Time-dependent Molecular Rates: A Very Rough Guide
|
|
- Cory Warner
- 5 years ago
- Views:
Transcription
1 Time-dependent Molecular Rates: A Very Rough Guide
2 Background / Introduction
3 - Time dependency of morphological evolution: inverse correlation with time interval over which the rate was measured rate of change between successive generations exceeded macroevolutionary rates by several orders of magnitude. (Kurtén 1959) o confirmed in a number of subsequent studies - The molecular clock: proteins experience amino acid replacements at a surprisingly consistent rate across very different species presumed single, uniform rate of genetic evolution. (Zuckerkandl & Pauling 1965) o Versatile tool for dating genetic events - The updated molecular clock: Rates can vary across various dimensions (Ho & Lee 2016) o Site effects: different parts of the genome o Lineage effects: taxa o And, seemingly, across time: Inverse correlation between measured rate and timescale of measurement time-dependent molecular rate (TDMR)
4 A B Site effect Lineage effect Time (My ago) Clade X Clad Clade X 200 C D Epoch effect Site & Lineage effects 0 Time (My ago) and ver, he ary ntially fossil ock n birds h radiated period e oldest h groups of the ular rigin of ms) more the first ar (Figure ncies il ned. As enerally ous fossils, mmal or y to be ation or t largely molecular more adiations, ences would be models to es. an also traits and evolution. nalyses ains ecular 100 Clade X Clade X 200 Key: Gene 1 Gene 2 Fast evolutionary rate Slow evolutionary rate Current Biology Figure 2. Modern molecular clocks can accommodate complex variation in rates of genetic change across the tree of life. (A) Rate variation across sites: gene 1 evolves rapidly but gene 2 evolves slowly, across all lineages. (B) Rate variation across lineages: genes 1 and 2 both evolve rapidly in clade X. (C) Rate variation across time periods or epochs : genes 1 and 2 both evolved rapidly between 140 and 80
5 What (is TDMR)
6 - Disparity between spontaneous mutation rates measured over short timescales and substitution rates over geological timescales - In other words: mutation rate (µ) vs. substitution rate (σ) - All mutations strictly neutral => σ = µ (Kimura 1968) - => Expect µ and σ to differ when many mutations aren t neutral - Rates on different timescales reflect different biological processes: o Very short (e.g. between successive generations): Can include all but the most detrimental mutations Approaches µ (discounting lethal mutations) o Very long (e.g. between distantly related species): Usually dominated by substitutions (fixed mutations) Approximates σ: < µ due to purifying (negative) selection
7 Present AB C D t 1 coalescent history of extant individuals t 2 between intraspecific genealogies and speciation event Past t 3 coalescent history of ancestral population prior to speciation Fig. 3 A simplified representation of genealogical history at a single locus in a pair of species. Each circle represents a randomly mating individual and each row represents one generation. The ancestral species (spanning the time period t 3 ) splits into two descendent species (spanning the periods t 2 and t 1 ). Four contemporary individuals labelled A, B, C and D are referred to in the text.
8 - A and B closely related individuals: Observed differences dominated by mutations - A and D from different species: Differences likely dominated by substitutions (fixed during t2, sometimes t3), though some may be polymorphisms (generally arising in t1) - Proportions of t1, t2, t3 -> relative influence of µ and σ on rate estimate from A-D comparison, e.g. o t2 long relative to t1, t3 => estimate approximates σ - Another factor: effective population size o E.g. if large and most mutations deleterious: estimate from A-C < estimate from A-B
9 How
10 The degree of divergence between 2 sequences is determined by: a. The rate of molecular change b. TMRCA (time to most recent common ancestor) => To estimate the rate (a), independent information about the evolutionary timescale (b) is needed.
11 Typical calibration techniques for the shortest timescales: - Laboratory mutation-accumulation lines (Keightley et al. 2009) - Studies of pedigrees (Haag-Liautard et al. 2008) - Heterochronous sampling: sampled sequences of different ages (Duchêne et al. 2015) o Also used for longer timescales, e.g. with adna (ancient DNA) o Calibration technique: temporal structure eliminates need for calibration by fixing an internal node at a point in time
12 Calibration techniques for longer timescales: - Dated geological events (Burridge et al. 2008) - Archaeological and anthropological evidence (Henn et al. 2009) Fossil record usually for calibrations at least several million years in age - Evidence for earliest appearance of members of separate lineages o Minimum age constraint for divergence event - Usually insufficient morphological variation on shorter timescales for reliable diagnostic usage
13 ANIMALS AND PLANTS Fossil record Geology/Biogeography Ancient DNA Pedigree Lab line Serial sampling Years before present Archaeology Ancient DNA BACTERIA AND VIRUSES Pop. co-divergence Species co-divergence Fig. 2 Typical age ranges of different forms of calibrating information.
