Extinction risk assessment for the species survival plan (SSP®) population of the Bali mynah (Leucopsar rothschildi)

The Bali mynah Species Survival Plan (SSP^®), an Association of Zoos and Aquariums program, strives to maintain the genetic and demographic health of its population, avoid unplanned changes in size, and minimize the risk of population extinction. The SSP population meets current demographic and genetic objectives with a population size of 209 birds at 61 institutions and 96% genetic diversity (GD) retained from the source population. However, participating institutions have expressed concerns regarding space allocation, target population size (TPS), breeding restrictions, inbreeding depression, and harvest in relation to future population availability and viability. Based on these factors, we assess five questions with a quantitative risk assessment, specifically a population viability analysis (PVA) using ZooRisk software. Using an individual-based stochastic model, we project potential population changes under different conditions (e.g. changes in TPS and genetic management) to identify the most effective management actions. Our projections indicate that under current management conditions, population decline and extinction are unlikely and that although GD will decline over 100 years the projected loss does not exceed levels acceptable to population managers (less than 90% GD retained). Model simulations indicate that the combination of two genetic management strategies (i.e. priority breeding based on mean kinship and inbreeding avoidance) benefits the retention of GD and reduces the accumulation of inbreeding. The current TPS (250) is greater than necessary to minimize the risk of extinction for the SSP population but any reduction in TPS must be accompanied by continued application of genetic management. If carefully planned, birds can be harvested for transfer to Bali for a reintroduction program without jeopardizing the SSP population. Zoo Biol 28:230–252, 2009. © 2009 Wiley-Liss, Inc.     

Image analysis of Daphnia populations: non-destructive determination of demography and biomass in cultures

SUMMARY 1. An image analysis technique was developed for the semiautomatic determination of abundance, size distribution and biomass in Daphnia cultures. This allowed detailed observations of growth, demography and biomass accumulation in live populations, avoiding artifacts caused by subsampling and sampling losses.
2. The image analysis method gave fast, non-destructive and reliable individual counts, even in cultures with high density and a large fraction of juveniles.
3. In Daphnia , animal width changes with nutritional status and growth within instar, while length changes only at the moult. Thus, estimation of individual biomass using an ellipsoidal model based on animal width gave improved biomass calculations compared to manual counting, sizing, and length : weight regressions.
4. The power of the image analysis technique for assessing population growth and size structure was demonstrated in two 40-day experiments, with Daphnia magna feeding on the green algae Selenastrum capricornutum in a two-stage chemostat system.     

Contrasting Patterns of Demography and Population Viability Among Gopher Tortoise Populations in Alabama

Population viability analyses are useful tools to predict abundance and extinction risk for imperiled species. In southeastern North America, the federally threatened gopher tortoise (Gopherus polyphemus) is a keystone species in the diverse and imperiled longleaf pine (Pinus palustris) ecosystem, and researchers have suggested that tortoise populations are declining and characterized by high extinction risk. We report results from a 30-year demographic study of gopher tortoises in southern Alabama (1991–2020), where 3 populations have been stable and 3 others have declined. To better understand the demographic vital rates associated with stable and declining tortoise populations, we used a multi-state hierarchical mark-recapture model to estimate sex- and stage-specific patterns of demographic vital rates at each population. We then built a predictive population model to project population dynamics and evaluate extinction risk in a population viability context. Population structure did not change significantly in stable populations, but juveniles became less abundant in declining populations over 30 years. Apparent survival varied by age, sex, and site; adults had higher survival than juveniles, but female survival was substantially lower in declining populations than in stable ones. Using simulations, we predicted that stable populations with high female survival would persist over the next 100 years but sites with lower female survival would decline, become male-biased, and be at high risk of extirpation. Stable populations were most sensitive to changes in apparent survival of adult females. Because local populations varied greatly in vital rates, our analysis improves upon previous demographic models for northern populations of gopher tortoises by accounting for population-level variation in demographic patterns and, counter to previous model predictions, suggests that small tortoise populations can persist when habitat is managed effectively. © 2021 The Wildlife Society.     

Deciphering the relative weights of demographic transition and vaccination in the decrease of measles incidence in Italy

In Italy, during the course of the past century to the present-day, measles incidence underwent a remarkable decreasing trend that started well before the introduction of the national immunization programme. In this work, we aim at examining to what extent both the demographic transition, characterized by declining mortality and fertility rates over time, and the vaccination programme are responsible for the observed epidemiological pattern. Making use of a non-stationary, age-structured disease transmission model, we show that in the pre-vaccination era, from 1901 to 1982, the decline in birth rates has resulted in a drastic decrease in the effective transmission rate, which in turn has determined a declining trend of measles incidence (from 25.2 to 10.3 infections per 1000 individuals). However, since 1983, vaccination appears to have become the major contributing factor in the decrease of measles incidence, which otherwise would have remained stable as a consequence of the nearly constant birth rates. This led to a remarkable decrease in the effective transmission rate, to a level well below the critical threshold for disease persistence. These findings call for the adoption of epidemiological models, which deviate the age structure from stationary equilibrium solutions, to better understand the biology of infectious diseases and evaluate immunization programmes.     

