The impact of Quaternary climate oscillations on divergence times and historical population sizes inThylamysopossums from the Andes

2015 ◽  
Vol 24 (10) ◽  
pp. 2495-2506 ◽  
Author(s):  
Thomas C. Giarla ◽  
Sharon A. Jansa
Keyword(s):  
Divergence Times ◽  
Climate Oscillations ◽  
The Andes ◽  
Quaternary Climate ◽  
Population Sizes ◽  
The Impact

Characterizing the impact of recovering sea otters on commercially important crabs in California estuaries

2020 ◽  
Vol 655 ◽  
pp. 123-137
Author(s):  
TM Grimes ◽  
MT Tinker ◽  
BB Hughes ◽  
KE Boyer ◽  
L Needles ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Sea Otter ◽  
Dungeness Crab ◽  
Sea Otters ◽  
Elkhorn Slough ◽  
Enhydra Lutris Nereis ◽  
Crab Abundance ◽  
Population Sizes ◽  
Commercially Important ◽  
The Impact

Protective legislation and management have led to an increase in California’s sea otter Enhydra lutris nereis population. While sea otter recovery has been linked to ecosystem benefits, sea otter predation may negatively affect commercially valuable species. Understanding the potential influence of sea otters is of particular importance as their range expands into estuaries that function as nurseries for commercially valuable species like Dungeness crab Metacarcinus magister. We consider how sea otter predation has affected the abundance and size of juvenile Dungeness crab in Elkhorn Slough, California, USA, and analyzed cancrid crab abundance and size across 4 California estuaries with and without sea otters to understand how biotic and abiotic factors contribute to observed variation in crab size and abundance. We compared trends in southern sea otters relative to Dungeness crab landings in California to assess whether increasing sea otter abundance have negatively impacted landings. In Elkhorn Slough, juvenile Dungeness crab abundance and size have declined since 2012, coinciding with sea otter population growth. However, the impact of sea otters on juvenile Dungeness crab size was habitat-specific and only significant in unvegetated habitat. Across estuaries, we found that cancrid crab abundance and size were negatively associated with sea otter presence. While abiotic factors varied among estuaries, these factors explained little of the observed variation in crab abundance or size. Although we found evidence that sea otters can have localized effects on cancrid crab populations within estuaries, we found no evidence that southern sea otters, at recent population sizes, have negatively impacted Dungeness crab landings in California from 2000-2014.

scholarly journals The Impact of Health Policies and Sociodemographic Factors on Doubling Time of the COVID-19 Pandemic in Mexico

2021 ◽  
Vol 18 (5) ◽  
pp. 2354
Author(s):  
Lina Díaz-Castro ◽  
Héctor Cabello-Rangel ◽  
Kurt Hoffman
Keyword(s):  
Population Density ◽  
Doubling Time ◽  
Sociodemographic Factors ◽  
Health Policies ◽  
Government Response ◽  
University Of Oxford ◽  
Negative Effect ◽  
Population Sizes ◽  
The University ◽  
The Impact

Background. The doubling time is the best indicator of the course of the current COVID-19 pandemic. The aim of the present investigation was to determine the impact of policies and several sociodemographic factors on the COVID-19 doubling time in Mexico. Methods. A retrospective longitudinal study was carried out across March–August, 2020. Policies issued by each of the 32 Mexican states during each week of this period were classified according to the University of Oxford Coronavirus Government Response Tracker (OxCGRT), and the doubling time of COVID-19 cases was calculated. Additionally, variables such as population size and density, poverty and mobility were included. A panel data model was applied to measure the effect of these variables on doubling time. Results. States with larger population sizes issued a larger number of policies. Delay in the issuance of policies was associated with accelerated propagation. The policy index (coefficient 0.60, p < 0.01) and the income per capita (coefficient 3.36, p < 0.01) had a positive effect on doubling time; by contrast, the population density (coefficient −0.012, p < 0.05), the mobility in parks (coefficient −1.10, p < 0.01) and the residential mobility (coefficient −4.14, p < 0.01) had a negative effect. Conclusions. Health policies had an effect on slowing the pandemic’s propagation, but population density and mobility played a fundamental role. Therefore, it is necessary to implement policies that consider these variables.

scholarly journals Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Dna Sequences ◽  
Gene Tree ◽  
Species Tree ◽  
Bayes Estimation ◽  
Ancestral Population ◽  
Divergence Times ◽  
Gene Trees ◽  
Species Divergence ◽  
Multiple Loci ◽  
Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

scholarly journals Predicting the Future Distribution of Ara rubrogenys, an Endemic Endangered Bird Species of the Andes, Taking into Account Trophic Interactions

