1. Population Genetics -- Auburn University Welcome to the population genetics Homepage LINKS to places of interestfor ZY 517 Course Syllabus; Research Project Instructions http://www.ag.auburn.edu/~mwooten/popgen.html

Welcome to the POPULATION GENETICS Homepage LINKS to places of interest for ZY 517 Course Syllabus Research Project Instructions and Information Final Exam Questions - Due Wed Noon National Science Foundation Population Genetics Literature MendelWeb Mendel's Original Papers and More! Beach Mouse InfoPage Molecular Ecology HomePage Genetics Information Links of All Kinds Quantiative Genetics Information Links How to Calculate Relatedness and Other Information Simulator for Hardy-Weinberg Software for Genetic Analysis A Little Net Writing Help Writing Across the Curriculum Home Page Elements of Style by Strunk AUBURN University Information Page

2. PBE&B Educational Index Biomath links About the Index population genetics Links. INDEX FOR THIS PAGE This review briefly discusses many population genetics concepts (among other things), including http://www.geocities.com/CapeCanaveral/Lab/4709/popgen.htm

Back to main index ] [PopGen links] [ PopEcol links Evol links Biomath links About the Index Population Genetics Links INDEX FOR THIS PAGE Courses Documents Resources Software ... Feedback Courses with Lecture Notes, Outlines, and Educational Materials "The Genetic Basis for Evolutionary Change", lecture notes Lecture 16 from the "Introduction to Global Change-I" on-line course at the U of Michigan. Lecture discusses (among other topics): sources of genetic variation, Hardy-Weinberg equilibrium, mutation, gene-flow, drift, non-random mating and selection. "... the materials... are available here free of charge, but we request that you register with us [course authorities] and follow our usage guidelines." Lecture outline by D. Bogler at the U of Texas-Austin. Selection index theory and introduction to best linear unbiased prediction (BLUP) Lecture notes (PS and MSWord format) by R. M. Bourdon and B. L. Golden at Colorado State Univ. Population and Quantitative Genetics Course by W. Engels at the U of Wisconsin. Quantitative Genetics Course by S. Haley at South Dakota State Univ. (Lecture notes in PDF format).

3. Population Genetics Web Pages Human Biology population genetics Web Pages. Hardy Weinberg Equation of population genetics. Direct Allele Frequency Calculation http://www.people.virginia.edu/~rjh9u/popgenes.html

Human Biology: Population Genetics Web Pages Hardy Weinberg Equation of Population Genetics Direct Allele Frequency Calculation (co-dominant trait) Indirect Allele Frequency Calculation (recessive trait) H-W Applied to 3 Alleles at a Gene Table of Simple Genotype Frequencies Graphic Form H-W Calculation Spreadsheet (requires a plug-in) Using H-W to Determine Dominant or Recessive MN Blood Group and Hardy Weinberg MNSs Allele Frequencies PKU and CF Frequencies ... Lactose Intolerance Frequencies Class Experiment on Hardy-Weinberg Fall, 1995 Fall, 1996 Fall, 1997 Fall, 1998 ... Sickle-Cell Hemoglobin This document maintained by Robert J. Huskey Last updated on October 13, 1998.

4. Basics Of Population Genetics population genetics I Random breeding. Ordinary genetics looks at how one selects breeding the best possible offspring. population genetics looks at the statistical distribution of http://bowlingsite.mcf.com/Genetics/PopGenI.html

Population Genetics I: Random breeding Ordinary genetics looks at how one selects breeding stock to produce the best possible offspring. Population genetics looks at the statistical distribution of genes in a particular breeding population, such as a breed of dog, and how different kinds of selection can affect that gene distribution. (Increasingly, population genetics also involves looking at the relationship between species by using gene sequencing as a tool.) You can think of ordinary genetics as predicting the phenotypic makup of the next generation, while population genetics predicts the genetic makeup of the breed as a whole, often several generations away. This article is based on the assumption that the population is random breeding - an animal is equally likely to mate with any other animal in the population. This is obviously not really true - a dog in California is much more likely to mate with another California dog than with one in New York, a Great Dane is more likely to mate with another Great Dane than with a Papillion, and many breeders of domesticated animals practice deliberate breeding to relatively close relatives. We'll look at possible effects of this later on (if I get around to it). Random breeding with selection based on a single gene is the simplest case, with which other possibilities can be compared. Unfortunately, I'll have to use a little algebra to do this. I promise I'll try to explain the results in non-mathematical terms.

