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230 results for “population decline”
Data from: Quantifying behavioral changes in territorial animals caused by sudden population declines
Although territorial animals are able to maintain exclusive use of certain regions of space, movement data from neighboring individuals often suggest overlapping home ranges. To explain and unify these two aspects of animal space use, we use recently developed mechanistic models of collective animal movement. We apply our approach to a natural experiment on an urban red fox (Vulpes vulpes) population that underwent a rapid decline in population density due to a sarcoptic mange epizooty. By extracting details of movement and interaction strategies from location data, we show how foxes alter their behavior, taking advantage of sudden population-level changes by acquiring areas vacated due to neighbor mortality, while ensuring territory boundaries remain contiguous. The rate of territory border movement increased eightfold as the population declined and the foxes' response time to neighboring scent reduced by a third. By demonstrating how observed, fluctuating territorial patterns emerge from movements and interactions of individual animals, our results give the first data-validated, mechanistic explanation of the elastic disc hypothesis, proposed nearly 80 years ago.
Data from: Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance
Non-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stochastic processes with stationary increments which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of beta-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://github.com/mrc-ide/skygrowth.
Data from: Estimating national population sizes: methodological challenges and applications illustrated in the common nightingale, a declining songbird in the UK
1. Estimation of national population size can be important for setting conservation priorities but its methodology has received little critical attention. Sites for highly aggregated species are often prioritised if they contain 1% of national or biogeographical populations but the utility of this approach for other species is unclear. 2. To make recommendations for study design, we present methods used to estimate the UK population size of the common nightingale Luscinia megarhynchos. We assess the sensitivity of the population estimate to the analytical method used and identify sites of national importance for this territorial songbird. 3. Survey effort was directed by prior knowledge of the species' distribution and the survey design maximised detectability by focussing on the period of greatest song output. We used three different statistical methods to account for detectability, estimating that 55–65% of the national population was detected during surveys. 4. Birds in areas not known to contain the species accounted for 13–23% of the population estimate. Methods to account for these individuals contributed the greatest uncertainty to the results, due to the difficulty of surveying a very large sample of random sites and consequent need to stratify the sample. 5. The 12 derived estimates ranged between 5094 and 5938 territorial males, with the confidence limits ranging from 4764 to 6534. Site delimitation, using clustering based on nearest-neighbour distances, identified one site clearly of national importance and several others potentially nationally important, depending on the population threshold and clustering distance used. 6. Synthesis and applications. National population estimation is difficult and requires that species-specific variability in detectability and individuals present outside surveyed areas are accurately accounted for through survey design and statistical analysis. Accounting for these sources of error will not always be possible and will hamper efforts to assess true population size and consequently to determine whether sites, however defined, exceed critical thresholds of importance. Resources may be better invested in other activities, for example in generating population trends based on relative indices. The latter are generally easier to produce, potentially more robust and arguably more suitable for many conservation applications.
Data from: Monarch butterfly population decline in North America: identifying the threatening processes
The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids). While climatic factors, principally breeding season temperature, were important determinants of annual variation in abundance, our results indicated strong negative relationships between population size and habitat loss variables, principally glyphosate use, but also weaker negative effects from the loss of overwinter forest and breeding season use of neonicotinoids. Further declines in population size because of glyphosate application are not expected. Thus, if remaining threats to habitat are mitigated we expect climate-induced stochastic variation of the eastern migratory population of monarch butterfly around a relatively stationary population size.