Integral projection models perform better for small demographic data sets than matrix population models: a case study of two perennial herbs

1. Matrix population models are widely used to describe population dynamics, conduct population viability analyses and derive management recommendations for plant populations. For endangered or invasive species, management decisions are often based on small demographic data sets. Hence, there is a need for population models which accurately assess population performance from such small data sets.
2. We used demographic data on two perennial herbs with different life histories to compare the accuracy and precision of the traditional matrix population model and the recently developed integral projection model (IPM) in relation to the amount of data.
3. For large data sets both matrix models and IPMs produced identical estimates of population growth rate (λ). However, for small data sets containing fewer than 300 individuals, IPMs often produced smaller bias and variance for λ than matrix models despite different matrix structures and sampling techniques used to construct the matrix population models.
4. Synthesis and applications . Our results suggest that the smaller bias and variance of λ estimates make IPMs preferable to matrix population models for small demographic data sets with a few hundred individuals. These results are likely to be applicable to a wide range of herbaceous, perennial plant species where demographic fate can be modelled as a function of a continuous state variable such as size. We recommend the use of IPMs to assess population performance and management strategies particularly for endangered or invasive perennial herbs where little demographic data are available.     

Is reversing the decline of Asian elephants in North American zoos possible? An individual‐based modeling approach

Demographic models are important tools for assessing population status, diagnosing potential causes of population decline, and comparing management strategies that might change population trajectory. The population of Asian elephants (Elephas maximus) maintained in North American zoos has been declining for the past decade, and Wiese ([2000] Zoo. Biol. 19:299–309) predicted a continued decline in the population using an age‐based matrix model. We developed an individual‐based model to further explore the demographic issues of the population. Our model allowed us to quantitatively evaluate the prospects for slowing or reversing the decline given the potential management strategies of improving reproduction, reducing infant mortality, altering birth sex ratio, and recruiting additional individuals from outside the population. Our simulations showed that if current demographic trends continued, the population would continue to decline at 2%/year. It was possible to create sustainable simulations, but these required a large increase in the annual number of births produced. Increasing reproduction was the most effective strategy to slow the decline, whereas other management strategies had the most impact when combined with increases in reproduction. Almost all simulations resulted in large changes in population structure, with increases in the male population and decreases in the female population. Given the population's demographic issues, it will be difficult to either increase the population substantially or sustain it at its current size. Zoo Biol 25:201–218, 2006. © 2005 Wiley‐Liss, Inc.     

Empirical Modelling of the Population Dynamics of a Small Population of the Threespine Stickleback, <Emphasis Type="Italic">Gasterosteus aculeatus</Emphasis>

Synopsis We estimated the abundance of a small population of threespine stickleback, Gasterosteus aculeatus, by mark-recapture over a 21 year period. Length-frequency analysis showed that the population in October consisted almost entirely of young-of-the-year. The per capita annual rate of increase was inversely related to abundance in October. Time series analysis suggested the presence of a cycle of abundance with a period of about 6 years. There was a significant inverse relationship between abundance in year t and in year t + 3. A simple, empirical, deterministic model based on this inverse relationship and run for 100 years predicted that population abundance showed damped oscillations leading to a stable abundance. When a stochastic component was added to the model, seven of 10 runs included a component with a period of about 6 years. These simulations suggest that the dynamics of this population are driven by an interaction between a deterministic (density-dependent) component and a stochastic component. We compare these results with time series of abundance of threespine stickleback obtained from the Thames Estuary in south-east England and Loch Lomond in Scotland.     

濒危植物沉水樟的种群生命表和谱分析

将林木依胸径大小分级,以林木径级结构代表年龄结构。采用分段匀滑技术,编制沉水樟种群特定时间生命表,绘制死亡率曲线、危险率曲线及存活曲线,分析沉水樟种群动态趋势。结果表明：沉水樟种群的存活曲线趋于Deevey-Ⅲ型,幼苗和中树稀缺是导致沉水樟濒危的重要原因。沉水樟种群天然更新过程的动态是通过沉水樟不同龄级的株数分布波动而表现的,种群动态的谱分析表明沉水樟种群动态除受基波的影响外,还显示出明显的小周期波动,在11龄级这一小周期波动与沉水樟高生长有关,在15龄级这一小周期的波动可能与沉水樟的生理特性有关。     

Sailing through the Late Pleistocene: unusual historical demography of an East Asian endemic, the Chinese Hwamei (Leucodioptron canorum canorum), during the last glacial period

