Browsing by Subject "Population Dynamics"

Now showing 1 - 20 of 31

Open Access
An age-structured extension to the vectorial capacity model.
(PLoS One, 2012) Novoseltsev, Vasiliy N; Michalski, Anatoli I; Novoseltseva, Janna A; Yashin, Anatoliy I; Carey, James R; Ellis, Alicia M
BACKGROUND: Vectorial capacity and the basic reproductive number (R(0)) have been instrumental in structuring thinking about vector-borne pathogen transmission and how best to prevent the diseases they cause. One of the more important simplifying assumptions of these models is age-independent vector mortality. A growing body of evidence indicates that insect vectors exhibit age-dependent mortality, which can have strong and varied affects on pathogen transmission dynamics and strategies for disease prevention. METHODOLOGY/PRINCIPAL FINDINGS: Based on survival analysis we derived new equations for vectorial capacity and R(0) that are valid for any pattern of age-dependent (or age-independent) vector mortality and explore the behavior of the models across various mortality patterns. The framework we present (1) lays the groundwork for an extension and refinement of the vectorial capacity paradigm by introducing an age-structured extension to the model, (2) encourages further research on the actuarial dynamics of vectors in particular and the relationship of vector mortality to pathogen transmission in general, and (3) provides a detailed quantitative basis for understanding the relative impact of reductions in vector longevity compared to other vector-borne disease prevention strategies. CONCLUSIONS/SIGNIFICANCE: Accounting for age-dependent vector mortality in estimates of vectorial capacity and R(0) was most important when (1) vector densities are relatively low and the pattern of mortality can determine whether pathogen transmission will persist; i.e., determines whether R(0) is above or below 1, (2) vector population growth rate is relatively low and there are complex interactions between birth and death that differ fundamentally from birth-death relationships with age-independent mortality, and (3) the vector exhibits complex patterns of age-dependent mortality and R(0) ∼ 1. A limiting factor in the construction and evaluation of new age-dependent mortality models is the paucity of data characterizing vector mortality patterns, particularly for free ranging vectors in the field.
Open Access
Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data.
(Mol Ecol, 2003-06) Palkovacs, EP; Marschner, M; Ciofi, C; Gerlach, J; Caccone, A
The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.
Open Access
Capacity shortfalls hinder the performance of marine protected areas globally.
(Nature, 2017-03-22) Gill, David A; Mascia, Michael B; Ahmadia, Gabby N; Glew, Louise; Lester, Sarah E; Barnes, Megan; Craigie, Ian; Darling, Emily S; Free, Christopher M; Geldmann, Jonas; Holst, Susie; Jensen, Olaf P; White, Alan T; Basurto, Xavier; Coad, Lauren; Gates, Ruth D; Guannel, Greg; Mumby, Peter J; Thomas, Hannah; Whitmee, Sarah; Woodley, Stephen; Fox, Helen E
Marine protected areas (MPAs) are increasingly being used globally to conserve marine resources. However, whether many MPAs are being effectively and equitably managed, and how MPA management influences substantive outcomes remain unknown. We developed a global database of management and fish population data (433 and 218 MPAs, respectively) to assess: MPA management processes; the effects of MPAs on fish populations; and relationships between management processes and ecological effects. Here we report that many MPAs failed to meet thresholds for effective and equitable management processes, with widespread shortfalls in staff and financial resources. Although 71% of MPAs positively influenced fish populations, these conservation impacts were highly variable. Staff and budget capacity were the strongest predictors of conservation impact: MPAs with adequate staff capacity had ecological effects 2.9 times greater than MPAs with inadequate capacity. Thus, continued global expansion of MPAs without adequate investment in human and financial capacity is likely to lead to sub-optimal conservation outcomes.
Open Access
Decoupling the effects of logging and hunting on an afrotropical animal community.
