Differential pathogenicity and lethality of bubonic plague (1720-1945) by sex, age and place.

COVID-19 brought back to the attention of the scientific community that males are more susceptible to infectious diseases. What is clear for other infections-that sex and gender differences influence both risk of infection and mortality-is not yet fully elucidated for plague, particularly bubonic plague, although this knowledge can help find specific defences against a disease for which a vaccine is not yet available. To address this question, we analysed data on plague from hospitals in different parts of the world since the early eighteenth century, which provide demographic information on individual patients, diagnosis and course of the disease in the pre-antibiotic era. Assuming that the two sexes were equally represented, we observe a worldwide prevalence of male cases hospitalized at any age, a result which seems better explained by gender-biased (thus cultural) behaviours than biological sex-related factors. Conversely, case fatality rates differ among countries and geographic macro-areas, while globally, lethality appears slightly prevalent in young females and older adults (regardless of sex). Logistic regression models confirm that the main risk factor for bubonic plague death was the geographical location of the cases and being older than 50 years, whereas sex only showcased a slight trend.

A genomic and historical synthesis of plague in 18th century Eurasia.

Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

Spatial ecology of coastal Atlantic cod Gadus morhua associated with parasite load.

Acoustic tags and receivers were used to investigate the spatial ecology of coastal Atlantic cod Gadus morhua (n = 32, mean fork length: 50 cm, range: 33-80 cm) on the Norwegian Skagerrak coast in 2012. Monthly home ranges (HR), swimming activity and depth use varied considerably among individuals and through the months of June, July and August. HR sizes for the period ranged from 0.25 to 5.20 km2 (mean = 2.30 km2. Two thirds of the tagged G. morhua were infected with black spot disease Cryptocotyle lingua parasites; these fish had larger HRs and occupied deeper water compared with non-infected fish. The infected fish also tended to be more active in terms of horizontal swimming. From an ecological and evolutionary perspective, any environmental change that modifies G. morhua behaviour may therefore also alter the parasite load of the population, and its conservation and fishery status.

A combination of hydrodynamical and statistical modelling reveals non-stationary climate effects on fish larvae distributions.

Biological processes and physical oceanography are often integrated in numerical modelling of marine fish larvae, but rarely in statistical analyses of spatio-temporal observation data. Here, we examine the relative contribution of inter-annual variability in spawner distribution, advection by ocean currents, hydrography and climate in modifying observed distribution patterns of cod larvae in the Lofoten-Barents Sea. By integrating predictions from a particle-tracking model into a spatially explicit statistical analysis, the effects of advection and the timing and locations of spawning are accounted for. The analysis also includes other environmental factors: temperature, salinity, a convergence index and a climate threshold determined by the North Atlantic Oscillation (NAO). We found that the spatial pattern of larvae changed over the two climate periods, being more upstream in low NAO years. We also demonstrate that spawning distribution and ocean circulation are the main factors shaping this distribution, while temperature effects are different between climate periods, probably due to a different spatial overlap of the fish larvae and their prey, and the consequent effect on the spatial pattern of larval survival. Our new methodological approach combines numerical and statistical modelling to draw robust inferences from observed distributions and will be of general interest for studies of many marine fish species.

Within and between species competition in a seabird community: statistical exploration and modeling of time-series data.

