Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with ... more Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Percontig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.
The dynamics of species interactions are of central importance for the understanding of ecologica... more The dynamics of species interactions are of central importance for the understanding of ecological coexistence, community structure and the effects of biological invasions. Using bark beetles that colonize the same habitat as an example, we explore species interactions in a resource-based model system with positive feedback between insect abundance and resource availability. The net interspecies interaction was found to be highly dynamic and may alternate in time between competition and mutualism. When both bark beetle species were able to kill trees (“aggressive”), our simulations showed strong facilitations between beetle species. This may lead to escape from control by competition, and increase the frequency of outbreaks of tree-killing. The frequency of net positive interactions varied with interaction strengths and the relative aggressiveness of the species and was highest when both species were strongly aggressive; which predicts disastrous outbreaks if, e.g., the European spruce bark beetle Ips typographus and the North American spruce beetle Dendroctonus rufipennis should become interacting species due to introductions. In imbalanced pairs, the relatively less aggressive species was facilitated more often than the aggressive species. Net positive interactions did not occur for strongly inferior species, but their survival was an increasing function of interaction strength with aggressive species and availability of resources. The benefits for the inferior species in the model are consistent with the structure of one aggressive and several less aggressive or non-aggressive species, which is common in bark beetle communities in many parts of the world.
Foraging patterns of large herbivores may give important clues as to why their life history varie... more Foraging patterns of large herbivores may give important clues as to why their life history varies depending on population density. In this landscape-scale experiment, domestic sheep Ovis aries were kept at high (80 sheep km À2 ) and low (25 sheep km À2 ) population densities during summer in high mountain pastures in Hol, Norway. We predicted an increasing use of less preferred plant species or habitat types with increasing sheep population density. Foraging behaviour was investigated by direct observations of individually marked sheep on different spatial scales, and diet composition was also assessed with microhistological analysis of faecal samples from known individuals. We found that the effects of density on foraging behaviour depended on scale and were only detected at the scale of diet choice. Use of the common grass species Deschampsia flexuosa, which provided the bulk forage (10-65% of the diet), remained constant throughout the season at low densities, but increased significantly over time at high densities. On a coarser spatial scale, neither within vegetation type nor between vegetation types, selection was affected by density, but vegetation type selection differed depending on whether the sheep were grazing or resting. Our study provides evidence of density dependence in foraging behaviour, but only at the finest spatial scale (diet choice).
A 56-year time series of human plague cases (Yersinia pestis) in the western United States was us... more A 56-year time series of human plague cases (Yersinia pestis) in the western United States was used to explore the effects of climatic patterns on plague levels. We found that the Pacific Decadal Oscillation (PDO), together with previous plague levels and above-normal temperatures, explained much of the plague variability. We propose that the PDO's impact on plague is conveyed via its effect on precipitation and temperature and the effect of precipitation and temperature on plague hosts and vectors: warmer and wetter climate leading to increased plague activity and thus an increased number of human cases. Our analysis furthermore provides insights into the consistency of plague mechanisms at larger scales.
Plague, caused by the bacterium Yersinia pestis, is a mammalian vector-borne disease, transmitted... more 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.
Proceedings of The National Academy of Sciences, 2011
Plague (caused by the bacterium Yersinia pestis) is a zoonotic reemerging infectious disease with... more Plague (caused by the bacterium Yersinia pestis) is a zoonotic reemerging infectious disease with reservoirs in rodent populations worldwide. Using one-half of a century of unique data from Kazakhstan on plague dynamics, including data on the main rodent host reservoir (great gerbil), main vector (flea), human cases, and external (climate) conditions, we analyze the full ecoepidemiological (bubonic) plague system. We show that two epidemiological threshold quantities play key roles: one threshold relating to the dynamics in the host reservoir, and the second threshold relating to the spillover of the plague bacteria into the human population.
