Coalescents. Joe Felsenstein. GENOME 453, Autumn Coalescents p.1/48
|
|
|
- Grant French
- 5 years ago
- Views:
Transcription
1 Coalescents p.1/48 Coalescents Joe Felsenstein GENOME 453, Autumn 2015
2 Coalescents p.2/48 Cann, Stoneking, and Wilson Becky Cann Mark Stoneking the late Allan Wilson Cann, R. L., M. Stoneking, and A. C. Wilson Mitochondrial DNA and human evolution. Nature 325:a
3 Mitochondrial Eve Coalescents p.3/48
4 Coalescents p.4/48 Genealogy of gene copies in a random-mating population Time
5 Coalescents p.5/48 Genealogy of gene copies in a random-mating population Time
6 Coalescents p.6/48 Genealogy of gene copies in a random-mating population Time
7 Coalescents p.7/48 Genealogy of gene copies in a random-mating population Time
8 Coalescents p.8/48 Genealogy of gene copies in a random-mating population Time
9 Coalescents p.9/48 Genealogy of gene copies in a random-mating population Time
10 Coalescents p.10/48 Genealogy of gene copies in a random-mating population Time
11 Coalescents p.11/48 Genealogy of gene copies in a random-mating population Time
12 Coalescents p.12/48 Genealogy of gene copies in a random-mating population Time
13 Coalescents p.13/48 Genealogy of gene copies in a random-mating population Time
14 Coalescents p.14/48 Genealogy of gene copies in a random-mating population Time
15 Coalescents p.15/48 Genealogy of gene copies in a random-mating population Time
16 Coalescents p.16/48 Untangling this genealogy by left-right swappings... Time
17 Coalescents p.17/48 Genealogy of a sample of gene copies Time
18 Coalescents p.18/48 Ancestry of a sample in the population pedigree Time
19 Coalescents p.19/48 Why lineages coalesce under the Wright Fisher model each gene comes from a random copy in the previous generation a chance of 1 out of 2N that another one comes from the same copy hence it takes about 2N generations for two lineages to coalesce
20 Coalescents p.20/48 Sir John Kingman J. F. C. Kingman in about 1983 Currently Emeritus Professor of Mathematics at Cambridge University, U.K., and former head of the Isaac Newton Institute of Mathematical Sciences.
21 Kingman s coalescent Random collision of lineages as go back in time (sans recombination) Collision is faster the smaller the effective population size u 9 u 8 u7 u6 u 5 u 4 u 3 u 2 In a diploid population of effective population size N e 4N e Average time for k copies to coalesce to k 1 = k(k 1) Average time for two copies to coalesce = 2N e generations Average time for n copies to coalesce = 4N e ( 1 1 n ( generations Coalescents p.21/48
22 Coalescents p.22/48 An accurate analogy: Bugs In A Box There is a box...
23 Coalescents p.23/48 An accurate analogy: Bugs In A Box with bugs that are...
24 Coalescents p.24/48 An accurate analogy: Bugs In A Box... hyperactive...
25 Coalescents p.25/48 An accurate analogy: Bugs In A Box... indiscriminate...
26 Coalescents p.26/48 An accurate analogy: Bugs In A Box... voracious...
27 Coalescents p.27/48 An accurate analogy: Bugs In A Box Gulp!... (eats other bug)...
28 Coalescents p.28/48 An accurate analogy: Bugs In A Box... and insatiable.
29 Random coalescents from the same population Coalescents p.29/48
30 Two sources of variability (1) Randomness of mutation affected by the mutation rate u can reduce variance of number of mutations per site per branch by examining more sites (2) Randomness of coalescence of lineages affected by effective population size N e coalescence times allow estimation of N e can reduce variability by looking at (i) more gene copies, or (ii) more loci Coalescents p.30/48
31 Coalescents p.31/48 Coalescent with population growth size of population During a population bottleneck there is expected to be a burst of coalescence Down near the root of the tree effects of population size become difficult to see
32 Coalescents p.32/48 Coalescent with migration Time population #1 population #2
33 Coalescents p.33/48 Coalescent with migration, untangled Time
34 Coalescents p.34/48 My ancestor? Charles the Great (Charlemagne) born 747 about 44 more generations Cornelia John Maud William Itzhak Jacob Helen Will Sheimdel Lev Eleanor Jake Joe 1850s 1880s 1910s 1942
35 Coalescents p.35/48 Chromosome 1, back up one lineage 6 (none) now
36 Coalescents p.36/48 Coalescent with recombination Different markers have slightly different coalescent trees Recomb.
37 Coalescents p.37/48 Coalescent with recombination
38 Coalescents p.38/48 A phylogeographic study The rotifer Brachionus plicatilis Mills, S., D. H. Lunt, and A. Gomez Global isolation by distance despite strong regional phylogeography in a small metazoan. BMC Evolutionary Biology 7: 225.
