Presentation of a paper by LMC & OKW. Devil in the details:Analysis of a coevolutionary model of language evolution via relaxation of selection. Advances in Artificial Life, ECAL 2011. Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems.
Neutral theory proposes that most mutations are neutral and do not affect fitness. Under neutral evolution, genetic drift is the main factor driving changes in allele frequencies in populations rather than natural selection. Tests based on polymorphism and divergence data can help determine if loci are evolving neutrally or under the influence of selection. Extended haplotype homozygosity (EHH) and cross population EHH (XPEHH) are methods used to detect signatures of positive selection by examining the breakdown of linkage disequilibrium around candidate regions.
Introduction to conservation genetics and genomicsRanajitDas12
1) The document introduces population genetics and its application to conservation. It defines key terms like allele frequency, genotype frequency, and Hardy-Weinberg equilibrium.
2) Mutation, recombination, migration, and natural selection are described as the main forces that can drive evolution by changing allele frequencies over time. Mutation introduces new variants while selection favors advantageous variants.
3) Models of mutation, migration, genetic drift and natural selection are presented to explain how they impact allele frequency changes in a population both qualitatively and quantitatively over multiple generations. The interaction between mutation and selection is also described.
The devil in the details by Carlos CortesYolanda Reyes
1. The document describes a German family - Heinzjuergen, his Filipina wife Cherilyn, and their 2-year old son Peter - attempting to fly from Cebu to Frankfurt via Singapore.
2. Upon checking their documents, the person in charge realizes Cherilyn's Schengen visa is not valid until May 4th, while their connecting flight would arrive in Frankfurt on April 5th.
3. They determine Cherilyn will only be allowed to travel to Singapore, and will need to change her flight to depart after May 3rd when her visa becomes valid. The inaccurate date on Cherilyn's visa leads to issues with her travel plans.
Analysis: Dead Stars by Paz Marquez BenitezSungwoonie
Alfredo Salazar was engaged to Esperanza but fell in love with Julia Salas. At their final meeting before his wedding, Julia told Alfredo to honor his commitment to Esperanza. Alfredo married Esperanza but never stopped thinking about Julia. Years later he visited Julia's hometown and found her still unmarried, realizing his love for her was just a memory.
This document provides an outline for a lecture on the genetic basis of evolution. It begins with introducing key terms like gene, locus, allele, genotype, and phenotype. It then discusses genetic drift and how drift is influenced by population size. Selection is also introduced and defined as a process where individuals with different genotypes have different fitnesses. The document emphasizes that both genetic drift and selection influence evolution, and neither process should be overemphasized. It aims to move people away from only considering selection (pan-selectionism) and highlights the importance of genetic drift.
Five factors drive evolution in populations: mutation, migration, genetic drift, natural selection, and nonrandom mating. Genetic drift is the change in allele frequencies that occurs due to random sampling error in small populations. It can cause alleles to be lost or fixed in a population by chance alone, independent of adaptive effects. The rate of genetic drift is influenced by population size, with smaller populations experiencing stronger drift effects due to increased sampling error. Effective population size is often much smaller than actual population size due to factors like unequal sex ratios. Genetic drift reduces genetic diversity over time and can cause maladaptive evolution if drift is stronger than selection.
This document provides an outline and content for a lecture on the genetic basis of evolution. The key points covered include:
- Genetic drift and natural selection both influence evolution but selection does not explain everything, as the "pan-selectionist" view suggests.
- Genetic drift, the random changes in allele frequencies between generations due to chance events, is an important evolutionary process that occurs in all populations. It accounts for genetic differences between individuals, populations, and species.
- Other topics that will be covered include defining terms like genes, loci, alleles, genotypes and phenotypes, and exploring the concepts of genetic drift and natural selection in more detail. The goal is to move beyond a "just-so"
Neutral theory proposes that most mutations are neutral and do not affect fitness. Under neutral evolution, genetic drift is the main factor driving changes in allele frequencies in populations rather than natural selection. Tests based on polymorphism and divergence data can help determine if loci are evolving neutrally or under the influence of selection. Extended haplotype homozygosity (EHH) and cross population EHH (XPEHH) are methods used to detect signatures of positive selection by examining the breakdown of linkage disequilibrium around candidate regions.
Introduction to conservation genetics and genomicsRanajitDas12
1) The document introduces population genetics and its application to conservation. It defines key terms like allele frequency, genotype frequency, and Hardy-Weinberg equilibrium.
2) Mutation, recombination, migration, and natural selection are described as the main forces that can drive evolution by changing allele frequencies over time. Mutation introduces new variants while selection favors advantageous variants.
3) Models of mutation, migration, genetic drift and natural selection are presented to explain how they impact allele frequency changes in a population both qualitatively and quantitatively over multiple generations. The interaction between mutation and selection is also described.
The devil in the details by Carlos CortesYolanda Reyes
1. The document describes a German family - Heinzjuergen, his Filipina wife Cherilyn, and their 2-year old son Peter - attempting to fly from Cebu to Frankfurt via Singapore.
2. Upon checking their documents, the person in charge realizes Cherilyn's Schengen visa is not valid until May 4th, while their connecting flight would arrive in Frankfurt on April 5th.