14 Where
15 - mtdna in: o Humans: pedigree rate of mtdna sequence divergence higher than phylogenetic rate (meta-analysis by Howell et al. 2003) o Fish (Burridge et al. 2008) o Birds (Subramanian et al. 2009) o Insects (Papadopoulou et al. 2010) - Bacteria (Comas et al. 2013) - Viruses (Aiewsakun & Katzourakis 2015)
16 It s Complicated
17 - The role of purifying selection in removing some mutations, and the existence of some degree of TDMR is uncontroversial - But: Magnitude of TDMR is debated - Support for order-of-magnitude differences - But that is disputed (e.g. on methodological grounds, e.g. Emerson & Hickerson 2015) - 2 illustrations of order-of-magnitude differences, 1 of sub-order-ofmagnitude difference:
18 Evolutionary rate (substitutions/site/year) (a) (c) (b) (d) Fig. 1 Time-dependent patterns in rate estimates have been observed in a variety of taxonomic groups, including: (a) noncoding mitochondrial DNA from amniotes (data from Fig. 1b in Molak & Ho 2015), (b) mitochondrial DNA from insects (data from Fig. 2 in Ho & Lo 2013), (c) genomic DNA from bacteria (data from Fig. 4 in Comas et al. 2013) and (d) genomic RNA and DNA from viruses (data from Fig. 1a in Duch^ene et al. 2014). Trend lines are based on those estimated in the original analyses of these data sets. In panel d, separate trend lines are given for RNA viruses (solid) and DNA viruses (dashed). Calibration age (years)
19 FIG. 4. Difference between mtdna mutation rate estimates and rates expected under the K2P þ c model. Phylogeny-based mutation rate estimates are drawn from tables 1 and 2. Solid black line: effective mutation rate under our general model of K2P þ c assuming published pedigreebased mutation rate (0.95/bp/My) taken from Howell et al. (2003), ts/tv 5 20/1, a We explored the sensitivity of the model parameters, examples for each parameter are displayed. Solid gray lines: effective mutation rate given alternative instantaneous pedigree mutation rates 1.20 and 0.75/bp/My. Dotted line: effective mutation rate given ts/tv 5 100/1. Dashed lines: effective mutation rate given alternative a and 0.2.
20
21 Why
22 Roughly classifiable into biological and methodological factors - Note: Only one purely biological factor, i.e. purifying selection - Most methodological factors involve inadequate modelling of biological processes - Relative importance of factors likely vary across cases Natural selection: purifying (negative) selection - Substantial proportion of slightly deleterious mutations lost continuously from mtdna gene pool over a prolonged period (Kivisild et al. 2006) - Time-dependent decline in the ratio of non-synonymous to synonymous changes in coding sequences (Peterson & Masel 2009)
23 Methodological factors Calibration error - For calibrations based on the presumed timing of population- or speciesdivergence event, genetic divergence typically assumed to coincide with population divergence. - Genetic divergence often precedes population/species divergence => underestimate of time since genetic divergence => rate overestimation - Can result in rate underestimation, when genetic divergence postdates calibration event - Magnitude of bias greatest on short timescales, where the difference between genetic and population divergence times is an appreciable proportion of the total time separating the two populations or species
24 T T split T T split Lineage 1 Lineage 2 T T split Species A Species B
25 Mutational saturation - E.g. when one nucleotide undergoes multiple substitutions from its initial state, and only the first and last states are observed - Unobserved substitutions bias rate estimates downward - Likely to be less of a problem over very short time frames, but important over longer time frames - Under-correction for saturation can contribute to time-dependent rates
26 Rate heterogeneity across sites (RHAS) - Genomic sites can evolve at significantly different rates o E.g. mtdna exhibits up to 1,000-fold difference between the fastest and slowest evolving sites - Decreases rate estimates through increasing saturation (more unobserved substitutions) at fast-evolving sites over time - Time-dependent underestimate more pronounced both when the proportion of mutational hotspots increases, and when the ratio between high and low rates increases in the data (Soubrier et al. 2012)
27 A B FIG. 3.Mathematical exploration of the relationship between divergence time, actual substitution rate, and inferred rate from the mathematical model. (A) Rates for various proportions of fastsites, when the ratio of fast to slow rates is 1,000. (B) Ratesforvariousratiosoffastto slow rates, when the proportion of fast sites is fixed at 10%. * represents the parameter values chosen in subsequent simulations.
