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ABSTRACT: BACKGROUND: Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche. RESULTS: Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles. CONCLUSIONS: Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.
BMC Genomics 02/2013; 14(1):81. · 4.07 Impact Factor
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Håvard Kauserud,
Einar Heegaard,
Ulf Büntgen,
Rune Halvorsen,
Simon Egli,
Beatrice Senn-Irlet,
Irmgard Krisai-Greilhuber,
Wolfgang Dämon,
Jenni Nordén,
Klaus Høiland,
Paul M Kirk,
Mikhail Semenov, Nils Chr Stenseth,
Lynne Boddy
Proceedings of the National Academy of Sciences 01/2013; 110(5):E335. · 9.68 Impact Factor
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ABSTRACT: AIM: A major challenge in metagenome studies is to estimate the true size of all combined genomes. Here, we present a novel approach to estimate the size of all combined genomes for low coverage Next Generation Sequencing (NGS) data through empirically determined copy numbers of random DNA fragments. METHODS AND RESULTS: Size estimates were made based on analyses of two experimental soil micro-ecosystems - simulating soil with and without earthworms. Our analyses showed combined genome sizes of about log 11 nucleotides for each of the soil micro-ecosystems, as estimated from qPCR determined copy numbers of random DNA fragments. This corresponds to more than 20 000 unique bacterial genomes in each sample. There seemed, however, to be a bacterial subpopulation in the earthworm soil, not being present in the non-earthworm soil. To describe the structure of the metagenomes, both total DNA and amplified 16S rRNA gene sequence libraries were generated with 454-sequencing. Bioinformatic analysis of 454 sequence libraries showed a large functional, but low taxonomic overlap between the samples with and without earthworms. A neutrality test indicated that rare species have a competitive advantage over abundant species in both micro-ecosystems providing a potential explanation for the large metagenome sizes. CONCLUSIONS: We have shown that the soil metagenome is very large, and that the large size is probably a consequence of top down selection of the dominant bacterial species. SIGNIFICANCE AND IMPACT: Estimates of metagenome size from low coverage NGS data will be important for guiding future NGS setups. © 2012The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.
Journal of Applied Microbiology 10/2012; · 2.34 Impact Factor
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ABSTRACT: Atlantic salmon populations are reported to be declining throughout its range, raising major management concerns. Variation in adult fish abundance may be due to variation in survival, growth, and timing of life history decisions. Given the complex life history, utilizing highly divergent habitats, the reasons for declines may be multiple and difficult to disentangle. Using recreational angling data of two sea age groups, one-sea-winter (1SW) and two-sea-winter (2SW) fish originated from the same smolt year class, we show that sea age at maturity of the returns has increased in 59 Norwegian rivers over the cohorts 1991-2005. By means of linear mixed-effects models we found that the proportion of 1SW fish spawning in Norway has decreased concomitant with the increasing sea surface temperature experienced by the fish in autumn during their first year at sea. Furthermore, the decrease in the proportion of 1SW fish was influenced by freshwater conditions as measured by water discharge during summer months 1 year ahead of seaward migration. These results suggest that part of the variability in age at maturity can be explained by the large-scale changes occurring in the north-eastern Atlantic pelagic food web affecting postsmolt growth, and by differences in river conditions influencing presmolt growth rate and later upstream migration.
Ecology and evolution. 09/2012; 2(9):2192-203.
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ABSTRACT: We consider the problem of analyzing long-term experiments with panels of nonlinear time-series data in the framework of generalized
additive models. Our approach is developed for testing and estimating the (partial) common dynamic structure across treatment
groups. We illustrate our approach with a detailed analysis of an ecotoxicological experiment on the effect of sublethal doses
of a toxic substance (cadmium) on the long-run dynamic structure of the greenbottle blowfly (Lucilia sericata). The general model for the blowfly experiment is a generalized additive model which is derived from a stage-structured ecological
model. We discuss the relationship between the components of the generalized additive model and those of the underlying stage-structured
model. In particular, our proposed approach casts new insights on the effect of toxic diet on the population dynamic structure
of the blowfly.
Journal of Agricultural Biological and Environmental Statistics 04/2012; 9(2):200-215. · 1.21 Impact Factor
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ABSTRACT: Fluctuations of fish populations abundances are shaped by the interplay between population dynamics and the stochastic forcing of the environment. Age-structured populations behave as a filter of the environment. This filter is characterised by the species-specific life cycle and life-history traits. An increased mortality of mature individuals alters these characteristics and may therefore induce changes in the variability of populations. The response of a generic age-structured model was analysed to investigate the expected changes in the fluctuations of fish populations in response to decreased adult survival. These expectations were then tested on an extensive dataset. In accordance with theory, the analyses revealed that decreased adult survival and mean age of spawners were linked to an increase in the relative importance of short-term fluctuations. It suggests that intensive exploitation can lead to a change in the variability of fish populations, an issue of central interest from both conservation and management perspectives.
