Mean Population Size Research Articles

Correction to ‘Historical DNA reveals the demographic history of Atlantic cod ( Gadus morhua ) in medieval and early modern Iceland’

[ Proc. R. Soc. B 281 , 20132976. (22 February 2014; Published online 8 January 2014) ([doi:10.1098/rspb.2013.2976][2])][2] Concerns with the original article [[1][2]] were originally brought to light by Prof Einar Arnason and his concerns are outlined here [[2][3]]. Moreover, there were errors in

The effect of alternative forms of hunting on the social organization of two small populations of lions Panthera leo in southern Africa

AbstractAfrican lion Panthera leo populations have declined as a result of various anthropogenic factors, and most extant populations are small, which further compromises their persistence. Lions in unfenced areas are more exposed to illegal hunting, snaring and poisoning, and populations in fenced reserves are subject to population control by removal of selected individuals from particular age and sex classes. During 2000–2011 19 lions from the mostly unfenced Northern Tuli Game Reserve in Botswana were shot, snared or poisoned. By contrast, only one lioness was shot outside the fenced Venetia Limpopo Nature Reserve 10 km away, in South Africa, where 29 lions were trophy hunted or culled. We found that the mean population size, sex ratio and litter size were the same for both reserves but population density, pride size and cub survival rate were significantly higher in the fenced reserve. The size of the population in Northern Tuli was constrained by a high rate of indiscriminate anthropogenic mortality, with 94.7% of adult mortality occurring outside the reserve. The different forms of anthropogenic suppression in evidence at the two reserves resulted in different population-level responses, which will ultimately affect population viability. As conservation strategies are attempting to remove fences and establish larger conservation areas, this study indicates how fences can influence population dynamics in areas where human presence threatens large carnivores.

Extinction risk and eco-evolutionary dynamics in a variable environment with increasing frequency of extreme events.

One of the most dramatic consequences of climate change will be the intensification and increased frequency of extreme events. I used numerical simulations to understand and predict the consequences of directional trend (i.e. mean state) and increased variability of a climate variable (e.g. temperature), increased probability of occurrence of point extreme events (e.g. floods), selection pressure and effect size of mutations on a quantitative trait determining individual fitness, as well as the their effects on the population and genetic dynamics of a population of moderate size. The interaction among climate trend, variability and probability of point extremes had a minor effect on risk of extinction, time to extinction and distribution of the trait after accounting for their independent effects. The survival chances of a population strongly and linearly decreased with increasing strength of selection, as well as with increasing climate trend and variability. Mutation amplitude had no effects on extinction risk, time to extinction or genetic adaptation to the new climate. Climate trend and strength of selection largely determined the shift of the mean phenotype in the population. The extinction or persistence of the populations in an 'extinction window' of 10 years was well predicted by a simple model including mean population size and mean genetic variance over a 10-year time frame preceding the 'extinction window', although genetic variance had a smaller role than population size in predicting contemporary risk of extinction.

Trichotomous noise controlled signal amplification in a generalized Verhulst model

The long-time limit of the probability distribution and statistical moments for a population size are studied by means of a stochastic growth model with generalized Verhulst self-regulation. The effect of variable environment on the carrying capacity of a population is modeled by a multiplicative three-level Markovian noise and by a time periodic deterministic component. Exact expressions for the moments of the population size have been calculated. It is shown that an interplay of a small periodic forcing and colored noise can cause large oscillations of the mean population size. The conditions for the appearance of such a phenomenon are found and illustrated by graphs. Implications of the results on models of symbiotic metapopulations are also discussed. Particularly, it is demonstrated that the effect of noise-generated amplification of an input signal gets more pronounced as the intensity of symbiotic interaction increases.

Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range.

Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (i) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics and (ii) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. In contrast, the fact that population variability is often related to mean population size implies that the spatial structure of the population size within the range of a species may also be a useful predictor of the spatial variation in temporal variability of population size over the range of the species. To explore how population temporal variability varies spatially and the underlying processes responsible for the spatial variation, we focused on the intertidal barnacle Chthamalus dalli and examined differences in its population dynamics along the tidal levels it inhabits. Changes in coverage of barnacle populations were monitored for 10.5 years at 25 plots spanning the elevational range of this species. Data were analysed by fitting a population dynamics model to estimate the effects of density-dependent and density-independent processes on population growth. We also examined the temporal mean-variance relationship of population size with parameters estimated from the population dynamics model. We found that the relative variability of populations tended to increase from the centre of the elevational range towards the margins because of an increase in the magnitude of stochastic fluctuations of growth rates. Thus, our results supported hypothesis (2). We also found that spatial variations in temporal population variability were well characterized by Taylor's power law, the relative population variability being inversely related to the mean population size. Results suggest that understanding the population dynamics of a species over its range may be facilitated by taking the spatial structure of population size into account as well as by considering changes in population processes as a function of position within the range of the species.