(Ecol Appl, 2011-07) Poulsen, JR; Clark, CJ; Bolker, BM
In tropical forests, hunting nearly always accompanies logging. The entangled nature of these disturbances complicates our ability to resolve applied questions, such as whether secondary and degraded forest can sustain populations of tropical animals. With the expansion of logging in central Africa, conservation depends on knowledge of the individual and combined impacts of logging and hunting on animal populations. Our goals were (1) to decouple the effects of selective logging and hunting on densities of animal guilds, including apes, duikers, monkeys, elephant, pigs, squirrels, and large frugivorous and insectivorous birds and (2) to compare the relative importance of these disturbances to the effects of local-scale variation in forest structure and fruit abundance. In northern Republic of Congo, we surveyed animals along 30 transects positioned in forest disturbed by logging and hunting, logging alone, and neither logging nor hunting. While sampling transects twice per month for two years, we observed 47 179 animals of 19 species and eight guilds in 1154 passages (2861 km). Species densities varied by as much as 480% among forest areas perturbed by logging and/or hunting, demonstrating the strong effects of these disturbances on populations of some species. Densities of animal guilds varied more strongly with disturbance type than with variation in forest structure, canopy cover, and fruit abundance. Independently, logging and hunting decreased density of some guilds and increased density of others: densities varied from 44% lower (pigs) to 90% higher (insectivorous birds) between logged and unlogged forest and from 61% lower (apes) to 77% higher (frugivorous birds) between hunted and unhunted forest. Their combined impacts exacerbated decreases in populations of some guilds (ape, duiker, monkey, and pig), but counteracted one another for others (squirrels, insectivorous and frugivorous birds). Together, logging and hunting shifted the relative abundance of the animal community away from large mammals toward squirrels and birds. Logged forest, even in the absence of hunting, does not maintain similar densities as unlogged forest for most animal guilds. To balance conservation with the need for economic development and wild meat in tropical countries, landscapes should be spatially managed to include protected areas, community hunting zones, and production forest.
Open Access
Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play.
(Philos Trans R Soc Lond B Biol Sci, 2009-06-12) Post, DM; Palkovacs, EP
Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer-algae chemostats; alewife-zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife-zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.
Open Access
Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers.
(eLife, 2017-07-25) Bauer, Matthias; Knebel, Johannes; Lechner, Matthias; Pickl, Peter; Frey, Erwin
Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via 'quorum sensing'. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits.
Open Access
Elevational ranges of birds on a tropical montane gradient lag behind warming temperatures.
(PloS one, 2011-01) Forero-Medina, German; Terborgh, John; Socolar, S Jacob; Pimm, Stuart L
Background
Species may respond to a warming climate by moving to higher latitudes or elevations. Shifts in geographic ranges are common responses in temperate regions. For the tropics, latitudinal temperature gradients are shallow; the only escape for species may be to move to higher elevations. There are few data to suggest that they do. Yet, the greatest loss of species from climate disruption may be for tropical montane species.
Methodology/principal findings
We repeat a historical transect in Peru and find an average upward shift of 49 m for 55 bird species over a 41 year interval. This shift is significantly upward, but also significantly smaller than the 152 m one expects from warming in the region. To estimate the expected shift in elevation we first determined the magnitude of warming in the locality from historical data. Then we used the temperature lapse rate to infer the required shift in altitude to compensate for warming. The range shifts in elevation were similar across different trophic guilds.
Conclusions
Endothermy may provide birds with some flexibility to temperature changes and allow them to move less than expected. Instead of being directly dependent on temperature, birds may be responding to gradual changes in the nature of the habitat or availability of food resources, and presence of competitors. If so, this has important implications for estimates of mountaintop extinctions from climate change.
Open Access
Experimental evaluation of evolution and coevolution as agents of ecosystem change in Trinidadian streams.
(Philos Trans R Soc Lond B Biol Sci, 2009-06-12) Palkovacs, EP; Marshall, MC; Lamphere, BA; Lynch, BR; Weese, DJ; Fraser, DF; Reznick, DN; Pringle, CM; Kinnison, MT
Evolution has been shown to be a critical determinant of ecological processes in some systems, but its importance relative to traditional ecological effects is not well known. In addition, almost nothing is known about the role of coevolution in shaping ecosystem function. Here, we experimentally evaluated the relative effects of species invasion (a traditional ecological effect), evolution and coevolution on ecosystem processes in Trinidadian streams. We manipulated the presence and population-of-origin of two common fish species, the guppy (Poecilia reticulata) and the killifish (Rivulus hartii). We measured epilithic algal biomass and accrual, aquatic invertebrate biomass, and detrital decomposition. Our results show that, for some ecosystem responses, the effects of evolution and coevolution were larger than the effects of species invasion. Guppy evolution in response to alternative predation regimes significantly influenced algal biomass and accrual rates. Guppies from a high-predation site caused an increase in algae relative to guppies from a low-predation site; algae effects were probably shaped by observed divergence in rates of nutrient excretion and algae consumption. Rivulus-guppy coevolution significantly influenced the biomass of aquatic invertebrates. Locally coevolved populations reduced invertebrate biomass relative to non-coevolved populations. These results challenge the general assumption that intraspecific diversity is a less critical determinant of ecosystem function than is interspecific diversity. Given existing evidence for contemporary evolution in these fish species, our findings suggest considerable potential for eco-evolutionary feedbacks to operate as populations adapt to natural or anthropogenic perturbations.