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 94
Author(s):  
Alain Hambuckers ◽  
Simon de Harenne ◽  
Eberth Rocha Ledezma ◽  
Lilian Zúñiga Zeballos ◽  
Louis François
Keyword(s):  
Food Resource ◽  
Bird Species ◽  
Co2 Concentration ◽  
Distribution Models ◽  
Plant Resources ◽  
Term Survival ◽  
The Andes ◽  
Vegetation Models ◽  
Fertilizing Effect ◽  
The Impact

Species distribution models (SDMs) are commonly used with climate only to predict animal distribution changes. This approach however neglects the evolution of other components of the niche, like food resource availability. SDMs are also commonly used with plants. This also suffers limitations, notably an inability to capture the fertilizing effect of the rising CO2 concentration strengthening resilience to water stress. Alternatively, process-based dynamic vegetation models (DVMs) respond to CO2 concentration. To test the impact of the plant modelling method to model plant resources of animals, we studied the distribution of a Bolivian macaw, assuming that, under future climate, DVMs produce more conservative results than SDMs. We modelled the bird with an SDM driven by climate. For the plant, we used SDMs or a DVM. Under future climates, the macaw SDM showed increased probabilities of presence over the area of distribution and connected range extensions. For plants, SDMs did not forecast overall response. By contrast, the DVM produced increases of productivity, occupancy and diversity, also towards higher altitudes. The results offered positive perspectives for the macaw, more optimistic with the DVM than with the SDMs, than initially assumed. Nevertheless, major common threats remain, challenging the short-term survival of the macaw.

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i884-i894
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

A Dynamic Theory of Populism in Power

2021 ◽  
Author(s):  
Julio F. Carrión
Keyword(s):  
Regime Change ◽  
Dynamic Theory ◽  
Empirical Relationship ◽  
The United States ◽  
Democratic Governance ◽  
Theory Of Change ◽  
Popular Participation ◽  
The Andes ◽  
The Impact ◽  
The Relationship

The relationship between populism and democracy is a hotly debated topic. Some believe that populism is inherently bad for democracy because it is anti-pluralist and confrontational. Others argue that populism can reinvigorate worn-out democracies in need of an infusion of greater popular participation. This book advances this debate by examining the empirical relationship between populism in power and democracy. Does populism in power always lead to regime change, that is, the demise of democracy? The answer is no. The impact of populism on democracy depends on the variety of populism in power: the worst outcomes in democratic governance are found under unconstrained populism. This book discusses the conditions that explain how populism becomes unconstrained, and advances a dynamic theory of change that shows how the late victories of populists build on early ones, resulting in greater power asymmetries. The book analyzes five populist presidencies in the Andes. In four of them (Bolivia, Ecuador, Peru, and Venezuela), populism became unconstrained and regime change followed. In one case, Colombia, populism in power was contained and democracy survived. The concluding chapter places the Andean cases in comparative perspective and discusses how unconstrained populism in other cases (Nicaragua and Hungary) also lead to the end of electoral democracy. Where populism in power was constrained (Honduras and the United States), regime change did not materialize. This book advances a theory of populism that help us understand how democracies transition into non-democracies. To that extent, the book illuminates the processes of democratic erosion in our time.

scholarly journals The impact of large terrestrial carnivores on Pleistocene ecosystems

2015 ◽  
Vol 113 (4) ◽  
pp. 862-867 ◽  
Author(s):  
Blaire Van Valkenburgh ◽  
Matthew W. Hayward ◽  
William J. Ripple ◽  
Carlo Meloro ◽  
V. Louise Roth
Keyword(s):  
Prey Size ◽  
Habitat Degradation ◽  
Terrestrial Ecosystems ◽  
Growth Data ◽  
Predator Prey ◽  
Body Sizes ◽  
Population Sizes ◽  
Potential Impact ◽  
The Impact ◽  
Ground Sloths

Large mammalian terrestrial herbivores, such as elephants, have dramatic effects on the ecosystems they inhabit and at high population densities their environmental impacts can be devastating. Pleistocene terrestrial ecosystems included a much greater diversity of megaherbivores (e.g., mammoths, mastodons, giant ground sloths) and thus a greater potential for widespread habitat degradation if population sizes were not limited. Nevertheless, based on modern observations, it is generally believed that populations of megaherbivores (>800 kg) are largely immune to the effects of predation and this perception has been extended into the Pleistocene. However, as shown here, the species richness of big carnivores was greater in the Pleistocene and many of them were significantly larger than their modern counterparts. Fossil evidence suggests that interspecific competition among carnivores was relatively intense and reveals that some individuals specialized in consuming megaherbivores. To estimate the potential impact of Pleistocene large carnivores, we use both historic and modern data on predator–prey body mass relationships to predict size ranges of their typical and maximum prey when hunting as individuals and in groups. These prey size ranges are then compared with estimates of juvenile and subadult proboscidean body sizes derived from extant elephant growth data. Young proboscideans at their most vulnerable age fall within the predicted prey size ranges of many of the Pleistocene carnivores. Predation on juveniles can have a greater impact on megaherbivores because of their long interbirth intervals, and consequently, we argue that Pleistocene carnivores had the capacity to, and likely did, limit megaherbivore population sizes.

