Selection against A 2 (upper row, s = 0.004) and for A 2 (lower row, s = ) N = 25 N = 250 N = 2500
|
|
- Horace Beasley
- 5 years ago
- Views:
Transcription
1 Why mitochondrial DN is simple Mitochondrial DN and the History of Population Size lan R Rogers January 4, 8 inherited from mother only no recombination evolves fast mean pairwise difference: average number of nucleotide site differences between mitochondria of pairs of individuals we will look at about 3 base pairs of mitochondrial DN / 5 / 5 Mitochondrial nucleotide differences (D-loop) Mean pairwise diff: between\within\net Major Human Populations European sian frican (N = ) (N = 7) (N = ) Eur 94 8 s f Chimpanzee Subspecies Pts Ptt Ptv (N = 4) (N = 8) (N = 8) Pts Ptt Ptv Genetic differences between human mitochondria are small between populations small within Eurasian populations somewhat larger within frica Suggests populations separated recently Eurasian populations less ancient 3 / 5 4 / 5 Movies of drift versus selection (N, s, and the fates of mutations) Selection against (upper row, s = 4) and for (lower row, s = -4) Each panel shows allele-freuency histories for a given N, s, and initial freuency Each history runs for generations or until fixation occurs Within each row of three panels, the population sizes are 5, 5, and 5 N = 5 N = 5 N = W( ) =, W( ) = -½s, and W( ) = -s The first set of cases (below) is a neutral control for the experiments in subseuent slides s =, = ½ (neutral case, pure drift) N = 5 fixations for : 48 N = 5 N = fixations for : 5 generations 4 generations generations 48 5 generations generations generations 5 / 5 Ns = Ns = Ns = 6 / 5
2 s = 4 = /N N = 5 N = 5 N = 5 Genealogy of genes s = -4 = /N s = - = /N N 99 7 / 5 8 / 5 Genealogy of 3 genes Genealogy of 4 genes C C N/3 N ( 3 + ) D N/6 N ( 6 + ) 3 N ( ) 9 / 5 / 5 Simulated gene genealogy of a sample of size 5 from a population of constant size Principles The expected length of a coalescent interval is long in large populations if there are only a few lineages What if the population changes in size? Terminal branches are short asal branch is long dditional samples don t tell us much about the ancient past / 5 / 5
3 Population Size Population Size N Effect of a population explosion 7 4 Mutational time before present Genealogy Mismatch Distribution Middle: comb-shaped (or star-shaped) genealogy of 5 individuals; dots are mutations mutational diff per time unit ottom: = simulated data, line = theory Wave peaks at population expansion Mutational time before present Genealogy Mismatch Distribution Simulation of euilibrium population No history of growth Deep genealogy Ragged mismatch distribution 7 4 Site Differences Site Differences 3 / 5 4 / 5 Mitochondrial Mismatch Distribution i ˆN =, 3 ˆN = 9, ˆt = 68, 7 open circles: data of Cann, Stoneking, & Wilson (7) solid line: fit to expansion model (Rogers & Harpending 99) implies expansion 7 kyr ago (or so we thought then) revised molecular clock: 45 kyr ago coincident with origin of modern humans Mismatch Distribution: 77 sian Subjects i open circles: sian data solid line: fit to expansion model (Rogers & Harpending 99) implies expansion 45 kyr ago coincident with origin of modern humans 5 / 5 6 / 5 Mismatch Distributions of merindian mtdn Haplogroups Genealogies of merindian mtdn Haplogroups Fagundes et al 8 Fagundes et al 8 7 / 5 8 / 5
4 Skyline Plot Hepatitus C virus in Egypt (Drummond et al 5) Use mutations to estimate length of each interval Long intervals imply large population size Won t work with nuclear DN: too few mutations per tree (Drummond et al 5) 9 / 5 / 5 Estimated Size of merindian Population Estimated Size of ison Population Fagundes et al 8 / 5 / 5 The Selection Hypothesis Problems with mitochondrial clock Suppose that a favorable mitochondrial mutation arose 6, years ago, and increased in freuency until everyone had it This is called a selective sweep Effect on mitochondrial variation is indistinguishable from that of population growth No recombination: deleterious mutations are hard to get rid of Hang around in mtdn longer than in ndn t short time scales, we overestimate the count of neutral differences Overestimate dates within past, years 3 / 5 4 / 5