Data from: Phage selection for bacterial cheats leads to population decline
While predators and parasites are known for their effects on bacterial population biology, their impact on the dynamics of bacterial social evolution remains largely unclear. Siderophores are iron-chelating molecules that are key to the survival of certain bacterial species in iron-limited environments, but their production can be subject to cheating by non-producing phenotypes. In a selection experiment conducted over c 20 bacterial generations and involving 140 populations of the pathogenic bacterium Pseudomonas aeruginosa PAO1, we assessed the impact of a lytic phage on competition between siderophore producers and non-producers. We show that the presence of lytic phages favours the non-producing genotype in competition, regardless of whether iron use relies on siderophores. Interestingly, phage pressure resulted in higher siderophore production, which constitutes a cost to the producers and may explain why they were outcompeted by non-producers. At the end of the experiment, however, cheating load reduced the fitness of mixed populations relative to producer monocultures, and only monocultures of producers managed to grow in the presence of phage in situations where siderophores were necessary to access iron. These results suggest that public goods production may be modulated in the presence of natural enemies with consequences for the evolution of social strategies.
Data from: Phenotypic biomarkers of climatic impacts on declining insect populations: a key role for decadal drought, thermal buffering and amplification effects and host plant dynamics
1. Widespread population declines have been reported for diverse Mediterranean butterflies over the last three decades, and have been significantly associated to increased global change impacts. The specific landscape and climatic drivers of these declines remain uncertain for most declining species. 2. Here we analyse whether plastic phenotypic traits of a model butterfly species (Pieris napi) perform as reliable biomarkers of vulnerability to extreme temperature impacts in natural populations, showing contrasting trends in thermally exposed and thermally buffered populations. 3. We also examine whether improved descriptions of thermal exposure of insect populations can be achieved by combining multiple information sources (i.e. integrating measurements of habitat thermal buffering, habitat thermal amplification, host plant transpiration, and experimental assessments of thermal death time (TDT), thermal avoidance behaviour (TAB) and thermally induced trait plasticity). These integrative analyses are conducted in two demographically declining and two non-declining populations of P. napi. 4. The results show that plastic phenotypic traits (butterfly body mass and wing size) are reliable biomarkers of population vulnerability to extreme thermal conditions. Butterfly wing size is strongly reduced only in thermally exposed populations during summer drought periods. Lab rearing of these populations documented reduced wing size due to significant negative effects of increased temperatures affecting larval growth. We conclude that these thermal biomarkers are indicative of the population vulnerability to increasing global warming impacts, showing contrasting trends in thermally exposed and buffered populations. 5. Thermal effects in host plant microsites significantly differ between populations, with stressful thermal conditions only effectively ameliorated in mid-elevation populations. In lowland populations we observe a six-fold reduction in vegetation thermal buffering effects, and larval growth occurs in these populations at significantly higher temperatures. Lowland populations show reduced host plant quality (C/N ratio), reduced leaf transpiration rates and complete aboveground plant senescence during the peak of summer drought. Amplified host plant temperatures are observed in open microsites, reaching thermal thresholds that can affect larval survival. 6. Overall, our results suggest that butterfly population vulnerability to long-term drought periods is associated to multiple co-occurring and interrelated ecological factors, including limited vegetation thermal buffering effects at lowland sites, significant drought impacts on host plant transpiration and amplified leaf surface temperature, as well as reduced leaf quality linked to the seasonal advance of plant phenology. Our results also identify multi-annual summer droughts affecting larval growing periods as a key driver of the recently reported butterfly population declines in the Mediterranean biome.
Data from: Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes
The rate and fitness effects of new mutations have been investigated by mutation accumulation (MA) experiments in which organisms are maintained at a constant minimal population size to facilitate the accumulation of mutations with minimal efficacy of selection. We evolved 35 MA lines of Caenorhabditis elegans in parallel for 409 generations at three population sizes (N = 1, 10, and 100), representing the first spontaneous long-term MA experiment at varying population sizes with corresponding differences in the efficacy of selection. Productivity and survivorship in the N = 1 lines declined by 44% and 12%, respectively. The average effects of deleterious mutations in N = 1 lines are estimated to be 16.4% for productivity and 11.8% for survivorship. Larger populations (N = 10 and 100) did not suffer a significant decline in fitness traits despite a lengthy and sustained regime of consecutive bottlenecks exceeding 400 generations. Together, these results suggest that fitness decline in very small populations is dominated by mutations with large deleterious effects. It is possible that the MA lines at larger population sizes contain a load of cryptic deleterious mutations of small to moderate effects that would be revealed in more challenging environments.