39 A phylogeographic study Coalescents p.39/48
40 Coalescents p.40/48 Why mitochondrial eve? The Out-Of-Africa Hypothesis Europe Asia Africa (vertical scale is not time or evolutionary change)
41 Coalescents p.41/48 Genomes from Neanderthals, and more Svante Pääbo Krings, M., H. Geisert, R. W. Schmitz, H. Krainitzki, and S. Paabo DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen. Proceedings of the Natonal Academy of Sciences USA 96: Green, R., 54 others, and S. Pääbo A draft sequence of the Neanderthal genome. Science 7 May 2010:
42 Neanderthals, Denisovans, and us But... can you make trees from closely-related genomes? Coalescents p.42/48
43 Coalescents p.43/48 Coalescents in related species Tree of gene copies, compared with the phylogeny of the species for the case in which effective population size is small compared to the number of generations between speciations The tree of gene copies has topology consistent with the phylogeny
44 Coalescents p.44/48 Coalescents in related species Tree of gene copies, compared with the phylogeny of the species for the case in which effective population size is large compared to the number of generations between speciations The tree of gene copies has topology inconsistent with the phylogeny
45 Coalescents p.45/48 Hey and Kliman Jody Hey Rich Kliman and friend Kliman, R. M., and J. Hey DNA sequence variation at the period locus within and among species of the Drosophila melanogaster complex. Genetics 133: Hey, J. and R. M. Kliman Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Molecular Biology Evolution 10:
46 Coalescents p.46/48 Ranges of East African Drosophila species East Africa Seychelles D. seychellea D. melanogaster D. simulans Madagascar Mauritius D. mauritianus
47 Coalescent among Drosophila species Coalescents p.47/48
48 Coalescent among Drosophila species Coalescents p.48/48
Coalescents. Joe Felsenstein. GENOME 453, Winter Coalescents p.1/39
Coalescents Joe Felsenstein GENOME 453, Winter 2007 Coalescents p.1/39 Cann, Stoneking, and Wilson Becky Cann Mark Stoneking the late Allan Wilson Cann, R. L., M. Stoneking, and A. C. Wilson. 1987. Mitochondrial
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from?
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? 28 July 2010. Joe Felsenstein Evening At The Genome Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? p.1/39 Evolutionary
Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!
Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Paul has many great tools for teaching phylogenetics at his web site: http://hydrodictyon.eeb.uconn.edu/people/plewis
Comparative method, coalescents, and the future
Comparative method, coalescents, and the future Joe Felsenstein Depts. of Genome Sciences and of Biology, University of Washington Comparative method, coalescents, and the future p.1/36 Correlation of
Comparative method, coalescents, and the future. Correlation of states in a discrete-state model
Comparative method, coalescents, and the future Joe Felsenstein Depts. of Genome Sciences and of Biology, University of Washington Comparative method, coalescents, and the future p.1/28 Correlation of
Evolutionary trees and population genetics: a family reunion
Evolutionary trees and population genetics: a family reunion 9 October 2009. Joe Felsenstein 500th anniversary (or something) of the University of Chicago Evolutionary trees and population genetics: a
can mathematicians find the woods?
Eolutionary trees, coalescents, and gene trees: can mathematicians find the woods? Joe Felsenstein Department of Genome Sciences and Department of Biology Eolutionary trees, coalescents, and gene trees:
Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms
Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms Magnus Nordborg University of Southern California The importance of history Genetic polymorphism data represent the outcome
Population Structure and Genealogies
Population Structure and Genealogies One of the key properties of Kingman s coalescent is that each pair of lineages is equally likely to coalesce whenever a coalescent event occurs. This condition is
BIOL Evolution. Lecture 8
BIOL 432 - Evolution Lecture 8 Expected Genotype Frequencies in the Absence of Evolution are Determined by the Hardy-Weinberg Equation. Assumptions: 1) No mutation 2) Random mating 3) Infinite population
The African Origin Hypothesis What do the data tell us?