5. Nearctica - Evolution - Population Genetics population genetics. Special Segments. General Topics. HardyWeinberg Equation. p2. + 2pq + q2 = 1. Buy Books about population genetics. Evolution and Selection of Quantitative Traits. Bruce Walsh http://www.nearctica.com/evolve/popgen.htm

Population Genetics Special Segments Butterflies of North America Conifers of North America Eastern Birds List of N.A. Insects Home Eastern Wildflowers General Topics Natural History Ecology Family Environment Evolution Home Education Home Conservation Geophysics Paleontology Commercial Organizations Hardy-Weinberg Equation p + 2pq + q Buy Books about Population Genetics Evolution and Selection of Quantitative Traits . Bruce Walsh, University of Arizona. This is volume 2 of a two volume work on quantitative genetics and deals with population genetics. These pages are preliminary drafts for a book and will probably only be around until the book is published. The chapters are arranged as a series of Adobe Acrobat files (pdf). The material is extremely technical, but the book is an incredible resource for the web. Highly recommended. Population Genetics Question Page . Michael Wooten, Auburn University. Here's your chance to ask an expert a question about population genetics or genetics. Population Genetics, Random Genetic Drift

6. Population And Evolutionary Genetics Evolutionary Genetics. Darwin's Theory of Natural Selection. Speciation. Study Questions. Population and Evolutiionary Genetics Overheads. Population and Evolutiionary Genetics WWW Links. Genetic Topics. The HardyWeinberg Law The unifying concept of population genetics is the Hardy-Weinberg Law (named after http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/popgen/popgen3.htm

Population Variability Deriving Genotypic and Allelic Frequencies Hardy-Weinberg Equilibrium Evolutionary Genetics Darwin's Theory of Natural Selection Speciation Study Questions ... Genetic Topics The Hardy-Weinberg Law The unifying concept of population genetics is the Hardy-Weinberg Law (named after the two scientists who simultaneously discovered the law). The law predicts how gene frequencies will be transmitted from generation to generation given a specific set of assumptions. Specifically, If an infinitely large, random mating population is free from outside evolutionaryforces (i.e. mutation, migration and natural selection), then the gene frequencies will not change over time and the frequencies in the next generation will be p for the AA genotype, 2 pq for the Aa genotype and q for the aa genotype. Let's examine the assumptions and conclusions in more detail starting first with the assumptions. Infinitely large population - No such population actually exists, but does this necessarily negate the Hardy-Weinberg Law? NO!! The effect that is of concern is genetic drift. Genetic drift is a change in gene frequency that is the result of chance deviation from expected genotypic frequencies. This is a problem in small population, but is minimal in moderate sized or larger populations. Random mating - Random mating refers to matings in a population that occur in proportion to their genotypic frequencies. For example, if the genotypic frequencies in a population are MM=0.83, MN=0.16 and NN=0.01 then we would expect that 68.9% (0.83 x 0.83 X 100) of the matings would occur between MM individuals. If a significant deviation from this expected value occurred, then random mating did not happen in this population. If significant deviations occurred in the other matings (for example MM x MN or MN x NN), again the assumption of random mating will have been violated.

