Increasing longevity through caloric restriction or rapamycin feeding in mammals: common mechanisms for common outcomes?

Significant extension of lifespan in important mammalian species is bound to attract the attention not only of the aging research community, but also the media and the wider public. Two recent papers published by Harrison et al. (2009) in Nature and by Colman et al. (2009) in Science report increased longevity of mice fed with rapamycin and of rhesus monkeys undergoing caloric restriction, respectively. These papers have generated considerable debate in the aging community. Here we assess what is new about these findings, how they fit with our knowledge of lifespan extension from other studies and what prospects this new work holds out for improvements in human longevity and human health span.     

Genetics of personalities: no simple answers for complex traits

Identifying the genes that underlie phenotypic variation in natural populations, and assessing the consequences of polymorphisms at these loci for individual fitness are major objectives in evolutionary biology. Yet, with the exception of a few success stories, little progress has been made, and our understanding of the link between genotype and phenotype is still in its infancy. For example, although body length in humans is largely genetically determined, with heritability estimates greater than 0.8, massive genome‐wide association studies (GWAS) have only been able to account for a very small proportion of this variation ( Gudbjartsson et al. 2008 ). If it is so difficult to explain the genetics behind relatively ‘simple’ traits, can we envision that it will at all be possible to find genes underlying complex behavioural traits in wild non‐model organisms? Some notable examples suggest that this can indeed be a worthwhile endeavour. Recently, the circadian rhythm gene Clock has been associated with timing of breeding in a wild blue tit population ( Johnsen et al. 2007 ; Liedvogel et al. 2009 ) and the Pgi gene to variation in dispersal and flight endurance in Glanville fritillary butterflies ( Niitepold et al. 2009 ). A promising candidate gene for influencing complex animal personality traits, also known as behavioural syndromes ( Sih et al. 2004 ), is the dopamine receptor D4 (DRD4) gene. Within the last decade, polymorphisms in this gene have been associated with variation in novelty seeking and exploration behaviour in a range of species, from humans to great tits ( Schinka et al. 2002 ; Fidler et al. 2007 ). In this issue, Korsten et al. (2010) attempt to replicate this previously observed association in wild‐living birds, and test for the generality of the association between DRD4 and personality across a number of European great tit populations.     

Lack of intermediate-scale disturbance data prevents robust extrapolation of plot-level tree mortality rates for old-growth tropical forests

Lloyd et al. (2009) question the methods, concepts and conclusions of Fisher et al. (2008) . We address these assertions, and place our work into a broader context. We demonstrate the veracity of Fisher et al. , and further show that lack of data for intermediate-scale tree mortality disturbance events for old-growth tropical forests might prevent robust extrapolation of forest plot biomass accumulation data, and accurate estimates of distribution parameters such as power-law exponents ( α ).     

Population genomics as a new tool for wildlife management

Admixture and introgression have varied effects on population viability and fitness. Admixture might be an important source of new alleles, particularly for small, geographically isolated populations. However, admixture might also cause outbreeding depression if populations are adapted to different ecological or climatic conditions. Because of the emerging use of translocation and admixture as a conservation and wildlife management strategy to reduce genetic load (termed genetic rescue), the possible effects of admixture have practical consequences ( Bouzat et al. 2009 ; Hedrick & Fredrickson 2010 ). Importantly, genetic load and local adaptation are properties of individual loci and epistatic interactions among loci rather than properties of genomes. Likewise, the outcome and consequences of genetic rescue depend on the fitness effects of individual introduced alleles. In this issue of Molecular Ecology, Miller et al. (2012) use model‐based, population genomic analyses to document locus‐specific effects of a recent genetic rescue in the bighorn sheep population within the National Bison Range wildlife refuge (NBR; Montana, USA). They find a subset of introduced alleles associated with increased fitness in NBR bighorn sheep, some of which experienced accelerated introgression following their introduction. These loci mark regions of the genome that could constitute the genetic basis of the successful NBR bighorn sheep genetic rescue. Although population genomic analyses are frequently used to study local adaptation and selection (e.g. Hohenlohe et al. 2010 ; Lawniczak et al. 2010 ), this study constitutes a novel application of this analytical framework for wildlife management. Moreover, the detailed demographic data available for the NBR bighorn sheep population provide a rare and powerful source of information and allow more robust population genomic inference than is often possible.     

