Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical bayesian model

The purpose of this study was to test for evidence that savannah baboons (Papio cynocephalus) underwent a population expansion in concert with a hypothesized expansion of African human and chimpanzee populations during the late Pleistocene. The rationale is that any type of environmental event sufficient to cause simultaneous population expansions in African humans and chimpanzees would also be expected to affect other codistributed mammals. To test for genetic evidence of population expansion or contraction, we performed a coalescent analysis of multilocus microsatellite data using a hierarchical Bayesian model. Markov chain Monte Carlo (MCMC) simulations were used to estimate the posterior probability density of demographic and genealogical parameters. The model was designed to allow interlocus variation in mutational and demographic parameters, which made it possible to detect aberrant patterns of variation at individual loci that could result from heterogeneity in mutational dynamics or from the effects of selection at linked sites. Results of the MCMC simulations were consistent with zero variance in demographic parameters among loci, but there was evidence for a 10- to 20-fold difference in mutation rate between the most slowly and most rapidly evolving loci. Results of the model provided strong evidence that savannah baboons have undergone a long-term historical decline in population size. The mode of the highest posterior density for the joint distribution of current and ancestral population size indicated a roughly eightfold contraction over the past 1,000 to 250,000 years. These results indicate that savannah baboons apparently did not share a common demographic history with other codistributed primate species.     

Estimates of vital rates and predictions of population dynamics change along a long-term monitoring program

Despite the widespread recognition of the importance of monitoring, only a few studies have explored how estimates of vital rates and predictions of population dynamics change with additional data collected along the monitoring program. We investigate how estimates of survival and individual growth, along with predictions about future population size, change with additional years of monitoring and data collected, using as a model system freshwater populations of marble (Salmo marmoratus), rainbow (Oncorhynchus mykiss), and brown trout (Salmo trutta L.) living in Western Slovenian streams. Fish were sampled twice a year between 2004 and 2015. We found that in 3 out of 4 populations, a few years of data (3 or 4 sampling occasions, between 300 and 500 tagged individuals for survival, 100–200 for growth) provided the same estimates of average survival and growth as those obtained with data from more than 15 sampling occasions, while the estimation of the range of survival (i.e., the difference, over all sampling occasions considered, between maximum and minimum survival estimated in a sampling occasion) required more sampling occasions (up to 22 for marble trout), with little reduction of uncertainty around the point estimates. Predictions of mean density and variation in density over time did not change with more data collected after the first 5 years (i.e., 10 sampling occasions) and overall were within 10% of the observed mean and variation in density over the whole monitoring program.     

Intensive trapping and increased fish predation cause massive population decline of an invasive crayfish

1. Invasive species frequently have adverse impacts on native communities and ecosystems. Management options are often limited. Our goal is to evaluate the effect of intensive trapping and fish predation on the population dynamics of an invasive crayfish. 2. From 2001 to 2005, we removed invasive rusty crayfish (Orconectes rusticus) by trapping in Sparkling Lake in northern WI. In addition, the Wisconsin Department of Natural Resources restricted harvest of fish species known to consume crayfish, thereby increasing predation on crayfish that are too small to trap. 3. After an initial increase, catch rates of rusty crayfish declined by approximately 95%, from 11 crayfish per trap per day in 2002 to 0.65 in 2004. The catch rate in 2005 remained low at 0.5 crayfish per trap. Females comprised nearly 50% of the catch from 2002 to 2004. Unlike rusty crayfish in Sparkling Lake, catch rates of O. rusticus and Orconectes propinquus in three nearby lakes increased or remained relatively constant over the 5‐year removal period. 4. We also examined the influence of habitat and temperature on crayfish catch rates. Catch rates were highest at water temperatures between 20 and 25 °C and on cobble, log or macrophyte habitats that may serve as refuge from fish predation. 5. Five summers of intensive trapping and fisheries management practices reduced abundances, but did not extirpate rusty crayfish in Sparkling Lake. To determine the potential of trapping as a management option for invasive crayfishes, these methods must be tested in other systems.     