5 Summary History of population size affects depth of gene trees, genetic variation, and length of MRC segments We can use these facts to infer the history of population size Mitochondrial DN suggest that human populations were small during the last ice age With mitochondrial DN, it is hard to distinguish the effect of population growth from that of selection 5 / 5
Neutral Theory of Molecular Evolution
Neutral Theory of Molecular Evolution Kimura Nature (968) 7:64-66 King and Jukes Science (969) 64:788-798 (Non-Darwinian Evolution) Neutral Theory of Molecular Evolution Describes the source of variation
More informationUnderstanding relationship between homologous sequences
Molecular Evolution Molecular Evolution How and when were genes and proteins created? How old is a gene? How can we calculate the age of a gene? How did the gene evolve to the present form? What selective
More informationHow robust are the predictions of the W-F Model?
How robust are the predictions of the W-F Model? As simplistic as the Wright-Fisher model may be, it accurately describes the behavior of many other models incorporating additional complexity. Many population
More informationGene Genealogies Coalescence Theory. Annabelle Haudry Glasgow, July 2009
Gene Genealogies Coalescence Theory Annabelle Haudry Glasgow, July 2009 What could tell a gene genealogy? How much diversity in the population? Has the demographic size of the population changed? How?
More informationClassical Selection, Balancing Selection, and Neutral Mutations
Classical Selection, Balancing Selection, and Neutral Mutations Classical Selection Perspective of the Fate of Mutations All mutations are EITHER beneficial or deleterious o Beneficial mutations are selected
More informationCasey Leonard. Multiregional model vs. Out of Africa theory SLCC
Casey Leonard Multiregional model vs. Out of Africa theory SLCC 2 It is debated where humans came from and how they spread across the world. Since people don't all look the same, or are categorized into
More informationApplication of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 5456 546, May 998 Statistics Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data ANDRZEJ
More information7. Tests for selection
Sequence analysis and genomics 7. Tests for selection Dr. Katja Nowick Group leader TFome and Transcriptome Evolution Bioinformatics group Paul-Flechsig-Institute for Brain Research www. nowicklab.info
More informationSolutions to Even-Numbered Exercises to accompany An Introduction to Population Genetics: Theory and Applications Rasmus Nielsen Montgomery Slatkin
Solutions to Even-Numbered Exercises to accompany An Introduction to Population Genetics: Theory and Applications Rasmus Nielsen Montgomery Slatkin CHAPTER 1 1.2 The expected homozygosity, given allele
More informationLecture 11 Friday, October 21, 2011
Lecture 11 Friday, October 21, 2011 Phylogenetic tree (phylogeny) Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system
More informationEvolution Problem Drill 10: Human Evolution
Evolution Problem Drill 10: Human Evolution Question No. 1 of 10 Question 1. Which of the following statements is true regarding the human phylogenetic relationship with the African great apes? Question
More information6 Introduction to Population Genetics
70 Grundlagen der Bioinformatik, SoSe 11, D. Huson, May 19, 2011 6 Introduction to Population Genetics This chapter is based on: J. Hein, M.H. Schierup and C. Wuif, Gene genealogies, variation and evolution,
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More informationQ1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate.