Ecology Letters 04/2012; 15(7):658-65. · 17.56 Impact Factor
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ABSTRACT: Assessment of future ecosystem risks should account for the relevant uncertainty sources. This means accounting for the joint effects of climate variables and using modelling techniques that allow proper treatment of uncertainties. We investigate the influence of three of the IPCC's scenarios of greenhouse gas emissions (special report on emission scenarios (SRES)) on projections of the future abundance of a bryophyte model species. We also compare the relative importance of uncertainty sources on the population projections. The whole chain global climate model (GCM)-regional climate model-population dynamics model is addressed. The uncertainty depends on both natural- and model-related sources, in particular on GCM uncertainty. Ignoring the uncertainties gives an unwarranted impression of confidence in the results. The most likely population development of the bryophyte Buxbaumia viridis towards the end of this century is negative: even with a low-emission scenario, there is more than a 65 per cent risk for the population to be halved. The conclusion of a population decline is valid for all SRES scenarios investigated. Uncertainties are no longer an obstacle, but a mandatory aspect to include in the viability analysis of populations.
Proceedings of the Royal Society B: Biological Sciences 03/2012; 279(1740):3098-105. · 5.41 Impact Factor
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ABSTRACT: Until recently, the Bale monkey (Chlorocebus djamdjamensis), an arboreal primate endemic to the southern Ethiopian highlands, remained virtually unstudied, and its distribution pattern inadequately documented. To broaden our knowledge of the species' distribution and abundance, we carried out interviews with local people and total count surveys for Bale monkeys across 67 fragmented forest sites in human-dominated landscapes in the Oromia and Southern Nations, Nationalities, and People's Regions, Ethiopia. From January 2010 to May 2011, we discovered 26 new Bale monkey populations inhabiting forest fragments at elevations ranging from 2,355 to 3,204 m asl. Across these populations, we recorded 37 groups ranging in size from 9 to 29 individuals (Mean = 19.5, SD = 4.5), for a total of 722 individuals. Black-and-white colobus monkeys (Colobus guereza) were sympatric with Bale monkeys at all sites, while grivet monkeys (Chlorocebus aethiops) were found only at sites where Bale monkeys did not occur. All of the newly discovered Bale monkey sites once contained bamboo forest, though at 35% of the sites bamboo forest had been eliminated during the past two decades. The persistence of Bale monkeys at fragmented sites lacking bamboo suggests greater habitat flexibility for the species than previously thought, though the long-term viability of populations both with and without bamboo remains uncertain. Human hunting in response to crop raiding, a behavior the monkeys engaged in at all sites, represents a major threat facing the newly discovered Bale monkey populations. Furthermore, despite their current lack of sympatry, apparently hybrid individuals between Bale monkeys and grivets were noted at three sites, posing yet another potential obstacle to Bale monkey conservation. Community conservation programs aimed at (1) protecting remaining habitat fragments, (2) planting bamboo and trees within and between fragments, and (3) reducing crop raiding represent the only hope for survival of the newly discovered Bale monkey populations.
American Journal of Primatology 02/2012; 74(5):423-32. · 2.22 Impact Factor
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ABSTRACT: Recently developed theoretical models of stage-structured consumer-resource systems have shown that stage-specific biomass overcompensation can arise in response to increased mortality rates. We parameterized a stage-structured population model to simulate the effects of increased adult mortality caused by a pathogen outbreak in the perch (Perca fluviatilis) population of Windermere (UK) in 1976. The model predicts biomass overcompensation by juveniles in response to increased adult mortality due to a shift in food-dependent growth and reproduction rates. Considering cannibalism between life stages in the model reinforces this compensatory response due to the release from predation on juveniles at high mortality rates. These model predictions are matched by our analysis of a 60-year time series of scientific monitoring of Windermere perch, which shows that the pathogen outbreak induced a strong decrease in adult biomass and a corresponding increase in juvenile biomass. Age-specific adult fecundity and size at age were higher after than before the disease outbreak, suggesting that the pathogen-induced mortality released adult perch from competition, thereby increasing somatic and reproductive growth. Higher juvenile survival after the pathogen outbreak due to a release from cannibalism likely contributed to the observed biomass overcompensation. Our findings have general implications for predicting population- and community-level responses to increased size-selective mortality caused by exploitation or disease outbreaks.
