Prediction and Estimation of Effective Population Size
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Effective Population Size and Genetic Conservation Criteria for Bull Trout
North American Journal of Fisheries Management 21:756±764, 2001 q Copyright by the American Fisheries Society 2001 Effective Population Size and Genetic Conservation Criteria for Bull Trout B. E. RIEMAN* U.S. Department of Agriculture Forest Service, Rocky Mountain Research Station, 316 East Myrtle, Boise, Idaho 83702, USA F. W. A LLENDORF Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA Abstract.ÐEffective population size (Ne) is an important concept in the management of threatened species like bull trout Salvelinus con¯uentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively. Although Ne strongly depends on census population size, it also depends on demographic and life history characteristics that complicate any estimates. This is an especially dif®cult problem for species like bull trout, which have overlapping generations; biologists may monitor annual population number but lack more detailed information on demographic population structure or life history. We used a generalized, age-structured simulation model to relate Ne to adult numbers under a range of life histories and other conditions characteristic of bull trout populations. Effective population size varied strongly with the effects of the demographic and environmental variation included in our simulations. Our most realistic estimates of Ne were between about 0.5 and 1.0 times the mean number of adults spawning annually. We conclude that cautious long-term management goals for bull trout populations should include an average of at least 1,000 adults spawning each year. Where local populations are too small, managers should seek to conserve a collection of interconnected populations that is at least large enough in total to meet this minimum. -
Routledge Handbook of Ecological and Environmental Restoration the Principles of Restoration Ecology at Population Scales
This article was downloaded by: 10.3.98.104 On: 26 Sep 2021 Access details: subscription number Publisher: Routledge Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: 5 Howick Place, London SW1P 1WG, UK Routledge Handbook of Ecological and Environmental Restoration Stuart K. Allison, Stephen D. Murphy The Principles of Restoration Ecology at Population Scales Publication details https://www.routledgehandbooks.com/doi/10.4324/9781315685977.ch3 Stephen D. Murphy, Michael J. McTavish, Heather A. Cray Published online on: 23 May 2017 How to cite :- Stephen D. Murphy, Michael J. McTavish, Heather A. Cray. 23 May 2017, The Principles of Restoration Ecology at Population Scales from: Routledge Handbook of Ecological and Environmental Restoration Routledge Accessed on: 26 Sep 2021 https://www.routledgehandbooks.com/doi/10.4324/9781315685977.ch3 PLEASE SCROLL DOWN FOR DOCUMENT Full terms and conditions of use: https://www.routledgehandbooks.com/legal-notices/terms This Document PDF may be used for research, teaching and private study purposes. Any substantial or systematic reproductions, re-distribution, re-selling, loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The publisher shall not be liable for an loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. 3 THE PRINCIPLES OF RESTORATION ECOLOGY AT POPULATION SCALES Stephen D. -
Population Size and the Rate of Evolution
Review Population size and the rate of evolution 1,2 1 3 Robert Lanfear , Hanna Kokko , and Adam Eyre-Walker 1 Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia 2 National Evolutionary Synthesis Center, Durham, NC, USA 3 School of Life Sciences, University of Sussex, Brighton, UK Does evolution proceed faster in larger or smaller popu- mutations occur and the chance that each mutation lations? The relationship between effective population spreads to fixation. size (Ne) and the rate of evolution has consequences for The purpose of this review is to synthesize theoretical our ability to understand and interpret genomic varia- and empirical knowledge of the relationship between tion, and is central to many aspects of evolution and effective population size (Ne, Box 1) and the substitution ecology. Many factors affect the relationship between Ne rate, which we term the Ne–rate relationship (NeRR). A and the rate of evolution, and recent theoretical and positive NeRR implies faster evolution in larger popula- empirical studies have shown some surprising and tions relative to smaller ones, and a negative NeRR implies sometimes counterintuitive results. Some mechanisms the opposite (Figure 1A,B). Although Ne has long been tend to make the relationship positive, others negative, known to be one of the most important factors determining and they can act simultaneously. The relationship also the substitution rate [5–8], several novel predictions and depends on whether one is interested in the rate of observations have emerged in recent years, causing some neutral, adaptive, or deleterious evolution. Here, we reassessment of earlier theory and highlighting some gaps synthesize theoretical and empirical approaches to un- in our understanding. -
Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation
Copyright 2000 by the Genetics Society of America Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation Yuseob Kim and Wolfgang Stephan Department of Biology, University of Rochester, Rochester, New York 14627 Manuscript received December 7, 1999 Accepted for publication March 20, 2000 ABSTRACT Due to relatively high rates of strongly selected deleterious mutations, directional selection on favorable alleles (causing hitchhiking effects on linked neutral polymorphisms) is expected to occur while a deleteri- ous mutation-selection balance is present in a population. We analyze this interaction of directional selection and background selection and study their combined effects on neutral variation, using a three- locus model in which each locus is subjected to either deleterious, favorable, or neutral mutations. Average heterozygosity is measured by simulations (1) at the stationary state under the assumption of recurrent hitchhiking events and (2) as a transient level after a single hitchhiking event. The simulation results are compared to theoretical predictions. It is shown that known analytical solutions describing the hitchhiking effect without background selection can be modi®ed such that they accurately predict the joint effects of hitchhiking and background on linked, neutral variation. Generalization of these results to a more appro- priate multilocus model (such that background selection can occur at multiple sites) suggests that, in regions of very low recombination rates, stationary levels of nucleotide diversity are primarily determined by hitchhiking, whereas in regions of high recombination, background selection is the dominant force. The implications of these results on the identi®cation and estimation of the relevant parameters of the model are discussed. -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
Evolutionary Restoration Ecology
ch06 2/9/06 12:45 PM Page 113 189686 / Island Press / Falk Chapter 6 Evolutionary Restoration Ecology Craig A. Stockwell, Michael T. Kinnison, and Andrew P. Hendry Restoration Ecology and Evolutionary Process Restoration activities have increased dramatically in recent years, creating evolutionary chal- lenges and opportunities. Though restoration has favored a strong focus on the role of habi- tat, concerns surrounding the evolutionary ecology of populations are increasing. In this con- text, previous researchers have considered the importance of preserving extant diversity and maintaining future evolutionary potential (Montalvo et al. 1997; Lesica and Allendorf 1999), but they have usually ignored the prospect of ongoing evolution in real time. However, such contemporary evolution (changes occurring over one to a few hundred generations) appears to be relatively common in nature (Stockwell and Weeks 1999; Bone and Farres 2001; Kin- nison and Hendry 2001; Reznick and Ghalambor 2001; Ashley et al. 2003; Stockwell et al. 2003). Moreover, it is often associated with situations that may prevail in restoration projects, namely the presence of introduced populations and other anthropogenic disturbances (Stockwell and Weeks 1999; Bone and Farres 2001; Reznick and Ghalambor 2001) (Table 6.1). Any restoration program may thus entail consideration of evolution in the past, present, and future. Restoration efforts often involve dramatic and rapid shifts in habitat that may even lead to different ecological states (such as altered fire regimes) (Suding et al. 2003). Genetic variants that evolved within historically different evolutionary contexts (the past) may thus be pitted against novel and mismatched current conditions (the present). The degree of this mismatch should then determine the pattern and strength of selection acting on trait variation in such populations (Box 6.1; Figure 6.1). -
An Unusually Low Microsatellite Mutation Rate in Dictyostelium Discoideum,An Organism with Unusually Abundant Microsatellites