The African Origin Hypothesis What do the data tell us? Mitochondrial DNA and Human Evolution Cann, Stoneking and Wilson, Nature 1987. WOS - 1079 citations Mitochondrial DNA and Human Evolution Cann, Stoneking
Coalescence. Outline History. History, Model, and Application. Coalescence. The Model. Application
Coalescence History, Model, and Application Outline History Origins of theory/approach Trace the incorporation of other s ideas Coalescence Definition and descriptions The Model Assumptions and Uses Application
Population Genetics using Trees. Peter Beerli Genome Sciences University of Washington Seattle WA
Population Genetics using Trees Peter Beerli Genome Sciences University of Washington Seattle WA Outline 1. Introduction to the basic coalescent Population models The coalescent Likelihood estimation of
2 The Wright-Fisher model and the neutral theory
0 THE WRIGHT-FISHER MODEL AND THE NEUTRAL THEORY The Wright-Fisher model and the neutral theory Although the main interest of population genetics is conceivably in natural selection, we will first assume
Coalescent Theory: An Introduction for Phylogenetics
Coalescent Theory: An Introduction for Phylogenetics Laura Salter Kubatko Departments of Statistics and Evolution, Ecology, and Organismal Biology The Ohio State University lkubatko@stat.ohio-state.edu
Algorithms for Genetics: Basics of Wright Fisher Model and Coalescent Theory
Algorithms for Genetics: Basics of Wright Fisher Model and Coalescent Theory Vineet Bafna Harish Nagarajan and Nitin Udpa 1 Disclaimer Please note that a lot of the text and figures here are copied from
Population genetics: Coalescence theory II
Population genetics: Coalescence theory II Peter Beerli August 27, 2009 1 The variance of the coalescence process The coalescent is an accumulation of waiting times. We can think of it as standard queuing
Viral epidemiology and the Coalescent
Viral epidemiology and the Coalescent Philippe Lemey and Marc A. Suchard Department of Microbiology and Immunology K.U. Leuven, and Departments of Biomathematics and Human Genetics David Geffen School
Analysis of geographically structured populations: Estimators based on coalescence
Analysis of geographically structured populations: Estimators based on coalescence Peter Beerli Department of Genetics, Box 357360, University of Washington, Seattle WA 9895-7360, Email: beerli@genetics.washington.edu
DISCUSSION: RECENT COMMON ANCESTORS OF ALL PRESENT-DAY INDIVIDUALS
Adv. Appl. Prob. 31, 1027 1035 (1999) Printed in Northern Ireland Applied Probability Trust 1999 DISCUSSION: RECENT COMMON ANCESTORS OF ALL PRESENT-DAY INDIVIDUALS It is a pleasure to be able to comment
Coalescence time distributions for hypothesis testing -Kapil Rajaraman 498BIN, HW# 2
Coalescence time distributions for hypothesis testing -Kapil Rajaraman (rajaramn@uiuc.edu) 498BIN, HW# 2 This essay will be an overview of Maryellen Ruvolo s work on studying modern human origins using
GENEALOGICAL TREES, COALESCENT THEORY AND THE ANALYSIS OF GENETIC POLYMORPHISMS
GENEALOGICAL TREES, COALESCENT THEORY AND THE ANALYSIS OF GENETIC POLYMORPHISMS Noah A. Rosenberg and Magnus Nordborg Improvements in genotyping technologies have led to the increased use of genetic polymorphism
arxiv: v1 [q-bio.pe] 4 Mar 2013
![arxiv: v1 [q-bio.pe] 4 Mar 2013](/thumbs/75/72248364.jpg "arxiv: v1 [q-bio.pe] 4 Mar 2013")
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees arxiv:1303.0673v1 [q-bio.pe] 4 Mar 2013 Sha Zhu 1,, James H Degnan 2 and Bjarki Eldon 3 1
Simulated gene genealogy of a sample of size 50 from a population of constant size. The History of Population Size from Whole Genomes.