Estimates of population differentiation in pink salmon Oncorhynchus gorbuscha with using of the microsatellite markers may be underestimated due to high population sizes

Data on the variation at eight microsatellite loci in the Far East salmon Oncorhynchus gorbuscha samples caught in 1984–1985 and 2001–2006 are analyzed. F-statistics indices at all levels of the hierarchical spatial structures are very small. At the same time, the differentiation between populations (according to F ST estimates) in the odd-year broodline of pink salmon does not exceed the temporal variation within populations. In the even-year broodline, the F-statistics indices at the interregional and intraregional levels are significantly greater than those in the odd-year broodline. F ST estimates (averaged over the same set of loci) vary widely within the range: the highest values are observed in populations of the coast of North America (except Alaska) and in the new range in the European North of Russia, whereas in the populations of the Asian part of the range and Alaska they are one order of magnitude smaller. The causes of the heterogeneity of the estimates of genetic differentiation within the range and between the broodlines of odd and even years are discussed. Since the mean population size estimates were correlated with the F ST values, it was assumed that the effect of random genetic drift, the main factor of population divergence in selectively neutral loci, weakens with an increase in the population size. Because of the greater population sizes in pink salmon compared to other salmon species, as well due to the uneven distribution of populations of different size, the usage of microsatellite markers may lead to an underestimation of the true divergence of populations and their regional groups and, consequently, to an overestimation of genetic migration.

Linking indices for biodiversity monitoring to extinction risk theory.

Biodiversity indices often combine data from different species when used in monitoring programs. Heuristic properties can suggest preferred indices, but we lack objective ways to discriminate between indices with similar heuristics. Biodiversity indices can be evaluated by determining how well they reflect management objectives that a monitoring program aims to support. For example, the Convention on Biological Diversity requires reporting about extinction rates, so simple indices that reflect extinction risk would be valuable. We developed 3 biodiversity indices that are based on simple models of population viability that relate extinction risk to abundance. We based the first index on the geometric mean abundance of species and the second on a more general power mean. In a third index, we integrated the geometric mean abundance and trend. These indices require the same data as previous indices, but they also relate directly to extinction risk. Field data for butterflies and woodland plants and experimental studies of protozoan communities show that the indices correlate with local extinction rates. Applying the index based on the geometric mean to global data on changes in avian abundance suggested that the average extinction probability of birds has increased approximately 1% from 1970 to 2009.Conectando Índices para el Monitoreo de la Biodiversidad con la Teoría de Riesgo de ExtinciónResumenLos índices de biodiversidad combinan frecuentemente los datos de diferentes especies cuando se usan en los programas de monitoreo. Las propiedades heurísticas pueden sugerir índices preferidos, pero carecemos de medios objetivos para discriminar a los índices con propiedades heurísticas similares. Los índices de biodiversidad pueden evaluarse al determinar qué tan bien reflejan los objetivos de manejo que un programa de monitoreo busca apoyar. Por ejemplo, la Convención sobre la Diversidad Biológica requiere reportar las tasas de extinción, así que los índices que reflejan el riesgo de extinción serían valiosos. Desarrollamos 3 índices de biodiversidad que se basan en modelos sencillos de viabilidad de población y que relacionan el riesgo de extinción con la abundancia. Basamos el primer índice en la media geométrica de la abundancia de especies, y el segundo en una media de poder más general. En el tercer índice integramos la media geométrica y la tendencia. Estos índices requieren los mismos datos que índices previos, pero también se relacionan directamente con el riesgo de extinción. La información de campo sobre mariposas y plantas de bosque, y los estudios experimentales de comunidades protozoarias, muestran que los índices se correlacionan con las tasas locales de extinción. Al aplicar el índice basado en la media geométrica sobre los datos globales de los cambios en la abundancia de aves, sugirió que la probabilidad de extinción promedio de aves ha incrementado aproximadamente 1% desde 1970 hasta 2009.Palabras ClaveÍndice de biodiversidad, media geométrica, medida de la biodiversidad, riesgo de extinción

Decline of a Callista chione (Bivalvia: Veneridae) bed in the Maresme coast (northwestern Mediterranean Sea)