Background Human cases of plague (Yersinia pestis) infection originate, ultimately, in the bacter... more Background Human cases of plague (Yersinia pestis) infection originate, ultimately, in the bacterium's wildlife host populations. The epidemiological dynamics of the wildlife reservoir therefore determine the abundance, distribution and evolution of the pathogen, which in turn shape the frequency, distribution and virulence of human cases. Earlier studies have shown clear evidence of climatic forcing on contemporary plague abundance in rodents and humans. Results We find that high-resolution palaeoclimatic indices correlate with plague prevalence and population density in a major plague host species, the great gerbil (Rhombomys opimus), over 1949-1995. Climate-driven models trained on these data predict independent data on human plague cases in early 20th-century Kazakhstan from 1904-1948, suggesting a consistent impact of climate on large-scale wildlife reservoir dynamics influencing human epidemics. Extending the models further back in time, we also find correspondence between their predictions and qualitative records of plague epidemics over the past 1500 years. Conclusions Central Asian climate fluctuations appear to have had significant influences on regional human plague frequency in the first part of the 20th century, and probably over the past 1500 years. This first attempt at ecoepidemiological reconstruction of historical disease activity may shed some light on how long-term plague epidemiology interacts with human activity. As plague activity in Central Asia seems to have followed climate fluctuations over the past centuries, we may expect global warming to have an impact upon future plague epidemiology, probably sustaining or increasing plague activity in the region, at least in the rodent reservoirs, in the coming decades. See commentary: http://www.biomedcentral.com/1741-7007/8/108
Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened ... more Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between ''endemic'' and ''epidemic'' regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics.
Proceedings of The Royal Society B: Biological Sciences, 2007
In central Asia, the great gerbil (Rhombomys opimus) is the main host for the bacterium Yersinia ... more In central Asia, the great gerbil (Rhombomys opimus) is the main host for the bacterium Yersinia pestis, the cause of bubonic plague. In order to prevent plague outbreaks, monitoring of the great gerbil has been carried out in Kazakhstan since the late 1940s. We use the resulting data to demonstrate that climate forcing synchronizes the dynamics of gerbils over large geographical areas. As it is known that gerbil densities need to exceed a threshold level for plague to persist, synchrony in gerbil abundance across large geographical areas is likely to be a condition for plague outbreaks at similar large scales. Here, we substantiate this proposition through autoregressive modelling involving the normalized differentiated vegetation index as a forcing covariate. Based upon predicted climate changes, our study suggests that during the next century, plague epizootics may become more frequent in central Asia.
Proceedings of The National Academy of Sciences, 2006
The bacterium Yersinia pestis causes bubonic plague. In Central Asia, where human plague is still... more The bacterium Yersinia pestis causes bubonic plague. In Central Asia, where human plague is still reported regularly, the bacterium is common in natural populations of great gerbils. By using field data from 1949 -1995 and previously undescribed statistical techniques, we show that Y. pestis prevalence in gerbils increases with warmer springs and wetter summers: A 1°C increase in spring is predicted to lead to a >50% increase in prevalence. Climatic conditions favoring plague apparently existed in this region at the onset of the Black Death as well as when the most recent plague pandemic arose in the same region, and they are expected to continue or become more favorable as a result of climate change. Threats of outbreaks may thus be increasing where humans live in close contact with rodents and fleas (or other wildlife) harboring endemic plague.
Proceedings of The National Academy of Sciences, 2010
Climate change has been identified as a causal factor for diverse ecological changes worldwide. W... more Climate change has been identified as a causal factor for diverse ecological changes worldwide. Warming trends over the last couple of decades have coincided with the collapse of long-term population cycles in a broad range of taxa, although causal mechanisms are not well-understood. Larch budmoth (LBM) population dynamics across the European Alps, a classic example of regular outbreaks, inexplicably changed sometime during the 1980s after 1,200 y of nearly uninterrupted periodic outbreak cycles. Herein, analysis of perhaps the most extensive spatiotemporal dataset of population dynamics and reconstructed Alpine-wide LBM defoliation records reveals elevational shifts in LBM outbreak epicenters that coincide with temperature fluctuations over two centuries. A population model supports the hypothesis that temperature-mediated shifting of the optimal elevation for LBM population growth is the mechanism for elevational epicenter changes. Increases in the optimal elevation for population growth over the warming period of the last century to near the distributional limit of host larch likely dampened population cycles, thereby causing the collapse of a millennium-long outbreak cycle. The threshold-like change in LBM outbreak pattern highlights how interacting species with differential response rates to climate change can result in dramatic ecological changes.
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Papers by Kyrre Kausrud