An exactly solvable model of population dynamics with density-dependent migrations and the Allee effect

We consider a single-species model of population dynamics allowing for migrations and the Allee effect. Two types of migration are taken into account: one caused by environmental factors (e.g., a passive transport with the wind or water current) and the other associated with biological mechanisms. While the first type is apparently density-independent, the speed of migration in the second one can depend on the population density. Mathematically, this model consists of a non-linear partial differential equation of advection-diffusion-reaction type. Using an appropriate change of variables, we obtain an exact solution of the equation describing propagation of travelling population fronts. We show that, depending on parameter values and thus on the relative intensity of density-dependent and density-independent factors, the direction of the propagation can be different thus describing either species invasion or species retreat.     

Directions in modelling partial migration: how adaptation can cause a population decline and why the rules of territory acquisition matter

Modelling of partial migration in birds has progressed from simple graphical representations to sophisticated analyses that use evolutionary invasion analysis to determine how the success of the two strategies (stay year round on the breeding grounds, or migrate) can become frequency dependent. Here I build two models to relax two assumptions commonly made in models and often violated in nature: that individuals do not vary in any trait other than their migratory propensity, and that the prior residence effect (which grants priority access of good habitats to non‐migrants) operates at maximum strength. The same framework can incorporate and merge aspects of various hypotheses proposed to explain partial migration (dominance, body size, arrival timing, and limited foraging opportunities), and shows that either small (subdominant) or large (dominant) individuals may emerge as the more likely migrants; the latter case occurs when it is easy for socially dominant migrants to win back prime breeding locations upon their arrival. The dynamics of territory acquisition is shown to be an important and understudied topic, as variations in the relative importance of prior residency versus resource holding power can shift a population from complete migration to complete year‐round residency. These models also highlight exceptions to a tacit assumption in discussions of evolution of migration under climate change, which is that populations can decline if genetic adaptation or phenotypic plasticity do not occur fast enough. Competition can also yield the opposite pattern where adaptation itself leads to a population decline.     

From snapshot information to long-term population dynamics of Acacias by a simulation model

The African Acacia species A. raddiana is believed to be endangered in the Negev desert of Israel. The ecology of this species is not well understood. The main idea of our study is to learn more about the long-term population dynamics of these trees using snapshot information in the form of size frequency distributions. These distributions are highly condensed indices of population dynamics acting over many years. In this paper, we analyse field data on recruitment, growth, and mortality and use an existing simulation model of the population dynamics of A. raddiana (SAM) to produce contrasting scenarios of these live history processes that are based on the analysed field evidence. The main properties of simulated as well as observed tree size frequency distributions are characterised with Simpson's index of dominance and a new permutation index. Finally, by running the SAM model under the different scenarios, we study the effect of these different processes on simulated size frequency distributions (pattern) and we compare them to size distributions observed in the field, in order to identify the processes acting in the field. Our study confirms rare recruitment events as a major factor shaping tree size frequency distributions and shows that the paucity of recruitment has been a normal feature of A. raddiana in the Negev over many years. Irregular growth, e.g., due to episodic rainfall, showed a moderate influence on size distributions. Finally, the size frequency distributions observed in the Negev reveal the information that, in this harsh environment, mortality of adult A. raddiana is independent of tree size (age).     

Unique population dynamics of Japanese field vole: Winter breeding and summer population decline

It is common knowledge that winter temperatures influence the life history of small mammals. Cold temperatures necessitate increased energy requirements for survival, and recent studies indicate that snow cover can have both negative and positive influences. With each new observation, we develop a more comprehensive understanding of the mechanisms that influence small mammal populations. Here we report on our recent study on Japanese field vole Microtus montebelli, which reaches its peak in population during the early spring and its low during the autumn. To understand the population dynamics of these voles, we conducted a capture-mark-recapture survey, then estimated the seasonal abundance, recruit, capture probabilities, and survival probabilities using the Bayesian hierarchical model. We also analyzed the impact of mammalian generalist predator visits on the survival probabilities. Our data indicates that the early spring peak in population is due to intensive winter breeding and the highest survival probabilities during the periods of deep snow cover. When snow cover reaches a certain depth, the circumstances can combine to raise survival probability and favor breeding. During the breeding season in May and June, on the contrary, the survival probability reached its lowest, resulting in a decrease in population despite breeding. The low survival probability between spring and autumn could be attributed to the impact of generalist predators, and low vegetation may have amplified the effect. In summary, the deep snow cover and generalist predators were considered to be the key factors shaping this unique population dynamics in this orchard area.     