Open Access
Impact of simian immunodeficiency virus infection on chimpanzee population dynamics.
(PLoS Pathog, 2010-09-23) Rudicell, RS; Jones, JH; Wroblewski, EE; Learn, GH; Li, Y; Robertson, JD; Greengrass, E; Grossmann, F; Kamenya, S; Pintea, L; Mjungu, DC; Lonsdorf, EV; Mosser, A; Lehman, C; Collins, DA; Keele, BF; Goodall, J; Hahn, BH; Pusey, AE; Wilson, ML
Like human immunodeficiency virus type 1 (HIV-1), simian immunodeficiency virus of chimpanzees (SIVcpz) can cause CD4+ T cell loss and premature death. Here, we used molecular surveillance tools and mathematical modeling to estimate the impact of SIVcpz infection on chimpanzee population dynamics. Habituated (Mitumba and Kasekela) and non-habituated (Kalande) chimpanzees were studied in Gombe National Park, Tanzania. Ape population sizes were determined from demographic records (Mitumba and Kasekela) or individual sightings and genotyping (Kalande), while SIVcpz prevalence rates were monitored using non-invasive methods. Between 2002-2009, the Mitumba and Kasekela communities experienced mean annual growth rates of 1.9% and 2.4%, respectively, while Kalande chimpanzees suffered a significant decline, with a mean growth rate of -6.5% to -7.4%, depending on population estimates. A rapid decline in Kalande was first noted in the 1990s and originally attributed to poaching and reduced food sources. However, between 2002-2009, we found a mean SIVcpz prevalence in Kalande of 46.1%, which was almost four times higher than the prevalence in Mitumba (12.7%) and Kasekela (12.1%). To explore whether SIVcpz contributed to the Kalande decline, we used empirically determined SIVcpz transmission probabilities as well as chimpanzee mortality, mating and migration data to model the effect of viral pathogenicity on chimpanzee population growth. Deterministic calculations indicated that a prevalence of greater than 3.4% would result in negative growth and eventual population extinction, even using conservative mortality estimates. However, stochastic models revealed that in representative populations, SIVcpz, and not its host species, frequently went extinct. High SIVcpz transmission probability and excess mortality reduced population persistence, while intercommunity migration often rescued infected communities, even when immigrating females had a chance of being SIVcpz infected. Together, these results suggest that the decline of the Kalande community was caused, at least in part, by high levels of SIVcpz infection. However, population extinction is not an inevitable consequence of SIVcpz infection, but depends on additional variables, such as migration, that promote survival. These findings are consistent with the uneven distribution of SIVcpz throughout central Africa and explain how chimpanzees in Gombe and elsewhere can be at equipoise with this pathogen.
Open Access
Impacts of shrub encroachment on ecosystem structure and functioning: towards a global synthesis
(Ecology Letters, 2011) Eldridge; DJ; Bowker, MA; Maestre, FT; Roger, E; REYNOLDS, JF; Whitford, WG
Encroachment of woody plants into grasslands has generated considerable interest among ecologists. Syntheses of encroachment effects on ecosystem processes have been limited in extent and confined largely to pastoral land uses or particular geographical regions. We used univariate analyses, meta-analysis and structural equation modelling to test the propositions that (1) shrub encroachment does not necessarily lead to declines in ecosystem functions and (2) shrub traits influence the functional outcome of encroachment. Analyses of 43 ecosystem attributes from 244 case studies worldwide showed that some attributes consistently increased with encroachment (e.g. soil C, N), and others declined (e.g. grass cover, pH), but most exhibited variable responses. Traits of shrubs were associated with significant, though weak, structural and functional outcomes of encroachment. Our review revealed that encroachment had mixed effects on ecosystem structure and functioning at global scales, and that shrub traits influence the functional outcome of encroachment. Thus, a simple designation of encroachment as a process leading to functionally, structurally or contextually degraded ecosystems is not supported by a critical analysis of existing literature. Our results highlight that the commonly established link between shrub encroachment and degradation is not universal.