Ecology 12/2011; 92(12):2175-82. · 4.85 Impact Factor
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ABSTRACT: This paper expands the Conspecific Community Dynamics (CCD) models on the issue of interaction between communities. In the first part, we consider a model for the standard types of interactions: predator-prey and competition for resources. Particular emphasis is placed on comparing the results of the classical models describing the interaction between species and their counterparts describing the interaction between single-species (conspecific) communities. Then, considering the coexistence of species under resource competition, it is shown that there is a definite relationship between the total number of organisms, the number of coexisting species and the variation between species carrying capacities. In the last part, the paper introduces a model for such type of interaction between communities, which may briefly be described as "warfare", which is a mixture of resource competition and the direct killing of rivals. As an example of such interactions, a model describing the emergence of phytoplankton toxic blooms is considered. Key words: Ecological community, conspecific community, prey-predator model, Lotka-Volterra competition model, the paradox of the plankton, phytoplankton toxic blooms
11/2011, Degree: PhD, Supervisor: Nils Chr. Stenseth
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ABSTRACT: The paper goes back to the basis of population dynamics, especially the works of Malthus, and tries to model his pioneering vision again, this time taking into account such of his postulates as the necessity of food for survival, the reproduction of each individual and inequities of resource distribution. We construct a Conspecific Community Dynamics Model (CCDM), which is based on these well-known postulates of Malthus. Nevertheless, analysis of the model reveals quite interesting results. (1) The size of the community nontrivially depends on the level of equality between its members (for example, there is a given level of equality in which the size of the community becomes a maximum). (2) The size of the community is limited not only by the amount of resources, but the community's ability to utilize these resources. (3) A high level of equality leads to a dynamical instability, which, in turn, under certain conditions, may lead to extinction. Thereafter, we included in the model the fact that the level of equality in the community may be constantly changing under the influence of co-selection. This in turn leads to changes in average demographic characteristics and associated life-history traits. It is interesting that this model demonstrates a so-called demographic-economic paradox, which is traditionally considered to be the main empirical argument against the Malthus theory. In conclusion, we consider the anti-Malthus or pro-Condorcet model in which resources available to the community can grow at the same pace as the population. Despite the fact that such a community has always been unstable (has no equilibrium size or carrying capacity), it may nevertheless be limited and exist for a long time due to co-selection. Analysis of this model demonstrates a significant similarity in the results with the empirical model of demographic transition.
11/2011, Degree: PhD, Supervisor: Nils Chr. Stenseth
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ABSTRACT: This paper introduces an integrated approach to the modeling of epidemics that combines nutrition-dependent physiology and nutrition-dependent immunology of an individual with differences among individuals within a conspecific community. This approach, based on a Conspecific Community Dynamics Model (CCDM), offers a new analytic platform for epidemiological and interdisciplinary studies, which allows for the inclusion into consideration of a greater number of essentially important components. This paper provides significant insight into the crucial role of heterogeneity among individuals in the epidemic process, showing that the inclusion of heterogeneity in the consideration may radically change the whole picture of epidemic dynamics.
11/2011, Degree: PhD, Supervisor: Nils Chr. Stenseth
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ABSTRACT: Fishes used to live under water. Fishes are not a floating biomass. Fishes differ among themselves, and not only in their taxonomical affiliation, sex, and age. Fishes need certain amount of food for survival and reproduction. Fishes used to live into groups. Fishes used to live in stochastic environment."-This is a list of basic facts that are still barely considered together, if at all, in models of fish population. The newly developed Conspecific Community Dynamics Model (CCDM) approach, in combination with optimal shoaling models (OSM) allows the taking into account of these facts and offers an analytical shoal-based model for fish population dynamics. This model provides convenient tools for investigating such issues as a density-dependence and bi-stability. The model gives insight into how species-specific physiology, involvement in shoaling behavior, resource availability and cannibalism affect fish population dynamics.
11/2011, Degree: PhD, Supervisor: Nils Chr. Stenseth
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ABSTRACT: Plague is enzootic in wildlife populations of small mammals in central and eastern Asia, Africa, South and North America, and has been recognized recently as a reemerging threat to humans. Its causative agent Yersinia pestis relies on wild rodent hosts and flea vectors for its maintenance in nature. Climate influences all three components (i.e., bacteria, vectors, and hosts) of the plague system and is a likely factor to explain some of plague's variability from small and regional to large scales. Here, we review effects of climate variables on plague hosts and vectors from individual or population scales to studies on the whole plague system at a large scale. Upscaled versions of small-scale processes are often invoked to explain plague variability in time and space at larger scales, presumably because similar scale-independent mechanisms underlie these relationships. This linearity assumption is discussed in the light of recent research that suggests some of its limitations.