Bivalves are considered key species in many marine communities and the decline of their populations usually causes changes in the structure of the ecosystems.The aim of the present study was to investigate changes in the spatial distribution and population structure of an exploited shellfish bed of Callista chione at a location of the northwestern Mediterranean Sea and analyse its potential causes. To this end field surveys for the years 2004 and 2010 covering the whole distribution area of the species were performed and all historical data on commercial landings, clam biomass and density, and locations and volume of dredged sand for beach nourishment were compiled. Results showed that the distribution had been hugely reduced, showing a sharp decline in density and biomass and a decrease in the mean population size in 2010. Our results confirm that the species is a slow-growing bivalve that is highly vulnerable to disturbances prolonged in time. Persistent sand dredging operations since 1987 have gradually reduced the distribution area of the smooth clam to the northeastern part of the clam bed. Consequently, fishing activity has concentrated on a smaller area, thus increasing the fishing effort in the northern part. Therefore, the results clearly suggest that the decline of C. chione bed was mainly caused by the interaction of two coastal uses: sand dredging and clam fisheries. Based on this study, some management guidelines are proposed.

Scaling of the mean and variance of population dynamics under fluctuating regimes

Theoretical ecologists have long sought to understand how the persistence of populations depends on the interactions between exogenous (biotic and abiotic) and endogenous (e.g., demographic and genetic) drivers of population dynamics. Recent work focuses on the autocorrelation structure of environmental perturbations and its effects on the persistence of populations. Accurate estimation of extinction times and especially determination of the mechanisms affecting extinction times is important for biodiversity conservation. Here we examine the interaction between environmental fluctuations and the scaling effect of the mean population size with its variance. We investigate how interactions between environmental and demographic stochasticity can affect the mean time to extinction, change optimal patch size dynamics, and how it can alter the often-assumed linear relationship between the census size and the effective population size. The importance of the correlation between environmental and demographic variation depends on the relative importance of the two types of variation. We found the correlation to be important when the two types of variation were approximately equal; however, the importance of the correlation diminishes as one source of variation dominates. The implications of these findings are discussed from a conservation and eco-evolutionary point of view.

Noise-Induced Transitions in a Population Growth Model Based on Size-Dependent Carrying Capacity

The stochastic dynamics of a population growth model with size-dependent carrying capacity is considered. The effect of a fluctuating environment on population growth is modeled as a multiplicative dichotomous noise. At intermediate values of population size the deterministic counterpart of the model behaves similarly to the Von Foerster model for human population, but at small and very large values of population size substantial differences occur. In the stochastic case, an exact analytical solution for the stationary probability distribution is found. It is established that variation of noise correlation time can cause noise-induced transitions between three different states of the system characterized by qualitatively different behaviors of the probability distributions of the population size. Also, it is shown that, in some regions of the system parameters, variation of the amplitude of environmental fluctuations can induce single unidirectional abrupt transitions of the mean population size.

Reducing the uncertainty of wildlife population abundance: model‐based versus design‐based estimates

Knowledge of population sizes in delimited spatial regions is crucial for most ecological research. Data from population surveys are collected with strip, line, or point transects sampling. These data are positively skewed and spatially autocorrelated, which makes estimation of uncertainty in the population size difficult. Thus, we propose a novel spatial‐based estimator from a hierarchical spatial model for count data where the inhomogeneous animal density is decomposed into a deterministic trend related to potential habitat and a stationary latent field modeled by geostatistics. An empirical estimate of the latent variable is obtained including corrective terms for non‐stationarity and variance resulting from a Poisson distribution of sightings. A novel block kriging estimator that takes into account both non‐stationarity and the nature of count data is derived to obtain a spatial estimate of animal total abundance and variance of errors of prediction. From spatial simulated count data and real count data of common guillemot wintering in the Bay of Biscay (France), we compare mean population size and variance estimates obtained from our model‐based approach to the design‐based estimator (i.e., block bootstrap). The novel Poisson block kriging estimates greatly reduces uncertainty of population size estimates while block bootstrap provides larger uncertainties. Copyright © 2013 John Wiley & Sons, Ltd.