Pleistocene climate fluctuations shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Late Pleistocene for East Asia, a region of great topographical complexity and presumably milder historical climate, remains poorly understood. We analysed 3.86 kb of the mitochondrial genome of 186 Chinese Hwamei birds, Leucodioptron canorum canorum , and found that contrary to the conventional expectation of population decline during cold periods (stadials), the demographic history of this species shows continuous population growth since the penultimate glacial period (about 170 000 years ago). Refugia were identified in the south, coastal regions, and northern inland areas, implying that topographic complexity played a substantial role in providing suitable habitats for the Chinese Hwamei during cold periods. Intermittent gene flow between these refugia during the warmer periods (interstadials) might have resulted in a large effective population of this bird through the last glacial period.     

From climate change to population change: the need to consider annual life cycles

Detailed studies of organisms' life cycles are important for understanding population response to climate change. However, in general one cannot make strong inference about the overall population response from such studies, unless the full annual cycle of the species in question is covered. Here, we present a theoretical framework for the understanding of population response to climate change. Owing to the combined effects of demography, intraspecific feedback, and a possible use of environmental cues, environmentally induced changes in survival and/or reproduction do not necessarily lead to a straightforward change in population size. This framework can guide our thinking about how abiotic conditions work their way to the population level. More specifically, it can help us to identify mechanisms that need to be examined when predicting population change in response to expected climate change.     

Population cycles in microtines: The senescence hypothesis

Summary The cause of population cycles in microtines (voles and lemmings) remains an enigma. I propose a new solution to this problem based on a crucial feature of microtine biology, shifts in age structure, that has been ignored until now. Empirical evidence indicates that age structure must shift markedly towards older animals during declines because of three characteristics of the previous peak year: a shortened breeding season, total replacement of the breeding population from peak to decline and density-dependent social inhibition of maturation of young. Declines become inevitable as populations composed of older animals survive and reproduce poorly because of the effects of senescence, possibly interacting with the experiences of peak density and I present both theoretical and empirical evidence for this hypothesis. Although a variety of physiological systems deteriorate with aging, I focus on a crucial one — the inability of older animals to effectively maintain homeostasis in the face of environmental challenges because of a progressive deterioration in the endocrine feedback mechanisms involved in the hippocampal—hypothalamic—pituitary—adrenal axis. Microtine populations will not exhibit cycles where age structure shifts are prevented owing to extrinsic factors such as intense predation. Six testable predictions are made that can falsify this hypothesis.     

Is climate change causing the range contraction of Cape Rock-jumpers (Chaetops frenatus)?

Species distribution models often suggest strong links between climate and species' distribution boundaries and project large distribution shifts in response to climate change. However, attributing distribution shifts to climate change requires more than correlative models. One idea is to examine correlates of the processes that cause distribution shifts, namely colonization and local extinction, by using dynamic occupancy models. The Cape Rock-jumper (Chaetops frenatus) has disappeared over most of its distribution where temperatures are the highest. We used dynamic occupancy models to analyse Cape Rock-jumper distribution with respect to climate (mean temperature and precipitation over the warmest annual quarter), vegetation (proportion of natural vegetation, fynbos) and land-use type (protected areas). Detection/non-detection data were collected over two phases of the Southern African Bird Atlas Project (SABAP): 1987–1991 (SABAP1) and 2008–2014 (SABAP2). The model described the contraction of the Cape Rock-jumper's distribution between SABAP1 and SABAP2 well. Occupancy probability during SABAP1 increased with the proportion of fynbos and protected area per grid cell, and decreased with increases in mean temperature and precipitation over the warmest annual quarter. Mean extinction probability increased with mean temperature and precipitation over the warmest annual quarter, although the associated confidence intervals were wide. Nonetheless, our results showed a clear correlation between climate and the distribution boundaries of the Cape Rock-jumper, and in particular, the species' aversion for higher temperatures. The data were less conclusive on whether the observed range contraction was linked to climate change or not. Examining the processes underlying distribution shifts requires large datasets and should lead to a better understanding of the drivers of these shifts.     

Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"?

The giant panda (Ailuropoda melanoleuca) is currently threatened by habitat loss, fragmentation, and human persecution. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an "evolutionary dead end," destined for deterministic extinction in the modern world. Here we examine this perception by a comprehensive investigation of its genetic diversity, population structure, and demographic history across its geographic range. We present analysis of 655 base pairs of mitochondrial (mt) control region (CR) DNA and 10 microsatellite loci for samples from its 5 extant mountain populations (Qinling, Minshan, Qionglai, Liangshan, and Lesser Xiangling). Surprisingly, extant populations display average to high levels of CR and microsatellite diversity compared with other bear species. Genetic differentiation among populations was significant in most cases but was markedly higher between Qinling and the other mountain ranges, suggesting, minimally, that the Qinling population should comprise a separate management unit for conservation purposes. Recent demographic inference using microsatellite markers demonstrated a clear genetic signature for population decline starting several thousands years ago or even further back in the past, and being accelerated and enhanced by the expansion of human populations. Importantly, these data suggest that the panda is not a species at an evolutionary "dead end," but in common with other large carnivores, has suffered demographically at the hands of human pressure. Conservation strategies should therefore focus on the restoration and protection of wild habitat and the maintenance of the currently substantial regional genetic diversity, through active management of disconnected populations.     