Intergenerational reproductive parasitism in a stingless bee

Insect colonies have been traditionally regarded as closed societies comprised of completely sterile workers ruled over by a single once-mated queen. However, over the past 15 years, microsatellite studies of parentage have revealed that this perception is far from the truth ( Beekman & Oldroyd 2008 ). First, we learned that honey bee queens are far more promiscuous than we had previously imagined ( Estoup et al. 1994 ), with one Apis dorsata queen clocked at over 100 mates ( Wattanachaiyingcharoen et al. 2003 ). Then Oldroyd et al. (1994) reported a honey bee colony from Queensland, where virtually all the males were sons of a single patriline of workers – a clear case of a cheater mutant that promoted intra-colonial reproductive parasitism. Then we learned that both bumble bee colonies ( Lopez-Vaamonde et al. 2004 ) and queenless honey bee colonies ( Nanork et al. 2005, 2007 ) are routinely parasitized by workers from other nests that fly in and lay male-producing eggs that are then reared by the victim colony. There is even evidence that in a thelytokous honey bee population, workers lay female-destined eggs directly into queen cells, thus reincarnating themselves as a queen ( Jordan et al. 2008 ). And let us not forget ants, where microsatellite studies have revealed equally bizarre and totally unexpected phenomena (e.g. Cahan & Keller 2003 ; Pearcy et al. 2004 ; Fournier et al. 2005 ). Now, in this issue, Alves et al. (2009) use microsatellites to provide yet another shocking and completely unexpected revelation about the nefarious goings-on in insect colonies: intergenerational reproductive parasitism by stingless bee workers.     

Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests

Both direct and indirect experimental evidence has shown signaling, communication and conductivity in microtubules (MTs). Theoretical models have predicted that MTs can be potentially used for both classical and quantum information processing although controversies arose in regard to physiological temperature effects on these capabilities. In this paper, MTs have been studied using well-established principles of classical statistical physics as applied to information processing, information storage and signal propagation. To investigate the existence of information processing in MTs we used cellular automata (CA) models with neighbor rules based on the electrostatic properties of the molecular structure of tubulin, and both synchronous and asynchronous updating methods. We obtained a phase diagram of possible dynamic behaviors in MTs that depend on the values of characteristic physical parameters that can be experimentally verified.     

Within-genotype epigenetic variation enables broad niche width in a flower living yeast

Niche theory is one of the central organizing concepts in ecology. Generally, this theory defines a given species niche as all of the factors that effect the persistence of the species as well as the impact of the species in a given location ( Hutchinson 1957 ; Chase 2011 ). Many studies have argued that phenotypic plasticity enhances niche width because plastic responses allow organisms to express advantageous phenotypes in a broader range of environments ( Bradshaw 1965 ; Van Valen 1965 ; Sultan 2001 ). Further, species that exploit habitats with fine‐grained variation, or that form metapopulations, are expected to develop broad niche widths through phenotypic plasticity ( Sultan & Spencer 2002 ; Baythavong 2011 ). Although a long history of laboratory, greenhouse and reciprocal transplant experiments have provided insight into how plasticity contributes to niche width ( Pigliucci 2001 ), recent advances in molecular approaches allow for a mechanistic understanding of plasticity at the molecular level ( Nicotra et al. 2010 ). In particular, variation in epigenetic effects is a potential source of the within‐genotype variation that underlies the phenotypic plasticity associated with broad niche widths. Epigenetic mechanisms can alter gene expression and function without altering DNA sequence ( Richards 2006 ) and may be stably transmitted across generations ( Jablonka & Raz 2009 ; Verhoeven et al. 2010 ). Also, epigenetic mechanisms may be an important component of an individual’s response to the environment ( Verhoeven et al. 2010 ). While these ideas are intriguing, few studies have made a clear connection between genome‐wide DNA methylation patterns and phenotypic plasticity (e.g. Bossdorf et al. 2010 ). In this issue of Molecular Ecology, Herrera et al. (2012) present a study that demonstrates epigenetic changes in genome‐wide DNA methylation are causally active in a species’ ability to exploit resources from a broad range of environments and are particularly important in harsh environments.     

Speciation genetics of biological invasions with hybridization

The negative effects of human‐induced habitat disturbance and modification on multiple dimensions of biological diversity are well chronicled ( Turner 1996 ; Harding et al. 1998 ; Lawton et al. 1998 ; Sakai et al. 2001 ). Among the more insidious consequences is secondary contact between formerly allopatric taxa ( Anderson & Hubricht 1938 ; Perry et al. 2002 ; Seehausen 2006 ). How the secondary contact will play out is unpredictable ( Ellstrand et al. 2010 ), but if the taxa are not fully reproductively isolated, hybridization is likely, and if the resulting progeny are fertile, the eventual outcome is often devastating from a conservation perspective ( Rhymer & Simberloff 1996 ; Wolf et al. 2001 ; McDonald et al. 2008 ). In this issue of Molecular Ecology, Steeves et al. (2010) present an analysis of hybridization between two avian species, one of which is critically endangered and the other of which is invasive. Their discovery that the endangered species has not yet been hybridized to extinction is promising and not what one would necessarily expect from theory.     