3. They determine Cherilyn will only be allowed to travel to Singapore, and will need to change her flight to depart after May 3rd when her visa becomes valid. The inaccurate date on Cherilyn's visa leads to issues with her travel plans.
Analysis: Dead Stars by Paz Marquez BenitezSungwoonie
Alfredo Salazar was engaged to Esperanza but fell in love with Julia Salas. At their final meeting before his wedding, Julia told Alfredo to honor his commitment to Esperanza. Alfredo married Esperanza but never stopped thinking about Julia. Years later he visited Julia's hometown and found her still unmarried, realizing his love for her was just a memory.
This document provides an outline for a lecture on the genetic basis of evolution. It begins with introducing key terms like gene, locus, allele, genotype, and phenotype. It then discusses genetic drift and how drift is influenced by population size. Selection is also introduced and defined as a process where individuals with different genotypes have different fitnesses. The document emphasizes that both genetic drift and selection influence evolution, and neither process should be overemphasized. It aims to move people away from only considering selection (pan-selectionism) and highlights the importance of genetic drift.
Five factors drive evolution in populations: mutation, migration, genetic drift, natural selection, and nonrandom mating. Genetic drift is the change in allele frequencies that occurs due to random sampling error in small populations. It can cause alleles to be lost or fixed in a population by chance alone, independent of adaptive effects. The rate of genetic drift is influenced by population size, with smaller populations experiencing stronger drift effects due to increased sampling error. Effective population size is often much smaller than actual population size due to factors like unequal sex ratios. Genetic drift reduces genetic diversity over time and can cause maladaptive evolution if drift is stronger than selection.
This document provides an outline and content for a lecture on the genetic basis of evolution. The key points covered include:
- Genetic drift and natural selection both influence evolution but selection does not explain everything, as the "pan-selectionist" view suggests.
- Genetic drift, the random changes in allele frequencies between generations due to chance events, is an important evolutionary process that occurs in all populations. It accounts for genetic differences between individuals, populations, and species.
- Other topics that will be covered include defining terms like genes, loci, alleles, genotypes and phenotypes, and exploring the concepts of genetic drift and natural selection in more detail. The goal is to move beyond a "just-so"
This document provides an overview of lectures for Week 6 on the genetic basis of evolution. The lectures will cover general introductions, defining key terms, genetic drift, and natural selection. Students are advised to read additional material on evolution. The lectures aim to move students away from overly simplistic "pan-selectionist" views and help them understand how genetic drift and natural selection both shape evolution. Genetic drift, the random changes in allele frequencies due to chance events in small populations, is a major factor in evolution and occurs in all populations.
2014 talk at NYU CUSP: "Biology Caught the Bus: Now what? Sequencing, Big Dat...c.titus.brown
This document summarizes a presentation on analyzing soil microbial communities through shotgun metagenomics. It begins with an analogy that sequencing environmental DNA is like shredding books and trying to reconstruct their contents computationally. It describes challenges like errors, rare sequences, and analyzing huge datasets. It outlines goals of understanding soil microbes' roles and responding to perturbations. It discusses using large datasets like the Great Prairie Grand Challenge to reconstruct metagenomes and answer ecological questions. It proposes two solutions: 1) partitioning data by binning reads, and 2) discarding redundant data through digital normalization to reduce memory needs and allow assembly of massive datasets.
This document discusses inbreeding in animal and plant breeding populations. It defines inbreeding as the mating of closely related individuals, which can decrease vigor but retain desirable traits. Inbreeding leads to inbreeding depression and higher inbreeding coefficients over time. The document illustrates how selection intensity and heritability impact inbreeding and kinship in a simulated population over generations. It provides examples of unintended inbreeding consequences in animal breeding and the intentional use of inbreeding to create hybrid plant varieties with heterosis effects.
EEB 321 Community Ecology: phylogenetics lecture Rachel Germain
This document outlines a lecture on community phylogenetics, which is the study of how evolutionary relationships among species affect community structure. It discusses classic theories of limiting similarity and how relatedness may influence communities. Contemporary approaches use phylogenetic tools to infer patterns of community assembly from evolutionary processes. The lecture also examines how phylogenetic distances can estimate species similarity and tests for phylogenetic over- and under-dispersion in communities. It further explores how differences in stabilizing niche differences versus fitness differences influence coexistence across evolutionary time.
p. 1Lab 6 Population Genetics Hardy-Weinberg TheoremOBJEC.docxalfred4lewis58146
p. 1Lab 6: Population Genetics: Hardy-Weinberg Theorem
OBJECTIVES
After completing this exercise, you should be able to:
1)
Explain Hardy‑Weinberg equilibrium in terms of allelic and genotypic frequencies and relate these to the expression (p+ q)2 = p2 + 2pq + q2 = 1.
2)
Describe the conditions necessary to maintain Hardy‑Weinberg equilibrium.
3)
Use a computer simulation to demonstrate conditions for evolution.
4)
Test hypotheses concerning the effects of evolutionary change (migration, genetic drift via bottleneck effect, and natural selection) using a computer model.