Influence of competition and age on tree growth in structurally complex old-growth forests in northern Minnesota, USA

Factors influencing tree growth in structurally complex forests remain poorly understood. Here we assessed the influence of competition on Pinus resinosa (n=224) and Pinus strobus (n=90) growth in four old-growth stands in Minnesota, using mixed effects models. A subset of trees, with accurate age estimates, was used to further test the influence of tree age. Our analyses included the weighted Voronoi diagram (WVD) as a novel competition index, representing a detailed description of the spatial structure of a tree’s neighborhood.Competition was variably expressed depending on stand developmental history and tree species. For P. resinosa in single-cohort stands, and P. strobus in multi-cohort stands, tree size relative to the population mean size best predicted tree growth. In contrast, for P. resinosa in multi-cohort stands, the spatial configuration of competitors became important, as shown by the superior performance of the WVD index. Surprisingly, while tree age had a negative influence on growth, it did not influence the intensity of competition.Our results highlight the importance of considering stand developmental history and tree age in analyses of tree growth and competition, and the potential for improving assessments of competition in complex stands, using detailed quantification of neighborhood structure.

Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets.

DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available. [Clusters; coalescent; DNA; genealogical; neutral; speciation; species.]

Ecological interactions between hatchery and wild fish: a case study based on the highly piscivorous Japanese Spanish mackerel

If the release of hatchery-reared juveniles exceeds the carrying capacity of the envi- ronment, the growth rate of wild fish may decrease or hatchery fish might displace wild fish because of competition for prey and space, or cannibalism. However, limited evidence is available to confirm these ecological effects. Therefore, we used census-marking experiments to investigate the ecological interactions between hatchery and wild fish in the large piscivorous species Japan- ese Spanish mackerel (JSM) Scomberomorus niphonius in the Seto Inland Sea. We analysed the relationship between the mean body weight and population size of Age 0 JSM, and the relation- ship between the biomass of juvenile Japanese anchovy Engraulis japonicus, which is the princi- pal prey fish of JSM, and that of Age 0 JSM. We also estimated the spawner−recruit relationship. We measured the body sizes of 5008 JSM juveniles during July and December between 1999 and 2005 in the eastern Seto Inland Sea, and 551 hatchery fish were identified in the sample based on examinations of marked otoliths. There was a negative correlation between the mean body weight and population size of Age 0 fish, which clearly demonstrated the density-dependent growth of Age 0 JSM. The ~35% variation in the biomass of Age 0 JSM was explained by the biomass of prey fish. Hatchery fish tended to be larger than wild fish, and they had better growth perform- ance. Our analysis showed that hatchery fish reduced the growth rate of wild fish and displaced the wild fish in terms of biomass when hatchery fish stocking exceeded the carrying capacity of the environment.

Quantifying the Mutational Meltdown in Diploid Populations

Mutational meltdown, in which demographic and genetic processes mutually reinforce one another to accelerate the extinction of small populations, has been poorly quantified despite its potential importance in conservation biology. Here we present a model-based framework to study and quantify the mutational meltdown in a finite diploid population that is evolving continuously in time and subject to resource competition. We model slightly deleterious mutations affecting the population demographic parameters and study how the rate of mutation fixation increases as the genetic load increases, a process that we investigate at two timescales: an ecological scale and a mutational scale. Unlike most previous studies, we treat population size as a random process in continuous time. We show that as deleterious mutations accumulate, the decrease in mean population size accelerates with time relative to a null model with a constant mean fixation time. We quantify this mutational meltdown via the change in the mean fixation time after each new mutation fixation, and we show that the meltdown appears less severe than predicted by earlier theoretical work. We also emphasize that mean population size alone can be a misleading index of the risk of population extinction, which could be better evaluated with additional information on demographic parameters.

A preliminary study of the Caprella scaura amphipod culture for potential use in aquaculture

The caprellid amphipod Caprella scaura Templeton, 1836 was investigated as a mass culture organism, for potential use as natural prey in aquaculture. C. scaura showed good population growth during 3months of culturing with nauplii of Artemia sp. and microalgae as food source. A final mean population size of 12,510.67individuals/tank and a maximum density of 10,460individualsm−2 were obtained; a 50-fold increase of the initial population was observed. Juveniles were the most abundant stage in the culture (86.0% of total), followed by mature females (5.4%) and immature males (3.1%). Three kinds of plastic mesh with different complexity levels were used as artificial substrates for amphipods to attach to and shelter. There were no significant differences in the total number of individuals present on each kind of mesh, although female and male adults were more abundant in folded meshes with larger pore diameter. This research demonstrated that the caprellid amphipod C. scaura may be readily cultured at high densities with a variety of mesh morphologies allowing more efficient use of tank volume and improved handling.

