Thursday – four out of seven PLoS journals publish new articles and I make my own picks. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth’s ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød) warming phase at 14.5 kyrs BP. Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population extinctions of collared lemmings would have severe effects on the arctic ecosystem, as collared lemmings are a key species in the trophic interactions and ecosystem processes in the Arctic.
This article describes the typical stages in the analysis of microarray data for non-specialist researchers in systems biology and medicine. Particular attention is paid to significant data analysis issues that are commonly encountered among practitioners, some of which need wider airing. The issues addressed include experimental design, quality assessment, normalization, and summarization of multiple-probe data. This article is based on the ISMB 2008 tutorial on microarray data analysis. An expanded version of the material in this article and the slides from the tutorial can be found at http://www.people.vcu.edu/~mreimers/OGMD A/index.html .
Uncertainties remain in the potential of forest plantations to sequestrate carbon (C). We synthesized 86 experimental studies with paired-site design, using a meta-analysis approach, to quantify the differences in ecosystem C pools between plantations and their corresponding adjacent primary and secondary forests (natural forests). Totaled ecosystem C stock in plant and soil pools was 284 Mg C ha−1 in natural forests and decreased by 28% in plantations. In comparison with natural forests, plantations decreased aboveground net primary production, litterfall, and rate of soil respiration by 11, 34, and 32%, respectively. Fine root biomass, soil C concentration, and soil microbial C concentration decreased respectively by 66, 32, and 29% in plantations relative to natural forests. Soil available N, P and K concentrations were lower by 22, 20 and 26%, respectively, in plantations than in natural forests. The general pattern of decreased ecosystem C pools did not change between two different groups in relation to various factors: stand age (<25 years vs. ≥25 years), stand types (broadleaved vs. coniferous and deciduous vs. evergreen), tree species origin (native vs. exotic) of plantations, land-use history (afforestation vs. reforestation) and site preparation for plantations (unburnt vs. burnt), and study regions (tropic vs. temperate). The pattern also held true across geographic regions. Our findings argued against the replacement of natural forests by the plantations as a measure of climate change mitigation.
Infections by the influenza A virus show highly seasonal patterns in temperate regions. Winter is flu season. Over the course of the autumn and winter, a small number of initial infections grow to encompass a significant proportion of the population. At the end of the winter, infection disappears. It has been suggested that the strains founding each temperate flu season originate from China and Southeast Asia, where influenza A is less seasonal. We test this hypothesis through analysis of genetic sequences from viruses sampled throughout the world between 1998 and 2009. We find that although China and Southeast Asia play the largest role in the migration network, temperate regions, particularly the USA, also make important contributions. Not all temperate strains of influenza die out with the end of the winter season. Instead many strains emigrate to more favorable climes. Thus, we find patterns of influenza transmission to be highly dynamic. Because of emigration out of temperate regions, mutations harbored by temperate strains of influenza A can spread to the global virus population. This means that regional public health decisions regarding influenza may have global impacts.
Membranous compartments of neurons such as axons, dendrites and modified primary cilia are defining features of neuronal phenotype. This is unlike organelles deep to the plasma membrane, which are for the most part generic and not related directly to morphological, neurochemical or functional specializations. However, here we use multi-label immunohistochemistry combined with confocal and electron microscopy to identify a very large (~6 microns in diameter), entirely intracellular neuronal organelle which occurs singly in a ubiquitous but neurochemically distinct and morphologically simple subset of sympathetic ganglion neurons. Although usually toroidal, it also occurs as twists or rods depending on its intracellular position: tori are most often perinuclear whereas rods are often found in axons. These ‘loukoumasomes’ (doughnut-like bodies) bind a monoclonal antibody raised against beta-III-tubulin (SDL.3D10), although their inability to bind other beta-III-tubulin monoclonal antibodies indicate that the responsible antigen is not known. Position-morphology relationships within neurons and their expression of non-muscle heavy chain myosin suggest a dynamic structure. They associate with nematosomes, enigmatic nucleolus-like organelles present in many neural and non-neural tissues, which we now show to be composed of filamentous actin. Loukoumasomes also separately interact with mother centrioles forming the basal body of primary cilia. They express gamma tubulin, a microtubule nucleator which localizes to non-neuronal centrosomes, and cenexin, a mother centriole-associated protein required for ciliogenesis. These data reveal a hitherto undescribed organelle, and depict it as an intracellular transport machine, shuttling material between the primary cilium, the nematosome, and the axon.
Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection. Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a ~30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location. This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.
When I took on the role of Editor-in-Chief of this open-access journal, I began, for the first time, to think about scholarly communication beyond submitting my papers and getting them published. This thinking led to previous Perspectives -, all of which shared an underlying theme–there are many opportunities to achieve better dissemination and comprehension of our science, and as producers of that output I believe authors have a responsibility to see it used in the best possible way.
In unearthing the genetic history of human populations, the recent pace of discovery has been so rapid that we can lose sight of the impact made by a single paper. In a 1987 Nature article, Rebecca Cann and her co-workers, Mark Stoneking and the late Allan Wilson, painstakingly analyzed mitochondrial DNA purified from placentas that had been collected from women of many different ancestral origins. By comparing the mitochondrial DNA variants to each other, the authors produced a phylogenetic tree that showed how human mitochondria are all related to each other and, by implication, how all living females, through whom mitochondria are transmitted, are descended from a single maternal ancestor. Not only that, they localized the root of the tree in Africa. The report left a wake, still rippling today, that stimulated not just geneticists and paleo-anthropologists, but the layperson as well, especially as the ancestor was quickly dubbed “Mitochondrial Eve.” Indeed, the cover of Newsweek one year later depicted an Eden, replete with apple tree and serpent, but with the iconic blonde couple of Dürer now supplanted by an Adam and Eve of African descent.
More than 25 years have passed since the discovery of HIV type 1, the causative agent of AIDS, and the first vaccine candidate to exhibit evidence for protection against infection was reported only recently . However, the extent and mode of protection are still under debate . Thus, a vaccine that effectively stimulates complete protective immunity by the cellular branch (cytotoxic T lymphocytes) and/or the humoral branch (antibodies) of the immune system has yet to emerge. Among the millions of people who have received treatment for the disease and the many more who have tested HIV positive, there exists no definitive case in which a potent neutralizing antibody response enabled an infected individual to successfully clear or control the infection. In a small percentage of cases, individuals will exhibit a natural ability to suppress viral replication and progression of the disease. However, the explanation for the existence of this rare phenotype has primarily converged on a robust cellular immune response, with evidence generally lacking for a significant contribution to viral control by antibodies -.
Decision analysis and game theory ,  have proved useful tools in various biodiversity conservation planning and modeling contexts -. This paper shows how game theory may be used to inform group decisions in biodiversity conservation scenarios by modeling conflicts between stakeholders to identify Pareto-inefficient Nash equilibria. These are cases in which each agent pursuing individual self-interest leads to a worse outcome for all, relative to other feasible outcomes. Three case studies from biodiversity conservation contexts showing this feature are modeled to demonstrate how game-theoretical representation can inform group decision-making. The mathematical theory of games is used to model three biodiversity conservation scenarios with Pareto-inefficient Nash equilibria: (i) a two-agent case involving wild dogs in South Africa; (ii) a three-agent raptor and grouse conservation scenario from the United Kingdom; and (iii) an n-agent fish and coral conservation scenario from the Philippines. In each case there is reason to believe that traditional mechanism-design solutions that appeal to material incentives may be inadequate, and the game-theoretical analysis recommends a resumption of further deliberation between agents and the initiation of trust–and confidence–building measures. Game theory can and should be used as a normative tool in biodiversity conservation contexts: identifying scenarios with Pareto-inefficient Nash equilibria enables constructive action in order to achieve (closer to) optimal conservation outcomes, whether by policy solutions based on mechanism design or otherwise. However, there is mounting evidence  that formal mechanism-design solutions may backfire in certain cases. Such scenarios demand a return to group deliberation and the creation of reciprocal relationships of trust.
One of the easiest ways for people to lower their risk of infection during an epidemic is for them to reduce their rate of contact with infectious individuals. However, the value of such actions depends on how the epidemic progresses. Few analyses of behavior change to date have accounted for how changes in behavior change the epidemic wave. In this paper, I calculate the tradeoff between daily social distancing behavior and reductions in infection risk now and in the future. The subsequent analysis shows that, for the parameters and functional forms studied, social distancing is most useful for moderately transmissible diseases. Social distancing is particularly useful when it is inexpensive and can delay the epidemic until a vaccine becomes widely available. However, the benefits of social distancing are small for highly transmissible diseases when no vaccine is available.
Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator’s functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator’s effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model’s predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.