Supplementary material 1 from: Thomaes A, Verschelde P, Mader D, Sprecher-Uebersax E, Fremlin M, Onkelinx T, Méndez M (2017) Can we successfully monitor a population density decline of elusive invertebrates? A statistical power analysis on Lucanus cervus. In: Campanaro A, Hardersen S, Sabbatini Peverieri G, Carpaneto GМ (Eds) Monitoring of saproxylic beetles and other insects protected in the European Union. Nature Conservation 19: 1-18. https://doi.org/10.3897/natureconservation.19.11761
Figures of statistical support : Data type: statistical data
Figure 6 in Populations of Microcondylaea bonellii (Férussac 1827), Unionidae - an european freshwater mussel at rapid decline - and Unio mancus in Istria, Croatia
Figure 6. Adult Microcondylaea bonellii from Butoniga (1.10.2011), note the arboriform siphonal papillae typical for this species.
Data from: Estimation of contemporary effective population size and population declines using RAD sequence data
Large genomic datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Using a linkage disequilibrium-based analysis, individual sampling (i.e., n ≥ 30) had the greatest effect on Ne estimation and the detection of population-size declines, with declines reliably detected across scenarios approximately 10 generations after they began. Coalescent-based inference required fewer sampled individuals (i.e., n = 15), and instead was most influenced by the size of the SNP dataset, with 25,000 to 50,000 SNPs required for accurate detection of population trends and at least 20 generations after decline began. The number of samples available and targeted number of RADseq loci are important criteria when choosing between these methods. Neither method suffered any apparent bias due to the effects of allele dropout typical of RAD data. With an understanding of the limitations and biases of these approaches, researchers can make more informed decisions when designing their sampling and analyses. Overall, our results reveal that demographic inference using RADseq data can be successfully applied to infer recent population size change and may be important tools for population monitoring and conservation biology.
Data from: Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus
Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short-term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17 populations spanning the geographic range of the endangered eastern massasauga rattlesnake (Sistrurus catenatus). First, we use SNP data to confirm previous reports that these populations exhibit high levels of genetic structure (overall Fst = 0.25). Second, we show that most populations have contemporary Ne estimates less than 50. Heterozygosity-fitness correlations in these populations provided no evidence for a genetic cost to living in small populations, though these tests may lack power. Third, model-based demographic analyses of individual populations indicate that all have experienced declines, with the onset of many of these declines occurring over timescales consistent with anthropogenic impacts (<200 years). Finally, forward simulations of the expected loss of variation in relatively large (Ne = 50) and small (Ne = 10) populations indicate they will lose a substantial amount of their current standing neutral variation (63% and 99%, respectively) over the next 100 years. Our results argue that drift has a significant and increasing impact on levels of genetic variation in isolated populations of this snake, and efforts to assess and mitigate associated impacts on adaptive variation should be components of the management of this endangered reptile.
Data from: Quantifying behavioral changes in territorial animals caused by sudden population declines
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Data from: Estimation of contemporary effective population size and population declines using RAD sequence data
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Data from: Estimating national population sizes: methodological challenges and applications illustrated in the common nightingale, a declining songbird in the UK
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Data from: Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance
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Data from: Phenotypic biomarkers of climatic impacts on declining insect populations: a key role for decadal drought, thermal buffering and amplification effects and host plant dynamics
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Data from: Monarch butterfly population decline in North America: identifying the threatening processes
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Data from: Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus
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Local human population increase in the non-breeding areas of long-distance migrant bird species is only weakly associated with their declines, even for synanthropic species
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Population genomics and conservation management of a declining tropical rodent
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International Brain Laboratory public data
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OpenNeuro
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