ResearchPad - population-growth https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Sustainability management of short-lived freshwater fish in human-altered ecosystems should focus on adult survival]]> https://www.researchpad.co/article/elastic_article_7859 Fish populations globally are susceptible to endangerment through exploitation and habitat loss. We present theoretical simulations to explore how reduced adult survival (age truncation) might affect short-lived freshwater fish species in human-altered contemporary environments. Our simulations evaluate two hypothetical "average fish" and five example fish species of age 1 or age 2 maturity. From a population equilibrium baseline representing a natural, unaltered environment we impose systematic reductions in adult survival and quantify how age truncation affects the causes of variation in population growth rate. We estimate the relative contributions to population growth rate arising from simulated temporal variation in age-specific vital rates and population structure. At equilibrium and irrespective of example species, population structure (first adult age class) and survival probability of the first two adult age classes are the most important determinants of population growth. As adult survival decreases, the first reproductive age class becomes increasingly important to variation in population growth. All simulated examples show the same general pattern of change with age truncation as known for exploited, longer-lived fish species in marine and freshwater environments. This implies age truncation is a general potential concern for fish biodiversity across life history strategies and ecosystems. Managers of short-lived, freshwater fishes in contemporary environments often focus on supporting reproduction to ensure population persistence. However, a strong focus on water management to support reproduction may reduce adult survival. Sustainability management needs a focus on mitigating adult mortality in human-altered ecosystems. A watershed spatial extent embracing land and water uses may be necessary to identify and mitigate causes of age truncation in freshwater species. Achieving higher adult survival will require paradigm transformations in society and government about water management priorities.

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<![CDATA[Time-lapse imaging of HeLa spheroids in soft agar culture provides virtual inner proliferative activity]]> https://www.researchpad.co/article/Nceafa1bd-f75c-4e08-9c15-587118f668b1

Cancer is a complex disease caused by multiple types of interactions. To simplify and normalize the assessment of drug effects, spheroid microenvironments have been utilized. Research models that involve agent measurement with the examination of clonogenic survival by monitoring culture process with image analysis have been developed for spheroid-based screening. Meanwhile, computer simulations using various models have enabled better predictions for phenomena in cancer. However, user-based parameters that are specific to a researcher’s own experimental conditions must be inputted. In order to bridge the gap between experimental and simulated conditions, we have developed an in silico analysis method with virtual three-dimensional embodiment computed using the researcher’s own samples. The present work focused on HeLa spheroid growth in soft agar culture, with spheroids being modeled in silico based on time-lapse images capturing spheroid growth. The spheroids in silico were optimized by adjusting the growth curves to those obtained from time-lapse images of spheroids and were then assigned virtual inner proliferative activity by using generations assigned to each cellular particle. The ratio and distribution of the virtual inner proliferative activities were confirmed to be similar to the proliferation zone ratio and histochemical profiles of HeLa spheroids, which were also consistent with those identified in an earlier study. We validated that time-lapse images of HeLa spheroids provided virtual inner proliferative activity for spheroids in vitro. The present work has achieved the first step toward an in silico analysis method using computational simulation based on a researcher’s own samples, helping to bridge the gap between experiment and simulation.

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<![CDATA[Environment-dependent pleiotropic effects of mutations on the maximum growth rate r and carrying capacity K of population growth]]> https://www.researchpad.co/article/5c57e656d5eed0c484ef2c2a

Maximum growth rate per individual (r) and carrying capacity (K) are key life-history traits that together characterize the density-dependent population growth and therefore are crucial parameters of many ecological and evolutionary theories such as r/K selection. Although r and K are generally thought to correlate inversely, both r/K tradeoffs and trade-ups have been observed. Nonetheless, neither the conditions under which each of these relationships occur nor the causes of these relationships are fully understood. Here, we address these questions using yeast as a model system. We estimated r and K using the growth curves of over 7,000 yeast recombinants in nine environments and found that the rK correlation among genotypes changes from 0.53 to −0.52 with the rise of environment quality, measured by the mean r of all genotypes in the environment. We respectively mapped quantitative trait loci (QTLs) for r and K in each environment. Many QTLs simultaneously influence r and K, but the directions of their effects are environment dependent such that QTLs tend to show concordant effects on the two traits in poor environments but antagonistic effects in rich environments. We propose that these contrasting trends are generated by the relative impacts of two factors—the tradeoff between the speed and efficiency of ATP production and the energetic cost of cell maintenance relative to reproduction—and demonstrate an agreement between model predictions and empirical observations. These results reveal and explain the complex environment dependency of the rK relationship, which bears on many ecological and evolutionary phenomena and has biomedical implications.