Simulated gene genealogy of a sample of size 50 from a population of constant size The History of Population Size from Whole Genomes Alan R Rogers October 1, 2018 Short terminal branches; long basal ones
TREES OF GENES IN POPULATIONS
1 TREES OF GENES IN POPULATIONS Joseph Felsenstein Abstract Trees of ancestry of copies of genes form in populations, as a result of the randomness of birth, death, and Mendelian reproduction. Considering
Human origins and analysis of mitochondrial DNA sequences
Human origins and analysis of mitochondrial DNA sequences Science, February 7, 1992 L. Vigilant et al. [1] recently presented "the strongest support yet for the placement of [their] common mtdna [mitochondrial
Forward thinking: the predictive approach
Coalescent Theory 1 Forward thinking: the predictive approach Random variation in reproduction causes random fluctuation in allele frequencies. Can describe this process as diffusion: (Wright 1931) showed
Bioinformatics I, WS 14/15, D. Huson, December 15,
Bioinformatics I, WS 4/5, D. Huson, December 5, 204 07 7 Introduction to Population Genetics This chapter is closely based on a tutorial given by Stephan Schiffels (currently Sanger Institute) at the Australian
Chapter 12 Gene Genealogies
Chapter 12 Gene Genealogies Noah A. Rosenberg Program in Molecular and Computational Biology. University of Southern California, Los Angeles, California 90089-1113 USA. E-mail: noahr@usc.edu. Phone: 213-740-2416.
The genealogical history of a population The coalescent process. Identity by descent Distribution of pairwise coalescence times
The coalescent The genealogical history of a population The coalescent process Identity by descent Distribution of pairwise coalescence times Adding mutations Expected pairwise differences Evolutionary
Ioanna Manolopoulou and Brent C. Emerson. October 7, Abstract
Phylogeographic Ancestral Inference Using the Coalescent Model on Haplotype Trees Ioanna Manolopoulou and Brent C. Emerson October 7, 2011 Abstract Phylogeographic ancestral inference is a question frequently
Ancestral Recombination Graphs
Ancestral Recombination Graphs Ancestral relationships among a sample of recombining sequences usually cannot be accurately described by just a single genealogy. Linked sites will have similar, but not
5 Inferring Population
5 Inferring Population History and Demography While population genetics was a very theoretical discipline originally, the modern abundance of population genetic data has forced the field to become more
Common ancestors of all humans
Definitions Skip the methodology and jump down the page to the Conclusion Discussion CAs using Genetics CAs using Archaeology CAs using Mathematical models CAs using Computer simulations Recent news Mark
Coalescent Theory. Magnus Nordborg. Department of Genetics, Lund University. March 24, 2000
Coalescent Theory Magnus Nordborg Department of Genetics, Lund University March 24, 2000 Abstract The coalescent process is a powerful modeling tool for population genetics. The allelic states of all homologous
Warning: software often displays unrooted trees like this:
Warning: software often displays unrooted trees like this: /------------------------------ Chara /-------------------------- Chlorella /---------16 \---------------------------- Volvox +-------------------17
MOLECULAR POPULATION GENETICS: COALESCENT METHODS BASED ON SUMMARY STATISTICS
MOLECULAR POPULATION GENETICS: COALESCENT METHODS BASED ON SUMMARY STATISTICS Daniel A. Vasco*, Keith A. Crandall* and Yun-Xin Fu *Department of Zoology, Brigham Young University, Provo, UT 8460, USA Human
Tópicos Depto. Ciencias Biológicas, UniAndes Profesor Andrew J. Crawford Semestre II
Tópicos Depto. Ciencias Biológicas, UniAndes Profesor Andrew J. Crawford Semestre 29 -II Lab Coalescent simulation using SIMCOAL 17 septiembre 29 Coalescent theory provides a powerful model
Kinship and Population Subdivision
Kinship and Population Subdivision Henry Harpending University of Utah The coefficient of kinship between two diploid organisms describes their overall genetic similarity to each other relative to some
Your mtdna Full Sequence Results