Analytic solution of a dynamic pool model incorporating constant marginal cost and discount rates

A simple dynamic pool model is extended to describe the economics of a single-species fishery by incorporating constant marginal cost and discount rates. Assuming that the population has already come to equilibrium under an initial fishing mortality rate and that any change in that rate is to be sustained indefinitely, the model can be solved analytically to yield the optimal fishing mortality rate. When this rate is expressed as a proportion of the natural mortality rate, the solution takes the form of a third-degree polynomial whose coefficients are simple functions of four other parameters. The solution exhibits positive conservation effects as long as all four parameters are sufficiently high. These conservation effects may be great enough to warrant closing the fishery when the marginal cost rate exceeds a well-defined limit.     

Interspecific population regulation and the stability of mutualism: fruit abortion and density-dependent mortality of pollinating seed-eating insects

Two questions central to the population ecology of mutualism include: (1) what mechanisms prevent the inherent positive feedback of mutualism from leading to unbounded population growth; and (2) what mechanisms prevent instability from arising due to overexploitation. Theory and empiricism suggest that preventing such instability requires density‐dependent processes. A recent theory proposes that if benefits and costs to a mutualist vary with the density of its partner, then instability can be prevented if the former species can control demographic rates and regulate (or limit) the population density of its partner. The ecological and evolutionary feasibility of this theory of interspecific population regulation has been demonstrated using quantitative models of mutualism between plants and pollinating seed‐consuming insects. In these models, resource‐limited fruit set and ensuing fruit abortion are mechanisms that can lead to density‐dependent recruitment and population regulation of the insects. Yet, there has been little interplay between these theoretical results and empirical research. A recent study empirically examined the density‐dependent effects of resource‐limited fruit set and fruit abortion in the Yucca/moth mutualism. An analysis of the study led to the conclusion that, even though fruit abortion can account for >95% of moth mortality, it is largely a density‐independent source of mortality that cannot regulate moth population density. Here, we re‐analyze those empirical data and conduct further theoretical analyses to examine the nature of fruit abortion on moth recruitment. We conclude that resource‐limited fruit set and fruit abortion can effectively regulate and limit moth populations, due to its density‐dependent feedback on moth recruitment. Nonetheless, in any given interaction, multiple sources of mortality may contribute to the regulation and limitation of populations, and hence the stability of mutualism, including, larval competition and mortality due to locule damage in the Yucca/moth mutualism.     

Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence

Viruses play diverse and important roles in ecosystems. In recent years, trade-offs between host and virus traits have gained increasing attention in viral ecology and evolution. However, microbial organism traits, and viral population parameters in particular, are challenging to monitor. Mathematical and individual-based models are useful tools for predicting virus-host dynamics. We have developed an individual-based evolutionary model to study ecological interactions and evolution between bacteria and viruses, with emphasis on the impacts of trade-offs between competitive and defensive host traits on bacteria-phage population dynamics and trait diversification. Host dynamics are validated with lab results for different initial virus to host ratios (VHR). We show that trade-off based, as opposed to random bacteria-virus interactions, result in biologically plausible evolutionary outcomes, thus highlighting the importance of trade-offs in shaping biodiversity. The effects of nutrient concentration and other environmental and organismal parameters on the virus-host dynamics are also investigated. Despite its simplicity, our model serves as a powerful tool to study bacteria-phage interactions and mechanisms for evolutionary diversification under various environmental conditions.     

Towards a model of a floodplain fish population and its fishery

Synopsis A model is developed which describes the way in which the fish populations of African rivers and their fisheries are influenced by the different types of flood Regime. Ichthyomass and fish catch are dependent on both the extent of flooding during high water and the amount of water remaining in the system during the dry season. The relative number and individual weight of fish are determined by the intensity of flooding, whereas the total number surviving to the next year depends more on the low water regime. Catch per unit effort falls with increasing difference between areas flooded at high and low water. A negative log-log relationship exists between catch and the ratio of maximum area flooded to minimum area of water remaining in the system. This relationship of catch to flood ratio may form the basis for a general index for the evaluation of both year-to-year variations within a floodplain, and differences between floodplains. Lines of equal catch are also derived for various combinations of high and low water areas; these might be used as guidelines for the hydrological management of tropical flood-plains.     