7. Human Genetics - Population Genetics for 1st YEAR STUDENTS. population genetics. INTRODUCTION. he applications of Mendelian genetics, chromosomal use the calculations of population genetics in medical practice, the http://www.uic.edu/classes/bms/bms655/lesson13.html

HUMAN GENETICS for 1st YEAR STUDENTS POPULATION GENETICS INTRODUCTION Population genetics is also the most widely misused area of human genetics, sometimes bordering on "vigilante genetics," a term coined by Newton Morton. Persons have mistakenly applied population genetics to "prove" race superiority for intelligence and aptitudes, and have misused it in eugenics. As an educated and, I hope, a respected member of your community you must be alert to "vigilante genetics." Population genetics is concerned with gene and genotype frequencies, the factors that tend to keep them constant, and the factors that tend to change them in populations. It is largely concerned with the study of polymorphisms. It directly impacts counseling, forensic medicine, and genetic screening. GENE AND GENOTYPE FREQUENCIES CODOMINANT ALLELES Consider a population of 1000 individuals all typed for the simplest test at the MN blood group locus. At its most simplistic form this locus can be reduced to a codominant system with two alleles M and N. (In reality it is considerably more complex than this but this simple form will suffice for our examples.) Every individual in the population will be either M (having two M alleles), MN (heterozygous), or N (having two N alleles). Suppose the blood typing results were as follows: 300 M individuals, 600MN individuals, and 100 N individuals. You probably want to ask, "What is the gene frequency of the M allele in the above population of 1000 individuals?" I'm glad you're interested!

8. Human Population Genetics Laboratory - Home Welcome to the Human population genetics Laboratory (HPGL). We are located inthe Department of Genetics at the Stanford University School of Medicine. http://hpgl.stanford.edu/

PERSONNEL PROJECTS PUBLICATIONS LINKS Welcome to the Human Population Genetics Laboratory (HPGL). We are located in the Department of Genetics at the Stanford University School of Medicine Human Population Genetics Laboratory Department of Genetics School of Medicine Stanford University Stanford, California 94305-5120 United States of America 650.723.7959 (voice) 650.498.6869 (facsimile) http://hpgl.stanford.edu/ info@hpgl.stanford.edu Comments and question to info@hpgl.stanford.edu Stanford University unless noted otherwise.

9. Essentials Of Genetics Provides a range of notes including landmarks, basic terms and rules, chromosomes and genes, population genetics, viral and bacterial genetics, and plant genetics. Includes links to related resources . http://home.att.net/~dorak/genetics.html

10. Kluwer Academic Publishers - Conservation Genetics Publish research papers in a variety of fields including population genetics, molecular ecology and biology, evolutionary biology, and systematics. Subscription information and instructions for authors. http://www.wkap.nl/journalhome.htm/1566-0621

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11. Population Genetics population genetics by Knud Christensen. Division of Animal Genetics.Contents. Chapter 1996. Download population genetics, Pdf file. http://www.kursus.kvl.dk/shares/vetgen/_Popgen/genetics/genetik.htm

Population genetics by Knud Christensen Division of Animal Genetics Contents Chapter 1. Introduction, quantitative versus qualitative (Mendelian) genetics Chapter 2. Hardy-Weinberg law for gene frequency stability in large populations Chapter 3. Deviations from Hardy-Weinberg equilibrium Chapter 4. Relationship and inbreeding Chapter 5. Test of simple genetic hypotheses, experimental or field data Chapter 6. Definition of quantitative traits, breeding values and heritability Chapter 7. Estimation of breeding values Chapter 8. Genetic changes by selection Chapter 9. Inbreeding, crossing and bred structure Chapter 10. Chromosomes and chromosome aberrations Chapter 11. Genetics of hair and coat colour in mammals (under construction) Chapter 12. Estimation- and bio-technology and disease resistance Chapter 13. Exercises and solutions, in Danish Chapter 14. Genetic calculations, applets and other programs Chapter 15. Input to genetic discussion club or former input Introduction The present genetics notes are produced as a substitute for ' Veterinary Genetics ' by FW.Nicolas, Oxford University Press, 1989. This book was not available after 1995.