Simulation of Evolutionary Change Using an Online Population Simulator
Under the conditions specified by the Hardy‑Weinberg model (random mating, large population, no mutation, no migration, and no selection), the genetic frequencies should not change, and evolution should not occur. In this exercise, the class will modify these conditions and determine the effect on genetic frequencies in subsequent generations.
Work in teams of two or three students to simulate three scenarios:
1. Genetic drift- simulated by applying a bottleneck event where a population experiences a drastic reduction in size due only to chance (no selection)
2. Gene flow- simulated by allowing migration to occur between populations
3. Natural selection- simulated by providing certain genotypes with different levels of fitness.
You will be using a computerized population simulator, a general introduction is shown below. The URL for the simulator is http://www.radford.edu/~rsheehy/Gen_flash/popgen/
Experiment A. Simulation of Genetic Drift
Introduction
Genetic drift is the change in allelic frequencies in small populations as a result of chance alone. In a small population, combinations of gametes may not be random, owing to sampling error. (If you toss a coin 500 times, you expect about a 50:50 ratio of heads to tails; but if you toss the coin only 10 times, the ratio may deviate greatly in a small sample owing to chance alone.) Genetic fixation, the loss of all but one possible allele at a gene locus in a population, is a common result of genetic drift in small natural populations. Genetic drift is a significant evolutionary force in situations known as the bottleneck effect (investigated here)and the founder effect.
A bottleneck occurs when a population undergoes a drastic reduction in size as a result of chance events (not differential selection), such as a volcanic eruption, hurricane, or sometimes human influence. (Bad luck, not bad genes!) In Figure 6.1, the marbles pass through a bottleneck, which results in an unpredictable combination of marbles that pass to the other side. These marbles would constitute the beginning of the next generation, but the allelic frequencies might be entirely different than the original population! In the computerized simulation, both the size and duration (number of generations) of a bottleneck can be altered. Each variable can influencing how t.
This document summarizes a research project that aims to model language competition and coexistence using mathematical models. The researchers intend to:
1) Develop a model that allows for the stable coexistence of languages with meaningful applications.
2) Understand how social factors like prestige and resistance to assimilation affect language integration within a bilingual model.
3) Understand how temporal and spatial parameters impact a language's social standing and resistance to assimilation.
This document discusses quantitative traits, which are traits influenced by multiple genes and the environment, resulting in continuous variation in phenotypes rather than discrete categories. It provides examples of quantitative traits like height and explains how Mendelian genetics can still underlie such traits. For example, wheat kernel color is influenced by three genes, with partial dominance of alleles resulting in a quantitative distribution of colors in offspring. The document also discusses statistics used to describe and analyze quantitative traits, like mean, variance, and heritability.
This document summarizes a presentation on genetic mapping and association mapping. It discusses genetic mapping, how it orders genes along chromosomes based on recombination frequency. It then introduces association mapping as an alternative that uses linkage disequilibrium to identify marker-trait associations in natural populations. Key factors that influence linkage disequilibrium like germplasm, recombination rates, and generations are described. The document contrasts linkage and association mapping, noting how association mapping allows for higher resolution mapping. Approaches for association mapping like candidate gene and genome-wide methods are outlined, along with their advantages and limitations.
1. The document discusses factors that can initiate microevolution by changing gene frequencies in populations.
2. It explains that microevolution occurs within populations and involves changes in gene frequency over time due to factors like mutation, natural selection, genetic drift, non-random mating, and gene flow.
3. For a population to evolve, at least one of the five conditions of Hardy-Weinberg equilibrium must be absent - no mutations, random mating, no natural selection, extremely large population size, or no gene flow.
This document discusses key concepts in statistical analysis, including parameters, statistics, and their uses. It provides examples to distinguish between population parameters and sample statistics. Parameters represent entire populations and are studied using all data, while statistics represent samples and are used to estimate parameters. The document also discusses defining problems, data collection methods like census and sampling, and the four basic steps of statistical data analysis: defining the problem, collecting data, analyzing data, and reporting results.
1) The chi-square test is a nonparametric test used to analyze categorical data when assumptions of parametric tests are violated. It compares observed frequencies to expected frequencies specified by the null hypothesis.
2) The chi-square test can test for goodness of fit, evaluating if sample proportions match population proportions. It can also test independence, assessing relationships between two categorical variables.
3) To perform the test, observed and expected frequencies are calculated and entered into the chi-square formula. The resulting statistic is compared to critical values of the chi-square distribution to determine significance.
This document provides information about an upcoming lecture on selection, gene flow, and mutation. It includes the following:
1) Announcements about an upcoming workshop assessment and tutorial.
2) An outline of the lecture topics: types of selection, gene flow, mutation, and a review session.
3) Details about different types of selection including dominant, recessive, heterozygote advantage and disadvantage. It discusses examples like sickle cell anemia.
4) A discussion of gene flow and how it affects genetic differentiation between populations.
5) A definition of mutation and different types like point mutations, insertions, deletions, and larger events. It also discusses mutation's interaction with drift
Genetic algorithms are a type of evolutionary algorithm that mimics natural selection. They operate on a population of potential solutions applying operators like selection, crossover and mutation to produce the next generation. The algorithm iterates until a termination condition is met, such as a solution being found or a maximum number of generations being produced. Genetic algorithms are useful for optimization and search problems as they can handle large, complex search spaces. However, they require properly defining the fitness function and tuning various parameters like population size, mutation rate and crossover rate.
