Organisms or biological individuals? Combining physiological and evolutionary individuality

The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the category of biological individuals should be divided into two subcategories: physiological individuals and evolutionary individuals, which suggests that the notions of organism and biological individual should not be used interchangeably. I suggest that the combination of an evolutionary and a physiological perspective will enable biologists and philosophers to supply an account of biological individuality that will be both more comprehensive and more in accordance with scientific practices.     

Hovering sunbirds in the Old World: occasional behaviour or evolutionary trend?

The nectarivory of sunbirds in the Old World and hummingbirds in the New World evolved independently. While both groups are specialised in their feeding apparatuses, hummingbirds are moreover famous for their adaptations to sustained hovering flight. Recently, an example of a pollination system of the invasive plant Nicotiana glauca has been used to show that less adapted sunbirds also are frequently able to hover. Nevertheless, the question has remained why plants adapted to bird hovering pollination do not occur outside the New World. In this paper we show that the long‐peduncle Cameroonian Impatiens sakeriana is not capable of autonomous selfing and can be pollinated only by two often hovering sunbirds, the Cameroon sunbird Cyanomitra oritis and the northern double‐collared sunbird Cinnyris reichenowi. Our study revealed that this plant is highly specialised for pollination by C. oritis. Cinnyris reichenowi hovers less frequently and often thieves nectar by piercing the flower spur when perching. This study shows that pollination systems occurring in the Old World follow similar evolutionary trends as systems including hovering hummingbirds in the New World.     

Gall-induction in insects: evolutionary dead-end or speciation driver?

Background

The tree of life is significantly asymmetrical - a result of differential speciation and extinction - but general causes of such asymmetry are unclear. Differences in niche partitioning are thought to be one possible general explanation. Ecological specialization might lead to increases in diversification rate or, alternatively, specialization might limit the evolutionary potential of specialist lineages and increase their extinction risk. Here we compare the diversification rates of gall-inducing and non-galling insect lineages. Compared with other insect herbivores feeding on the same host plant, gall-inducing insects feed on plant tissue that is more nutritious and less defended, and they do so in a favorable microhabitat that may also provide some protection from natural enemies. We use sister-taxon comparisons to test whether gall-inducing lineages are more host-specific than non-galling lineages, and more or less diverse than non-gallers. We evaluate the significance of diversity bipartitions under Equal Rates Markov models, and use maximum likelihood model-fitting to test for shifts in diversification rates.

Results

We find that, although gall-inducing insect groups are more host-specific than their non-galling relatives, there is no general significant increase in diversification rate in gallers. However, gallers are found at both extremes - two gall-inducing lineages are exceptionally diverse (Euurina sawflies on Salicaceae and Apiomorpha scale insects on Eucalytpus), and one gall-inducing lineage is exceptionally species-poor (Maskellia armored scales on Eucalyptus).

Conclusions

The effect of ecological specialization on diversification rates is complex in the case of gall-inducing insects, but host range may be an important factor. When a gall-inducing lineage has a host range approximate to that of its non-galling sister, the gallers are more diverse. When the non-galler clade has a much wider host range than the galler, the non-galler is also much more diverse. There are also lineage-specific effects, with gallers on the same host group exhibiting very different diversities. No single general model explains the observed pattern.     

Nongenomic actions of aldosterone: physiological or pathophysiological role?

The actions of aldosterone are usually divided into persistent genomic mediated by the classical mineralocorticoid receptor versus acute nongenomic actions. Rapid, nongenomic effects of aldosterone have been shown in a variety of tissues, although the physiological relevance of these nongenomic actions remains to be established. There is now growing evidence that both the nongenomic and genomic actions of aldosterone, are mediated via the same classical mineralocorticoid receptor, and there is cross talk between the nongenomic and classical actions of steroid hormones. Activation of tissue-specific, second messenger pathways may contribute to integration of nongenomic and classical actions of aldosterone. Further studies are required to determine the physiological or pathophysiological role of these nongenomic actions of aldosterone and whether they might amplify pathophysiological effects of aldosterone.     

Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata

Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species (‘common GO’) within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.     

BSE risk assessments in the UK: a risk tradeoff?