12. Population Genetics Made Simple population genetics Made Simple. David A. Plaisted. We give a brief survey ofsome of the points of population genetics most relevant for this purpose. http://www.cs.unc.edu/~plaisted/ce/genetics.html

Population Genetics Made Simple David A. Plaisted In order to understand discussions about evolution, even from a creationist viewpoint, it is helpful to have some background in population genetics. We give a brief survey of some of the points of population genetics most relevant for this purpose. The characteristics of organisms are determined by their genetic material (DNA), and random mutations (changes) in the DNA can result in slight changes in organisms. As these accumulate, there can be changes in organisms, resulting in evolution. Population genetics attempts to analyze this process mathematically. Harmful mutations result in organisms less likely to survive, and so these mutations tend to be eliminated from the population (group of organisms in a species). Beneficial mutations also tend to be eliminated by chance, but less often, and tend to be preserved. As these accumulate, the species can gradually adapt to its environment. Neutral mutations are generally eliminated, curiously, but sometimes can spread to the whole population. We then say that the mutation has fixed in the population. The rate of evolution is the rate at which mutations fix in the population. These can be either beneficial or neutral mutations. If the offspring have on the average one harmful mutation each, then the population will degenerate; this is called "error catastrophe." This puts a bound on how many non-neutral mutations can occur per generation. It cannot be much more than about one per generation, and in fact, it must be significantly less, since most non-neutral mutations are harmful.

13. A Population Genetics For Small Evolution A population genetics for Small Evolution. David A. Plaisted. The standardmodel of population genetics on which the theory of evolution http://www.cs.unc.edu/~plaisted/ce/challenge11.html

A Population Genetics for Small Evolution David A. Plaisted My purpose is not to refute evolution or prove creation. I don't think that either is possible, but prefer to reason based on the weight of evidence, which I believe is in favor of creation.. The simple (standard?) population genetics model in which beneficial mutations are not too rare and, when combined, are still beneficial, does not correspond to reality in all cases, as a number of considerations can show. And of course, this is undoubtedly no surprise to population geneticists. In fact, if beneficial mutations are not too rare and can always combine and remain beneficial, then under certain reasonable assumptions, one can show that a random genome would be better adapted than an existing organism. So we can say that a portion of the genome is tightly correlated (highly constrained) if separate mutations A and B in this portion combine as mentioned above. In such a tightly correlated region, mutations must accumulate sequentially. However, there may be more than one such region, and these regions may be independent of one another. Thus, the two regions could evolve independently, increasing the possible rate of evolution. There may also be loosely correlated (loosely constrained) regions of the genome. In the loosely correlated regions, beneficial mutations may be more numerous. Also, I imagine that in a tightly correlated region of the genome, the probability of a beneficial mutation is more like 1/1000 or one in a million, since each change is affecting so many other parts of the organism. This would probably lead to a rate of one beneficial mutation in about 10 or 20 generations, and probably many more generations would be required. If there were a number of tightly correlated regions, largely independent of each other, the rate of evolution could be greater. For example, lungs and legs could evolve in parallel. It is also possible that a tightly correlated region of the organism cannot evolve significantly at all. In a loosely constrained region of the genome, beneficial mutations may be much more common, and evolution could occur much faster.

14. PBE&B Educational Index Index of Educationoriented links for population genetics, PopulationEcology, Evolution, and Biomathematics. population genetics Links. http://www.geocities.com/CapeCanaveral/Lab/4709/

Internet Guide to Education-oriented Resources for Population Genetics, Population Ecology, Evolution, and Biomathematics (Level: College and above) Starting Nov '97, Indexation date of links will be shown in parenthesis Some of the links in these pages contain information in a format different from HTML. Both PDF (Portable Document Format) and PostScript (PS) format links can be viewed with the help of GSview (Ghostscript also required), freely available from the Ghostscript World Wide Web Home Page . Alternatively, PDF documents can be viewed with the Adobe Acrobat Reader , also freely available. See their respective documentation to configure your browser. Population Genetics Links Contains links to: Courses with Lecture Notes, Outlines and Educational Materials On-line Papers and Other Documents Population Genetics Resources Software for Education and Research ... Population Ecology Links Contains links to: Courses with Lecture Notes and On-line Papers Population Ecology Resources Software for Education and Research Conservation ... Evolution Links Contains links to: Courses with Lecture Notes and Outlines On-line Papers, Books and other Documents

15. Basic Population Genetics [M.Tevfik Dorak] Back to HLABack to MHCGlossaryHomepage. BASIC population genetics. M.Tevfik Dorak, M.D physician) independently worked out the mathematical basis of population genetics in 1908 http://dorakmt.tripod.com/genetics/popgen.html