Human population dynamics revisited with the logistic model: How much can be modeled and predicted?

Decrease or growth of population comes from the interplay of death and birth (and locally, migration). We revive the logistic model, which was tested and found wanting in early-20th-century studies of aggregate human populations, and apply it instead to life expectancy (death) and fertility (birth), the key factors totaling population. For death, once an individual has legally entered society, the logistic portrays the situation crisply. Human life expectancy is reaching the culmination of a two-hundred year-process that forestalls death until about 80 for men and the mid-80's for women. No breakthroughs in longevity are in sight unless genetic engineering comes to help. For birth, the logistic covers quantitatively its actual morphology. However, because we have not been able to model this essential parameter in a predictive way over long periods, we cannot say whether the future of human population is runaway growth or slow implosion. Thus, we revisit the logistic analysis of aggregate human numbers. From a niche point of view, resources are the limits to numbers, and access to resources depends on technologies. The logistic makes clear that for homo faber, the limits to numbers keep shifting. These moving edges may most confound forecasting the long-run size of humanity.     

A model incorporating a reduction in carrying capacity translates brood size trends into a population decline: the case of Finnish starlings, 1951–2005

Finnish starlings Sturnus vulgaris declined by 80% during the 1970s and 1980s, but during this time mean brood size increased. On the basis of previous results, we assumed that the carrying capacity K of breeding habitats declined, especially in southern Finland, the phenomenon being due to regional diversification in agriculture and a corresponding decline in dairy farming. We further assumed that following the changes in agriculture, poorly productive starling habitats (sinks) increased at the expense of highly productive ones (sources). We used nestling ringing data from 1951 to 2005 to estimate trends in brood size and population change. The results showed that mean brood size was greater during stable population stages (at the beginning and end of the study period) than during the years of collapse. The coefficient of variation displayed a contrary pattern to the mean brood size, being at its highest during the decline. We modelled the relation of population dynamics and environmental change with a density-dependent matrix model that assumed a 80% decline in K. The modelling results obtained were similar to the population dynamics actually observed. The model showed a decrease in per-capita reproduction rate as a response to habitat deterioration. This was due to a time lag in response to the declining K. On the basis of the dynamics observed and the population model, we concluded that during the decline, a larger proportion of starlings bred in sub-optimal sink habitats than during the stable population phases, and that this caused the low in the mean and the high in the coefficient of variation of brood size. Survival analyses on nest-card data (using the Mayfield method) supported our conclusion that the population decline was due to a decreased brood size caused by decreased K.     

Socially informed random walks: incorporating group dynamics into models of population spread and growth

Simple correlated random walk (CRW) models are rarely sufficient to describe movement of animals over more than the shortest time scales. However, CRW approaches can be used to model more complex animal movement trajectories by assuming individuals move in one of several different behavioural or movement states, each characterized by a different CRW. The spatial and social context an individual experiences may influence the proportion of time spent in different movement states, with subsequent effects on its spatial distribution, survival and fecundity. While methods to study habitat influences on animal movement have been previously developed, social influences have been largely neglected. Here, we fit a 'socially informed' movement model to data from a population of over 100 elk (Cervus canadensis) reintroduced into a new environment, radio-collared and subsequently tracked over a 4-year period. The analysis shows how elk move further when they are solitary than when they are grouped and incur a higher rate of mortality the further they move away from the release area. We use the model to show how the spatial distribution and growth rate of the population depend on the balance of fission and fusion processes governing the group structure of the population. The results are briefly discussed with respect to the design of species reintroduction programmes.     

The gene pool of Belgorod oblast population: the distribution of immunological and biochemical gene markers

The frequencies of 33 alleles of 12 loci of immunological and biochemical gene markers (ABO, RH, HP, GC, TF, PI, C'3, ACP1, GLO1, PGM1, ESD, and 6-PGD) have been estimated in the indigenous Russian and Ukrainian populations of Belgorod oblast. Differences of the Belgorod population from other populations of Russia with respect to the genetic structure have been determined. It has been found that the frequency distributions of all alleles studied in the Belgorod population are similar to those typical of the genetic structure of Caucasoid populations.     