PLoS Pathogens 09/2011; 7(9):e1002160. · 9.13 Impact Factor
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ABSTRACT: Plague, caused by the bacterium Yersinia pestis, is a mammalian vector-borne disease, transmitted by fleas that serve as the vector between rodent hosts. For many pathogens, including Y. pestis, there are strong evolutionary pressures that lead to a reduction in 'useless genes', with only those retained that reflect function in the specific environment inhabited by the pathogen. Genetic traits critical for survival and transmission between two environments, the rodent and the flea, are conserved in epizootic/epidemic plague strains. However, there are genes that remain conserved for which no function in the flea-rodent cycle has yet been observed, indicating an additional environment may exist in the transmission cycle of plague. Here, we present evidence for highly conserved genes that suggests a role in the persistence of Y. pestis after death of its host. Furthermore, maintenance of these genes points to Y. pestis traversing a post-mortem path between, and possibly within, epizootic periods and offering insight into mechanisms that may allow Y. pestis an alternative route of transmission in the natural environment.
The ISME Journal 08/2011; 6(2):231-6. · 7.38 Impact Factor
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Bastiaan Star,
Alexander J Nederbragt,
Sissel Jentoft,
Unni Grimholt,
Martin Malmstrøm,
Tone F Gregers,
Trine B Rounge,
Jonas Paulsen,
Monica H Solbakken,
Animesh Sharma, [......],
Richard Reinhardt,
Lei Du,
Steinar D Johansen,
Steve Searle,
Sigbjørn Lien,
Frank Nilsen,
Inge Jonassen,
Stig W Omholt, Nils Chr Stenseth,
Kjetill S Jakobsen
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ABSTRACT: Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
Nature 08/2011; 477(7363):207-10. · 36.28 Impact Factor
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ABSTRACT: Biotic interactions via the struggle for control of energy and the interactive effects of biota with their physical environment characterize Van Valen's Red Queen (VRQ). Here, we review new evidence for and against a VRQ view of the world from studies of increasing temporal and spatial scales. Interactions among biota and with the physical environment are important for generating and maintaining diversity on diverse timescales, but detailed mechanisms remain poorly understood. We recommend directly estimating the effect of biota and the physical environment on ecological and evolutionary processes. Promising approaches for elucidating VRQ include using mathematical modelling, controlled experimental systems, sampling and processes-oriented approaches for analysing data from natural systems, while paying extra attention to biotic interactions discernable from the fossil record.
Trends in Ecology & Evolution 07/2011; 26(7):349-58. · 15.75 Impact Factor
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ABSTRACT: Over the years, plague has caused a large number of deaths worldwide and subsequently changed history, not the least during the period of the Black Death. Of the three plague pandemics, the third is believed to have originated in China. Using the spatial and temporal human plague records in China from 1850 to 1964, we investigated the association of human plague intensity (plague cases per year) with proxy data on climate condition (specifically an index for dryness/wetness). Our modeling analysis demonstrates that the responses of plague intensity to dry/wet conditions were different in northern and southern China. In northern China, plague intensity generally increased when wetness increased, for both the current and the previous year, except for low intensity during extremely wet conditions in the current year (reflecting a dome-shaped response to current-year dryness/wetness). In southern China, plague intensity generally decreased when wetness increased, except for high intensity during extremely wet conditions of the current year. These opposite effects are likely related to the different climates and rodent communities in the two parts of China: In northern China (arid climate), rodents are expected to respond positively to high precipitation, whereas in southern China (humid climate), high precipitation is likely to have a negative effect. Our results suggest that associations between human plague intensity and precipitation are nonlinear: positive in dry conditions, but negative in wet conditions.
Proceedings of the National Academy of Sciences 06/2011; 108(25):10214-9. · 9.68 Impact Factor
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ABSTRACT: The objectives pursued by governments managing fisheries may include maximizing profits, minimizing the impact on the marine ecosystem, or securing employment, which all require adjusting the composition of the fishing fleet. We develop a management plan that can be adapted to those objectives and allows the regulator to compare the long-run profits between the various management options. We apply the model to the case of Northeast Arctic cod, and estimate the cost and harvesting functions of various vessel types, the demand function, and a biological model to provide key insights regarding the optimal management of this valuable fish species.
Environment & Natural Resources eJournal. 06/2011;