Congratulations! You are one of the first to have your entire mitochondrial DNA (DNA) sequenced! Testing the full sequence has already become the standard practice used by researchers studying the DNA,
Estimating Ancient Population Sizes using the Coalescent with Recombination
Estimating Ancient Population Sizes using the Coalescent with Recombination Sara Sheehan joint work with Kelley Harris and Yun S. Song May 26, 2012 Sheehan, Harris, Song May 26, 2012 1 Motivation Introduction
MODERN population genetics is data driven and
Copyright Ó 2009 by the Genetics Society of America DOI: 10.1534/genetics.108.092460 Note Extensions of the Coalescent Effective Population Size John Wakeley 1 and Ori Sargsyan Department of Organismic
The Structure of Genealogies and the Distribution of Fixed Differences Between DNA Sequence Samples From Natural Populations
Copyright 0 1991 by the Genetics Society of America The Structure of Genealogies the Distribution of Fixed Differences Between DNA Sequence Samples From Natural Populations Department of Biological Sciences,
The Two Phases of the Coalescent and Fixation Processes
The Two Phases of the Coalescent and Fixation Processes Introduction The coalescent process which traces back the current population to a common ancestor and the fixation process which follows an individual
POPULATION GENETICS: WRIGHT FISHER MODEL AND COALESCENT PROCESS. Hailong Cui and Wangshu Zhang. Superviser: Prof. Quentin Berger
POPULATIO GEETICS: WRIGHT FISHER MODEL AD COALESCET PROCESS by Hailong Cui and Wangshu Zhang Superviser: Prof. Quentin Berger A Final Project Report Presented In Partial Fulfillment of the Requirements
Research Article The Ancestry of Genetic Segments
International Scholarly Research Network ISRN Biomathematics Volume 2012, Article ID 384275, 8 pages doi:105402/2012/384275 Research Article The Ancestry of Genetic Segments R B Campbell Department of
Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling
Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling Mary K. Kuhner, Jon Yamato, and Joseph Felsenstein Department of Genetics, University of Washington
Contributed by "Kathy Hallett"
National Geographic: The Genographic Project Name Background The National Geographic Society is undertaking the ambitious process of tracking human migration using genetic technology. By using the latest
Testing Multiregionality of Modern Human Origins
Testing Multiregionality of Modern Human Origins Naoyuki Takahata, Sang-Hee Lee, and Yoko Satta Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, Kanagawa, Japan In order
DNA CHARLOTTE COUNTY GENEALOGICAL SOCIETY - MARCH 30, 2013 WALL STREET JOURNAL ARTICLE
DNA CHARLOTTE COUNTY GENEALOGICAL SOCIETY - MARCH 30, 2013 WALL STREET JOURNAL ARTICLE NATIONAL GEOGRAPHIC GENOGRAPHIC PROJECT ABOUT NEWS RESULTS BUY THE KIT RESOURCES Geno 2.0 - Genographic Project
Bottlenecks reduce genetic variation Genetic Drift
Bottlenecks reduce genetic variation Genetic Drift Northern Elephant Seals were reduced to ~30 individuals in the 1800s. Rare alleles are likely to be lost during a bottleneck Two important determinants
Part I. Concepts and Methods in Bacterial Population Genetics COPYRIGHTED MATERIAL
Part I Concepts and Methods in Bacterial Population Genetics COPYRIGHTED MATERIAL Chapter 1 The Coalescent of Bacterial Populations Mikkel H. Schierup and Carsten Wiuf 1.1 BACKGROUND AND MOTIVATION Recent
STAT 536: The Coalescent
STAT 536: The Coalescent Karin S. Dorman Department of Statistics Iowa State University November 7, 2006 Wright-Fisher Model Our old friend the Wright-Fisher model envisions populations moving forward
Growing the Family Tree: The Power of DNA in Reconstructing Family Relationships
Growing the Family Tree: The Power of DNA in Reconstructing Family Relationships Luke A. D. Hutchison Natalie M. Myres Scott R. Woodward Sorenson Molecular Genealogy Foundation (www.smgf.org) 2511 South
DNA and Ancestry. An Update on New Tests. Steve Louis. Jewish Genealogical Society of Washington State. January 13, 2014
DNA and Ancestry An Update on New Tests Steve Louis Jewish Genealogical Society of Washington State January 13, 2014 DISCLAIMER This document was prepared as a result of independent work and opinions of
[CLIENT] SmithDNA1701 DE January 2017