28 Demographic factors - E.g. population expansions o For humans, purifying selection further weakened by population expansions associated with the out-of Africa migration and the end of the Last Ice Age. (Henn et al. 2009) o => Higher rate estimates for timescales since then compared to before
29 References Burridge CP, Craw D, Fletcher D, Waters JM (2008). Geological dates and molecular rates: fish DNA sheds light on time dependency. Molecular Biology and Evolution 25: Comas I, Coscolla M, Luo T et al. (2013). Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genetics 45: Duchêne S, Duchêne D, Holmes EC, Ho SYW (2015). The performance of the date-randomisation test in phylogenetic analyses of time-structured virus data. Molecular Biology and Evolution 32: Haag-Liautard C, Coffey N, Houle D et al. (2008). Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biology 6:e204. Henn BM, Gignoux CR, Feldman MW, Mountain JL (2009). Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Molecular Biology and Evolution 26: Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C (2003). The pedigree rate of sequence divergence in the human mitochondrial genome. There is a difference between phylogenetic and pedigree rates. Am J Hum Genet 72: Keightley PD, Trivedi U, Thomson M et al. (2009). Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Research 19: Kimura M (1968). Evolutionary rate at the molecular level. Nature 217:
30 Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K et al. (2006). The role of selection in the evolution of human mitochondrial genomes. Genetics 172: Lee MSY, Ho SYW (2016). Molecular clocks. Current Biology 26:R387-R407 Loogväli EL, Kivisild T, Margus T, Villems R (2009). Explaining the imperfection of the molecular clock of hominid mitochondria. PLoS ONE 4:e8260. Papadopoulou A, Anastasiou I, Vogler AP (2010). Revisiting the insect mitochondrial molecular clock: the mid- Aegean trench calibration. Molecular Biology and Evolution 27: Peterson GI, Masel J (2009). Quantitative prediction of molecular clock and Ka Ks at short timescales. Molecular Biology and Evolution 26: Soubrier J, Steel M, Lee MSY et al. (2012). The influence of rate heterogeneity among sites on the time dependence of molecular rates. Molecular Biology and Evolution 29: Subramanian S, Denver DR, Millar CD et al. (2009). High mitogenomic evolutionary rates and time dependency. Trends in Genetics 25: Zuckerkandl E, and Pauling L (1962). Molecular disease, evolution, and genic heterogeneity. In Horizons in Biochemistry, M. Kasha, and B. Pullman, eds. (New York: Academic Press):
Chapter 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 informationPHYLOGENY AND SYSTEMATICS
AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study
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 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 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 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 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 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 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 informationChapter 16: Reconstructing and Using Phylogenies
Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/
More informationSEQUENCE DIVERGENCE,FUNCTIONAL CONSTRAINT, AND SELECTION IN PROTEIN EVOLUTION
Annu. Rev. Genomics Hum. Genet. 2003. 4:213 35 doi: 10.1146/annurev.genom.4.020303.162528 Copyright c 2003 by Annual Reviews. All rights reserved First published online as a Review in Advance on June 4,
More informationUoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)
- Phylogeny? - Systematics? The Phylogenetic Systematics (Phylogeny and Systematics) - Phylogenetic systematics? Connection between phylogeny and classification. - Phylogenetic systematics informs the
More informationOutline. Genome Evolution. Genome. Genome Architecture. Constraints on Genome Evolution. New Evolutionary Synthesis 11/8/16
Genome Evolution Outline 1. What: Patterns of Genome Evolution Carol Eunmi Lee Evolution 410 University of Wisconsin 2. Why? Evolution of Genome Complexity and the interaction between Natural Selection
More informationUsing phylogenetics to estimate species divergence times... Basics and basic issues for Bayesian inference of divergence times (plus some digression)
Using phylogenetics to estimate species divergence times... More accurately... Basics and basic issues for Bayesian inference of divergence times (plus some digression) "A comparison of the structures
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 informationSPECIATION. REPRODUCTIVE BARRIERS PREZYGOTIC: Barriers that prevent fertilization. Habitat isolation Populations can t get together
SPECIATION Origin of new species=speciation -Process by which one species splits into two or more species, accounts for both the unity and diversity of life SPECIES BIOLOGICAL CONCEPT Population or groups
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 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 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 informationSCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology
SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION Using Anatomy, Embryology, Biochemistry, and Paleontology Scientific Fields Different fields of science have contributed evidence for the theory of
More informationPhylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationEvolution Problem Drill 09: The Tree of Life
Evolution Problem Drill 09: The Tree of Life Question No. 1 of 10 Question 1. The age of the Earth is estimated to be about 4.0 to 4.5 billion years old. All of the following methods may be used to estimate
More informationBig Idea #1: The process of evolution drives the diversity and unity of life
BIG IDEA! Big Idea #1: The process of evolution drives the diversity and unity of life Key Terms for this section: emigration phenotype adaptation evolution phylogenetic tree adaptive radiation fertility
More informationBustamante et al., Supplementary Nature Manuscript # 1 out of 9 Information #
Bustamante et al., Supplementary Nature Manuscript # 1 out of 9 Details of PRF Methodology In the Poisson Random Field PRF) model, it is assumed that non-synonymous mutations at a given gene are either
More informationOutline. Genome Evolution. Genome. Genome Architecture. Constraints on Genome Evolution. New Evolutionary Synthesis 11/1/18
Genome Evolution Outline 1. What: Patterns of Genome Evolution Carol Eunmi Lee Evolution 410 University of Wisconsin 2. Why? Evolution of Genome Complexity and the interaction between Natural Selection
More informationHow should we organize the diversity of animal life?
How should we organize the diversity of animal life? The difference between Taxonomy Linneaus, and Cladistics Darwin What are phylogenies? How do we read them? How do we estimate them? Classification (Taxonomy)
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 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 informationPhylogeny 9/8/2014. Evolutionary Relationships. Data Supporting Phylogeny. Chapter 26
Phylogeny Chapter 26 Taxonomy Taxonomy: ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences Carolus Linnaeus developed binomial nomenclature,
More informationChapter 27: Evolutionary Genetics
Chapter 27: Evolutionary Genetics Student Learning Objectives Upon completion of this chapter you should be able to: 1. Understand what the term species means to biology. 2. Recognize the various patterns
More informationChapter 19: Taxonomy, Systematics, and Phylogeny
Chapter 19: Taxonomy, Systematics, and Phylogeny AP Curriculum Alignment Chapter 19 expands on the topics of phylogenies and cladograms, which are important to Big Idea 1. In order for students to understand
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 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 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 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 informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Chapter focus Shifting from the process of how evolution works to the pattern evolution produces over time. Phylogeny Phylon = tribe, geny = genesis or origin
More informationName: Class: Date: ID: A
Class: _ Date: _ Ch 17 Practice test 1. A segment of DNA that stores genetic information is called a(n) a. amino acid. b. gene. c. protein. d. intron. 2. In which of the following processes does change
More informationMETHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.
Chapter 12 (Strikberger) Molecular Phylogenies and Evolution METHODS FOR DETERMINING PHYLOGENY In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task. Modern
More informationRate of Evolution Juliana Senawi
Rate of Evolution Juliana Senawi Rate of Evolution Measurement of the change in an evolutionary lineage overtime Radiometric and paleomagnetic dating provide an effective basis for determining the age
More informationWelcome to Evolution 101 Reading Guide
Name: Welcome to Evolution 101 Reading Guide http://evolution.berkeley.edu/evolibrary/article/evo_01 Read the information on the website. Click on the next arrow at the bottom of each page to move to the
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 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 informationOrganizing Life s Diversity
17 Organizing Life s Diversity section 2 Modern Classification Classification systems have changed over time as information has increased. What You ll Learn species concepts methods to reveal phylogeny
More informationBiology 211 (2) Week 1 KEY!
Biology 211 (2) Week 1 KEY Chapter 1 KEY FIGURES: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 VOCABULARY: Adaptation: a trait that increases the fitness Cells: a developed, system bound with a thin outer layer made of
More informationAP Biology Review Packet 5- Natural Selection and Evolution & Speciation and Phylogeny
AP Biology Review Packet 5- Natural Selection and Evolution & Speciation and Phylogeny 1A1- Natural selection is a major mechanism of evolution. 1A2: Natural selection acts on phenotypic variations in
More informationLecture 7 Mutation and genetic variation
Lecture 7 Mutation and genetic variation Thymidine dimer Natural selection at a single locus 2. Purifying selection a form of selection acting to eliminate harmful (deleterious) alleles from natural populations.