An Experimental Study of Natural Selection and Relative Fitness .docxamrit47
An Experimental Study of Natural Selection and Relative Fitness
Introduction (2/3 or 2/4)
Biological evolution is a fundamental concept in biology that helps us understand the natural world i.e., the history and diversity of life on Earth. At the most basic definition, biological evolution is descent with modification. That is, subsequent generations change over time. Biological evolution can be subdivided into microevolution and macroevolution. Microevolution involves small-scale changes in allele frequencies in a population from one generation to the next. Macroevolution encompasses large-scale changes that produces different species from common ancestors over many generations. Since macroevolution requires an extensive period of time (most are beyond human lifetimes), macroevolutionary studies are largely observational. In other words, we cannot create experiments to test macroevolutionary hypotheses. Instead, we observe patterns and infer the processes from those patterns. Alternatively, microevolution studies require a relatively short period of time such that hypotheses testing can be observational or experimentational (we can create experiments).
Performing microevolution experiments requires an understanding of the Hardy-
Weinberg equilibrium principle. Hardy-Weinberg equilibrium is a simple mathematical model
that assumes a single population’s gene pool does not change in frequency from one generation
to the next. The model is represented by two algebraic equations: the allele frequency equation (p
+ q = 1) and the genotype frequency equation (p2 + 2pq + q2 = 1). To illustrate these equations,
let’s consider a simple dominant/recessive relationship of a character (mouse fur color,
represented by the letter “b”) with two traits (brown and white). This means we will have two
alleles and three genotypes. The lower-case b allele represents the white fur trait and the upper-
case B allele represents the brown fur trait, while the white fur phenotype is represented by the
ww genotype and the brown fur phenotype is represented by the WW and Ww genotypes. With
respect to the frequencies, f(w) is represented by q and f(W) is represented by p, while ww is 22
represented by q , Ww is represented by pq and WW is represented by p . This lab consists of using these equations to determine whether microevolution has occurred, so make sure you understand them.
In simpler terms, this means that if 60% of a population of mice have the white fur trait and 40% have the brown fur trait, this proportion will be the same in the next generation regardless of population size. There may be more individuals in the next generation, but the ratio remains the same (three white fur traits to two brown fur traits). As a principle, this expectation makes sense. However, there are mechanisms of evolutionary change that violate this Hardy- Weinberg equilibrium principle that need to be understood.
There are five recognized mechanisms that disrupt the Ha.
Association mapping for improvement of agronomic traits in riceSopan Zuge
This document summarizes a seminar on association mapping in plants. It discusses how association mapping offers greater precision in locating quantitative trait loci (QTLs) than family-based linkage analysis by taking advantage of linkage disequilibrium across diverse populations. The key steps in association mapping are described, including population selection and structure analysis, high-throughput phenotyping and genotyping, measuring linkage disequilibrium, and association analysis to identify marker-trait links. Software for conducting association mapping and case studies in rice are also reviewed.
This document discusses genetic algorithms and provides an overview of their key concepts and components. It describes how genetic algorithms are inspired by Darwinian evolution and use techniques like selection, crossover and mutation to evolve solutions to optimization problems. It also outlines various parameters and strategies used in genetic algorithms, including chromosome representation, population size, selection methods, and termination criteria. A wide range of applications are mentioned where genetic algorithms have been applied successfully.
This document discusses how populations evolve through changes in allele frequencies over generations due to various evolutionary mechanisms. It explains that evolution occurs at the population level, driven by mutations which introduce genetic variation, and natural selection which causes some genotypes to reproduce more successfully than others based on environmental pressures. Genetic drift, the chance fluctuation of allele frequencies especially in small populations, is another factor that can drive evolutionary change.
Genetic algorithms are computational models inspired by biological evolution. They work by encoding potential solutions to a problem as strings called chromosomes. An initial population of random chromosomes is generated. The chromosomes are then evaluated and reproductive opportunities are allocated based on fitness, with better solutions more likely to reproduce. Operators like crossover and mutation combine parts of existing chromosomes to form new ones for the next generation. This process is repeated until a termination criterion is reached, with the goal of evolving better and better solutions over generations based on the principle of survival of the fittest.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
This document provides an overview of lectures for Week 6 on the genetic basis of evolution. The lectures will cover general introductions, defining key terms, genetic drift, and natural selection. Students are advised to read additional material on evolution. The lectures aim to move students away from overly simplistic "pan-selectionist" views and help them understand how genetic drift and natural selection both shape evolution. Genetic drift, the random changes in allele frequencies due to chance events in small populations, is a major factor in evolution and occurs in all populations.
2014 talk at NYU CUSP: "Biology Caught the Bus: Now what? Sequencing, Big Dat...c.titus.brown
This document summarizes a presentation on analyzing soil microbial communities through shotgun metagenomics. It begins with an analogy that sequencing environmental DNA is like shredding books and trying to reconstruct their contents computationally. It describes challenges like errors, rare sequences, and analyzing huge datasets. It outlines goals of understanding soil microbes' roles and responding to perturbations. It discusses using large datasets like the Great Prairie Grand Challenge to reconstruct metagenomes and answer ecological questions. It proposes two solutions: 1) partitioning data by binning reads, and 2) discarding redundant data through digital normalization to reduce memory needs and allow assembly of massive datasets.