OEB 242 Exam Practice Problems Answer Key Q1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate. First, recall
More informationPhylogeny and Molecular Evolution. Introduction
Phylogeny and Molecular Evolution Introduction 1 Credit Serafim Batzoglou (UPGMA slides) http://www.stanford.edu/class/cs262/slides Notes by Nir Friedman, Dan Geiger, Shlomo Moran, Ron Shamir, Sagi Snir,
More information6 Introduction to Population Genetics
Grundlagen der Bioinformatik, SoSe 14, D. Huson, May 18, 2014 67 6 Introduction to Population Genetics This chapter is based on: J. Hein, M.H. Schierup and C. Wuif, Gene genealogies, variation and evolution,
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
More informationEvidence of evolution
The Theory of Evolution Charles Darwin Evidence for evolution Mechanisms for evolution Natural selection Speciation Evidence of evolution Structural adaptations Mimicry Camouflage Physiological adaptations
More informationIntraspecific gene genealogies: trees grafting into networks
Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation
More informationSelection and Population Genetics
Selection and Population Genetics Evolution by natural selection can occur when three conditions are satisfied: Variation within populations - individuals have different traits (phenotypes). height and
More informationEstimating Evolutionary Trees. Phylogenetic Methods
Estimating Evolutionary Trees v if the data are consistent with infinite sites then all methods should yield the same tree v it gets more complicated when there is homoplasy, i.e., parallel or convergent
More informationEndowed with an Extra Sense : Mathematics and Evolution
Endowed with an Extra Sense : Mathematics and Evolution Todd Parsons Laboratoire de Probabilités et Modèles Aléatoires - Université Pierre et Marie Curie Center for Interdisciplinary Research in Biology
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More informationGENETICS OF MODERN HUMAN ORIGINS AND DIVERSITY
Annu. Rev. Anthropol. 1998. 27:1 23 Copyright 1998 by Annual Reviews. All rights reserved GENETICS OF MODERN HUMAN ORIGINS AND DIVERSITY John H. Relethford Department of Anthropology, State University
More informationEvolutionary Rates in mtdna Sequences: Forensic Applications and Implications
Evolutionary Rates in mtdn Sequences: Forensic pplications and Implications Thomas J. Parsons Director of Forensic Sciences International Commission on Missing Persons 1 Obligatory Reminders, The mtdn
More information8/23/2014. Phylogeny and the Tree of Life
Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major
More informationUnit 5: Taxonomy. KEY CONCEPT Organisms can be classified based on physical similarities.
KEY CONCEPT Organisms can be classified based on physical similarities. Linnaeus developed the scientific naming system still used today. Taxonomy is the science of naming and classifying organisms. White
More informationTaming the Beast Workshop
Workshop and Chi Zhang June 28, 2016 1 / 19 Species tree Species tree the phylogeny representing the relationships among a group of species Figure adapted from [Rogers and Gibbs, 2014] Gene tree the phylogeny
More informationEvolutionary trees. Describe the relationship between objects, e.g. species or genes
Evolutionary trees Bonobo Chimpanzee Human Neanderthal Gorilla Orangutan Describe the relationship between objects, e.g. species or genes Early evolutionary studies The evolutionary relationships between
More informationSurfing genes. On the fate of neutral mutations in a spreading population
Surfing genes On the fate of neutral mutations in a spreading population Oskar Hallatschek David Nelson Harvard University ohallats@physics.harvard.edu Genetic impact of range expansions Population expansions
More informationPopulation Genetics I. Bio
Population Genetics I. Bio5488-2018 Don Conrad dconrad@genetics.wustl.edu Why study population genetics? Functional Inference Demographic inference: History of mankind is written in our DNA. We can learn
More informationEvolution & Natural Selection
Evolution & Natural Selection Learning Objectives Know what biological evolution is and understand the driving force behind biological evolution. know the major mechanisms that change allele frequencies
More informationSupplemental Information Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles
Supplemental Information Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles John Novembre and Montgomery Slatkin Supplementary Methods To
More informationC3020 Molecular Evolution. Exercises #3: Phylogenetics
C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from
More informationObservation: we continue to observe large amounts of genetic variation in natural populations
MUTATION AND GENETIC VARIATION Observation: we continue to observe large amounts of genetic variation in natural populations Problem: How does this variation arise and how is it maintained. Here, we look
More informationNotes 20 : Tests of neutrality
Notes 0 : Tests of neutrality MATH 833 - Fall 01 Lecturer: Sebastien Roch References: [Dur08, Chapter ]. Recall: THM 0.1 (Watterson s estimator The estimator is unbiased for θ. Its variance is which converges
More informationInferring Phylogenetic Trees. Distance Approaches. Representing distances. in rooted and unrooted trees. The distance approach to phylogenies
Inferring Phylogenetic Trees Distance Approaches Representing distances in rooted and unrooted trees The distance approach to phylogenies given: an n n matrix M where M ij is the distance between taxa
More informationTemporal Trails of Natural Selection in Human Mitogenomes. Author. Published. Journal Title DOI. Copyright Statement.