The gene pool of Belgorod oblast population: The distribution of immunological and biochemical gene markers

The frequencies of 33 alleles of 12 loci of immunological and biochemical gene markers (AB0, RH, HP, GC, TF, PI, C′3, ACP1, GLO1, PGM1, ESD, and 6-PGD) have been estimated in the indigenous Russian and Ukrainian populations of Belgorod oblast. Differences of the Belgorod population from other populations of Russia with respect to the genetic structure have been determined. It has been found that the frequency distributions of all alleles studied in the Belgorod population are similar to those typical of the genetic structure of Caucasoid populations.     

Estimating population cause-specific mortality fractions from in-hospital mortality: validation of a new method

Background

Cause-of-death data for many developing countries are not available. Information on deaths in hospital by cause is available in many low- and middle-income countries but is not a representative sample of deaths in the population. We propose a method to estimate population cause-specific mortality fractions (CSMFs) using data already collected in many middle-income and some low-income developing nations, yet rarely used: in-hospital death records.

Methods and Findings

For a given cause of death, a community''s hospital deaths are equal to total community deaths multiplied by the proportion of deaths occurring in hospital. If we can estimate the proportion dying in hospital, we can estimate the proportion dying in the population using deaths in hospital. We propose to estimate the proportion of deaths for an age, sex, and cause group that die in hospital from the subset of the population where vital registration systems function or from another population. We evaluated our method using nearly complete vital registration (VR) data from Mexico 1998–2005, which records whether a death occurred in a hospital. In this validation test, we used 45 disease categories. We validated our method in two ways: nationally and between communities. First, we investigated how the method''s accuracy changes as we decrease the amount of Mexican VR used to estimate the proportion of each age, sex, and cause group dying in hospital. Decreasing VR data used for this first step from 100% to 9% produces only a 12% maximum relative error between estimated and true CSMFs. Even if Mexico collected full VR information only in its capital city with 9% of its population, our estimation method would produce an average relative error in CSMFs across the 45 causes of just over 10%. Second, we used VR data for the capital zone (Distrito Federal and Estado de Mexico) and estimated CSMFs for the three lowest-development states. Our estimation method gave an average relative error of 20%, 23%, and 31% for Guerrero, Chiapas, and Oaxaca, respectively.

Conclusions

Where accurate International Classification of Diseases (ICD)-coded cause-of-death data are available for deaths in hospital and for VR covering a subset of the population, we demonstrated that population CSMFs can be estimated with low average error. In addition, we showed in the case of Mexico that this method can substantially reduce error from biased hospital data, even when applied to areas with widely different levels of development. For countries with ICD-coded deaths in hospital, this method potentially allows the use of existing data to inform health policy.     

Delayed density-dependent parasitism of eggs and pupae as a contributor to the cyclic population dynamics of the autumnal moth

Many populations of forest Lepidoptera exhibit 10-year cycles in densities, with impressive outbreaks across large regions. Delayed density-dependent interactions with natural enemies are recognized as key factors driving these cyclic population dynamics, but emphasis has typically been on the larval stages. Eggs, pupae and adults also suffer mortality from predators, parasitoids and pathogens, but little is known about possible density relationships between mortality factors and these non-feeding life stages. In a long-term field study, we experimentally deployed autumnal moth (Epirrita autumnata) eggs and pupae to their natural enemies yearly throughout the 10-year population cycle in northern Norway. The abundance of another geometrid, the winter moth (Operophtera brumata), increased in the study area, permitting comparisons between the two moth species in predation and parasitism. Survival of autumnal moth eggs and pupae was related to the moth abundance in an inverse and delayed manner. Egg and pupal parasitoids dominated as density-dependent mortality factors and predicted the subsequent growth rate of the host population size. In contrast, effects of egg and pupal predators were weakly density dependent, and generally predation remained low. Parasitism rates did not differ between the autumnal and winter moth pupae, whereas predators preferred winter moth pupae over those of the autumnal moth. We conclude that parasitism of the autumnal moth by egg and pupal parasitoids can be related to the changes of the moth density in a delayed density-dependent manner. Furthermore, egg and pupal parasitoids cannot be overlooked as causal factors for the population cycles of forest Lepidoptera in general.