Back to Genetics Back to Evolution Back to Biostatistics Back to HLA ... Homepage BASIC POPULATION GENETICS M.Tevfik Dorak, M.D., Ph.D. G.H. Hardy (the English mathematician) and W. Weinberg (the German physician) independently worked out the mathematical basis of population genetics in 1908. Their formula predicts the expected genotype frequencies using the allele frequencies in a diploid Mendelian population. They were concerned with questions like "what happens to the frequencies of alleles in a population over time?" and "would you expect to see alleles disappear or become more frequent over time?" Hardy and Weinberg showed in the following manner that if the population is very large and random mating is taking place, allele frequencies remain unchanged (or in equilibrium) over time unless some other factors intervene. If the frequencies of allele A and a (of a biallelic locus) are p and q, then (p + q) = 1. This means (p + q = 1 too. It is also correct that (p + q = p + 2pq +q = 1. In this formula, p

16. Population Biology Simulations Simple Java simulations of basic population genetic processes I haveused (or plan to use) in teaching. them. population genetics. http://darwin.eeb.uconn.edu/simulations/simulations.html

Population Biology Simulations Collected here are a few simple simulations (written in Java) I use (or plan to use) when teaching principles of population genetics and population ecology in various courses. If you have suggestions for improving them or ideas for other simulations that might be useful, please contact me at kent@darwin.eeb.uconn.edu . I can't promise that I'll have the time to adopt any suggestions you make, but I promise that I'll consider them. Population Genetics Wahlund effect and F-statistics This applet illustrates the Wahlund effect and partitioning of genetic diversity for five populations. Users may select from a variety of allele frequency configurations and several different inbreeding coefficients within populations (all populations are assumed to have the same inbreeding coefficient). EM algorithm for ABO frequencies This applet illustrates the EM algorithm for estimating allele frequencies in the ABO blood system. Users may select from a variety of sample configurations (including random allocation of phenotypes with three different sample sizes) and several different starting guesses (including random frequencies). Results from each iteration are displayed, but only six iterations can be displayed simultaenously. Genetic drift This simulation illustrates how allele frequencies change over time as a result of genetic drift in small populations. Users may select from three different starting allele frequenciese (0.1, 0.5, 0.9), five different population sizes (10, 25, 50, 100, 250), and three different numbers of generations for the simulation (50, 100, 250). Results from up to eight simulations are displayed simultaneously in different colors.

17. PopGen HomePage Software that models population genetics with emphasis on genetic drift, selection, and migration. http://cc.oulu.fi/~jaspi/popgen/popgen.htm

Welcome to PopGen 1.0 1. What is PopGen PopGen is a simulation program designed to clarify various population genetic events. It is aimed mainly for teaching purposes. It has been programmed by Jouni Aspi using Microsoft's Visual Basic. The code is based on previous GW-Basic and QuickBasic programs by Jaakko Lumme and Jouni Aspi. 2. General description With PopGen you can simulate some deterministic and stochastic population genetic processes in a simple one locus, two allele system. There are two alleles A1 and A2. Frequency of allele A1 is p and frequency of allele A2 is q. Genotypes of individuals and their frequencies are: Genotype A A A A A A Frequency p q With the models of PopGen you can study how these allele frequencies are affected by: Genetic drift Selection Migration You can also study sample sizes you need to detect significant deviations from Hardy-Weinberg proportions, when: The studied population is divided to two subpopulations 2. Allele frequencies are not similar in different sexes 3. The mating is not random, but there is some inbreeding in the population 3. Download PopGen for Windows is now available for Windows 3.x and Windows'95. See

18. Papers By Lee Altenberg On-Line Research publications in mathematical population genetics, evolutionary computation, and genetic algorithms. http://dynamics.org/~altenber/PAPERS/