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<![CDATA[Genetic and environmental influences on the size-fecundity relationship in Aedes albopictus (Diptera: Culicidae): Impacts on population growth estimates?]]> https://www.researchpad.co/article/5b6da1be463d7e4dccc5faf3

Population growth models are integral to ecological studies by providing estimates of population performance across space and time. Several models have been developed that estimate population growth through correlates of demographic traits, as measuring each parameter of the model can be prohibitive in experimental studies. Since differences in female size can accurately reflect changes in fecundity for many taxa, Livdahl and Sugihara developed a population growth index that incorporates size-fecundity relationships as a proxy for fecundity. To investigate the extent to which this model is robust to variation of this proxy, we tested if genetic (source population), temperature and resource treatments affect the size-fecundity relationship in Aedes albopictus (Skuse), the Asian tiger mosquito. We then determined if variation in the size-fecundity relationship alters the population growth estimates, lambda (λ), when applied to Livdahl and Sugihara’s model. We performed 2 laboratory experiments in which we reared cohorts of four different geographic populations of A. albopictus across 5 temperature treatments (18, 21, 25, 18, 31°C) and three resource treatments (low, medium, high larval resources). We determined if the slope of the size-fecundity relationship varied by source population, temperature, or resource; and if variation in this relationship affects lambda (λ) estimates in a competition study between A. albopictus and Culex pipiens (Linnaeus), the northern house mosquito. Temperature treatments significantly affected the size-fecundity relationship, resource level marginally affected the relationship, while source population had no effect. We found positive relationships between size and fecundity when mosquito larvae were reared at high temperatures and low resource levels but the relationship disappeared when mosquitoes were reared at a low temperature or with high levels of resources. The variation in the size-fecundity relationship produced from different temperatures resulted in statistically different lambda (λ) estimates. However, these changes in lambda (λ) did not alter the trends in the population performance across treatments or conclusions of the competition study. This study provides evidence that the population growth model is sensitive to variation in size-fecundity relationships and we recommend biologists apply the most compatible size-fecundity relationship to the models to obtain the most accurate estimates of population performance.

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<![CDATA[A Stochastic Version of the Brass PF Ratio Adjustment of Age-Specific Fertility Schedules]]> https://www.researchpad.co/article/5989daf3ab0ee8fa60bc1fbf

Estimates of age-specific fertility rates based on survey data are known to suffer down-bias associated with incomplete reporting. Previously, William Brass (1964, 1965, 1968) proposed a series of adjustments of such data to reflect more appropriate levels of fertility through comparison with data on children-ever-born by age, a measure of cohort-specific cumulative fertility. His now widely-used Parity/Fertility or PF ratio method makes a number of strong assumptions, which have been the focus of an extended discussion in the literature on indirect estimation. However, while it is clear that the measures used in making adjusted age-specific fertility estimates with this method are captured with statistical uncertainty, little discussion of the nature of this uncertainty around PF-ratio based estimates of fertility has been entertained in the literature. Since both age-specific risk of childbearing and cumulative parity (children ever born) are measured with statistical uncertainty, an unknown credibility interval must surround every PF ratio-based estimate. Using the standard approach, this is unknown, limiting the ability to make statistical comparisons of fertility between groups or to understand stochasticity in population dynamics. This paper makes use of approaches applied to similar problems in engineering, the natural sciences, and decision analysis—often discussed under the title of uncertainty analysis or stochastic modeling—to characterize this uncertainty and to present a new method for making PF ratio-based fertility estimates with 95 percent uncertainty intervals. The implications for demographic analysis, between-group comparisons of fertility, and the field of statistical demography are explored.