Risk assessments for bovine spongiform encephalopathy (BSE) should be based on the group risk and not the median individual risk. The group risk is calculated from the arithmetic mean risk, which in the case of dorsal root ganglia, is a factor of 50-fold higher than the median. For environmental routes, the arithmetic mean exposure is sufficient for risk assessment, while for food-borne routes failure to accommodate the variation in exposures to individuals across the UK population could overestimate the group risk considerably. Ignoring prion destruction by cooking could overestimate the food-borne risks still further. The recent estimate for the arithmetic mean cow-to-man species barrier of 4000 does not take into accounts either of these factors and thus may be too high. Until evidence for a threshold dose is demonstrated, public health scientists should avoid assessing safety on the basis of a 'minimum infective dose'. The incubation period observed in cattle-feeding studies, when completed, would continue to increase with decreasing dose below the ID50if there is a threshold or co-operative effect. The question is raised of whether fears over BSE in drinking water contributed to the spread of foot-and-mouth disease across the UK in 2001; a risk tradeoff.     

Desert spring refugia: museums of diversity or evolutionary cradles?

Refugia play a critical role in preserving species unable to move or adapt to cope with environmental change. The role of refugia as ‘museums of diversity’ means these environments have a high conservation priority. Less well known, however, is the role that isolated and fragmented refugia can play in the generation of new diversity. Here, we examined the diversification and evolutionary history of a community of endemic invertebrates that inhabit Australian desert spring refugia. We compared the phylogenies of seven endemic groups (Haloniscus and Phreatomerus isopods, chiltoniid amphipods, Ngarawa ostracods, Trochidrobia and Fonscochlea snails and Gymnochthebius beetles) from these springs and examine the rates and timing of diversification and reconstructed the phylogeographic history of each taxon. Despite major life‐history differences among these taxa, they demonstrate remarkable similarities in their evolutionary histories. All groups have multiple lineages that extend back to a time before the formation of present‐day deserts, and significant geographic‐based diversification since adapting to a refugial habitat. The results provide further evidence that refugia act as museums of biodiversity, preserving lineages that would have otherwise gone extinct. However, we also observed that isolation in refugia corresponds with significant diversification, leading to a recently evolved, novel endemic fauna, supporting the idea that fragmented refugia provide ideal conditions for the generation of future biodiversity hotspots.     

Organic nitrogen in precipitation: real problem or sampling artefact?

Published observations of organic nitrogen (N) compounds in precipitation go back almost a century. Several different methods have been used to measure both the total and ionic concentrations of N. There is therefore some uncertainty as to whether reported "organic N" is real, or simply the result of uncertainties in chemical analyses or inadequate sampling methods. We found that the materials from which the collector was made (polypropylene, steel, or glass) had no significant effect on the composition of dissolved organic N (DON). The use of a biocide was found to be very important during sampling and storage of samples before analysis. We set up a network of seven collectors across the U.K., from the Cairngorms to Dorset, all operating to the same protocol, and including a biocide. Samples were analysed centrally, using proven methods. Over 6 months, organic N contributed about 20% to the total N in U.K. precipitation, but with a large variation across the country. This means that current estimates of wet deposited N to the U.K., which are based only on the ammonium and nitrate concentrations, are too small. Organic N is not an artefact, but a real problem that needs to be addressed.     

Carbon or nitrogen limitation in marine copepods?

The elemental limitation of copepod production can be studiedusing stoichiometric models, which balance carbon (C) and nitrogen(N) in ingested food and predator biomass, and assume that theelement in shortest supply is used as efficiently as possible.A model of this type was developed which has two important features:(i) it is assumed that a maximum N net production efficiencyof 1.0 is possible, although assimilation of N may be <1.0;and (ii) assimilation of C in the gut is handled by dividingfood into biochemical compounds. Model results suggested thatmarine copepods should commonly be limited by C, owing to theirlow C net production efficiency, and the low food C:N ratiostypical of the upper ocean. Nevertheless, the work demonstratedthat copepods might still preferentially ingest protein-richprey to maximize production because the associated C is easilyassimilated. A comparison of model predictions with two experimentalstudies, however, revealed that in the studies copepods werenot utilizing N as efficiently as would be expected by stoichiometrictheory. This finding suggests that copepod nutrition is morecomplicated than simple elemental limitation by C or N: imbalancesof specific compounds, such as essential amino acids, may becontrolling production. In addition, the nutritional requirementsof copepods may vary on a seasonal basis in a complex manner.     