![[CLIENT] SmithDNA1701 DE January 2017](/thumbs/93/113058427.jpg "[CLIENT] SmithDNA1701 DE January 2017")
[CLIENT] SmithDNA1701 DE1704205 11 January 2017 DNA Discovery Plan GOAL Create a research plan to determine how the client s DNA results relate to his family tree as currently constructed. The client s
Your web browser (Safari 7) is out of date. For more security, comfort and the best experience on this site: Update your browser Ignore
Your web browser (Safari 7) is out of date. For more security, comfort and the best experience on this site: Update your browser Ignore Activitydevelop U SING GENETIC MARKERS TO CREATE L INEAGES How do
Using Mitochondrial DNA (mtdna) for Genealogy Debbie Parker Wayne, CG, CGL SM
Using Mitochondrial DNA (mtdna) for Genealogy Debbie Parker Wayne, CG, CGL SM This is one article of a series on using DNA for genealogical research. There are several types of DNA tests offered for genealogical
DNA Haplogroups Report
DNA Haplogroups Report for Matthew Mayberry Generated and printed on Sep 25 2011, 01:59 pm X This is a mtdna Haplogroup Report This is a mtdna Subclade Report Search criteria used in this report: HVR-1
Coalescent Likelihood Methods. Mary K. Kuhner Genome Sciences University of Washington Seattle WA
Coalescent Likelihood Methods Mary K. Kuhner Genome Sciences University of Washington Seattle WA Outline 1. Introduction to coalescent theory 2. Practical example 3. Genealogy samplers 4. Break 5. Survey
Coalescent genealogy samplers: windows into population history
Review Coalescent genealogy samplers: windows into population history Mary K. Kuhner Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA 98195-5065, USA Coalescent genealogy
DNA Testing. February 16, 2018
DNA Testing February 16, 2018 What Is DNA? Double helix ladder structure where the rungs are molecules called nucleotides or bases. DNA contains only four of these nucleotides A, G, C, T The sequence that
Autosomal-DNA. How does the nature of Jewish genealogy make autosomal DNA research more challenging?
Autosomal-DNA How does the nature of Jewish genealogy make autosomal DNA research more challenging? Using Family Finder results for genealogy is more challenging for individuals of Jewish ancestry because
Evaluating the performance of likelihood methods for. detecting population structure and migration
Molecular Ecology (2004) 13, 837 851 doi: 10.1111/j.1365-294X.2004.02132.x Evaluating the performance of likelihood methods for Blackwell Publishing, Ltd. detecting population structure and migration ZAID
CONGEN. Inbreeding vocabulary
CONGEN Inbreeding vocabulary Inbreeding Mating between relatives. Inbreeding depression Reduction in fitness due to inbreeding. Identical by descent Alleles that are identical by descent are direct descendents
Mitochondrial DNA (mtdna) JGSGO June 5, 2018
Mitochondrial DNA (mtdna) JGSGO June 5, 2018 MtDNA - outline What is it? What do you do with it? How do you maximize its value? 2 3 mtdna a double-stranded, circular DNA that is stored in mitochondria
G ene tree discordance, phylogenetic inference and the m ultispecies coalescent
Review G ene tree discordance, phylogenetic inference and the m ultispecies coalescent Ja m es H. Degnan 1,2 and N oah A. Rosenberg 1,3,4 1 Department of Human Genetics, University of Michigan, Ann Arbor,
A Likelihood Method to Estimate/Detect Gene Flow and A Distance Method to. Estimate Species Trees in the Presence of Gene Flow.
A Likelihood Method to Estimate/Detect Gene Flow and A Distance Method to Estimate Species Trees in the Presence of Gene Flow Thesis Presented in Partial Fulfillment of the Requirements for the Degree
Report on the VAN_TUYL Surname Project Y-STR Results 3/11/2013 Rory Van Tuyl
Report on the VAN_TUYL Surname Project Y-STR Results 3/11/2013 Rory Van Tuyl Abstract: Recent data for two descendants of Ott van Tuyl has been added to the project, bringing the total number of Gameren
6.047/6.878 Lecture 21: Phylogenomics II
Guest Lecture by Matt Rasmussen Orit Giguzinsky and Ethan Sherbondy December 13, 2012 1 Contents 1 Introduction 3 2 Inferring Orthologs/Paralogs, Gene Duplication and Loss 3 2.1 Species Tree..............................................