Open Access
Implications of long-term care capacity response policies for an aging population: a simulation analysis.
(Health policy (Amsterdam, Netherlands), 2014-05) Ansah, John P; Eberlein, Robert L; Love, Sean R; Bautista, Mary Ann; Thompson, James P; Malhotra, Rahul; Matchar, David B
Introduction
The demand for long-term care (LTC) services is likely to increase as a population ages. Keeping pace with rising demand for LTC poses a key challenge for health systems and policymakers, who may be slow to scale up capacity. Given that Singapore is likely to face increasing demand for both acute and LTC services, this paper examines the dynamic impact of different LTC capacity response policies, which differ in the amount of time over which LTC capacity is increased, on acute care utilization and the demand for LTC and acute care professionals.
Methods
The modeling methodology of System Dynamics (SD) was applied to create a simplified, aggregate, computer simulation model for policy exploration. This model stimulates the interaction between persons with LTC needs (i.e., elderly individuals aged 65 years and older who have functional limitations that require human assistance) and the capacity of the healthcare system (i.e., acute and LTC services, including community-based and institutional care) to provide care. Because the model is intended for policy exploration, stylized numbers were used as model inputs. To discern policy effects, the model was initialized in a steady state. The steady state was disturbed by doubling the number of people needing LTC over the 30-year simulation time. Under this demand change scenario, the effects of various LTC capacity response policies were studied and sensitivity analyses were performed.
Results
Compared to proactive and quick adjustment LTC capacity response policies, slower adjustment LTC capacity response policies (i.e., those for which the time to change LTC capacity is longer) tend to shift care demands to the acute care sector and increase total care needs.
Conclusions
Greater attention to demand in the acute care sector relative to demand for LTC may result in over-building acute care facilities and filling them with individuals whose needs are better suited for LTC. Policymakers must be equally proactive in expanding LTC capacity, lest unsustainable acute care utilization and significant deficits in the number of healthcare professionals arise. Delaying LTC expansion could, for example, lead to increased healthcare expenditure and longer wait lists for LTC and acute care patients.
Open Access
Inference for nonlinear epidemiological models using genealogies and time series.
(PLoS Comput Biol, 2011-08) Rasmussen, David A; Ratmann, Oliver; Koelle, Katia
Phylodynamics - the field aiming to quantitatively integrate the ecological and evolutionary dynamics of rapidly evolving populations like those of RNA viruses - increasingly relies upon coalescent approaches to infer past population dynamics from reconstructed genealogies. As sequence data have become more abundant, these approaches are beginning to be used on populations undergoing rapid and rather complex dynamics. In such cases, the simple demographic models that current phylodynamic methods employ can be limiting. First, these models are not ideal for yielding biological insight into the processes that drive the dynamics of the populations of interest. Second, these models differ in form from mechanistic and often stochastic population dynamic models that are currently widely used when fitting models to time series data. As such, their use does not allow for both genealogical data and time series data to be considered in tandem when conducting inference. Here, we present a flexible statistical framework for phylodynamic inference that goes beyond these current limitations. The framework we present employs a recently developed method known as particle MCMC to fit stochastic, nonlinear mechanistic models for complex population dynamics to gene genealogies and time series data in a Bayesian framework. We demonstrate our approach using a nonlinear Susceptible-Infected-Recovered (SIR) model for the transmission dynamics of an infectious disease and show through simulations that it provides accurate estimates of past disease dynamics and key epidemiological parameters from genealogies with or without accompanying time series data.
Open Access
Migration and fishing in Indonesian coastal villages.
(Ambio, 2002-06) Kramer, Randall A; Simanjuntak, Sahat MH; Liese, Christopher
The coastal ecosystems in Southeast Asia are under increased pressure from local and global change. This paper examines human migration and the use of marine resources in coastal villages in the Minahasa district of North Sulawesi, Indonesia. Primary data were collected through interviews with village leaders, focus groups, and a sample survey of 600 fishing households. Migration is responsible for at least one quarter of the total growth during the past decade. All groups of fishermen report falling productivity of the nearshore fisheries. Econometric analysis is used to examine the weekly fish catch of the artisanal fishing sector. Migration status and socioeconomic variables seem to have no systematic effect, while fishing effort (labor, boat, and gear), the degree of specialization, and the remoteness of villages are found to be positively related to weekly fish catches.