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.     

Managing for naturalness alone is not an effective way to preserve all the valuable natural features of the Białowieża Forest – a reply to Jaroszewicz et al.

Currently, Brzeziecki et al. 2016 (Journal of Vegetation Science 27: 460–467.) are using data from permanent study plots established in 1936 in Bia?owie?a National Park (NE Poland) to develop theoretical equilibrium tree size distributions and to then compare modelled and actual distributions with a view to assessing the population dynamics of the species involved. As part of their discussion, the authors address the question of possible consequences for the overall diversity of forest ecosystems under strict protection if long‐term trends relating to tree population densities and size structures are maintained. In the overall context of the above, the goal of the present paper is to respond to Jaroszewicz et al. (Journal of Vegetation Science 28: 218–222.) who suggest that the paper of Brzeziecki et al. (2016) is not representative for the whole Bia?owie?a National Park, and that – in this connection – strict protection should not be seen as a cause for concern. In this paper, we show that the data analysed by Brzeziecki et al. (2016) adequately characterize conditions in the wider Park. We also point out that the thorough scientific understanding of the long‐term dynamics of woodland communities under strict protection should indeed be taken into account as efforts are made to arrive at an effective conservation strategy capable of ensuring that the uniquely valuable features of the Bia?owie?a Forest are retained.     

North Atlantic marine communities through time

How and why ecological communities change their species membership over time and space is a central issue in ecology and evolution. Phylogeographic approaches based on animal mitochondrial DNA sequences have been important for revealing historical patterns of individual species and can provide qualitative comparisons among species. Exciting new methods, particularly implementing approximate Bayesian computation (ABC – Beaumont et al. 2002 ), now allow model‐based quantitative comparisons among species and permit the probabilistic exploration of alternative community‐level hypotheses (see review by Hickerson et al. 2010 ). In this issue of Molecular Ecology, Ilves et al. (2010) use an ABC approach to bring fresh insights into the well‐studied question of how North Atlantic coastal species contracted and expanded their ranges in response to late Pleistocene/Holocene climate fluctuations.     

Bacterial biofilms in a 'genes-to-ecosystems' context

In ecology, there is an increasing amount of research dedicated to understanding how intraspecific genetic diversity can extend beyond the population level to influence the assembly of communities and the functioning of ecosystems. In this issue of Molecular Ecology, Koh et al. (2012) take this exploration to a new level using bacterial biofilms and protozoan grazers. They show that there is heritable variation in the phenotypes of different variants of biofilms of Serratia marcescens and that these strains display complementarity when combined in a diverse assemblage. Mixtures of variants were significantly more resistant to protozoan grazing than either wild‐type or variant biofilms grown in monocultures. While similar biodiversity effects of genotype mixtures have been observed in other systems, Koh et al. (2012) link phenotype variation of the biofilms to a single nucleotide polymorphism in one regulatory gene. Importantly, the authors demonstrate that minimal changes in a genotype can result in substantial shifts in interspecific ecological interactions.     

A miniscule optimized visual system in the Lower Cambrian

Simultaneously with the development of animal body plans, probably before the Precambrian, there was an explosive diversification of visual systems. Competition of performance in these visual systems was a critical factor in the evolution of life systems.
Here we analyse the visual system in the lobopod Miraluolishania haikouensis ( Liu et al ., 2004 ) from the Lower Cambrian Chengjiang Lagerstätte, Kunming, China. It consists of a very small eye with a miniscule lens. A physical problem lies in the fact that due to the usual refractive conditions of such a lens, it hardly represents an improvement of the visual quality over the basal pit- or pinhole camera eyes. To develop such a lavish visual system, however, would not have been of any value, if it achieved no more than an equal level or represented even a retrograde step in evolutionary progress. We show how this system may have allowed pattern recognition even under poor light conditions. Optimization of such a tiny eye is costly but is not 'a wasted effort' in evolution. In M. haikouensis ( Liu et al. , 2004 ), an excellently adapted miniscule visual system has become possible.     