Recap: Properties of Trees. Rooting an unrooted tree. Questions trees can address: Data for phylogeny reconstruction. Rooted vs unrooted trees:
Pairwise sequence alignment (global and local) Recap: Properties of rees Multiple sequence alignment global local ubstitution matrices atabase ing L equence statistics Leaf nodes contemporary taxa Internal
Before India: Exploring Your Ancestry With DNA By David G. Mahal
Before India: Exploring Your Ancestry With DNA By David G. Mahal You then receive an email notifying you that your results are ready to explore on utilize your DNA results for family history by Ancestry.com
Population Genetics. Joe Felsenstein. GENOME 453, Autumn Population Genetics p.1/70
Population Genetics Joe Felsenstein GENOME 453, Autumn 2013 Population Genetics p.1/70 Godfrey Harold Hardy (1877-1947) Wilhelm Weinberg (1862-1937) Population Genetics p.2/70 A Hardy-Weinberg calculation
Every human cell (except red blood cells and sperm and eggs) has an. identical set of 23 pairs of chromosomes which carry all the hereditary
Introduction to Genetic Genealogy Every human cell (except red blood cells and sperm and eggs) has an identical set of 23 pairs of chromosomes which carry all the hereditary information that is passed
On the nonidentifiability of migration time estimates in isolation with migration models
Molecular Ecology (2011) 20, 3956 3962 doi: 10.1111/j.1365-294X.2011.05247.x NEWS AND VIEWS COMMENT On the nonidentifiability of migration time estimates in isolation with migration models VITOR C. SOUSA,
Population Genetics. Joe Felsenstein. GENOME 453, Autumn Population Genetics p.1/74
Population Genetics Joe Felsenstein GENOME 453, Autumn 2011 Population Genetics p.1/74 Godfrey Harold Hardy (1877-1947) Wilhelm Weinberg (1862-1937) Population Genetics p.2/74 A Hardy-Weinberg calculation
Identification of the Hypothesized African Ancestry of the Wife of Pvt. Henry Windecker Using Genomic Testing of the Autosomes.
Identification of the Hypothesized African Ancestry of the Wife of Pvt. Henry Windecker Using Genomic Testing of the Autosomes Introduction African Ancestry: The hypothesis, based on considerable circumstantial
Ernie Ebayley s Adventure in DNA-Land. A Resource for Beginning Your Own Adventure into Genealogical Genetics
Ernie Ebayley s Adventure in DNA-Land A Resource for Beginning Your Own Adventure into Genealogical Genetics 2006 C.E. Smith Museum of Anthropology College of Arts, Letters, and Social Sciences (CLASS)
Gene Genealogy in Three Related Populations: Consistency Probability Between Gene and Population Trees
Copyright 0 989 by the Genetics Society of America Gene Genealogy in Three Related Populations: Consistency Probability Between Gene and Population Trees Naoyuki Takahata National Institute of Genetics,
Theoretical Population Biology. An approximate likelihood for genetic data under a model with recombination and population splitting
Theoretical Population Biology 75 (2009) 33 345 Contents lists available at ScienceDirect Theoretical Population Biology journal homepage: www.elsevier.com/locate/tpb An approximate likelihood for genetic
Coalescent Theory for a Partially Selfing Population
Copyright 6 1997 by the Genetics Society of America T Coalescent Theory for a Partially Selfing Population Yun-xin FU Human Genetics Center, University of Texas, Houston, Texas 77225 Manuscript received
THE estimation of population genetics parameters such as
INVESTIGATION A Continuous Method for Gene Flow Michal Palczewski 1 and Peter Beerli Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306 ABSTRACT Most modern population
Behavioral Adaptations for Survival 1. Co-evolution of predator and prey ( evolutionary arms races )
Behavioral Adaptations for Survival 1 Co-evolution of predator and prey ( evolutionary arms races ) Outline Mobbing Behavior What is an adaptation? The Comparative Method Divergent and convergent evolution
ESTIMATION OF THE NUMBER OF INDIVIDUALS FOUNDING COLONIZED POPULATIONS
ORIGINAL ARTICLE doi:1.1111/j.1558-5646.7.8.x ESTIMATION OF THE NUMBER OF INDIVIDUALS FOUNDING COLONIZED POPULATIONS Eric C. Anderson 1, and Montgomery Slatkin 3,4 1 Fisheries Ecology Division, Southwest
Pedigree Reconstruction using Identity by Descent
Pedigree Reconstruction using Identity by Descent Bonnie Kirkpatrick Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2010-43 http://www.eecs.berkeley.edu/pubs/techrpts/2010/eecs-2010-43.html
Meek DNA Project Group B Ancestral Signature
Meek DNA Project Group B Ancestral Signature The purpose of this paper is to explore the method and logic used by the author in establishing the Y-DNA ancestral signature for The Meek DNA Project Group
Genesis and Genetics Matthew Price
Genesis and Genetics Matthew Price Apologetics and Creation Camp 16 June 2018 Karakariki Christian Camp, Waikato, NZ 1 What is Science? 2 What is Science? Hypothesis Theory Start with a hypothesis; a reasonable
Coalescent vs. Time-forward Simulations in the Problem of the Detection of Past Population Expansion
Issue, Volume, 8 Coalescent vs. Time-forward Simulations in the Problem of the Detection of Past Population Expansion Krzysztof A. Cyran, Dariusz Myszor Abstract The objective of this article is to show
What Can I Learn From DNA Testing?