In a changing environment, the maintenance of communities is subject to many constraints (phenology, resources, climate, etc.). One such constraint is the relationship between conspecifics and competitors. In mixed colonies, seabirds may have to cope with interspecific and intraspecific competition for both space and food resources. We applied competitive interaction models to data on three seabird breeding populations: black-legged kittiwake (Rissa tridactyla), common guillemot (Uria aalge) and Brünnich's guillemot (Uria lomvia) collected over 27-years at Kharlov Island in the Barents Sea. We found a competitive effect only for the kittiwake breeding population size on the common guillemot breeding population size when kittiwakes were abundant. The timing of kittiwake breeding negatively affected the number of breeding Brünnich's guillemots. The timing of breeding was negatively correlated to biomass of the main pelagic fish in the Barents Sea, the capelin (Mallotus villosus), which suggests an indirect action. The community matrix shows that the community was not stable. The kittiwake population did not decrease as seen in north Norwegian populations. Likewise, the common guillemot population, after a crash in 1985, was recovering at Kharlov while Norwegian populations were decreasing. Only the Brünnich's guillemot showed a decrease at Kharlov until 1999. We suggest that the stability of the kittiwake and common guillemot populations at Kharlov is due to better feeding conditions than in colonies of the Norwegian coast, linked to a possible eastward shift of the capelin population with the temperature increase of the Barents Sea.

Are low but statistically significant levels of genetic differentiation in marine fishes 'biologically meaningful'? A case study of coastal Atlantic cod.

A key question in many genetic studies on marine organisms is how to interpret a low but statistically significant level of genetic differentiation. Do such observations reflect a real phenomenon, or are they caused by confounding factors such as unrepresentative sampling or selective forces acting on the marker loci? Further, are low levels of differentiation biologically trivial, or can they represent a meaningful and perhaps important finding? We explored these issues in an empirical study on coastal Atlantic cod, combining temporally replicated genetic samples over a 10-year period with an extensive capture-mark-recapture study of individual mobility and population size. The genetic analyses revealed a pattern of differentiation between the inner part of the fjord and the open skerries area at the fjord entrance. Overall, genetic differentiation was weak (average F(ST) = 0.0037), but nevertheless highly statistical significant and did not depend on particular loci that could be subject to selection. This spatial component dominated over temporal change, and temporal replicates clustered together throughout the 10-year period. Consistent with genetic results, the majority of the recaptured fish were found close to the point of release, with <1% of recaptured individuals dispersing between the inner fjord and outer skerries. We conclude that low levels of genetic differentiation in this marine fish can indeed be biologically meaningful, corresponding to separate, temporally persistent, local populations. We estimated the genetically effective sizes (N(e) ) of the two coastal cod populations to 198 and 542 and found a N(e) /N (spawner) ratio of 0.14.

Complex interplays among population dynamics, environmental forcing, and exploitation in fisheries.

The patterns of variations in fisheries time series are known to result from a complex combination of species and fisheries dynamics all coupled with environmental forcing (including climate, trophic interactions, etc.). Disentangling the relative effects of these factors has been a major goal of fisheries science for both conceptual and management reasons. By examining the variability of 169 tuna and billfish time series of catch and catch per unit effort (CPUE) throughout the Atlantic as well as their linkage to the North Atlantic Oscillation (NAO), we find that the importance of these factors differed according to the spatial scale. At the scale of the entire Atlantic the patterns of variations are primarily spatially structured, whereas at a more regional scale the patterns of variations were primarily related to the fishing gear. Furthermore, the NAO appeared to also structure the patterns of variations of tuna time series, especially over the North Atlantic. We conclude that the patterns of variations in fisheries time series of tuna and billfish only poorly reflect the underlying dynamics of these fish populations; they appear to be shaped by several successive embedded processes, each interacting with each other. Our results emphasize the necessity for scientific data when investigating the population dynamics of large pelagic fishes, because CPUE fluctuations are not directly attributable to change in species' abundance.

Territory location and quality, together with climate, affect the timing of breeding in the white-throated dipper.