Temporal Trails of Natural Selection in Human Mitogenomes Author Sankarasubramanian, Sankar Published 2009 Journal Title Molecular Biology and Evolution DOI https://doi.org/10.1093/molbev/msp005 Copyright
More informationPhylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
More informationPhylogeny and Molecular Evolution. Introduction
Phylogeny and Molecular Evolution Introduction 1 2/62 3/62 Credit Serafim Batzoglou (UPGMA slides) http://www.stanford.edu/class/cs262/slides Notes by Nir Friedman, Dan Geiger, Shlomo Moran, Ron Shamir,
More informationthat of Phylotree.org, mtdna tree Build 1756 (Supplementary TableS2). is resulted in 78 individuals allocated to the hg B4a1a1 and three individuals to hg Q. e control region (nps 57372 and nps 1602416526)
More information122 9 NEUTRALITY TESTS
122 9 NEUTRALITY TESTS 9 Neutrality Tests Up to now, we calculated different things from various models and compared our findings with data. But to be able to state, with some quantifiable certainty, that
More informationGenetic Drift in Human Evolution
Genetic Drift in Human Evolution (Part 2 of 2) 1 Ecology and Evolutionary Biology Center for Computational Molecular Biology Brown University Outline Introduction to genetic drift Modeling genetic drift
More informationTheory a well supported testable explanation of phenomenon occurring in the natural world.
Evolution Theory of Evolution Theory a well supported testable explanation of phenomenon occurring in the natural world. Evolution the process by which modern organisms changed over time from ancient common
More informationI. Short Answer Questions DO ALL QUESTIONS
EVOLUTION 313 FINAL EXAM Part 1 Saturday, 7 May 2005 page 1 I. Short Answer Questions DO ALL QUESTIONS SAQ #1. Please state and BRIEFLY explain the major objectives of this course in evolution. Recall
More informationConcepts and Methods in Molecular Divergence Time Estimation
Concepts and Methods in Molecular Divergence Time Estimation 26 November 2012 Prashant P. Sharma American Museum of Natural History Overview 1. Why do we date trees? 2. The molecular clock 3. Local clocks
More informationGenetic Admixture in the Late Pleistocene
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1OO:l-5 (1996) Genetic Admixture in the Late Pleistocene ELISABETH J. MANDERSCHEID AND ALAN R. ROGERS Department of Anthropology, University of Utah, Salt Lake
More informationLecture Notes: BIOL2007 Molecular Evolution
Lecture Notes: BIOL2007 Molecular Evolution Kanchon Dasmahapatra (k.dasmahapatra@ucl.ac.uk) Introduction By now we all are familiar and understand, or think we understand, how evolution works on traits
More informationMolecular phylogeny How to infer phylogenetic trees using molecular sequences
Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 2009 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues
More informationBioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony
ioinformatics -- lecture 9 Phylogenetic trees istance-based tree building Parsimony (,(,(,))) rees can be represented in "parenthesis notation". Each set of parentheses represents a branch-point (bifurcation),
More informationBio 1B Lecture Outline (please print and bring along) Fall, 2007
Bio 1B Lecture Outline (please print and bring along) Fall, 2007 B.D. Mishler, Dept. of Integrative Biology 2-6810, bmishler@berkeley.edu Evolution lecture #5 -- Molecular genetics and molecular evolution
More informationMultiple Sequence Alignment. Sequences
Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe
More informationMolecular phylogeny How to infer phylogenetic trees using molecular sequences
Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 200 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues
More informationProcesses of Evolution
15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection
More informationLecture 18 : Ewens sampling formula
Lecture 8 : Ewens sampling formula MATH85K - Spring 00 Lecturer: Sebastien Roch References: [Dur08, Chapter.3]. Previous class In the previous lecture, we introduced Kingman s coalescent as a limit of
More informationEvidence of Evolution
Evidence of Evolution Biogeography The Age of Earth and Fossils Ancient artiodactyl Modern whale Ancestors of Whales Ambulocetus could both swim in shallow water and walk on land. Rodhocetus probably spent
More informationExtranuclear Inheritance
Extranuclear Inheritance Extranuclear Inheritance The past couple of lectures, we ve been exploring exceptions to Mendel s principles of transmission inheritance. Scientists have observed inheritance patterns
More informationMethods to reconstruct phylogene1c networks accoun1ng for ILS
Methods to reconstruct phylogene1c networks accoun1ng for ILS Céline Scornavacca some slides have been kindly provided by Fabio Pardi ISE-M, Equipe Phylogénie & Evolu1on Moléculaires Montpellier, France
More informationConstructing a Pedigree
Constructing a Pedigree Use the appropriate symbols: Unaffected Male Unaffected Female Affected Male Affected Female Male carrier of trait Mating of Offspring 2. Label each generation down the left hand
More informationThere are 3 parts to this exam. Use your time efficiently and be sure to put your name on the top of each page.
EVOLUTIONARY BIOLOGY EXAM #1 Fall 2017 There are 3 parts to this exam. Use your time efficiently and be sure to put your name on the top of each page. Part I. True (T) or False (F) (2 points each). Circle
More informationEstimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates
Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates JOSEPH FELSENSTEIN Department of Genetics SK-50, University
More informationReading for Lecture 13 Release v10
Reading for Lecture 13 Release v10 Christopher Lee November 15, 2011 Contents 1 Evolutionary Trees i 1.1 Evolution as a Markov Process...................................... ii 1.2 Rooted vs. Unrooted Trees........................................
More informationPhylogenetic Trees. How do the changes in gene sequences allow us to reconstruct the evolutionary relationships between related species?
Why? Phylogenetic Trees How do the changes in gene sequences allow us to reconstruct the evolutionary relationships between related species? The saying Don t judge a book by its cover. could be applied
More informationWarm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab
Date: Agenda Warm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab Ask questions based on 5.1 and 5.2 Quiz on 5.1 and 5.2 How
More informationA stochastic model for the mitochondrial Eve
K. Lachhab A stochastic model for the mitochondrial Eve Bachelorthesis Supervisor: dr. M.O. Heydenreich 4 August 2014 Mathematical Institute of Leiden University Abstract The existence of the most recent
More informationGroup activities: Making animal model of human behaviors e.g. Wine preference model in mice
Lecture schedule 3/30 Natural selection of genes and behaviors 4/01 Mouse genetic approaches to behavior 4/06 Gene-knockout and Transgenic technology 4/08 Experimental methods for measuring behaviors 4/13
More informationCladistics and Bioinformatics Questions 2013
AP Biology Name Cladistics and Bioinformatics Questions 2013 1. The following table shows the percentage similarity in sequences of nucleotides from a homologous gene derived from five different species
More informationchatper 17 Multiple Choice Identify the choice that best completes the statement or answers the question.