Open Access
Mycobacterium tuberculosis Beijing family: analysis of the epidemiological and clinical factors associated with an emerging lineage in the urban area of Milan.
(Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2014-07) Zanini, Fabio; Carugati, Manuela; Schiroli, Consuelo; Lapadula, Giuseppe; Lombardi, Alessandra; Codecasa, Luigi; Gori, Andrea; Franzetti, Fabio
The Mycobacterium tuberculosis Beijing genotype raises major concern because of global spreading, hyper-virulence and association with multi-drug resistance (MDR). The aims of the study were to evaluate role of Beijing family in the epidemiological setting of Milan and to identify predictors associated with the spreading of this lineage. Overall 3830TB cases were included. Beijing family accounted for 100 isolates (2.6%). Prevalence grew from 1.7% to 5.4% in the period 1996-2009. Foreign origin increased significantly the risk of having a Beijing strain: the greatest risk was observed among patients coming either from China [AOR=57.7, 95%CI (26.3-126.8)] or from Former Soviet countries [AOR=33.9, 95%CI (12.8-99.6)]. Also MDR was independently associated with Beijing family [AOR=2.7, 95%CI (1.3-5.8)], whereas male gender and younger age only approximated the statistical significance [p 0.051 and p 0.099, respectively]. However, the percentage of cases attributable to MDR strains decreased over time, both in the Beijing group and in the non-Beijing group. 97 isolates were grouped in 37 sub-lineages: MT11, MT33 were predominant. Beijing family is an emerging lineage in Milan. Origin from countries like China and Ukraine and MDR are significantly associated with Beijing. The broad range of the sub-lineages reflects the recent dynamics of the migration flows to our area. This scenario can prelude to a constant increase in the spreading of Beijing strains in the near future.
Open Access
Natal emigration by both sexes in the La Pacifica population of mantled howlers: when do some stay?
(Am J Primatol, 2008-02) Clarke, Margaret R; Glander, Kenneth E
We have reported previously that all male and female mantled howlers emigrate from natal groups at Hacienda La Pacifica, Costa Rica. In the years since that report, a small number of juveniles have stayed in the natal group without experiencing a solitary phase. Here, we present a post hoc analysis on juvenile emigration in six groups of howlers under observation for varying amounts of time between 1972 and 2005. Our records revealed 139 juveniles for whom emigration status was certain, and 125 of these did emigrate. There was a significant association between presence of mother and emigration: juveniles without mothers were more likely to remain in their natal group (chi(1)(2) = 53.1, P<.0001). The mean age of emigration for all juveniles (n = 125) was 2.47 years (SD = 0.9, range = 1.5-6.5). There was no difference in age of emigration by adult male composition (one-male, multi-male, both), but juveniles of unknown sex emigrated younger than either known males or females (F(2,116) = 4.4, P<.02). For emigrating juveniles of known sex (n = 99), both males and females without mothers left at a later age than those with mothers (F(1,95) = 6.5, P<.02). Although philopatry or delayed emigration occurs in a few motherless animals, most males and females do emigrate from their natal groups at ages consistent with those reported for other species of howlers.
Open Access
Quantitative analysis of forest fragmentation in the atlantic forest reveals more threatened bird species than the current red list.
(PloS one, 2013-01) Schnell, Jessica K; Harris, Grant M; Pimm, Stuart L; Russell, Gareth J
Habitat loss and attendant fragmentation threaten the existence of many species. Conserving these species requires a straightforward and objective method that quantifies how these factors affect their survival. Therefore, we compared a variety of metrics that assess habitat fragmentation in bird ranges, using the geographical ranges of 127 forest endemic passerine birds inhabiting the Atlantic Forest of Brazil. A common, non-biological metric - cumulative area of size-ranked fragments within a species range - was misleading, as the least threatened species had the most habitat fragmentation. Instead, we recommend a modified version of metapopulation capacity. The metric links detailed spatial information on fragment sizes and spatial configuration to the birds' abilities to occupy and disperse across large areas (100,000+ km(2)). In the Atlantic Forest, metapopulation capacities were largely bimodal, in that most species' ranges had either low capacity (high risk of extinction) or high capacity (very small risk of extinction). This pattern persisted within taxonomically and ecologically homogenous groups, indicating that it is driven by fragmentation patterns and not differences in species ecology. Worryingly, we found IUCN considers some 28 of 58 species in the low metapopulation capacity cluster to not be threatened. We propose that assessing the effect of fragmentation will separate species more clearly into distinct risk categories than does a simple assessment of remaining habitat.
