one mice with NETs received ¹⁷⁷Lu-octreotate at day 0. MR experiments (day ?1, 1, 3, 8, and 13) included T2-weighted, dynamic contrast-enhanced (DCE) and diffusion-weighted imaging (DWI) and relaxation measurements (T1/T2*). Tumor tissue was analyzed using proteomics. MR-derived parameters were evaluated for each examination day and for different radial distances from the tumor center. Response assessment efficacy and biological associations were evaluated using feature selection and protein expression correlations, respectively. Reduced tumor growth rate or shrinkage was observed until day 8, followed by reestablished growth in most tumors. The most important MR parameter for response prediction was DCE-MRI–derived pretreatment signal enhancement ratio (SER) at 40% to 60% radial distance, where it correlated significantly also with centrally sampled protein CCD89 (association: DNA damage and repair, proliferation, cell cycle arrest). The second most important was changed diffusion (D) between day ?1 and day 3, at 60% to 80% radial distance, where it correlated significantly also with peripherally sampled protein CATA (association: oxidative stress, proliferation, cell cycle arrest, apoptotic cell death). Important information regarding tumor biology in response to radionuclide therapy is reflected in several MR parameters, SER and D in particular. The spatial and temporal information provided by MR methods increases the sensitivity for tumor therapy response.     

Dead-End Based Modeling Tools to Explore the Sequence Space That Is Compatible with a Given Scaffold

The dead-end elimination algorithm has proven to be a powerful tool in protein homology modeling since it allows one to determine rapidly the global minimum-energy conformation (GMEC) of an arbitrarily large collection of side chains, given fixed backbone coordinates. After introducing briefly the necessary background, we focus on logic arguments that increase the efficacy of the dead-end elimination process. Second, we present new theoretical considerations on the use of the dead-end elimination method as a tool to identify sequences that are compatible with a given scaffold structure. Third, we initiate a search for properties derived from the computed GMEC structure to predict whether a given sequence can be well packed in the core of a protein. Three properties will be considered: the nonbonded energy, the accessible surface area, and the extent by which the GMEC side-chain conformations deviate from a locally optimal conformation.     

Physiological and Genomic Consequences of Intermittent Hypoxia: Selected Contribution: Role of spleen emptying in prolonging apneas in humans

This study addressed the interaction between short-termadaptation to apneas with face immersion and erythrocyte release from the spleen. Twenty healthy volunteers, including ten splenectomized subjects, participated. After prone rest, they performed five maximal-duration apneas with face immersion in 10°C water, with 2-minintervals. Cardiorespiratory parameters and venous blood samples werecollected. In subjects with spleens, hematocrit and hemoglobinconcentration increased by 6.4% and 3.3%, respectively, over theserial apneas and returned to baseline 10 min after the series. A delayof the physiological breaking point of apnea, by 30.5% (17 s), wasseen only in this group. These parameters did not change in thesplenectomized group. Plasma protein concentration, preapneic alveolarPCO₂, inspired lung volume, and divingbradycardia remained unchanged throughout the series in both groups.Serial apneas thus triggered the hematological changes that have been previously observed after long apneic diving shifts; they were rapidlyreversed and did not occur in splenectomized subjects. This suggeststhat splenic contraction occurs in humans as a part of the divingresponse and may prolong repeated apneas.

     

Interaction of bovine coagulation factor X and its glutamic-acid-containing fragments with phospholipid membranes. A surface plasmon resonance study.

The interaction of blood coagulation factor X and its Gla-containing fragments with negatively charged phospholipid membranes composed of 25 mol% phosphatidylserine (PtdSer) and 75 mol% phosphatidylcholine (PtdCho) was studied by surface plasmon resonance. The binding to 100 mol% PtdCho membranes was negligible. The calcium dependence in the membrane binding was evaluated for intact bovine factor X (factor X) and the fragment containing the Gla-domain and the N-terminal EGF (epidermal growth factor)-like domain, Gla-EGFN, from factor X. Both proteins show the same calcium dependence in the membrane binding. Calcium binding is cooperative and half-maximum binding was observed at 1.5 mm and 1.4 mm, with the best fit to the experimental data with three cooperatively bound calcium ions for both the intact protein and the fragment. The dissociation constant (Kd) for binding to membranes containing 25 mol% PtdSer decreased from 4.6 microm for the isolated Gla-domain to 1 microm for the fragments Gla-EGFN and Gla-EGFNC (the Gla-domain and both EGF-like domains) fragments and to 40 nm for the entire protein as zymogen, activated enzyme or in the active-site inhibited form. Analysis of the kinetics of adsorption and desorption confirmed the equilibrium binding data.     

Fish-mediated indirect effects in a littoral food web

The strength of the direct effect by scraping cladocerans and the indirect effect of nutrient regeneration by filtering herbivorous cladocerans on periphyton growth was investigated in a littoral food web. Ten enclosures were erected in a lake in an area with artificial vegetation. Five enclosures were stocked with juvenile perch ( Perca fluviatilis ) and five lacked fish. In addition, a reference area in the artificial vegetation was sampled. The mesh size of the net surrounding the cages was chosen to allow an inflow of phytoplankton into the cages from the surrounding water. The periphyton and filtering herbivorous cladoceran biomasses were highest in the fish-free treatment. There was no difference in phytoplankton biomass between treatments despite the large difference in filtering herbivorous cladoceran biomass, suggesting that the inflow of phytoplankton into enclosures completely compensated for the loss due to filtering. The reference area and the enclosure with fish showed the same patterns in developments with respect to filtering herbivorous cladocerans and periphyton. Scraping cladoceran biomass was higher in the fish-free treatment resulting in a positive correlation between scraping cladoceran and periphyton biomass. Our results suggest that the positive indirect effect of filtering herbivorous cladoceran nutrient regeneration on periphyton was stronger than the negative direct effect of grazing by scraping cladocerans on periphyton in this semi-open system, and that pelagic production by phytoplankton may foster periphyton growth in the littoral habitat via filtering herbivorous cladocerans. Furthermore, heterogeneity within trophic levels involving primary producers of different growth forms such as phytoplankton and periphyton may enhance the potential for compensatory responses via nutrient recycling.