chatper 17 Multiple Choice Identify the choice that best completes the statement or answers the question. 1. If a mutation introduces a new skin color in a lizard population, which factor might determine
More informationMolecular evolution. Joe Felsenstein. GENOME 453, Autumn Molecular evolution p.1/49
Molecular evolution Joe Felsenstein GENOME 453, utumn 2009 Molecular evolution p.1/49 data example for phylogeny inference Five DN sequences, for some gene in an imaginary group of species whose names
More informationExamining the Fossil Record
Examining the Fossil Record Objectives: analyze characteristics of fossils compare placement of fossils and determine relative ages develop a model evolutionary tree based on the morphology and age of
More informationIntroduction to Advanced Population Genetics
Introduction to Advanced Population Genetics Learning Objectives Describe the basic model of human evolutionary history Describe the key evolutionary forces How demography can influence the site frequency
More informationPopulation Genetics: a tutorial
: a tutorial Institute for Science and Technology Austria ThRaSh 2014 provides the basic mathematical foundation of evolutionary theory allows a better understanding of experiments allows the development
More informationModern Evolutionary Classification. Section 18-2 pgs
Modern Evolutionary Classification Section 18-2 pgs 451-455 Modern Evolutionary Classification In a sense, organisms determine who belongs to their species by choosing with whom they will mate. Taxonomic
More information- point mutations in most non-coding DNA sites likely are likely neutral in their phenotypic effects.
January 29 th, 2010 Bioe 109 Winter 2010 Lecture 10 Microevolution 3 - random genetic drift - one of the most important shifts in evolutionary thinking over the past 30 years has been an appreciation of
More informationGenomics refutes an exclusively African origin of humans
Journal of Human Evolution 49 (25) 1e18 Genomics refutes an exclusively African origin of humans Vinayak Eswaran a, Henry Harpending b, *, Alan R. Rogers c a Department of Mechanical Engineering, Indian
More informationDemography April 10, 2015
Demography April 0, 205 Effective Population Size The Wright-Fisher model makes a number of strong assumptions which are clearly violated in many populations. For example, it is unlikely that any population
More informationMitochondrial DNA and its Role in Contemporary Paleoanthropology
Mitochondrial DNA and its Role in Contemporary Paleoanthropology D. John Doyle April 2012 Mitochondria are extraordinarily complex biochemical structures ( organelles ) located inside eucaryotic cells
More informationThe neutral theory of molecular evolution
The neutral theory of molecular evolution Introduction I didn t make a big deal of it in what we just went over, but in deriving the Jukes-Cantor equation I used the phrase substitution rate instead of
More informationChapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships
Chapter 26: Phylogeny and the Tree of Life You Must Know The taxonomic categories and how they indicate relatedness. How systematics is used to develop phylogenetic trees. How to construct a phylogenetic
More informationExamples of Phylogenetic Reconstruction
Examples of Phylogenetic Reconstruction 1. HIV transmission Recently, an HIV-positive Florida dentist was suspected of having transmitted the HIV virus to his dental patients. Although a number of his
More informationGENETICS - CLUTCH CH.22 EVOLUTIONARY GENETICS.