More informationMultiple Sequence Alignment. Sequences
Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe
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 informationMacroevolution Part I: Phylogenies
Macroevolution Part I: Phylogenies Taxonomy Classification originated with Carolus Linnaeus in the 18 th century. Based on structural (outward and inward) similarities Hierarchal scheme, the largest most
More informationMajor questions of evolutionary genetics. Experimental tools of evolutionary genetics. Theoretical population genetics.
Evolutionary Genetics (for Encyclopedia of Biodiversity) Sergey Gavrilets Departments of Ecology and Evolutionary Biology and Mathematics, University of Tennessee, Knoxville, TN 37996-6 USA Evolutionary
More informationIntegrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;
More informationEvolutionary Patterns, Rates, and Trends
Evolutionary Patterns, Rates, and Trends Macroevolution Major patterns and trends among lineages Rates of change in geologic time Comparative Morphology Comparing body forms and structures of major lineages
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 informationSelection against A 2 (upper row, s = 0.004) and for A 2 (lower row, s = ) N = 25 N = 250 N = 2500
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
More informationChapter 16: Evolutionary Theory
Chapter 16: Evolutionary Theory Section 1: Developing a Theory Evolution: Artificial Selection: Evolution: I. A Theory to Explain Change Over Time B. Charles Darwin C. Theory: D. Modern evolutionary theory
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 informationName: Period Study Guide 17-1 and 17-2
Name: Period Study Guide 17-1 and 17-2 17-1 The Fossil Record (pgs. 417-422) 1. What is the fossil record? 2. What evidence does the fossil record provide? 1. 2. 3. List the 2 techniques paleontologists
More informationChapter 7: Covalent Structure of Proteins. Voet & Voet: Pages ,
Chapter 7: Covalent Structure of Proteins Voet & Voet: Pages 163-164, 185-194 Slide 1 Structure & Function Function is best understood in terms of structure Four levels of structure that apply to proteins
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 information5/31/17. Week 10; Monday MEMORIAL DAY NO CLASS. Page 88
Week 10; Monday MEMORIAL DAY NO CLASS Page 88 Week 10; Wednesday Announcements: Family ID final in lab Today Final exam next Tuesday at 8:30 am here Lecture: Species concepts & Speciation. What are species?
More informationPhylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationLesson 1 Syllabus Reference
Lesson 1 Syllabus Reference Outcomes A student Explains how biological understanding has advanced through scientific discoveries, technological developments and the needs of society. Content The theory
More informationEvidence for Evolution
Evidence for Evolution 1. 2. 3. 4. 5. Paleontology Comparative Anatomy Embryology Comparative Biochemistry Geographical Distribution How old is everything? The History of Earth as a Clock Station 1: Paleontology
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 informationSWEEPFINDER2: Increased sensitivity, robustness, and flexibility
SWEEPFINDER2: Increased sensitivity, robustness, and flexibility Michael DeGiorgio 1,*, Christian D. Huber 2, Melissa J. Hubisz 3, Ines Hellmann 4, and Rasmus Nielsen 5 1 Department of Biology, Pennsylvania
More informationBIOLOGY 432 Midterm I - 30 April PART I. Multiple choice questions (3 points each, 42 points total). Single best answer.
BIOLOGY 432 Midterm I - 30 April 2012 Name PART I. Multiple choice questions (3 points each, 42 points total). Single best answer. 1. Over time even the most highly conserved gene sequence will fix mutations.
More informationPage 1. Evolutionary Trees. Why build evolutionary tree? Outline
Page Evolutionary Trees Russ. ltman MI S 7 Outline. Why build evolutionary trees?. istance-based vs. character-based methods. istance-based: Ultrametric Trees dditive Trees. haracter-based: Perfect phylogeny
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 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 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 informationEvaluate evidence provided by data from many scientific disciplines to support biological evolution. [LO 1.9, SP 5.3]
Learning Objectives Evaluate evidence provided by data from many scientific disciplines to support biological evolution. [LO 1.9, SP 5.3] Refine evidence based on data from many scientific disciplines
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 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 informationIn a way, organisms determine who belongs to their species by choosing with whom they will! MODERN EVOLUTIONARY CLASSIFICATION 18-2 MATE
MODERN EVOLUTIONARY CLASSIFICATION 18-2 In a way, organisms determine who belongs to their species by choosing with whom they will! MATE Taxonomic groups are invented by scientists to group organisms with
More informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence
More informationAP Biology Notes Outline Enduring Understanding 1.B. Big Idea 1: The process of evolution drives the diversity and unity of life.