Copyright Ó 2007 by the Genetics Society of America DOI: 10.1534/genetics.107.076067 An Unusually Low Microsatellite Mutation Rate in Dictyostelium discoideum,an Organism With Unusually Abundant Microsatellites Ryan McConnell, Sara Middlemist, Clea Scala, Joan E. Strassmann and David C. Queller1 Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005 Manuscript received May 18, 2007 Accepted for publication September 4, 2007 ABSTRACT The genome of the social amoeba Dictyostelium discoideum is known to have a very high density of microsatellite repeats, including thousands of triplet microsatellite repeats in coding regions that apparently code for long runs of single amino acids. We used a mutation accumulation study to see if unusually high microsatellite mutation rates contribute to this pattern. There was a modest bias toward mutations that increase repeat number, but because upward mutations were smaller than downward ones, this did not lead to a net average increase in size. Longer microsatellites had higher mutation rates than shorter ones, but did not show greater directional bias. The most striking finding is that the overall mutation rate is the lowest reported for microsatellites: 1 3 10À6 for 10 dinucleotide loci and 6 3 10À6 for 52 trinucleotide loci (which were longer). High microsatellite mutation rates therefore do not explain the high incidence of microsatellites. The causal relation may in fact be reversed, with low mutation rates evolving to protect against deleterious fitness effects of mutation at the numerous microsatellites. ICROSATELLITES, also known as simple se- In humans, certain triplet repeats that occur in or M quence repeats, are long stretches of a short near coding regions are subject to expansions that (1–6 bp), tandemly repeated DNA unit, such as the directly cause genetic diseases (Ashley and Warren motif CAA repeated 20 times. -
Adaptive Tuning of Mutation Rates Allows Fast Response to Lethal Stress In
Manuscript 1 Adaptive tuning of mutation rates allows fast response to lethal stress in 2 Escherichia coli 3 4 a a a a a,b 5 Toon Swings , Bram Van den Bergh , Sander Wuyts , Eline Oeyen , Karin Voordeckers , Kevin J. a,b a,c a a,* 6 Verstrepen , Maarten Fauvart , Natalie Verstraeten , Jan Michiels 7 8 a 9 Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 10 3001 Leuven, Belgium b 11 VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie (VIB) Bioincubator 12 Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium c 13 Smart Systems and Emerging Technologies Unit, imec, Kapeldreef 75, 3001 Leuven, Belgium * 14 To whom correspondence should be addressed: Jan Michiels, Department of Microbial and 2 15 Molecular Systems (M S), Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 16 2460, 3001 Leuven, Belgium, [email protected], Tel: +32 16 32 96 84 1 Manuscript 17 Abstract 18 19 While specific mutations allow organisms to adapt to stressful environments, most changes in an 20 organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often 21 considered a slowly-evolving parameter. In contrast, we demonstrate an unexpected flexibility in 22 cellular mutation rates as a response to changes in selective pressure. We show that hypermutation 23 independently evolves when different Escherichia coli cultures adapt to high ethanol stress. 24 Furthermore, hypermutator states are transitory and repeatedly alternate with decreases in mutation 25 rate. Specifically, population mutation rates rise when cells experience higher stress and decline again 26 once cells are adapted. -
Population Genetics I
21 March, 2016: Population genetics I 529053 Evolutionary Genomics Ari Löytynoja / [email protected] Background reading This book is OK primer to pop.gen. in genomics era - focus on coalescent theory and SNP data - unfortunately it contains lots of typos 529053 Evolutionary Genomics Ari Löytynoja / [email protected] Population genetics Definition - studies distributions & changes of allele frequencies in populations over time - effects considered: - natural selection, genetic drift, mutation and gene flow - recombination, population subdivision and population structure - allows inferring past events as well as predicting future History - fundamental work by Haldane, Wright and Fisher on first half of 20th century - recent development: coalescent theory by Kingman in 1980’s - suitable for SNPs data - computationally highly efficient 529053 Evolutionary Genomics Ari Löytynoja / [email protected] Population genetics basics (1) Allele - one of alternative forms of a gene or same genetic locus - used to be visible gene product (e.g. blond vs. red hair) - now typically SNP (e.g. rs1805007(C) vs. rs1805007(T)) 529053 Evolutionary Genomics Ari Löytynoja / [email protected] Population genetics basics (1) Allele - one of alternative forms of a gene or same genetic locus - used to be visible gene product (e.g. blond vs. red hair) - now typically SNP (e.g. rs1805007(C) vs. rs1805007(T)) 529053 Evolutionary Genomics Ari Löytynoja / [email protected] Population genetics basics (1) Allele - one of alternative forms of a gene or same genetic locus - used to be visible gene product (e.g. blond vs. red hair) - now typically SNP (e.g. rs1805007(C) vs. rs1805007(T)) 529053 Evolutionary Genomics Ari Löytynoja / [email protected] Population genetics basics (1) Allele - one of alternative forms of a gene or same genetic locus - used to be visible gene product (e.g. -
Population Biology & Life Tables