This document discusses inbreeding in animal and plant breeding populations. It defines inbreeding as the mating of closely related individuals, which can decrease vigor but retain desirable traits. Inbreeding leads to inbreeding depression and higher inbreeding coefficients over time. The document illustrates how selection intensity and heritability impact inbreeding and kinship in a simulated population over generations. It provides examples of unintended inbreeding consequences in animal breeding and the intentional use of inbreeding to create hybrid plant varieties with heterosis effects.
EEB 321 Community Ecology: phylogenetics lecture Rachel Germain
This document outlines a lecture on community phylogenetics, which is the study of how evolutionary relationships among species affect community structure. It discusses classic theories of limiting similarity and how relatedness may influence communities. Contemporary approaches use phylogenetic tools to infer patterns of community assembly from evolutionary processes. The lecture also examines how phylogenetic distances can estimate species similarity and tests for phylogenetic over- and under-dispersion in communities. It further explores how differences in stabilizing niche differences versus fitness differences influence coexistence across evolutionary time.
p. 1Lab 6 Population Genetics Hardy-Weinberg TheoremOBJEC.docxalfred4lewis58146
p. 1Lab 6: Population Genetics: Hardy-Weinberg Theorem
OBJECTIVES
After completing this exercise, you should be able to:
1)
Explain Hardy‑Weinberg equilibrium in terms of allelic and genotypic frequencies and relate these to the expression (p+ q)2 = p2 + 2pq + q2 = 1.
2)
Describe the conditions necessary to maintain Hardy‑Weinberg equilibrium.
3)
Use a computer simulation to demonstrate conditions for evolution.
4)
Test hypotheses concerning the effects of evolutionary change (migration, genetic drift via bottleneck effect, and natural selection) using a computer model.
Simulation of Evolutionary Change Using an Online Population Simulator
Under the conditions specified by the Hardy‑Weinberg model (random mating, large population, no mutation, no migration, and no selection), the genetic frequencies should not change, and evolution should not occur. In this exercise, the class will modify these conditions and determine the effect on genetic frequencies in subsequent generations.
Work in teams of two or three students to simulate three scenarios:
1. Genetic drift- simulated by applying a bottleneck event where a population experiences a drastic reduction in size due only to chance (no selection)
2. Gene flow- simulated by allowing migration to occur between populations
3. Natural selection- simulated by providing certain genotypes with different levels of fitness.
You will be using a computerized population simulator, a general introduction is shown below. The URL for the simulator is http://www.radford.edu/~rsheehy/Gen_flash/popgen/
Experiment A. Simulation of Genetic Drift
Introduction
Genetic drift is the change in allelic frequencies in small populations as a result of chance alone. In a small population, combinations of gametes may not be random, owing to sampling error. (If you toss a coin 500 times, you expect about a 50:50 ratio of heads to tails; but if you toss the coin only 10 times, the ratio may deviate greatly in a small sample owing to chance alone.) Genetic fixation, the loss of all but one possible allele at a gene locus in a population, is a common result of genetic drift in small natural populations. Genetic drift is a significant evolutionary force in situations known as the bottleneck effect (investigated here)and the founder effect.
A bottleneck occurs when a population undergoes a drastic reduction in size as a result of chance events (not differential selection), such as a volcanic eruption, hurricane, or sometimes human influence. (Bad luck, not bad genes!) In Figure 6.1, the marbles pass through a bottleneck, which results in an unpredictable combination of marbles that pass to the other side. These marbles would constitute the beginning of the next generation, but the allelic frequencies might be entirely different than the original population! In the computerized simulation, both the size and duration (number of generations) of a bottleneck can be altered. Each variable can influencing how t.
This document summarizes a research project that aims to model language competition and coexistence using mathematical models. The researchers intend to:
1) Develop a model that allows for the stable coexistence of languages with meaningful applications.
2) Understand how social factors like prestige and resistance to assimilation affect language integration within a bilingual model.
3) Understand how temporal and spatial parameters impact a language's social standing and resistance to assimilation.
This document discusses quantitative traits, which are traits influenced by multiple genes and the environment, resulting in continuous variation in phenotypes rather than discrete categories. It provides examples of quantitative traits like height and explains how Mendelian genetics can still underlie such traits. For example, wheat kernel color is influenced by three genes, with partial dominance of alleles resulting in a quantitative distribution of colors in offspring. The document also discusses statistics used to describe and analyze quantitative traits, like mean, variance, and heritability.
This document summarizes a presentation on genetic mapping and association mapping. It discusses genetic mapping, how it orders genes along chromosomes based on recombination frequency. It then introduces association mapping as an alternative that uses linkage disequilibrium to identify marker-trait associations in natural populations. Key factors that influence linkage disequilibrium like germplasm, recombination rates, and generations are described. The document contrasts linkage and association mapping, noting how association mapping allows for higher resolution mapping. Approaches for association mapping like candidate gene and genome-wide methods are outlined, along with their advantages and limitations.