Open Access
Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam.
(Mol Biol Evol, 2014-02) Rasmussen, David A; Boni, Maciej F; Koelle, Katia
Coalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches-often referred to as phylodynamic methods-have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred from viral genealogies often differ widely from those observed from other sources of epidemiological data, such as hospitalization records. We demonstrate how a modeling framework that allows for the direct fitting of mechanistic epidemiological models to genealogies can be used to test different hypotheses about what ecological factors cause phylodynamic inferences to differ from observed dynamics. We use this framework to test different hypotheses about why dengue serotype 1 (DENV-1) population dynamics in southern Vietnam inferred using existing phylodynamic methods differ from hospitalization data. Specifically, we consider how factors such as seasonality, vector dynamics, and spatial structure can affect inferences drawn from genealogies. The coalescent models we derive to take into account vector dynamics and spatial structure reveal that these ecological complexities can substantially affect coalescent rates among lineages. We show that incorporating these additional ecological complexities into coalescent models can also greatly improve estimates of historical population dynamics and lead to new insights into the factors shaping viral genealogies.
Open Access
Reproduction and population growth in free-ranging mantled howling monkeys.
(Am J Phys Anthropol, 1980-07) Glander, KE
Free-ranging mantled howling monkey (Alouatta palliata Gray) females experienced a regular estrus cycle averaging 16.3 days, demonstrated sexual skin changes, and participated in multiple matings before becoming pregnant. Gestation averaged 186 days. The average interval between births was 22.5 months. Sexual maturity occurred at approximately 36 and 42 months for females and males, respectively. Female age at first birth was about 3 1/2 years. Births were scattered during some years and clustered during others. The age, rank, and parity of the females affected infant survival. More female than male infants survived to one year of age. Increased population size was the result of immigration rather than births.
Open Access
Reproductive improvement and senescence in a long-lived bird.
(Proc Natl Acad Sci U S A, 2010-04-27) Rebke, Maren; Coulson, Tim; Becker, Peter H; Vaupel, James W
Heterogeneity within a population is a pervasive challenge for studies of individual life-histories. Population-level patterns in age-specific reproductive success can be broken down into relative contributions from selective disappearance, selective appearance of individuals into the study population, and average change in performance for survivors (average ontogenetic development). In this article, we provide an exact decomposition. We apply our formula to data on the reproductive performance of a well characterized population of common terns (Sterna hirundo). We show that improvements with age over most of adult life and senescence at old ages are primarily due to a genuine change in the mean among surviving individuals rather than selective disappearance or selective appearance of individuals. Average ontogenetic development accounts for approximately 87% of the overall age-specific population change.
Open Access
Rise, stagnation, and rise of Danish women's life expectancy.
(Proc Natl Acad Sci U S A, 2016-04-12) Lindahl-Jacobsen, Rune; Rau, Roland; Jeune, Bernard; Canudas-Romo, Vladimir; Lenart, Adam; Christensen, Kaare; Vaupel, James W
Health conditions change from year to year, with a general tendency in many countries for improvement. These conditions also change from one birth cohort to another: some generations suffer more adverse events in childhood, smoke more heavily, eat poorer diets, etc., than generations born earlier or later. Because it is difficult to disentangle period effects from cohort effects, demographers, epidemiologists, actuaries, and other population scientists often disagree about cohort effects' relative importance. In particular, some advocate forecasts of life expectancy based on period trends; others favor forecasts that hinge on cohort differences. We use a combination of age decomposition and exchange of survival probabilities between countries to study the remarkable recent history of female life expectancy in Denmark, a saga of rising, stagnating, and now again rising lifespans. The gap between female life expectancy in Denmark vs. Sweden grew to 3.5 y in the period 1975-2000. When we assumed that Danish women born 1915-1945 had the same survival probabilities as Swedish women, the gap remained small and roughly constant. Hence, the lower Danish life expectancy is caused by these cohorts and is not attributable to period effects.

Browsing by Subject "Population Dynamics"

Background

Methodology/principal findings

Conclusions

Introduction

Methods

Results

Conclusions