EXERCISE 3 Population Biology: Life Tables & Theoretical Populations The purpose of this lab is to introduce the basic principles of population biology and to allow you to manipulate and explore a few of the most common equations using some simple Mathcad© wooksheets. A good introduction of this subject can be found in a general biology text book such as Campbell (1996), while a more complete discussion of pop- ulation biology can be found in an ecology text (e.g., Begon et al. 1990) or in one of the references listed at the end of this exercise. Exercise Objectives: After you have completed this lab, you should be able to: 1. Give deÞnitions of the terms in bold type. 2. Estimate population size from capture-recapture data. 3. Compare the following sets of terms: semelparous vs. iteroparous life cycles, cohort vs. static life tables, Type I vs. II vs. III survivorship curves, density dependent vs. density independent population growth, discrete vs. continuous breeding seasons, divergent vs. dampening oscillation cycles, and time lag vs. generation time in population models. 4. Calculate lx, dx, qx, R0, Tc, and ex; and estimate r from life table data. 5. Choose the appropriate theoretical model for predicting growth of a given population. 6. Calculate population size at a particular time (Nt+1) when given its size one time unit previous (Nt) and the corre- sponding variables (e.g., r, K, T, and/or L) of the appropriate model. 7. Understand how r, K, T, and L affect population growth. Population Size A population is a localized group of individuals of the same species. -
Estimating Effective Population Size Or Mutation Rate Using the Frequencies of Mutations of Various Classes in a Sample of DNA Sequences
Copyright 0 1994 by the Genetics Society of America Estimating Effective Population Size or Mutation Rate Using the Frequencies of Mutations of Various Classes in a Sample of DNA Sequences Yun-xin FU Center for Demographic and Population Genetics, University of Texas, Houston, Texas 77225 Manuscript received February 18, 1994 Accepted for publication August 27, 1994 ABSTRACT Mutations resulting in segregating sites of a sample of DNA sequences can be classified by size and type and the frequencies of mutations of different sizes and types can be inferred from the sample. A framework for estimating the essential parameter 8 = 4Nu utilizing the frequencies of mutations of various sizes and types is developed in this paper, where N is the effective size of a population and p is mutation rate per sequence per generation.The framework is a combination of coalescent theory, general linear model and Monte-Carlo integration, which leads to two new estimators 6, and 6, as well as a general Watterson’s estimator 6, and a general Tajima’s estimator 6,. The greatest strength of the framework is that it can be used under a variety of population models. The properties of the framework and the four estimators bK, e,,, 6, and 6, are investigated under three important population models: the neutral Wright-Fisher model, the neutral model with recombination and the neutral Wright’s finite-islands model. Under all these models, it is shown that 6, is the best estimator among the four even when recombination rate or migration rate has to be estimated. Under the neutral Wright-Fisher model, it is shown that the new estimator 6,has avariance close to alower bound ofvariances of allunbiased estimators of Owhichsuggests that 6, is a:ery efficient estimator. -
Detecting the Form of Selection from DNA Sequence Data
Outlook COMMENT Male:female mutation ratio muscular dystrophy, neurofibromatosis and retinoblast- outcome of further investigation, this unique transposition oma), there is a large male excess. So, I believe the evidence event and perhaps others like it are sure to provide impor- is convincing that the male base-substitution rate greatly tant cytogenetic and evolutionary insights. exceeds the female rate. There are a number of reasons why the historical Acknowledgements male:female mutation ratio is likely to be less than the I have profited greatly from discussions with my colleagues current one, the most important being the lower age of B. Dove, B. Engels, C. Denniston and M. Susman. My reproduction in the earliest humans and their ape-like greatest debt is to D. Page for a continuing and very fruitful ancestors. More studies are needed. But whatever the dialog and for providing me with unpublished data. References Nature 406, 622–625 6 Engels, W.R. et al. (1994) Long-range cis preference in DNA 1 Vogel, F. and Motulsky, A. G. (1997) Human Genetics: 4 Shimmin, L.C. et al. (1993) Potential problems in estimating homology search over the length of a Drosophila chromosome. Problems and Approaches. Springer-Verlag the male-to-female mutation rate ratio from DNA sequence Science 263, 1623–1625 2 Crow, J. F. (1997) The high spontaneous mutation rate: is it a data. J. Mol. Evol. 37, 160–166 7 Crow, J.F. (2000) The origins, patterns and implications of health risk? Proc. Natl. Acad. Sci. U. S. A. 94, 8380–8386 5 Richardson, C. et al.