Transport of multiple nicotinic acetylcholine receptors in the rat optic nerve: high densities of receptors containing alpha6 and beta3 subunits

Neuronal nicotinic acetylcholine receptors (nAChRs) are abundant in the rat retina and at least seven heteromeric subtypes have been detected. Axons of retinal ganglion cells form the optic nerve and innervate areas of the brain important for visual processing, including the lateral geniculate nucleus, the superior colliculus, and the pretectal nucleus. Development of eye-specific layers in these projection areas are dependent upon retinal waves which are initially mediated by nAChRs [ Feller et al. , Science 272 (1996), 1182 ; Penn et al. , Science 279 (1998), 2108 ; Bansal et al. , J. Neurosci. 20 (2000), 7672 ]. Unilateral eye-enucleation studies in the rat indicate that nAChRs are on the terminals of optic nerve axons, where they may mediate influences of acetylcholine on visual pathways. In this study, we use radioligand binding and immunoprecipitation with subunit-selective antibodies to investigate the subunit composition of nAChRs in the rat optic nerve. We found multiple nAChR subtypes in the optic nerve, all of which contain the β2 subunit. Most of these receptors are mixed heteromeric subtypes, composed of at least three different subunits. Included among these subtypes is the highest percentage and density of α6- and β3-containing nAChRs of any area of the rat CNS that has been reported.     

Sowing (and mapping) the wild oats

Both ecological and molecular methods have been applied to the study of locally adapted populations. While Clausen et al . (1940) were the pioneers of field transplant studies, the work of Robert Allard et al . on the invasive species Avena barbata is a classic example of using molecular evidence to infer adaptation via correlation of particular alleles with environmental gradients. In a new study published in this issue of Molecular Ecology, Latta (2009) combines ecological methods (reciprocal environment studies) with quantitative genetic techniques (recombinant inbred lines and quantitative trait analysis) to provide new evidence for local adaptation within this well known system. The conclusions are orthogonal to the original hypothesis, and instead, provide evidence that factors other than local adaptation were likely responsible for the historically observed patterns. This new evidence suggests that one ecotype is generally more fit than the other in both a moist and a dry environment, and accordingly, it appears to be increasing in frequency in historically surveyed populations.     

Crystallographic studies of the anthrax lethal toxin

Anthrax lethal toxin comprises two proteins: protective antigen (PA; MW 83 kDa) and lethal factor (LF; MW 87 kDa). We have recently determined the crystal structure of the 735-residue PA in its monomeric and heptameric forms ( Petosa et al . 1997 ). It bears no resemblance to other bacterial toxins of known three-dimensional structure, and defines a new structural class which includes homologous toxins from other Gram-positive bacteria. We have proposed a model of membrane insertion in which the water-soluble heptamer undergoes a substantial pH-induced conformational change involving the creation of a 14-stranded β-barrel. Recent work by Collier's group ( Benson et al . 1998 ) lends strong support to our model of membrane insertion. 'Lethal factor' is the catalytic component of anthrax lethal toxin. It binds to the surface of the cell-bound PA heptamer and, following endocytosis and acidification of the endosome, translocates to the cytosol. We have made substantial progress towards an atomic resolution crystal structure of LF. Progress towards a structure of the 7:7 translocation complex between the PA heptamer and LF will also be discussed.     

Tracing the recombination and colonization history of hybrid species in space and time

Hybrid speciation has long fascinated evolutionary biologists and laymen alike, presumably because it challenges our classical view of evolution as a ‘one‐way street’ leading to strictly tree‐like patterns of ancestry and descent. Homoploid hybrid speciation (HHS) has been a particularly interesting puzzle, as it appears to occur extremely rapidly, perhaps within less than 50 generations ( McCarthy et al. 1995 ; Buerkle et al. 2000 ). Nevertheless, HHS may sometimes involve extended or repeated periods of recombination and gene exchange between populations subject to strong divergent natural selection ( Buerkle & Rieseberg 2008 ). Thus, HHS provides a highly interesting setting for understanding the drivers and tempo of adaptive divergence and speciation in the face of gene flow ( Arnold 2006 ; Rieseberg & Willis 2007 ; Nolte & Tautz 2009). In the present issue of Molecular Ecology, Wang et al. (2011) explore a particularly challenging issue connected to HHS: they attempt to trace the colonization and recombination history of an ancient (several MYA) hybrid species, from admixture and recombination in the ancestral hybrid zone to subsequent range shifts triggered by tectonic events (uplift of the Tibetan plateau) and climatic shifts (Pleistocene ice ages). This work is important because it addresses key issues related to the origin of the standing genetic variation available for adaptive responses (e.g. to climate change) and speciation in temperate species, which are topics of great current interest ( Rieseberg et al. 2003 ; Barrett & Schluter 2008 ; de Carvalho et al. 2010 ).