Comparative density,demography, and ranging behavior of Barbary macaques (Macaca sylvanus) in marginal and prime conifer habitats

A semiisolated study population of 162 Barbary macaques (six groups) inhabiting the Ghomaran fir forests of the Moroccan Rif mountains has a density of 6.73 individuals/km ². The adult sex ratio is 0.725, and immatures comprise 46.9% of the population. Births are seasonal, occurring from April to June, and the adult female birth rate is 0.58 per annum. Mortality appears relatively low in all age classes until old age. Group size ranges from 12 to 59 individuals, with a median value of 24. Home-range sizes vary between 3 and 9 km², with a mean of 7.2 km². Home-range overlap is approximately 80%. On the basis of macaque density, conifer density, and herding competition from domestic animals, the Ghomaran environment can be considered “marginal” compared to the Moyen Atlas. Despite the marginal habitat of the Ghomaran population, it is surprisingly similar in demographic characteristics to a Barbary macaque population in the Moyen Atlas. Two characteristics of the population dynamics in the Ghomara differentiate it from the former. (1) The mean home range is five times larger in the Ghomara, roughly inversely proportional to the sixfold decrease in macaque density, confirming Caldecott’s (1986) principle that, in macaque species, range size adjustments are a primary proximate response to poor-quality habitat. (2) Smaller groups in the marginal habitat of the Ghomara appear to have better rates of growth than small groups in prime habitat. This may result from an overall decreased home-range defensibility in marginal habitat (larger home ranges), resulting in an ecological and demographic release of small groups from the levels of intergroup competition they would normally experience in prime habitat.     

Population modelling of Gelidium sesquipedale (Rhodophyta, Gelidiales)

A matrix population model of Gelidium sesquipedale, a commercial agarophyte from the Northeast Atlantic, was developed based on demographic data obtained during two years in a commercial stand of Cape Espichel, Portugal. G. sesquipedale individuals were classified into categories such as life cycle phase, spores, juveniles and adult frond size, because the species vital rates, fecundity, fertility, survival, growth and breakage depend on them. We also exemplify the use of a user-friendly modelling software, Stella, to develop a structured-population model. This is the first time this software has been used to model the demography of seaweed populations. The Stella model developed here behaved very similarly to the matrix model, because of its particular construction, which causes the forcing functions to be discrete rather than continuous. The relative importance of spore recruitment and vegetative growth of new fronds in both population growth and population structure was investigated. Elasticity analysis suggests that vegetative recruitment is the most important demographic parameter controlling population growth together with survival and transitions between juveniles (1–6 cm fronds) and class 1 fronds (6–9 cm fronds). On the other hand, sexual reproduction may, by itself, efficiently control the relative proportion of gametophytes and tetrasporophytes in the population, even though its contribution to recruitment is extremely small. A 40% difference in the growth rates of gametophyte and tetrasporophyte submatrices resulted from natural differences in spore recruitment rates. This revised version was published online in June 2006 with corrections to the Cover Date.     

Pitfalls to avoid in nonlinear perturbation analysis of structured population models

Despite the ubiquity of nonlinear functional relationships in nature we tend to characterize mechanisms in science using more tractable linear functions. In demographic modeling, transfer function analysis is used to calculate the nonlinear response of population growth rate to a theoretical perturbation of one or more matrix elements. This elegant approach is not yet popular in ecology. Inconveniently, using transfer function without care can produce erroneous results without warning. We used a large matrix projection model database to explore the potential pitfalls to be avoided in using transfer function analysis. We asked a fundamental population control question, what matrix element perturbation would be needed to reach a minimum goal of replacement population growth? We then tracked instances in which transfer function yields erroneous output and explored these cases in detail to measure how frequently it occurs. We developed a phylogenetically-corrected mixed effects logistic regression model in a Bayesian framework to test the effect of species traits and the identity of matrix elements on the probability that transfer function yields errors. We found in 16% of cases the transfer function yielded erroneous outcomes. These errors were more likely when perturbing demographic stasis and also for shrubs more than any other life form. Errors in transfer function analysis were often due to perturbing matrix elements beyond their biological limits, even when this is still mathematically correct. To use transfer function analysis properly in demographic modeling and avoid erroneous results, input must be carefully selected to include only a biologically admissible set of perturbations.