scholarly journals Eco-evolutionary dynamics: fluctuations in population growth rate reduce effective population size in chinook salmon

Ecology ◽  
2010 ◽  
Vol 91 (3) ◽  
pp. 902-914 ◽  
Author(s):  
Robin S. Waples ◽  
David W. Jensen ◽  
Michelle McClure
Keyword(s):  
Growth Rate ◽  
Population Growth ◽  
Population Size ◽  
Effective Population Size ◽  
Chinook Salmon ◽  
Population Growth Rate ◽  
Evolutionary Dynamics ◽  
Effective Population

scholarly journals Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

2017 ◽  
Author(s):  
Erik M. Volz ◽  
Xavier Didelot
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Growth Rates ◽  
Sequence Data ◽  
Demographic History ◽  
Parametric Models ◽  
Effective Population ◽  
Epidemic Dynamics ◽  
Non Parametric

AbstractNon-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 stationary stochastic processes 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 β-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://mrc-ide.github.io/skygrowth/.

Global changes explain the long-term demographic trend of the Eurasian common lizard (Squamata: Lacertidae)

2021 ◽  
Author(s):  
Jose L Horreo ◽  
Patrick S Fitze
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Climatic Changes ◽  
Vegetation Changes ◽  
Effective Population ◽  
Short Term ◽  
Demographic Trend ◽  
Common Lizard

Abstract The demographic trend of a species depends on the dynamics of its local populations, which can be compromised by local or by global phenomena. However, the relevance of local and global phenomena has rarely been investigated simultaneously. Here we tested whether local phenomena compromised a species’ demographic trend using the Eurasian common lizard Zootoca vivipara, the terrestrial reptile exhibiting the widest geographic distribution, as a model species. We analysed the species’ ancient demographic trend using genetic data from its six allopatric genetic clades and tested whether its demographic trend mainly depended on single clades or on global phenomena. Zootoca vivipara’s effective population size increased since 2.3 million years ago and started to increase steeply and continuously from 0.531 Mya. Population growth rate exhibited two maxima, both occurring during global climatic changes and important vegetation changes on the northern hemisphere. Effective population size and growth rate were negatively correlated with global surface temperatures, in line with global parameters driving long-term demographic trends. Zootoca vivipara’s ancient demography was not driven by a single clade, nor by the two clades that colonized huge geographic areas after the last glaciation. The low importance of local phenomena, suggests that the experimentally demonstrated high sensitivity of this species to short-term ecological changes is a response in order to cope with short-term and local changes. This suggests that what affected its long-term demographic trend the most, were not these local changes/responses, but rather the important and prolonged global climatic changes and important vegetation changes on the northern hemisphere, including the opening up of the forest by humans.

Maximum Likelihood Estimation of Population Growth Rates Based on the Coalescent

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 429-434 ◽  
Author(s):  
Mary K Kuhner ◽  
Jon Yamato ◽  
Joseph Felsenstein
Keyword(s):  
Growth Rate ◽  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Population Growth ◽  
Growth Rates ◽  
Population Growth Rate ◽  
Likelihood Estimation ◽  
Effective Population ◽  
Population Growth Rates ◽  
Neutral Mutation Rate

Abstract We describe a method for co-estimating 4Neμ (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Neμ is low; there is also a slight upwards bias in the estimate of 4Neμ itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.

Effective Population Size in Winter-Run Chinook Salmon

1995 ◽  
Vol 9 (3) ◽  
pp. 615-624 ◽  
Author(s):  
Philip W. Hedrick ◽  
Dennis Hedgecock ◽  
Scott Hamelberg
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Chinook Salmon ◽  
Effective Population

scholarly journals The effective population size and mutation rate of influenza A virus in acutely infected individuals

2020 ◽  
Author(s):  
John T. McCrone ◽  
Robert J. Woods ◽  
Arnold S. Monto ◽  
Emily T. Martin ◽  
Adam S. Lauring
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
Effective Population

AbstractThe global evolutionary dynamics of influenza viruses ultimately derive from processes that take place within and between infected individuals. Recent work suggests that within-host populations are dynamic, but an in vivo estimate of mutation rate and population size in naturally infected individuals remains elusive. Here we model the within-host dynamics of influenza A viruses using high depth of coverage sequence data from 200 acute infections in an outpatient, community setting. Using a Wright-Fisher model, we estimate a within-host effective population size of 32-72 and an in vivo mutation rate of 3.4×10−6 per nucleotide per generation.

scholarly journals Coalescent inference using serially sampled, high-throughput sequencing data from intra-host HIV infection

2015 ◽  
Author(s):  
Kevin Dialdestoro ◽  
Jonas Andreas Sibbesen ◽  
Lasse Maretty ◽  
Jayna Raghwani ◽  
Astrid Gall ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
High Throughput ◽  
Deep Sequencing ◽  
Evolutionary Dynamics ◽  
Viral Population ◽  
Single Infection ◽  
Sequencing Data ◽  
Effective Population ◽  
Population Size Estimates

ABSTRACTHuman immunodeficiency virus (HIV) is a rapidly evolving pathogen that causes chronic infections, so genetic diversity within a single infection can be very high. High-throughput “deep” sequencing can now measure this diversity in unprecedented detail, particularly since it can be performed at different timepoints during an infection, and this offers a potentially powerful way to infer the evolutionary dynamics of the intra-host viral population. However, population genomic inference from HIV sequence data is challenging because of high rates of mutation and recombination, rapid demographic changes, and ongoing selective pressures. In this paper we develop a new method for inference using HIV deep sequencing data using an approach based on importance sampling of ancestral recombination graphs under a multi-locus coalescent model. The approach further extends recent progress in the approximation of so-calledconditional sampling distributions, a quantity of key interest when approximating co-alescent likelihoods. The chief novelties of our method are that it is able to infer rates of recombination and mutation, as well as the effective population size, while handling sampling over different timepoints and missing data without extra computational difficulty. We apply our method to a dataset of HIV-1, in which several hundred sequences were obtained from an infected individual at seven timepoints over two years. We find mutation rate and effective population size estimates to be comparable to those produced by the software BEAST. Additionally, our method is able to produce local recombination rate estimates. The software underlying our method, Coalescenator, is freely available.

Population size affects vital rates but not population growth rate of a perennial plant

Ecology ◽  
2010 ◽  
Vol 91 (11) ◽  
pp. 3210-3217 ◽  
Author(s):  
Annette Kolb ◽  
Johan P. Dahlgren ◽  
Johan Ehrlén
Keyword(s):  
Growth Rate ◽  
Population Growth ◽  
Population Size ◽  
Population Growth Rate ◽  
Vital Rates ◽  
Perennial Plant
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