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<![CDATA[Mate-Finding as an Overlooked Critical Determinant of Dispersal Variation in Sexually-Reproducing Animals]]> https://www.researchpad.co/article/5989da9eab0ee8fa60ba4d61

Dispersal is a critically important process in ecology, but robust predictive models of animal dispersal remain elusive. We identify a potentially ubiquitous component of variation in animal dispersal that has been largely overlooked until now: the influence of mate encounters on settlement probability. We use an individual-based model to simulate dispersal in sexually-reproducing organisms that follow a simple set of movement rules based on conspecific encounters, within an environment lacking spatial habitat heterogeneity. We show that dispersal distances vary dramatically with fluctuations in population density in such a model, even in the absence of variation in dispersive traits between individuals. In a simple random-walk model with promiscuous mating, dispersal distributions become increasingly ‘fat-tailed’ at low population densities due to the increasing scarcity of mates. Similar variation arises in models incorporating territoriality. In a model with polygynous mating, we show that patterns of sex-biased dispersal can even be reversed across a gradient of population density, despite underlying dispersal mechanisms remaining unchanged. We show that some widespread dispersal patterns found in nature (e.g. fat tailed distributions) can arise as a result of demographic variability in the absence of heterogeneity in dispersive traits across the population. This implies that models in which individual dispersal distances are considered to be fixed traits might be unrealistic, as dispersal distances vary widely under a single dispersal mechanism when settlement is influenced by mate encounters. Mechanistic models offer a promising means of advancing our understanding of dispersal in sexually-reproducing organisms.

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<![CDATA[Genetic Structure and Inferences on Potential Source Areas for Bactrocera dorsalis (Hendel) Based on Mitochondrial and Microsatellite Markers]]> https://www.researchpad.co/article/5989d9f5ab0ee8fa60b6fc05

Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan.

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<![CDATA[Cellular Growth Arrest and Persistence from Enzyme Saturation]]> https://www.researchpad.co/article/5989dafcab0ee8fa60bc518d

Metabolic efficiency depends on the balance between supply and demand of metabolites, which is sensitive to environmental and physiological fluctuations, or noise, causing shortages or surpluses in the metabolic pipeline. How cells can reliably optimize biomass production in the presence of metabolic fluctuations is a fundamental question that has not been fully answered. Here we use mathematical models to predict that enzyme saturation creates distinct regimes of cellular growth, including a phase of growth arrest resulting from toxicity of the metabolic process. Noise can drive entry of single cells into growth arrest while a fast-growing majority sustains the population. We confirmed these predictions by measuring the growth dynamics of Escherichia coli utilizing lactose as a sole carbon source. The predicted heterogeneous growth emerged at high lactose concentrations, and was associated with cell death and production of antibiotic-tolerant persister cells. These results suggest how metabolic networks may balance costs and benefits, with important implications for drug tolerance.

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<![CDATA[Comparing multi-criteria decision analysis and integrated assessment to support long-term water supply planning]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf617

We compare the use of multi-criteria decision analysis (MCDA)–or more precisely, models used in multi-attribute value theory (MAVT)–to integrated assessment (IA) models for supporting long-term water supply planning in a small town case study in Switzerland. They are used to evaluate thirteen system scale water supply alternatives in four future scenarios regarding forty-four objectives, covering technical, social, environmental, and economic aspects. The alternatives encompass both conventional and unconventional solutions and differ regarding technical, spatial and organizational characteristics. This paper focuses on the impact assessment and final evaluation step of the structured MCDA decision support process. We analyze the performance of the alternatives for ten stakeholders. We demonstrate the implications of model assumptions by comparing two IA and three MAVT evaluation model layouts of different complexity. For this comparison, we focus on the validity (ranking stability), desirability (value), and distinguishability (value range) of the alternatives given the five model layouts. These layouts exclude or include stakeholder preferences and uncertainties. Even though all five led us to identify the same best alternatives, they did not produce identical rankings. We found that the MAVT-type models provide higher distinguishability and a more robust basis for discussion than the IA-type models. The needed complexity of the model, however, should be determined based on the intended use of the model within the decision support process. The best-performing alternatives had consistently strong performance for all stakeholders and future scenarios, whereas the current water supply system was outperformed in all evaluation layouts. The best-performing alternatives comprise proactive pipe rehabilitation, adapted firefighting provisions, and decentralized water storage and/or treatment. We present recommendations for possible ways of improving water supply planning in the case study and beyond.