AP Biology Notes Outline Enduring Understanding 1.B Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring Understanding 1.B: Organisms are linked by lines of descent from
More informationReconstructing the history of lineages
Reconstructing the history of lineages Class outline Systematics Phylogenetic systematics Phylogenetic trees and maps Class outline Definitions Systematics Phylogenetic systematics/cladistics Systematics
More informationThe practice of naming and classifying organisms is called taxonomy.
Chapter 18 Key Idea: Biologists use taxonomic systems to organize their knowledge of organisms. These systems attempt to provide consistent ways to name and categorize organisms. The practice of naming
More informationMolecular Markers, Natural History, and Evolution
Molecular Markers, Natural History, and Evolution Second Edition JOHN C. AVISE University of Georgia Sinauer Associates, Inc. Publishers Sunderland, Massachusetts Contents PART I Background CHAPTER 1:
More informationUON, CAS, DBSC, General Biology II (BIOL102) Dr. Mustafa. A. Mansi. The Origin of Species
The Origin of Species Galápagos Islands, landforms newly emerged from the sea, despite their geologic youth, are filled with plants and animals known no-where else in the world, Speciation: The origin
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 informationClassification and Phylogeny
Classification and Phylogeny The diversity of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme
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 informationThe Tempo of Macroevolution: Patterns of Diversification and Extinction
The Tempo of Macroevolution: Patterns of Diversification and Extinction During the semester we have been consider various aspects parameters associated with biodiversity. Current usage stems from 1980's
More informationHow Molecules Evolve. Advantages of Molecular Data for Tree Building. Advantages of Molecular Data for Tree Building
How Molecules Evolve Guest Lecture: Principles and Methods of Systematic Biology 11 November 2013 Chris Simon Approaching phylogenetics from the point of view of the data Understanding how sequences evolve
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 informationC.DARWIN ( )
C.DARWIN (1809-1882) LAMARCK Each evolutionary lineage has evolved, transforming itself, from a ancestor appeared by spontaneous generation DARWIN All organisms are historically interconnected. Their relationships
More informationPOPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics
POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the
More informationChapter 7. Evolution and the Fossil Record
Chapter 7 Evolution and the Fossil Record 1 Guiding Questions What lines of evidence convinced Charles Darwin that organic evolution produced the species of the modern world? What are the two components
More information9/19/2012. Chapter 17 Organizing Life s Diversity. Early Systems of Classification
Section 1: The History of Classification Section 2: Modern Classification Section 3: Domains and Kingdoms Click on a lesson name to select. Early Systems of Classification Biologists use a system of classification
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 informationClassification and Phylogeny
Classification and Phylogeny The diversity it of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme
More informationPhylogeny and the Tree of Life
LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 26 Phylogeny and the Tree of Life
More informationBiology. Slide 1 of 24. End Show. Copyright Pearson Prentice Hall
Biology 1 of 24 18-2 Modern Evolutionary Classification 2 of 24 18-2 Modern Evolutionary Classification Evolutionary Classification Evolutionary Classification Phylogeny is the study of evolutionary relationships
More informationOutline. Classification of Living Things
Outline Classification of Living Things Chapter 20 Mader: Biology 8th Ed. Taxonomy Binomial System Species Identification Classification Categories Phylogenetic Trees Tracing Phylogeny Cladistic Systematics
More information10 Biodiversity Support. AQA Biology. Biodiversity. Specification reference. Learning objectives. Introduction. Background
Biodiversity Specification reference 3.4.5 3.4.6 3.4.7 Learning objectives After completing this worksheet you should be able to: recall the definition of a species and know how the binomial system is
More informationOrigin and Evolution of Life
Origin and Evolution of Life OCN 201 Science of the Sea Biology Lecture 2 The Handfish -BBC Blue Planet!1!1 Evolution Nothing in biology makes sense except in the light of evolution I am a creationist
More informationThursday, January 14. Teaching Point: SWBAT. assess their knowledge to prepare for the Evolution Summative Assessment. (TOMORROW) Agenda:
Thursday, January 14 Teaching Point: SWBAT. assess their knowledge to prepare for the Evolution Summative Assessment. (TOMORROW) Agenda: 1. Show Hinsz your completed Review WS 2. Discuss answers to Review
More informationGenomes and Their Evolution
Chapter 21 Genomes and Their Evolution PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationTheory of Evolution Charles Darwin
Theory of Evolution Charles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (83-36) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties
More information