1. The document discusses factors that can initiate microevolution by changing gene frequencies in populations.
2. It explains that microevolution occurs within populations and involves changes in gene frequency over time due to factors like mutation, natural selection, genetic drift, non-random mating, and gene flow.
3. For a population to evolve, at least one of the five conditions of Hardy-Weinberg equilibrium must be absent - no mutations, random mating, no natural selection, extremely large population size, or no gene flow.
This document discusses key concepts in statistical analysis, including parameters, statistics, and their uses. It provides examples to distinguish between population parameters and sample statistics. Parameters represent entire populations and are studied using all data, while statistics represent samples and are used to estimate parameters. The document also discusses defining problems, data collection methods like census and sampling, and the four basic steps of statistical data analysis: defining the problem, collecting data, analyzing data, and reporting results.
1) The chi-square test is a nonparametric test used to analyze categorical data when assumptions of parametric tests are violated. It compares observed frequencies to expected frequencies specified by the null hypothesis.
2) The chi-square test can test for goodness of fit, evaluating if sample proportions match population proportions. It can also test independence, assessing relationships between two categorical variables.
3) To perform the test, observed and expected frequencies are calculated and entered into the chi-square formula. The resulting statistic is compared to critical values of the chi-square distribution to determine significance.
This document provides information about an upcoming lecture on selection, gene flow, and mutation. It includes the following:
1) Announcements about an upcoming workshop assessment and tutorial.
2) An outline of the lecture topics: types of selection, gene flow, mutation, and a review session.
3) Details about different types of selection including dominant, recessive, heterozygote advantage and disadvantage. It discusses examples like sickle cell anemia.
4) A discussion of gene flow and how it affects genetic differentiation between populations.
5) A definition of mutation and different types like point mutations, insertions, deletions, and larger events. It also discusses mutation's interaction with drift
Genetic algorithms are a type of evolutionary algorithm that mimics natural selection. They operate on a population of potential solutions applying operators like selection, crossover and mutation to produce the next generation. The algorithm iterates until a termination condition is met, such as a solution being found or a maximum number of generations being produced. Genetic algorithms are useful for optimization and search problems as they can handle large, complex search spaces. However, they require properly defining the fitness function and tuning various parameters like population size, mutation rate and crossover rate.
An Experimental Study of Natural Selection and Relative Fitness .docxamrit47
An Experimental Study of Natural Selection and Relative Fitness
Introduction (2/3 or 2/4)
Biological evolution is a fundamental concept in biology that helps us understand the natural world i.e., the history and diversity of life on Earth. At the most basic definition, biological evolution is descent with modification. That is, subsequent generations change over time. Biological evolution can be subdivided into microevolution and macroevolution. Microevolution involves small-scale changes in allele frequencies in a population from one generation to the next. Macroevolution encompasses large-scale changes that produces different species from common ancestors over many generations. Since macroevolution requires an extensive period of time (most are beyond human lifetimes), macroevolutionary studies are largely observational. In other words, we cannot create experiments to test macroevolutionary hypotheses. Instead, we observe patterns and infer the processes from those patterns. Alternatively, microevolution studies require a relatively short period of time such that hypotheses testing can be observational or experimentational (we can create experiments).
Performing microevolution experiments requires an understanding of the Hardy-
Weinberg equilibrium principle. Hardy-Weinberg equilibrium is a simple mathematical model
that assumes a single population’s gene pool does not change in frequency from one generation
to the next. The model is represented by two algebraic equations: the allele frequency equation (p
+ q = 1) and the genotype frequency equation (p2 + 2pq + q2 = 1). To illustrate these equations,
let’s consider a simple dominant/recessive relationship of a character (mouse fur color,
represented by the letter “b”) with two traits (brown and white). This means we will have two
alleles and three genotypes. The lower-case b allele represents the white fur trait and the upper-
case B allele represents the brown fur trait, while the white fur phenotype is represented by the
ww genotype and the brown fur phenotype is represented by the WW and Ww genotypes. With
respect to the frequencies, f(w) is represented by q and f(W) is represented by p, while ww is 22
represented by q , Ww is represented by pq and WW is represented by p . This lab consists of using these equations to determine whether microevolution has occurred, so make sure you understand them.
In simpler terms, this means that if 60% of a population of mice have the white fur trait and 40% have the brown fur trait, this proportion will be the same in the next generation regardless of population size. There may be more individuals in the next generation, but the ratio remains the same (three white fur traits to two brown fur traits). As a principle, this expectation makes sense. However, there are mechanisms of evolutionary change that violate this Hardy- Weinberg equilibrium principle that need to be understood.
There are five recognized mechanisms that disrupt the Ha.
Association mapping for improvement of agronomic traits in riceSopan Zuge
This document summarizes a seminar on association mapping in plants. It discusses how association mapping offers greater precision in locating quantitative trait loci (QTLs) than family-based linkage analysis by taking advantage of linkage disequilibrium across diverse populations. The key steps in association mapping are described, including population selection and structure analysis, high-throughput phenotyping and genotyping, measuring linkage disequilibrium, and association analysis to identify marker-trait links. Software for conducting association mapping and case studies in rice are also reviewed.