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<![CDATA[Shewanella oneidensis MR-1-Induced Fe(III) Reduction Facilitates Roxarsone Transformation]]> https://www.researchpad.co/article/5989da1bab0ee8fa60b7ce91

Although microbial activity and associated iron (oxy)hydroxides are known in general to affect the environmental dynamics of 4-hydroxy-3-nitrobenzenearsonic acid (roxarsone), the mechanistic understanding of the underlying biophysico-chemical processes remains unclear due to limited experimental information. We studied how Shewanella oneidensis MR-1 –a widely distributed metal-reducing bacterium, in the presence of dissolved Fe(III), affects roxarsone transformations and biogeochemical cycling in a model aqueous system. The results showed that the MR-1 strain was able to anaerobically use roxarsone as a terminal electron acceptor and to convert it to a single product, 3-amino-4-hydroxybenzene arsonic acid (AHBAA). The presence of Fe(III) stimulated roxarsone transformation via MR-1-induced Fe(III) reduction, whereby the resulting Fe(II) acted as an efficient reductant for roxarsone transformation. In addition, the subsequent secondary Fe(III)/Fe(II) mineralization created conditions for adsorption of organoarsenic compounds to the yielded precipitates and thereby led to arsenic immobilization. The study provided direct evidence of Shewanella oneidensis MR-1-induced direct and Fe(II)-associated roxarsone transformation. Quantitative estimations revealed a candidate mechanism for the early-stage environmental dynamics of roxarsone in nature, which is essential for understanding the environmental dynamics of roxarsone and successful risk assessment.

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<![CDATA[Social and Demographic Effects of Anthropogenic Mortality: A Test of the Compensatory Mortality Hypothesis in the Red Wolf]]> https://www.researchpad.co/article/5989da4cab0ee8fa60b8cf70

Whether anthropogenic mortality is additive or compensatory to natural mortality in animal populations has long been a question of theoretical and practical importance. Theoretically, under density-dependent conditions populations compensate for anthropogenic mortality through decreases in natural mortality and/or increases in productivity, but recent studies of large carnivores suggest that anthropogenic mortality can be fully additive to natural mortality and thereby constrain annual survival and population growth rate. Nevertheless, mechanisms underlying either compensatory or additive effects continue to be poorly understood. Using long-term data on a reintroduced population of the red wolf, we tested for evidence of additive vs. compensatory effects of anthropogenic mortality on annual survival and population growth rates, and the preservation and reproductive success of breeding pairs. We found that anthropogenic mortality had a strong additive effect on annual survival and population growth rate at low population density, though there was evidence for compensation in population growth at high density. When involving the death of a breeder, anthropogenic mortality was also additive to natural rates of breeding pair dissolution, resulting in a net decrease in the annual preservation of existing breeding pairs. However, though the disbanding of a pack following death of a breeder resulted in fewer recruits per litter relative to stable packs, there was no relationship between natural rates of pair dissolution and population growth rate at either high or low density. Thus we propose that short-term additive effects of anthropogenic mortality on population growth in the red wolf population at low density were primarily a result of direct mortality of adults rather than indirect socially-mediated effects resulting in reduced recruitment. Finally, we also demonstrate that per capita recruitment and the proportion of adults that became reproductive declined steeply with increasing population density, suggesting that there is potential for density-dependent compensation of anthropogenically-mediated population regulation.

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<![CDATA[Child malnutrition in sub-Saharan Africa: A meta-analysis of demographic and health surveys (2006-2016)]]> https://www.researchpad.co/article/5989db5aab0ee8fa60bdf71a

Background

Sub-Saharan Africa has one of the highest levels of child malnutrition globally. Therefore, a critical look at the distribution of malnutrition within its sub-regions is required to identify the worst affected areas. This study provides a meta-analysis of the prevalence of malnutrition indicators (stunting, wasting and underweight) within four sub-regions of sub-Saharan Africa.

Methods

Cross-sectional data from the most recent Demographic and Health Surveys (2006–2016) of 32 countries in sub-Saharan Africa were used. The countries were grouped into four sub-regions (East Africa, West Africa, Southern Africa and Central Africa), and a meta-analysis was conducted to estimate the prevalence of each malnutrition indicator within each of the sub-regions. Significant heterogeneity was detected among the various surveys (I2 >50%), hence a random effect model was used, and sensitivity analysis was performed, to examine the effects of outliers. Stunting was defined as HAZ<-2; wasting as WHZ<-2 and underweight as WAZ<-2.