Recent climate change has led to advanced spring phenology in many temperate regions. The phenological response to variation in the local environment, such as the habitat characteristics of the territories birds occupy, is less clear. The aim of this study is to understand how ecological conditions affect breeding time, and its consequences for reproduction, in a white-throated dipper Cinclus cinclus population in a river system in Norway during 34 years (1978-2011). Hatching date advanced almost nine days, indicating a response to higher temperatures and the advanced phenology in the area. Earlier breeding was found in warm springs and at lower altitudes. High population density facilitated earlier breeding close to the coast. Furthermore, when population density was low, breeding was early at territories that were rarely occupied, while in years with high density, breeding was early at territories that were frequently occupied. Also, when population density was low, earlier breeding occurred at territories that on average produced more offspring than other territories, while there was no difference in breeding time in high population years. Selection for early breeding was dependent on spring temperatures and high spring temperatures contributed to higher breeding success during the study period. We found that breeding phenology may have strong effects on fitness in the white-throated dipper, and thus that breeding time is an important ecological factor in a species that feeds mainly on aquatic rather than terrestrial prey.

Estimating the functional form for the density dependence from life history data.

Two contrasting approaches to the analysis of population dynamics are currently popular: demographic approaches where the associations between demographic rates and statistics summarizing the population dynamics are identified; and time series approaches where the associations between population dynamics, population density, and environmental covariates are investigated. In this paper, we develop an approach to combine these methods and apply it to detailed data from Soay sheep (Ovis aries). We examine how density dependence and climate contribute to fluctuations in population size via age- and sex-specific demographic rates, and how fluctuations in demographic structure influence population dynamics. Density dependence contributes most, followed by climatic variation, age structure fluctuations and interactions between density and climate. We then simplify the density-dependent, stochastic, age-structured demographic model and derive a new phenomenological time series which captures the dynamics better than previously selected functions. The simple method we develop has potential to provide substantial insight into the relative contributions of population and individual-level processes to the dynamics of populations in stochastic environments.

The effects of oil spills on marine fish: Implications of spatial variation in natural mortality.

The effects of oil spills on marine biological systems are of great concern, especially in regions with high biological production of harvested resources such as in the Northeastern Atlantic. The scientific studies of the impact of oil spills on fish stocks tend to ignore that spatial patterns of natural mortality may influence the magnitude of the impact over time. Here, we first illustrate how spatial variation in natural mortality may affect the population impact by considering a thought experiment. Second, we consider an empirically based example of Northeast Arctic cod to extend the concept to a realistic setting. Finally, we present a scenario-based investigation of how the degree of spatial variation in natural mortality affects the impact over a gradient of oil spill sizes. Including the effects of spatial variations in natural mortality tends to widen the impact distribution, hence increasing the probability of both high and low impact events.

Reproductive asynchrony increases with environmental disturbance.

While it is widely recognized that the manner in which organisms adjust their timing of reproduction reflects evolutionary strategies aimed at minimizing offspring mortality or maximizing reproductive output, the conditions under which the evolutionarily stable strategy involves synchronous or asynchronous reproduction is a matter of considerable discord. A recent theoretical model predicts that whether a population displays reproductive synchrony or asynchrony will depend on the relative scales of intrinsic regulation and environmental disturbance experienced by reproducing individuals. This model predicts that, under conditions of negligible competition and large-scale environmental perturbation, evolution of a single mixed strategy will result in asynchronous reproduction. We tested this prediction using empirical data on large-scale climatic fluctuation and the annual timing of reproduction by three species of flowering plants covering 1300-population-years and four degrees of latitude in Norway. In agreement with model predictions, within populations of all three species reproductive asynchrony increased with the magnitude of large-scale climatic perturbation, but bore no relation to the strength of local density dependence. These results suggest that mixed evolutionarily stable strategies can arise from the interplay of combinations of agents of selection and the scale at which they operate; hence it is fruitless to associate synchronous versus asynchronous timing with particular single factors like climate, competition, or predation.

A new geographical gradient in vole population dynamics.

A new geographical gradient in the dynamics of small rodents is demonstrated by analysing 29 time series of density indices of the common vole (Microtus arvalis) from Poland, the Czech Republic and the Slovak Republic. This gradient extends from more stable northerly populations in coastal Poland to more variable and cyclic populations in the southernmost parts of the Slovak Republic, and is hence a reversal of the Fennoscandian gradient. All studied variables (such as mean density, cycle amplitude, density variability and the coefficients in a second-order autoregressive model) exhibit consistent latitudinal variation. Possible underlying factors are discussed. In particular, we suggest that seasonality may be a key element in explaining the observed new gradient.