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EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
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ECAL11 Paris - August 2011
1. Devil in the Details: Analysis of a Coevolutionary
Model of Language Evolution via Relaxation of
Selection
Luke McCrohon & Olaf Witkowski
University of Tokyo
Japan
2. A Model of Linguistic
Gene-Culture Coevolution
<source:Y&H2010>
Yamauchi & Hashimoto 2010
2
3. Yamauchi & Hashimoto 2010 :
The Baldwin Effect
• Learned behavior gradually assimilated into the agents genetic repertoire
Fitness
Landscape
Learning
No learning
3
4. • Culture compensating for genetically maladaptive traits
• e.g. biosynthesis of vitamin C
Yamauchi & Hashimoto 2010 :
Cultural Masking
4
5. Yamauchi & Hashimoto 2010:
Why Do We Care ?
• Shows cyclic repetition of stages
• Biological selection is masked, innate behavior degrades
• Selection is unmasked, behaviors are nativized (Baldwin)
• We initially wanted to investigate the influence of the rates of cultural change
5
6. Yamauchi & Hashimoto 2010
• Agents
• Chromosome: Length 12 Array (0 or 1)
• Grammar: Length 12 Array (0, 1 or null)
• Learning resource: Integer value (initially 24)
• Fitness: Integer value (initially 1)
chromosome
grammar
6
7. Yamauchi & Hashimoto 2010
• Every generation, for each agent:
• Learning: exposed to the utterances of
the previous generation, with a chance
to learn them
• Invention: if still null values in grammar,
he has a chance to invent new values
• Communication: interaction with
neighbors in the current generation to
determine his fitness
• Reproduction: new generation created,
replacing the previous one
Figure 3: The spatial organization of the population.
26
<source:Y&H2010>
chromosome
grammar
7
8. Yamauchi & Hashimoto 2010
• An agent learning a word
• matching grammar: $1
• mismatching grammar: $4
Figure 3: The spatial organization of the
teacher
grammar
learner
grammar
utterance
8
9. Yamauchi & Hashimoto 2010
• Every generation, for each agent:
• Learning: exposed to the utterances of
the previous generation, with a chance
to learn them
• Invention: if still null values in grammar,
he has a chance to invent new values
• Communication: interaction with
neighbors in the current generation to
determine his fitness
• Reproduction: new generation created,
replacing the previous one
Figure 3: The spatial organization of the population.
26
<source:Y&H2010>
chromosome
grammar
9
10. Yamauchi & Hashimoto 2010
• Every generation, for each agent:
• Learning: exposed to the utterances of
the previous generation, with a chance
to learn them
• Invention: if still null values in grammar,
he has a chance to invent new values
• Communication: interaction with
neighbors in the current generation to
determine his fitness
• Reproduction: new generation created,
replacing the previous one
Figure 3: The spatial organization of the population.
26
<source:Y&H2010>
chromosome
grammar
10
11. Yamauchi & Hashimoto 2010
• Every generation, for each agent:
• Learning: exposed to the utterances of
the previous generation, with a chance
to learn them
• Invention: if still null values in grammar,
he has a chance to invent new values
• Communication: interaction with
neighbors in the current generation to
determine his fitness
• Reproduction: new generation created,
replacing the previous one
Figure 3: The spatial organization of the population.
26
<source:Y&H2010>
chromosome
grammar
11
13. Yamauchi & Hashimoto 2010 : The Original Results
• Stage 1: Baldwin effect,
Niche Construction
• Agents go from no
culturally transmitted
language, to a highly
uniform language
shared between agents,
and consequently a
high fitness
LearningIntensity
Gene-GrammarMatch
Generations
1 2 3 2*
0 1000 2000 3000 4000 5000
0
4
8
12
16
20
24
0
2
4
6
8
10
12
Learning Intensity
Gene-Grammar
Match
(a) Overall Result
0
4
8
12
16
20
24
LearningIntensity
0
1224 24
13
14. Yamauchi & Hashimoto 2010 : The Original Results
• Stage 1: Baldwin effect,
Niche Construction
• Agents go from no
culturally transmitted
language, to a highly
uniform language
shared between agents,
and consequently a
high fitness
14
15. Yamauchi & Hashimoto 2010 : The Original Results
!
• Stage 2: Functional
Redundancy
• Cultural transmission
masks biological
selection, progressive
drop of correlation
between the gene pool
and the environment
LearningIntensity
Gene-GrammarMatch
Generations
1 2 3 2*
0 1000 2000 3000 4000 5000
0
4
8
12
16
20
24
0
2
4
6
8
10
12
Learning Intensity
Gene-Grammar
Match
(a) Overall Result
0
4
8
12
16
20
24
LearningIntensity
0
1224 24
15
16. Yamauchi & Hashimoto 2010 : The Original Results
• Stage 3: Unmasking of
Natural Selection
• Convergence on
different languages, so
that the gene-grammar
match has deteriorated
so much that biological
selection is no longer
masked.