Results

Stunting was highest in Burundi (57.7%) and Malawi (47.1%) in East Africa; Niger (43.9%), Mali (38.3%), Sierra Leone (37.9%) and Nigeria (36.8%) in West Africa; Democratic Republic of Congo (42.7%) and Chad (39.9%) in Central Africa. Wasting was highest in Niger (18.0%), Burkina Faso (15.50%) and Mali (12.7%) in West Africa; Comoros (11.1%) and Ethiopia (8.70%) in East Africa; Namibia (6.2%) in Southern Africa; Chad (13.0%) and Sao Tome & Principle (10.5%) in Central Africa. Underweight was highest in Burundi (28.8%) and Ethiopia (25.2%) in East Africa; Niger (36.4%), Nigeria (28.7%), Burkina Faso (25.7%), Mali (25.0%) in West Africa; and Chad (28.8%) in Central Africa.

Conclusion

The prevalence of malnutrition was highest within countries in East Africa and West Africa compared to the WHO Millennium development goals target for 2015. Appropriate nutrition interventions need to be prioritised in East Africa and West Africa if sub-Saharan Africa is to meet the WHO global nutrition target of improving maternal, infant and young child nutrition by 2025.

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<![CDATA[Massive Nest-Box Supplementation Boosts Fecundity, Survival and Even Immigration without Altering Mating and Reproductive Behaviour in a Rapidly Recovered Bird Population]]> https://www.researchpad.co/article/5989dac1ab0ee8fa60bb0e28

Habitat restoration measures may result in artificially high breeding density, for instance when nest-boxes saturate the environment, which can negatively impact species' demography. Potential risks include changes in mating and reproductive behaviour such as increased extra-pair paternity, conspecific brood parasitism, and polygyny. Under particular cicumstances, these mechanisms may disrupt reproduction, with populations dragged into an extinction vortex. With the use of nuclear microsatellite markers, we investigated the occurrence of these potentially negative effects in a recovered population of a rare secondary cavity-nesting farmland bird of Central Europe, the hoopoe (Upupa epops). High intensity farming in the study area has resulted in a total eradication of cavity trees, depriving hoopoes from breeding sites. An intensive nest-box campaign rectified this problem, resulting in a spectacular population recovery within a few years only. There was some concern, however, that the new, high artificially-induced breeding density might alter hoopoe mating and reproductive behaviour. As the species underwent a serious demographic bottleneck in the 1970–1990s, we also used the microsatellite markers to reconstitute the demo-genetic history of the population, looking in particular for signs of genetic erosion. We found i) a low occurrence of extra-pair paternity, polygyny and conspecific brood parasitism, ii) a high level of neutral genetic diversity (mean number of alleles and expected heterozygosity per locus: 13.8 and 83%, respectively) and, iii) evidence for genetic connectivity through recent immigration of individuals from well differentiated populations. The recent increase in breeding density did thus not induce so far any noticeable detrimental changes in mating and reproductive behaviour. The demographic bottleneck undergone by the population in the 1970s-1990s was furthermore not accompanied by any significant drop in neutral genetic diversity. Finally, genetic data converged with a concomitant demographic study to evidence that immigration strongly contributed to local population recovery.

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<![CDATA[Unwanted Pregnancy and Associated Factors among Pregnant Married Women in Hosanna Town, Southern Ethiopia]]> https://www.researchpad.co/article/5989daf1ab0ee8fa60bc161b

Of an estimated 210 million pregnancies that occur in the world each year, 38% are unplanned, out of which 22% end in abortion. In Ethiopia, the estimates of unintended pregnancy indicate that it is one of the major reproductive health problems with all its adverse outcomes. Women risk their lives in by seeking illegal abortions following unintended pregnancies. Thus, this study aims to determine the prevalence of unintended pregnancy and associated factors among pregnant married women residing in Hossana, Southern Ethiopia. A community-based cross-sectional study involving both qualitative and quantitative data collection methods was carried out in Hossana from April 02 to 15, 2011. 385 pregnant married women randomly selected from the census were included for the quantitative data and took in-depth interviews for the qualitative. Descriptive, binary and multiple logistic regression analyses were performed using SPSS version 16. Out of the total pregnancies, 131 (34%) were unintended and 254 (66%) were reported to be intended. A history of previous unintended pregnancy, the husband not wanting to limit family size, a desire for at least two children, the number of pregnancy 3–4 and parity of 5 and above were factors significantly associated with unintended pregnancy. With over one third of pregnancies unintended, having a previous unintended pregnancy, the number of previous pregnancies, and husbands’ disagreement over family size, and the desired number of children are factors that reproductive health programs should aim to focus on to reduce unintended pregnancy.