!! www.clutchprep.com CONCEPT: OVERVIEW OF EVOLUTION Evolution is a process through which variation in individuals makes it more likely for them to survive and reproduce There are principles to the theory
More informationMolecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016
Molecular phylogeny - Using molecular sequences to infer evolutionary relationships Tore Samuelsson Feb 2016 Molecular phylogeny is being used in the identification and characterization of new pathogens,
More informationCHAPTERS 24-25: Evidence for Evolution and Phylogeny
CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology
More informationEffective population size and patterns of molecular evolution and variation
FunDamental concepts in genetics Effective population size and patterns of molecular evolution and variation Brian Charlesworth Abstract The effective size of a population,, determines the rate of change
More informationDrosophila melanogaster and D. simulans, two fruit fly species that are nearly
Comparative Genomics: Human versus chimpanzee 1. Introduction The chimpanzee is the closest living relative to humans. The two species are nearly identical in DNA sequence (>98% identity), yet vastly different
More informationHUMAN EVOLUTION 17 APRIL 2013
HUMAN EVOLUTION 17 APRIL 2013 Lesson Description In this lesson, we: Consider the following aspects of Human Evolution: - Interpretation of a phylogenetic tree to show the place of the family Hominidae
More informationBINF6201/8201. Molecular phylogenetic methods
BINF60/80 Molecular phylogenetic methods 0-7-06 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics
More informationExtranuclear Inheritance. Dr.Shivani Gupta, PGGCG-11, Chandigarh
Extranuclear Inheritance Dr.Shivani Gupta, PGGCG-11, Chandigarh Commonly defined as transmission through the cytoplasm (or things in the cytoplasm, including organelles) rather than the nucleus Generally
More informationEvolution in a spatial continuum
Evolution in a spatial continuum Drift, draft and structure Alison Etheridge University of Oxford Joint work with Nick Barton (Edinburgh) and Tom Kurtz (Wisconsin) New York, Sept. 2007 p.1 Kingman s Coalescent
More informationFrequency Spectra and Inference in Population Genetics
Frequency Spectra and Inference in Population Genetics Although coalescent models have come to play a central role in population genetics, there are some situations where genealogies may not lead to efficient
More informationHuman Evolution
http://www.pwasoh.com.co Human Evolution Cantius, ca 55 mya The continent-hopping habits of early primates have long puzzled scientists, and several scenarios have been proposed to explain how the first
More informationHuman Evolution. Darwinius masillae. Ida Primate fossil from. in Germany Ca.47 M years old. Cantius, ca 55 mya
http://www.pwasoh.com Human Evolution Cantius, ca 55 mya The continent-hopping habits of early primates have long puzzled scientists, and several scenarios have been proposed to explain how the first true
More informationThe abundance of deleterious polymorphisms in humans
Genetics: Published Articles Ahead of Print, published on February 23, 2012 as 10.1534/genetics.111.137893 Note February 3, 2011 The abundance of deleterious polymorphisms in humans Sankar Subramanian
More informationEvolution of Populations. Chapter 17
Evolution of Populations Chapter 17 17.1 Genes and Variation i. Introduction: Remember from previous units. Genes- Units of Heredity Variation- Genetic differences among individuals in a population. New
More informationChallenges when applying stochastic models to reconstruct the demographic history of populations.
Challenges when applying stochastic models to reconstruct the demographic history of populations. Willy Rodríguez Institut de Mathématiques de Toulouse October 11, 2017 Outline 1 Introduction 2 Inverse
More informationSequence Divergence & The Molecular Clock. Sequence Divergence
Sequence Divergence & The Molecular Clock Sequence Divergence v simple genetic distance, d = the proportion of sites that differ between two aligned, homologous sequences v given a constant mutation/substitution
More informationThe Theory of Evolution
The Theory of Evolution Matthew Ferry Evolution The process by which different kinds of living organisms are thought to have developed and diversified from earlier forms during the history of the Earth.
More informationBi1: The Great Ideas of Biology Homework 3 Due Date: Thursday, April 27, 2017
Bi1: The Great Ideas of Biology Homework 3 Due Date: Thursday, April 27, 2017 Patience is a virtue which is very easily apt to be fatigued by exercise. - Henry Fielding, Tom Jones 1. Deep time and earth
More informationGene Genealogies Strongly Distorted By Weakly Interfering. Mutations in Constant Environments
Genetics: Published Articles Ahead of Print, published on December 4, 2009 as 10.1534/genetics.109.103556 Gene Genealogies Strongly Distorted By Weakly Interfering Mutations in Constant Environments Jon
More informationIntroduction to population genetics & evolution
Introduction to population genetics & evolution Course Organization Exam dates: Feb 19 March 1st Has everybody registered? Did you get the email with the exam schedule Summer seminar: Hot topics in Bioinformatics
More information