Permanent and new arable field margins support large earthworm communities but do not increase in-field populations

The maintenance of uncultivated field margins and the creation of new field margin strips are standard agri-environmental measures aimed at enhancing above-ground biodiversity, but their effects on below-ground biodiversity (in margins and also in-field) are insufficiently known. This study compared earthworm communities in permanent (grassy) margins, newly created field margin strips (unsown) and in-field in five arable fields in Ireland over a 3-year period. Permanent field margins initially supported highest earthworm abundance, biomass and species richness compared to the newly created margin strips and in-field at three conventional and two minimum (conservation) tillage sites. However, after three years, mean earthworm populations in the newly created margin strips (371±181individualsm−2 and 91.9±41.7gbiomassm−2) approached those observed in the permanent margins (470±47individualsm−2 and 126.5±14.7gbiomassm−2) in the three conventional tillage field sites. By contrast, overall mean population sizes inside conventionally tilled fields were 155±46individualsm−2 and 38.3±12.5gbiomassm−2. Similar trends were observed at the two minimum tillage sites. Permanent field margins supported somewhat larger mean species numbers compared to in-field at conventional and minimum tillage field sites, but most species still occurred, at significantly lower abundances, inside fields. Spatially defined transect sampling (at 1, 3, 10 and 50m in-field) at all study sites did not provide evidence for increased populations nearer to the margins or margin strips, even under reduced cultivation. It is concluded that permanent and newly created margin strips in arable systems support larger earthworm populations than are found in-field, but field margins did not appear to enhance in-field populations through colonisation or spill-over effects documented for more mobile, above-ground invertebrate taxa.

Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations.

Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways.

Interspecific differences in stochastic population dynamics explains variation in Taylor's temporal power law

Taylor’s power law, i.e. that the slope for the increase in variance with mean population size is between 1 and 2 at a logarithmic scale, provides one of the few quantitative relationships in population ecology, yet the underlying ecological mechanisms are only poorly understood. Stochastic theory of population dynamics predicts that demographic and environmental stochasticity will affect the slope differently. In a stable environment under the influence of demographic stochasticity alone the slope will be equal to 1. In large populations in which demographic variance will have a negligible effect on the dynamics the slope will approach 2. In addition, the slope will also be influenced by how the strength of density dependence is related to mean population size. To disentangle the relative contribution of these processes we estimate the mean‐variance relationship for a large number of populations of British birds. The variance in population size of most species decreased with the mean due to decreased influence of demographic stochasticity at larger population sizes. Interspecific differences in demographic stochasticity was the main factor influencing variation in slopes of Taylor’s power law among species through a significant negative relationship between the slope and demographic variance. In addition, slopes were influenced by interspecific variation in life history parameters such as adult survival and clutch size. These analyses show that Taylor’s power law is generated from an interplay between stochastic and density dependent factors, modulated by life history.

Reconstruction and prediction of invasive mongoose population dynamics from history of introduction and management: aBayesian state‐space modelling approach

Summary An understanding of the underlying processes and comprehensive history of invasive species is necessary to assess the long‐term effectiveness of invasive species management. However, continuous, long‐term labour‐intensive population surveys on invasive species are often not feasible. Thus, it is important to learn about their dynamics through management action and its consequences. Amami Island, Japan, has an ongoing large‐scale and long‐term eradication programme of invasive small Indian mongooses. To estimate the long‐term pattern of population size and the parameters determining the dynamics, including anthropogenic removal, we applied a surplus‐production model within a Bayesian state‐space formulation incorporating the initial population size, number of captures and capture effort. Using the estimated process model directly, we conducted stochastic simulations to evaluate the feasibility of eradication. Estimated 32‐year annual capture probability of mongooses has increased since their introduction. The population size started to decline in 2001; mean population size in 2000 was 6141 (95%CI: 5415–6817), and declined to 169 (95%CI: 42–408) by 2011. Parameter estimates of a Weibull catchability model indicated that there was large individual heterogeneity in the probability of being captured, and per‐effort capture probability declined with an increase in annual capture effort. The simulation study indicated that the eradication feasibility in 2023 would be over 90% if the same annual capture effort is upheld as in 2010 (2 075 760 corrected trap‐days). However, increasing annual capture effort would have little effect on shortening the time to eradication. Synthesis and applications. A hierarchical model that incorporates multiple types of data to reveal long‐term population dynamics has the potential to be updated with the outcomes of control efforts, and will enhance adaptive management of invasive species. This approach will offer valuable information about trade‐offs between time to eradication success and effort per unit time in a long‐term eradication project, and the length of time needed to continue management actions to achieve eradication success.