What Can I Learn From DNA Testing? From where did my ancestors migrate? What is my DNA Signature? Was my ancestor a Jewish Cohanim Priest? Was my great great grandmother really an Indian Princes? I was
BI515 - Population Genetics
BI515 - Population Genetics Fall 2014 Michael Sorenson msoren@bu.edu Office hours (BRB529): M, Th, F 4-5PM or by appt. (send e-mail) My research: Avian behavior, systematics, population genetics, and molecular
An Introduction. Your DNA. and Your Family Tree. (Mitochondrial DNA) Presentation by: 4/8/17 Page 1 of 10
An Introduction Your DNA and Your Family Tree (Mitochondrial DNA) Presentation by: FredCoffey@aol.com 4/8/17 Page 1 of 10 Coffey Surname, y-dna Project We're now ready to move on and look at the type of
Where do evolutionary trees comes from?
Probabilistic models of evolutionary trees Joint work with Outline of talk Part 1: History, overview Part 2: Discrete models of tree shape Part 3: Continuous trees Part 4: Applications: phylogenetic diversity,
TRACK 1: BEGINNING DNA RESEARCH presented by Andy Hochreiter
TRACK 1: BEGINNING DNA RESEARCH presented by Andy Hochreiter 1-1: DNA: WHERE DO I START? Definition Genetic genealogy is the application of genetics to traditional genealogy. Genetic genealogy uses genealogical
Halley Family. Mystery? Mystery? Can you solve a. Can you help solve a
Can you solve a Can you help solve a Halley Halley Family Family Mystery? Mystery? Who was the great grandfather of John Bennett Halley? He lived in Maryland around 1797 and might have been born there.
The Coalescent. Chapter Population Genetic Models
Chapter 3 The Coalescent To coalesce means to grow together, to join, or to fuse. When two copies of a gene are descended from a common ancestor which gave rise to them in some past generation, looking
Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations
Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters
The Coalescent Model. Florian Weber
The Coalescent Model Florian Weber 23. 7. 2016 The Coalescent Model coalescent = zusammenwachsend Outline Population Genetics and the Wright-Fisher-model The Coalescent on-constant population-sizes Further
PHYLOGEOGRAPHIC BREAKS WITHOUT GEOGRAPHIC BARRIERS TO GENE FLOW
Evolution, 56(1), 00, pp. 383 394 PHYLOGEOGRAPHIC BREAKS WITHOUT GEOGRAPHIC BARRIERS TO GENE FLOW DARREN E. IRWIN 1 Section for Animal Ecology, Department of Ecology, Lund University, S-3 6 Lund, Sweden
Evolutions of communication
Evolutions of communication Alex Bell, Andrew Pace, and Raul Santos May 12, 2009 Abstract In this paper a experiment is presented in which two simulated robots evolved a form of communication to allow
Using Y-DNA for Genealogy Debbie Parker Wayne, CG, CGL SM
Using Y-DNA for Genealogy Debbie Parker Wayne, CG, CGL SM This is one article of a series on using DNA for genealogical research. There are several types of DNA tests offered for genealogical purposes.