Glacial survival of the Norwegian lemming (Lemmus lemmus) in Scandinavia: inference from mitochondrial DNA variation.

In order to evaluate the biogeographical hypothesis that the Norwegian lemming (Lemmus lemmus) survived the last glacial period in some Scandinavian refugia, we examined variation in the nucleotide sequence of the mitochondrial control region (402 base pairs (bp)) and the cytochrome b (cyt b) region (633 bp) in Norwegian and Siberian (Lemmus sibiricus) lemmings. The phylogenetic distinction and cyt b divergence estimate of 1.8% between the Norwegian and Siberian lemmings suggest that their separation pre-dated the last glaciation and imply that the Norwegian lemming is probably a relic of the Pleistocene populations from Western Europe. The star-like control region phylogeny and low mitochondrial DNA diversity in the Norwegian lemming indicate a reduction in its historical effective size followed by population expansion. The average estimate of post-bottleneck time (19-21 kyr) is close to the last glacial maximum (18-22 kyr BP). Taking these findings and the fossil records into consideration, it seems likely that, after colonization of Scandinavia in the Late Pleistocene, the Norwegian lemming suffered a reduction in its population effective size and survived the last glacial maximum in some local Scandinavian refugia, as suggested by early biogeographical work.

A gradient from stable to cyclic populations of Clethrionomys rufocanus in Hokkaido, Japan.

A total of 31 years of abundance data from 90 populations of the grey-sided vole (Clethrionomys rufocanus) in northern Hokkaido (Japan) were analysed with respect to population dynamic characteristics. Both non-periodic and multi-annually periodic fluctuations occur among the studied populations. The length of the period varies from 2 to 5 years. The dynamics appear approximately linear on a logarithmic scale, and a log-linear stochastic difference model with one time-lag is found to recreate the periodograms of the time series. The deterministic (log-linear) component of these models determines the periodicity while stochasticity sustains the cycles. The dynamics of the Hokkaidian vole populations are found to vary clinally from the western coast eastwards and towards the interior of the study area. This gradient corresponds superficially to the latitudinal gradient seen in microtine populations in Fennoscandia. However, under close scrutiny, these gradients differ greatly: the Hokkaidian gradient is caused by a cline in delayed density dependence. Statistical delayed density dependence is more negative towards the east and the interior.

Bootstrap estimated uncertainty of the dominant Lyapunov exponent for Holarctic microtine rodents.

The dominant Lyapunov exponent, as estimated from time series using the Jacobian-based method, is often used for indicating whether the underlying dynamic system is chaotic or not. The Jacobian-based method together with Response Surface Methodology has been suggested as a method for detecting chaotic dynamics in ecological time series. Besides pointing out that this may not be an appropriate method, we report on estimates of the uncertainty in the estimates of the dominant Lyapunov exponent. For this purpose, we have used time series data on Holarctic microtines. On the basis of our analyses, we are unable to find general evidence for chaotic dynamics in northern microtine populations (north of 60 degrees N) as recently suggested in the ecological literature. It seems, however, that the dynamic properties of the northern and southern populations are different. These patterns are supported by testing for nonlinearity.

Is spacing behaviour coupled with predation causing the microtine density cycle? A synthesis of current process-oriented and pattern-oriented studies.

Current ecological information on periodically fluctuating microtine populations are demonstrated to support a hypothesis involving both predation and intrinsic self-regulation as necessary and sufficient factors for explaining the "microtine density cycle'. The structure of the cyclic time series is largely two dimensional with strong delayed density dependence. Together with recent field studies on rodent demography, our modelling suggests that trophic interaction is a likely candidate to generate the dimensionality observed for northern microtine rodent dynamics. It is shown that the trophic interaction must be fairly strong. This suggests that specialist predation is the most likely one among the classes of trophic interactions. We also argue that some - but not too strong - self-regulation must occur to generate the structure of the available time series on northern European microtines.