Calpains: a physiological regulator of the endothelial barrier?

The intracellular protease calpain, abundant in endothelial cells (EC), is assumed to be inactive under physiological conditions but may account for Ca2+ -linked pathophysiological events. However, nonstimulated EC contained autolyzed, activated calpain. Adding 12-48 microM calpain inhibitor I (CI) or 0.5-1 microM of the novel, membrane-permeable conjugate of calpastatin peptide-penetratin (CPP) caused rapid rounding and retraction of cultured EC (phase contrast, capacitance) and translocation of Syk, Rac, and Rho to the membrane, signifying activation upon inhibition of calpain. Isolated hearts (guinea pig) perfused with 12 microM CI or 0.5 muM CPP developed coronary leak. We conclude that calpain is constitutively active in EC and regulates vascular permeability by governing cell-cell attachment.     

Inference of evolutionary patterns of the land snail Albinaria in the Aegean archipelago: is vicariance enough?

Mitochondrial DNA sequences from 16S rRNA and ATPase8 genes were used to investigate phylogeographic patterns of the land snail Albinaria (Gastropoda: Clausiliidae) in the Aegean archipelago. Forty-two populations of Albinaria were analyzed, mainly A. turrita, A. caerulea and A. brevicollis, collected from 22 Aegean islands and certain surrounding regions. Maximum parsimony, maximum likelihood and Bayesian analyses on 16S rRNA and combined datasets produced trees that share significant similarity and reveal a phylogeny with distinct branches which are in general, but not full, agreement with current taxonomy. The Aegean taxa are not monophyletic as a whole, since A. turrita does not cluster with A. caerulea and A. brevicollis. The latter form a distinct monophyletic cluster, within which two groups are evident. These groups do not readily correspond to currently accepted morphospecies; one contains the populations that inhabit the central part of the archipelago plus some eastern islands, while the other contains populations whose geographic distribution is restricted to the southeastern part of the archipelago. The divergence between these two groups is attributed to vicariance events that primarily shape contemporary distributions. Although dispersal may also be present, certain small- and large-scale vicariance events can be traced; alternative phylogeographic hypotheses are discussed in view of the historical biogeography of the region.     

Drug resistance in parasites: can we stay ahead of the evolutionary curve?

The articles in this special issue of Trends in Parasitology document the current status of drug discovery in various helminth and protozoan parasitic infections. Parasitic diseases present a unique challenge to those who try to prevent or treat them. In most cases, the parasite has evolved to evade the human immune system, so the human host can control, but not eliminate, the parasite. Design of effective vaccines against these diseases presents daunting difficulties; therefore, drugs are currently the only way to prevent or treat parasitic diseases. Under these circumstances, selection of resistance to any effective, well-tolerated drug is inevitable; the question is not if, but when. The goal of this review is to try to draw general conclusions about the measurement and selection of resistance to drugs directed against a variety of very different parasites.     

Oxidative stress in Alzheimer's disease: Primary villain or physiological by-product?

Abstract

The prevalence of Alzheimer's disease (AD) is increasing rapidly worldwide due to an ageing population and largely ineffective treatments. In AD cognitive decline is due to progressive neuron loss that begins in the medial temporal lobe and spreads through many brain regions. Despite intense research the pathogenesis of the common sporadic form of AD remains largely unknown. The popular amyloid cascade hypothesis suggests that the accumulation of soluble oligomers of beta amyloid peptides (Aβ) initiates a series of events that cause neuronal loss. Among their putative toxic effects, Aβ oligomers are thought to act as pro-oxidants combining with redox-active metals to produce excessive reactive oxygen and nitrogen species. However, to date the experimental therapies that reduce Aβ load in AD have failed to halt cognitive decline. Another hypothesis proposed by the late Mark Smith and colleagues is that oxidative stress, rather than Aβ, precipitates the pathogenesis of AD. That is, Aβ and microtubule-associated protein tau are upregulated to address the redox imbalance in the AD brain. As the disease progresses, excess Aβ and tau oligomerise to further accelerate the disease process. Here, we discuss redox balance in the human brain and how this balance is affected by ageing. We then discuss where oxidative stress is most likely to act in the disease process and the potential for intervention to reduce its effects.     

Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?

Cultivation-independent molecular surveys show that members of the kingdom Crenarchaeota within the domain Archaea represent a substantial component of microbial communities in aquatic and terrestrial environments. Recently, metagenomic studies have revealed that such Crenarchaeota contain and express genes related to those of bacterial ammonia monooxygenases. Furthermore, a marine chemolithoautotrophic strain was isolated that uses ammonia as a sole energy source. Considering the ubiquity and abundance of Crenarchaeota, these findings considerably challenge the accepted view of the microbial communities involved in global nitrogen cycling. However, the quantitative contribution of Archaea to nitrification in marine and terrestrial environments still remains to be elucidated.     

Are glycosyltransferases the evolutionary antecedents of the immunoglobulins?

The glycosyltransferases may be the evolutionary precursors of the immunoglobulins, although critical evidence for this hypothesis is not yet available. The transferases add sugars to non-glycosylated proteins, lipids, and organic molecules, as well as to oligosaccharides, glycoproteins, and glycolipids. The enzymes are specific, extremely polymorphic, occasionally inducible, and may be structurally related to one another. Circumstantial evidence links the transferases to both the MHC and T/t loci in the mouse. Finally, antibodies against purified transferases are difficult to produce and sometimes they react with immunoglobulins. The present hypothesis predicts that transferases should show some sequence homology with immunoglobulins, and that some MHC proteins will be glycosyltransferases.     

Glucose-induced buffering of cytoplasmic Ca2+ in the pancreatic beta-cell--an artifact or a physiological phenomenon?

The effects of stimulated metabolism on the cytoplasmic Ca2+ concentration (Ca2+i) of insulin-releasing pancreatic beta-cells were studied. When the glucose concentration was increased from 5 to 20 mM, some cell preparations responded with initial lowering of Ca2+i followed by a rise, whereas Ca2+i only increased in others. After prolonged exposure to 5 or 10 mM of the sugar, depolarization with high concentrations of sulfonylurea or K+ caused rapid increases of Ca2+i. However, when subsequently raising glucose to 20 mM there were pronounced temporary decreases of Ca2+i. Marked Ca2+i reducing effects were also obtained after prolonged exposure to 20 mM glucose, when metabolism was augmented further by exposure to leucine or beta-2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid. The results indicate that buffering of Ca2+i is not an artifact but may have physiological significance.     

The physiological role of GLP-1 in human: incretin, ileal brake or more?

The proglucagon-derived peptide glucagon-like peptide-1 (GLP-1) is an intestinal signal peptide postprandially released from the L cells of the lower gut. Exogenously administered the synthetic hormone exerts a glucose-dependent insulinotropic effect at the pancreatic beta-cells and lowers plasma glucagon by an inhibitory effect against the alpha-cells. It delays gastric emptying by relaxation of the gastric fundus, inhibition of antral contractility, and stimulation of both the tonic and phasic motility of the pyloric sphincter. Enhancement of insulin, suppression of glucagon, and inhibition of gastric emptying are the main determinants controlling glucose homeostasis with GLP-1. Human studies employing the specific GLP-1 receptor antagonist exendin(9-39) show that endogenously released GLP-1 likewise controls fasting plasma glucagon, stimulates insulin, and influences all the motoric mechanisms known to control gastric emptying. Therefore, GLP-1 is discussed as an incretin hormone and as an enterogastrone in man. Synthetic GLP-1 also suppresses gastric acid and pancreatic enzyme secretion. The inhibitory effects on upper gastrointestinal functions are at least partly mediated by vagal-cholinergic inhibition and may involve interactions with vagal afferent pathways and/or circumventricular regions within the CNS. GLP-1 is a candidate humoral mediator of the 'ileal brake' exerting inhibition of upper gastrointestinal function preventing malabsorption and postprandial metabolic disturbances. As human studies indicate a central action of GLP-1 in reduction of food intake, it is uncertain if this is a consequence of induction of satiety or of transduction of visceral aversive stress signals.