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<![CDATA[Living on the Edge: Assessing the Extinction Risk of Critically Endangered Bonelli’s Eagle in Italy]]> https://www.researchpad.co/article/5989dae9ab0ee8fa60bbe920

Background

The population of Bonelli’s eagle (Aquila fasciata) has declined drastically throughout its European range due to habitat degradation and unnatural elevated mortality. There are less than 1500 breeding pairs accounted for in Europe, and the species is currently catalogued as Critically Endangered in Italy, where the 22 territories of Sicily, represent nearly 95% of the entire Italian population. However, despite national and European conservation concerns, the species currently lacks a specific conservation plan, and no previous attempts to estimate the risk of extinction have been made.

Methodology/Principal Findings

We incorporated the most updated demographic information available to assess the extinction risk of endangered Bonelli’s eagle in Italy through a Population Viability Analysis. Using perturbation analyses (sensitivity and elasticity), and a combination of demographic data obtained from an assortment of independent methods, we evaluated which demographic parameters have more influence on the population’s fate. We also simulated different scenarios to explore the effects of possible management actions. Our results showed that under the current conditions, Bonelli’s eagle is expected to become extinct in Italy in less than 50 years. Stand-alone juvenile mortality was the most critical demographic parameter with the strongest influence on population persistence with respect to other demographic parameters. Measures aimed at either decreasing juvenile mortality, adult mortality or decreasing both juvenile and adult mortality resulted in equivalent net positive effects on population persistence (population growth rate λ>1). In contrast, changes aimed at increasing breeding success had limited positive effects on demographic trends.

Conclusions/Significance

Our PVA provides essential information to direct the decision-making process and exposes gaps in our previous knowledge. To ensure the long-term persistence of the species in Italy, measures are urgently needed to decrease both adult mortality due to poaching and juvenile mortality due to nest plundering, the top ranking mortality causes.

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<![CDATA[Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data]]> https://www.researchpad.co/article/5989db53ab0ee8fa60bdce55

Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness landscapes of arbitrary phenotypic traits, using genealogical data in the form of population lineage trees which can include phenotypic data of various kinds. Our inference methodology for fitness landscapes determines how reproductivity is correlated to cellular phenotypes, and provides a natural generalization of bulk growth rate measures for single-cell histories. Using this technique, we quantify the strength of selection acting on different cellular phenotypic traits within populations, which allows us to determine whether a change in population growth is caused by individual cells’ response, selection within a population, or by a mixture of these two processes. By applying these methods to single-cell time-lapse data of growing bacterial populations that express a resistance-conferring protein under antibiotic stress, we show how the distributions, fitness landscapes, and selection strength of single-cell phenotypes are affected by the drug. Our work provides a unified and practical framework for quantitative measurements of fitness landscapes and selection strength for any statistical quantities definable on lineages, and thus elucidates the adaptive significance of phenotypic states in time series data. The method is applicable in diverse fields, from single cell biology to stem cell differentiation and viral evolution.

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<![CDATA[Biodiversity Areas under Threat: Overlap of Climate Change and Population Pressures on the World’s Biodiversity Priorities]]> https://www.researchpad.co/article/5989db4fab0ee8fa60bdba2c

Humans and the ecosystem services they depend on are threatened by climate change. Places with high or growing human population as well as increasing climate variability, have a reduced ability to provide ecosystem services just as the need for these services is most critical. A spiral of vulnerability and ecosystem degradation often ensues in such places. We apply different global conservation schemes as proxies to examine the spatial relation between wet season precipitation, population change over three decades, and natural resource conservation. We pose two research questions: 1) Where are biodiversity and ecosystem services vulnerable to the combined effects of climate change and population growth? 2) Where are human populations vulnerable to degraded ecosystem services? Results suggest that globally only about 20% of the area between 50 degrees latitude North and South has experienced significant change–largely wetting–in wet season precipitation. Approximately 40% of rangelands and 30% of rainfed agriculture lands have experienced significant precipitation changes, with important implications for food security. Over recent decades a number of critical conservation areas experienced high population growth concurrent with significant wetting or drying (e.g. the Horn of Africa, Himalaya, Western Ghats, and Sri Lanka), posing challenges not only for human adaptation but also to the protection and sustenance of biodiversity and ecosystem services. Identifying areas of climate and population risk and their overlap with conservation priorities can help to target activities and resources that promote biodiversity and ecosystem services while improving human well-being.