A geographic gradient in small rodent density fluctuations: a statistical modelling approach.

The patterns of density dependence in Fennoscandian rodents are investigated statistically using a linear autoregressive scheme. Nineteen time series of microtine abundances along a latitudinal gradient in Fennoscandia from 60 degrees N to 69 degrees N are analysed. We provide statistical evidence that there exists a latitudinal gradient in density dependence in Fennoscandian microtines. Southern populations experience significantly stronger direct density dependence than northern populations. Delayed density dependence was significantly negative throughout the region and appeared constant across the latitudinal gradient. The populations consistently exhibit dynamics of second order throughout the region. Together, the clinal direct density dependence and constant delayed density dependence give rise to a cline in cycle period from 3 to 4.5 years. The statistical results are compared to assumptions and predictions made in previous studies on the geographic gradient in the population dynamics of these rodents. The results are in agreement with the predictions of the 'generalist predator hypothesis'.

Common structure in panels of short ecological time-series.

Typically, in many studies in ecology, epidemiology, biomedicine and others, we are confronted with panels of short time-series of which we are interested in obtaining a biologically meaningful grouping. Here, we propose a bootstrap approach to test whether the regression functions or the variances of the error terms in a family of stochastic regression models are the same. Our general setting includes panels of time-series models as a special case. We rigorously justify the use of the test by investigating its asymptotic properties, both theoretically and through simulations. The latter confirm that for finite sample size, bootstrap provides a better approximation than classical asymptotic theory. We then apply the proposed tests to the mink-muskrat data across 81 trapping regions in Canada. Ecologically interpretable groupings are obtained, which serve as a necessary first step before a fuller biological and statistical analysis of the food chain interaction.

Parasites and supernormal manipulation.

Social parasites may exploit their hosts by mimicking other organisms that the hosts normally benefit from investing in or responding to in some other way. Some parasites exaggerate key characters of the organisms they mimic, possibly in order to increase the response from the hosts. The huge gape and extreme begging intensity of the parasitic common cuckoo chick (Cuculus canorus) may be an example. In this paper, the evolutionary stability of manipulating hosts through exaggerated signals is analysed using game theory. Our model indicates that a parasite's signal intensity must be below a certain threshold in order to ensure acceptance and that this threshold depends directly on the rate of parasitism. The only evolutionarily stable strategy (ESS) combination is when hosts accept all signallers and parasites signal at their optimal signal intensity, which must be below the threshold. Supernormal manipulation by parasites is only evolutionarily stable under sufficiently low rates of parasitism. If the conditions for the ESS combination are not satisfied, rejector hosts can invade using signal intensity as a cue for identifying parasites. These qualitative predictions are discussed with respect to empirical evidence from parasitic mimicry systems that have been suggested to involve supernormal signalling, including evicting avian brood parasites and insect-mimicking Ophrys orchids.

The timing of life-history events in a changing climate.

Although empirical and theoretical studies suggest that climate influences the timing of life-history events in animals and plants, correlations between climate and the timing of events such as egg-laying, migration or flowering do not reveal the mechanisms by which natural selection operates on life-history events. We present a general autoregressive model of the timing of life-history events in relation to variation in global climate that, like autoregressive models of population dynamics, allows for a more mechanistic understanding of the roles of climate, resources and competition. We applied the model to data on 50 years of annual dates of first flowering by three species of plants in 26 populations covering 4 degrees of latitude in Norway. In agreement with earlier studies, plants in most populations and all three species bloomed earlier following warmer winters. Moreover, our model revealed that earlier blooming reflected increasing influences of resources and density-dependent population limitation under climatic warming. The insights available from the application of this model to phenological data in other taxa will contribute to our understanding of the roles of endogenous versus exogenous processes in the evolution of the timing of life-history events in a changing climate.