scholarly journals COVID-19 Cases and Deaths: A Comparison among Bangladesh, India and Pakistan

2021 ◽  
Vol 3 (5) ◽  
pp. 01-06
Author(s):  
B. M. Kibria
Keyword(s):  
Population Sizes ◽  
The Impact

This paper compares the number of infected cases and deaths of an ongoing pandemic of COVID-19 outbreak for Bangladesh, India and Pakistan for the period of March 8, 2020 to September 21, 2020. Comparisons among countries using absolute numbers are not comparable due to different factors, such as population sizes, rates of per 100,000 and also because not all countries are affected equally and at the same time. Following Middelburg and Rosendaal (2020), we graphically compare the number of cases and deaths expressed as a percentage of the cases and deaths on the reference day 25 after the first reported death. To see the impact of reference days, several later reference days are also considered in this study. From these comparisons, clear differences were observed among countries. Among these three countries, it is observed that Bangladesh had the most extreme flattening of the curve, followed by Pakistan and then India. We observed that the epidemic developed in India much more rapidly as compare to Bangladesh and Pakistan.

scholarly journals On mechanisms of trophic cascade caused by anti-predation response in food chain systems

2020 ◽  
Vol 1 (2) ◽  
pp. 1-27
Author(s):  
Yang Wang ◽  
Xingfu Zou
Keyword(s):  
Food Chain ◽  
Trophic Cascade ◽  
Predation Rate ◽  
Model Systems ◽  
Large Carnivores ◽  
Response Level ◽  
Population Sizes ◽  
The Cost ◽  
The Impact ◽  
D Model

Motivated by a recent field study [Nat. Commun. 7(2016), 10698] on the impact of fear of large carnivores on the populations in a cascading ecosystem of food chain type with the large carnivores as the top predator, in this paper we propose two model systems in the form of ordinary differential equations to mechanistically explore the cascade of such a fear effect. The models are of the Lotka-Volterra type, one is three imensional and the other four dimensional. The 3-D model only considers the cost of the anti-predation response reflected in the decrease of the production, while the 4-D model considers also the benefit of the response in reducing the predation rate, in addition to the cost by reducing the production. We perform a thorough analysis on the dynamics of the two models. The results reveal that the 3-D model and 4-model demonstrate opposite patterns for trophic cascade in terms of the dependence of population sizes for each species at the co-existence equilibrium on the anti-predation response level parameter, and such a difference is attributed to whether or not there is a benefit for the anti-predation response by the meso-carnivore species.

scholarly journals Incorporating genetic selection into individual-based models (IBMs) of malaria and other infectious diseases

2019 ◽  
Author(s):  
Ian M. Hastings ◽  
Raman Sharma
Keyword(s):  
Control Strategies ◽  
Genetic Parameter ◽  
Genetic Selection ◽  
Wait Time ◽  
Antimicrobial Drug Resistance ◽  
Infinite Population ◽  
Individual Based Models ◽  
Population Sizes ◽  
Human Infections ◽  
The Impact

AbstractOptimal control strategies for human infections are often investigated by computational approaches using individual-based models (IBMs). These typically track humans and evaluate the impact of control interventions in terms of human deaths, clinical cases averted, interruption of transmission etc. Genetic selection can be incorporated into these IBMs and used to track the spread of mutations whose origin and spread are often driven by the intervention, and which subsequently undermine the control strategy; for example, mutations which encode antimicrobial drug resistance or diagnosis- or vaccine-escape phenotypes. Basic population genetic descriptions of selection are based on infinite population sizes (so that chance fluctuations in allele frequency are absent) but IBMs track finite population sizes. We describe how the finite sizes of IBMs affect simulating the dynamics of genetic selection and how best to incorporate genetic selection into these models. We use the OpenMalaria IBM of malaria as an example, but the same principles apply to IBMs of other diseases. We identify four strategies to incorporate selection into IBMs and make the following four recommendations. Firstly, calculate and report the selection coefficients, s, of the advantageous allele as the key genetic parameter. Secondly, use these values of ‘s’ to calculate the wait-time until a mutation successful establishes itself in the population. The wait time for the mutation can be added to speed of selection, s, to calculate when the mutation will reach significant, operationally important levels. Thirdly, quantify the ability of the IBM to robustly estimate small selection coefficients. Fourthly, optimise computational efficacy: when ‘s’ is small it is plausible that fewer replicates of larger IBMs will be more efficient than a larger number of replicates of smaller size.

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