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<![CDATA[Temperature-dependent phenology of Plutella xylostella (Lepidoptera: Plutellidae): Simulation and visualization of current and future distributions along the Eastern Afromontane]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbe58

There is a scarcity of laboratory and field-based results showing the movement of the diamondback moth (DBM) Plutella xylostella (L.) across a spatial scale. We studied the population growth of the diamondback moth (DBM) Plutella xylostella (L.) under six constant temperatures, to understand and predict population changes along altitudinal gradients and under climate change scenarios. Non-linear functions were fitted to continuously model DBM development, mortality, longevity and oviposition. We compiled the best-fitted functions for each life stage to yield a phenology model, which we stochastically simulated to estimate the life table parameters. Three temperature-dependent indices (establishment, generation and activity) were derived from a logistic population growth model and then coupled to collected current (2013) and downscaled temperature data from AFRICLIM (2055) for geospatial mapping. To measure and predict the impacts of temperature change on the pest’s biology, we mapped the indices along the altitudinal gradients of Mt. Kilimanjaro (Tanzania) and Taita Hills (Kenya) and assessed the differences between 2013 and 2055 climate scenarios. The optimal temperatures for development of DBM were 32.5, 33.5 and 33°C for eggs, larvae and pupae, respectively. Mortality rates increased due to extreme temperatures to 53.3, 70.0 and 52.4% for egg, larvae and pupae, respectively. The net reproduction rate reached a peak of 87.4 female offspring/female/generation at 20°C. Spatial simulations indicated that survival and establishment of DBM increased with a decrease in temperature, from low to high altitude. However, we observed a higher number of DBM generations at low altitude. The model predicted DBM population growth reduction in the low and medium altitudes by 2055. At higher altitude, it predicted an increase in the level of suitability for establishment with a decrease in the number of generations per year. If climate change occurs as per the selected scenario, DBM infestation may reduce in the selected region. The study highlights the need to validate these predictions with other interacting factors such as cropping practices, host plants and natural enemies.

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<![CDATA[Population Dynamics of Aphids on Cereals: Digging in the Time-Series Data to Reveal Population Regulation Caused by Temperature]]> https://www.researchpad.co/article/5989da35ab0ee8fa60b86085

Aphid populations show periodic fluctuations and many causes are attributed to their dynamic. We investigated the regulation by temperature of the aphid populations composed of Metopolophium dirhodum, Sitobion avenae, and Rhopalosiphum padi on winter wheat using a 24 years long time series data. We computed the sum of daily temperatures above 5°C, the threshold temperature for aphid development, and the sum of daily temperatures within the [0(threshold for wheat development),5] °C interval. Applying Generalised Additive Model framework we tested influences of temperature history expressed via degree days before the start of the aphid immigration on the length of their occurrence. We aimed to estimate the magnitude and direction of this influence, and how far to the past before the start of the aphid season the temperature effect goes and then identify processes responsible for the effect. We fitted four models that differed in the way of correcting for abundance in the previous year and in specification of temperature effects. Abundance in the previous year did not affect the length of period of aphid population growth on wheat. The temperature effect on the period length increased up to 123 days before the start of the current season, i.e. when wheat completed vernalization. Increased sum of daily temperatures above 5°C and the sum of daily temperatures within the [0,5] °C interval both shortened the length of period of aphid population growth. Stronger effect of the latter suggests that wheat can escape from aphid attacks if during winter temperatures range from 0 to 5°C. The temperature influence was not homogeneous in time. The strongest effect of past temperature was about 50 to 80 and 90 to 110 days before the beginning of the current aphid season indicating important role of termination of aphid egg dormancy and egg hatching.

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<![CDATA[Population Growth Rates of Reef Sharks with and without Fishing on the Great Barrier Reef: Robust Estimation with Multiple Models]]> https://www.researchpad.co/article/5989dad2ab0ee8fa60bb68b2

Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple assessment methods, to obtain robust estimates of population trends in species threatened by overfishing.

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