• Biological assimilatory
process like in 1, leads
to cycles between 2
and 3
LearningIntensity
Gene-GrammarMatch
Generations
1 2 3 2*
0 1000 2000 3000 4000 5000
0
4
8
12
16
20
24
0
2
4
6
8
10
12
Learning Intensity
Gene-Grammar
Match
(a) Overall Result
0
4
8
12
16
20
24
LearningIntensity
0
1224 24
16
17. Yamauchi & Hashimoto 2010 : The Original Results
• Stage 3: Unmasking of
Natural Selection
• Convergence on
different languages, so
that the gene-grammar
match has deteriorated
so much that biological
selection is no longer
masked.
• Biological assimilatory
process like in 1, leads
to cycles between 2
and 3
17
19. Analysis : Genetic Diversity
• Is “Stage 1” really showing of a
Baldwin effect ?
• We ran the simulation with
neutral biological selection,
ignoring fitness
• The same reduction of genetic
diversity is observed
19
20. • The diversity oscillates between 5 and 10, because of genetic drift
• Fast-forward simulation. Ready ?
Analysis : Genetic Diversity
20
21. • The diversity wanders between 5 and 10, because of genetic drift
• Fast-forward simulation. Ready ?
• Results:
Analysis : Genetic Diversity
21
22. Analysis : Genetic Diversity
• Phenotypes (grammars) are even fewer
22
(10 separate runs, over 20000 generations)
23. Analysis : Masked Genetic Selection
• We observe no significant drop
below 8. Why ?
• 24 learning resources = 4 * 4
non-matching + 1 * 8 matching
• Any agent dropping below an 8
match would have its fitness
penalized.
(10 separate runs, over 10000 generations)
23
24. Analysis : Coevolutionary Attractors
• A few values of gene-grammar
match occur more frequently
than others, showing potential
local attractors
• This is caused by language
uniformity and lack of genetic
variation
• Attractors are around integer
values
(5 separate runs, over 5000 generations)
24
25. • State Transitions Graph and Density Plot
Analysis : Coevolutionary Attractors
gene-grammar matches as attractor states in the simulation,
despite them potentially representing a number of different
underlying gene-culture states.
to 12 to 11 to 10 to 9 to 8
from 12 .55 .05 .00 .00 .00
from 11 .01 .52 .07 .01 .00
from 10 .00 .02 .42 .08 .00
from 9 .00 .00 .02 .61 .03
from 8 .00 .00 .00 .04 .78
We calculated the likelihood of the simulation jumping
between each of these attractor states (±0.2 units) over a pe-
riod of 200 generations. The transition probability matrix is
presented in the table above and in the transition diagram in
figure 8. We tested these results compared against equally
sized intervals directly between the attractor states and ob-
tained probabilities of the simulation staying in the same
range approximately 5 times lower than in the case of the
attractors. This indicates that the attractors are significantly
more stable.
Figure 8: State Transition Diagram [Seed=1303037425613,
Runs=50, Generations=20000]
grammar matches that result in agents exhibiting the same
gene-grammar match value. However, as nothing in the
gent’s learning algorithm changes their probability of learn-
ng individual grammatical alleles due to a particular set of
genetic biases (only the number of matches ultimately in-
fluences learning), these different model states will behave
dentically. Because of this it is safe to view the integer value
gene-grammar matches as attractor states in the simulation,
despite them potentially representing a number of different
underlying gene-culture states.
to 12 to 11 to 10 to 9 to 8
from 12 .55 .05 – – –
from 11 .01 .52 .07 .01 –
from 10 – .02 .42 .08 –
from 9 – – .02 .61 .03
from 8 – – – .04 .78
We calculated the likelihood of the simulation jumping
between each of these attractor states (±0.2 units) over a pe-
iod of 200 generations. The transition probability matrix
s presented in the table above and in the transition diagram
n figure 8. We tested these results against transitions be-
ween equally sized intervals positioned directly between the
ttractor states and obtained probabilities of the simulation
taying in those intervals approximately 5 times lower than
n the case of the attractors. This indicates that the attractors
re significantly more stable.
• Shape of the attractors
• attractors not symmetrical
• deviation downward more
probable
• result of biological change:
random change from
optimal is often sub-
optimal
End-3 slides
26. Analysis: Steady State in the Long Run
• Transient can be
ignored
• Lower attractors
favored in the long run
End-2
27. Analysis : Sensitivity to Initial Conditions
400 agents
1000 agents
50 agents
• Changing the population size, we get
this kind of density for the gene-
grammar matches.
• Drift effect masked for a higher
population
• Qualitatively different behavior
End-1
28. End
Conclusions
• The model from Yamauchi & Hashimoto 2010 does capture some of the
intended phenomena (e.g. Cultural Shielding, Niche Construction)
• “Stage 2” does not show the claimed degradation of gene-grammar matches,
but rather is a random walk between a set of attractors
• Observed model behavior is the result of limited Cultural and Biological
Diversity which are themselves the result of the small agent population
• Population Structure and Organization are factors that can potentially
increase diversity without the computational costs of a larger agent
population
30. Devil in the Details: Analysis of a Coevolutionary
Model of Language Evolution via Relaxation of
Selection
Luke McCrohon & Olaf Witkowski
University of Tokyo
Japan