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.

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.

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.

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.

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.

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.

Detecting genetic structure in migrating bowhead whales off the coast of Barrow, Alaska.

We develop a general framework for analysing and testing genetic structure within a migratory assemblage that is based on measures of genetic differences between individuals. We demonstrate this method using microsatellite DNA data from the Bering-Chukchi-Beaufort stock of bowhead whales (Balaena mysticetus), sampled via Inuit hunting during the spring and autumn migration off Barrow, Alaska. This study includes a number of covariates such as whale ages and the time separation between captures. Applying the method to a sample of 117 bowhead whales, we use permutation methods to test for temporal trends in genetic differences that can be ascribed to age-related effects or to timing of catches during the seasons. The results reveal a pattern with elevated genetic differences among whales caught about a week apart, and are statistically significant for the autumn migration. In contrast, we find no effects of time of birth or age-difference on genetic differences. We discuss possible explanations for the results, including population substructuring, demographic consequences of historical overexploitation, and social structuring during migration.

Cryptic population structuring in Scandinavian lynx: reply to Pamilo.

In a recent Commentary in this journal, Pamilo (2004) criticized our analysis of the spatial genetic structure of the Eurasian lynx in Scandinavia (Rueness et al. 2003). The analyses uncovered a marked geographical differentiation along the Scandinavian peninsula with an apparent linear gradient in the north-south direction. We used computer simulations to check on the proposition that the observed geographical structure could have arisen by genetic drift and isolation by distance in the approximate 25 generations that have passed since the last bottleneck. Pamilo disapproved of our choice of population model and also how we compared the outcome of the simulations with data. As these issues should be of interest to a wider audience we discuss them in some detail.

Cryptic population structure in a large, mobile mammalian predator: the Scandinavian lynx.

The Eurasian lynx (Lynx lynx) is an example of a species that has gone through a severe bottleneck, leading to near extinction in Scandinavia around 1930-- a pattern shared with several other large carnivorous mammals. Here we extend previous genetic analyses of northern European lynx, confirming that lynx from the Scandinavian Peninsula represent a distinct clade differing clearly from European conspecifics. Furthermore, and despite a recent bottleneck and subsequent range expansion, we detect marked genetic differentiation within Scandinavia. This differentiation is largely manifested as a north-south gradient, with a linear increase in the quantity FST/(1 - FST). Aided by computer simulations we find that this pattern is unlikely to have arisen by random genetic drift in the short time since lynx started to expand in the 1950s, suggesting that the spatial structure may predate the bottleneck. Individual-based analyses indicate that, instead of a continuous gradient, Scandinavian lynx may be structured into three more or less distinct groups, possibly corresponding to northern, central and southern subpopulations. The presence of such structuring was unknown previously and was unexpected from general considerations on the mobility of the species, historical data and the absence of geographical barriers. Our study demonstrates how molecular markers may be used to detect cryptic population structure, invisible using traditional methods.

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.

Phase coupling and synchrony in the spatiotemporal dynamics of muskrat and mink populations across Canada.

Population ecologists have traditionally focused on the patterns and causes of population variation in the temporal domain for which a substantial body of practical analytic techniques have been developed. More recently, numerous studies have documented how populations may fluctuate synchronously over large spatial areas; analyses of such spatially extended time-series have started to provide additional clues regarding the causes of these population fluctuations and explanations for their synchronous occurrence. Here, we report on the development of a phase-based method for identifying coupling between temporally coincident but spatially distributed cyclic time-series, which we apply to the numbers of muskrat and mink recorded at 81 locations across Canada. The analysis reveals remarkable parallel clines in the strength of coupling between proximate populations of both species--declining from west to east--together with a corresponding increase in observed synchrony between these populations the further east they are located.

Genetic structure of Siberian lemmings (Lemmus sibiricus) in a continuous habitat: large patches rather than isolation by distance.

In a continuous habitat, restricted dispersal and local genetic drift are likely to create a pattern of increasing genetic differentiation with distance. Here, we describe the genetic structure of Siberian lemming (Lemmus sibiricus) populations in a continuous tundra habitat on the western coast of the Taimyr Peninsula, in order to determine the spatial scale at which genetic differentiation and isolation by distance occur. Sampling was carried out at three different geographical scales: (1) a continuous 11 km transect; (2) localities 10-30 km apart; and (3) two localities at 300 and 600 km from the main study area. Two types of genetic markers were used: partial sequences of the mitochondrial DNA control region and four microsatellite loci. On this basis the study populations were genetically quite homogeneous within patches extending over 8 km or more. Contrary to theoretical predictions, no pattern of isolation by distance among patches could be identified. This observation was interpreted as representing populations in migration-drift disequilibrium after a recent major mixing event. The lack of concordance between mtDNA haplotype phylogeny and the geographical distribution of haplotypes supported this interpretation. Spatial autocorrelation among individual genotypes on a local scale was weak and observed only in females, indicating a considerable amount of mostly male-mediated gene flow. Average gene flow per generation was estimated to be in the range of several hundred metres.

Demography and population dynamics of the mouse opossum (Thylamys elegans) in semi-arid Chile: seasonality, feedback structure and climate.

Here we present, to the authors' knowledge for the very first time for a small marsupial, a thorough analysis of the demography and population dynamics of the mouse opossum (Thylamys elegans) in western South America. We test the relative importance of feedback structure and climatic factors (rainfall and the Southern Oscillation Index) in explaining the temporal variation in the demography of the mouse opossum. The demographic information was incorporated into a stage-structured population dynamics model and the model's predictions were compared with observed patterns. The mouse opossum's capture rates showed seasonal (within-year) and between-year variability, with individuals having higher capture rates during late summer and autumn and lower capture rates during winter and spring. There was also a strong between-year effect on capture probabilities. The reproductive (the fraction of reproductively active individuals) and recruitment rates showed a clear seasonal and a between-year pattern of variation with the peak of reproductive activity occuring during winter and early spring. In addition, the fraction of reproductive individuals was positively related to annual rainfall, while population density and annual rainfall positively influenced the recruitment rate. The survival rates were negatively related to annual rainfall. The average finite population growth rate during the study period was estimated to be 1.011 +/- 0.0019 from capture-recapture estimates. While the annual growth rate estimated from the seasonal linear matrix models was 1.026, the subadult and adult survival and maturation rates represent between 54% (winter) and 81% (summer) of the impact on the annual growth rate.

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.

Life-history traits of voles in a fluctuating population respond to the immediate environment.

Life-history traits relating to growth and reproduction vary greatly among species and populations and among individuals within populations. In vole populations, body size and age at maturation may vary considerably among locations and among years within the same location. Individuals in increasing populations are typically larger and start reproduction earlier in the spring than those in declining populations. The cause of such life-history variation within populations has been subject of much discussion. Much of the controversy concerns whether the memory of past conditions, leading to delayed effects on life-history traits, resides in the environment (for example, predators, pathogens or food) or intrinsically within populations or individuals (age distribution, physiological state, genetic or maternal effects). Here we report from an extensive field transplant experiment in which voles were moved before the breeding season between sites that differed in average overwintering body mass. Transplanted voles did not retain the characteristics of their source population, and we demonstrate an over-riding role of the immediate environment in shaping life-history traits of small rodents.

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.

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.