Lee Altenberg's Home Page Curriculum Vitae Papers Evolved Graphics ... document.write(""); Papers by Lee Altenberg On-Line The following is a list of my recent papers and articles. Select Title to see a summary page with abstract and links to download the full paper. List of papers in BibTeX bibliography database format Select [... KB] below to download the paper in specified format. In case you experience http time-outs due to narrow bandwidth Web channels, you can also download the papers from an alternative FTP site Evolutionary Computation Title [click for abstract] Year *.ps.gz *.pdf Tutorial: Evolutionary Computation Models from Population Genetics: Part 2: An Historical Toolbox [120 KB] [418 KB] ... [156 KB] Evolutionary Theory Title [click for abstract] Year *.ps.gz *.pdf Modularity: Understanding the Development and Evolution of Complex Natural Systems [570 KB] [517 KB] Evolvability Checkpoints Against Evolutionary Pathologies ... A Generalization of Theory on the Evolution of Modifier Genes, Ph.D. Dissertation Ecology and Society The Ecological Living Group The Student-Run Course Catalyst: The Second National Student Environmental Conference Member Financing of the People's Intergalactic Food Conspiracy: ... From the Bedroom to the Bomb: An Interview with Paul Ehrlich Letters to the Editor Outdoor Lighting Standards Bill Citizen Ballot Initiatives on Maui Ads Invade Telephone White Pages Functional Villages vs. Gridlock

19. EEB 348 -- Population Genetics population genetics. Spring, 2004. Instructor Kent E. Holsinger. Office TLS 112.Phone 4864059. E-mail kent@darwin.eeb.uconn.edu. Office Hours by appointment. http://darwin.eeb.uconn.edu/eeb348/

Population Genetics Spring, 2004 Instructor: Kent E. Holsinger Office: TLS 112 Phone: E-mail: kent@darwin.eeb.uconn.edu Office Hours: by appointment Teaching Assistant: Robynn Shannon Office: TLS 461 Phone: E-mail: dshannon01@snet.net Office Hours: by appointment Lectures: MWF, 9:00AM, TLS 301 Emergency closing information Announcements April 27, 2004 AMOVA I've posted notes (and a link to a paper) on analysis of molecular variance. One way or the other we'll get started on AMOVA tomorrow even if I have to cut the discussion of evolution in multigene families a little short. It would be a disservice to you not to give you a little exposure to AMOVA and nested clade analysis before the course is over. Posted by Kent at 04:33 PM Comments (0) TrackBack (0) April 25, 2004 Project #3 Project #3 is now posted if you want to get an early look. Posted by Kent at 09:48 PM Comments (0) TrackBack (0) Multigene family notes (final) The notes on multigene families are now complete. You'll notice that I've revised the lecture schedule (a little) to reflect where we stand. The lecture last Friday is labeled as "Tajima's D." We'll finish our discussion of Tajima's D on Monday and start our discussion of evolution in multigene families. I don't expect that we'll finish it. But we will finish it on Wednesday. And we'll finish off the course with a discussion of phylogeography on Wednesday and Friday. Three other organizational items of which you should be aware: I'll be asking Robynn to leave lecture 10 minutes early on Wednesday so that I can distribute an evaluation form with which you can provide me and the department with your evalution of Robynn's performance.

20. Forensic Mathematics DNA identification, biostatistics, and recreational aspects of population genetics. Reports, software, links. http://dna-view.com/

Forensic Mathematics ... is the best short description that I have found to describe the work that I do, which mostly pertains to DNA identification, and includes consulting , writing software DNA-VIEW academic activities in mathematics , biostatistics, and recreational aspects of population genetics. Charles H. Brenner, Ph.D. Consulting in Forensic Mathematics 6801 Thornhill Drive (new) Oakland, California 94611-1336 USA phone fax chb@dna-view.com new pages: technical notes Contents index of this web site Vita Presentations and posters Quote for today ... A challenge: Why confidence limits? forthcoming conferences English Speaking Working Group of the International Society for Forensic Genetics June 17-20, 2004 in Zandvoort, the Netherlands Mediterranean Academy of Forensic Sciences (MAFS) Workshop June 11-12, Calabria Italy Index Situs The site indexing doesn't seem to be comprehensive. Try the search if you like, but sometimes you will have more luck just reading the web page names on this index page. Search this site Site search Website search technology courtesy FreeFind.com

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