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Human Evolution Timelines

Human Evolution Timelines. Research History. Evolution History. Source: Jobling, Hurles & Tyler-Smith (2004) Human Evolutionary Genetics. Human Evolution. The Data Genetic: Allele Frequencies, SNPs, Haplotypes Non-genetic: Language, culture, pets,pathogens, culture,.. The Dynamics

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Human Evolution Timelines

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  1. Human Evolution Timelines Research History Evolution History Source: Jobling, Hurles & Tyler-Smith (2004) Human Evolutionary Genetics.

  2. Human Evolution The Data Genetic: Allele Frequencies, SNPs, Haplotypes Non-genetic: Language, culture, pets,pathogens, culture,.. The Dynamics Mutation, selection, recombination, The Genealogical Structure Phylogeny, Ancestral Recombination Graph, Pedigree Relationship to the great Apes, Ancestral Population of Human/Chimp Ancestor, Out of Africa Ancestral Population Structure, Selection, Migrations & Age of Alleles. Genealogies Iceland Models of Pedigrees Languages & Pathogens

  3. Populations & Basic Genealogical Structures Pedigree: Trace the ancestry of individuals Grand parents Phylogeny: Trace the ancestry of sequence points. Parents ARG: Trace the ancestry of sequences Now Other Genealogical Structures are possible network, language merging, population splitting

  4. Recombination Recombination: Gene Conversion: 1 meiosis • Total Haploid length males: 25.9 M - females: 44.6 M. • Gene conversions 1-2 orders higher. Length 300-2000 pb. Lander et al.(2001) “Initial sequencing and analysis of the human genome” Nature 409.860-912. + Kong,E. et al.(2002) “A high resolution recombination map of the human genome” Nature Genetics

  5. A A A C C A A A C C A A A C C Mutations and Mutation Rates 1 mitosis or generation Average Number of Mitoses Per Male generation (15:35 .. 20:150) Per Female generation: ~24 • Single nucleotide substitutions: ~10-7 • Microsatellites (~100.000): ~10-2 • Small insertion deletions: ~10-8 Selection: Positive & Negative Crow,JF (2000) “The Origins, Patterns and Implications of Human Spontaneous Mutation” Nature Review Genetics 1.1.40-47 + Strachan and Read (2004) chapter 11 +Jobling, Hurles and Tyler-Smith (2004) chapter 2

  6. Coalescent Issues The number of genetic ancestors When gene-trees differ from species trees Out of Africa Ages of Alleles Allele Gradients Number of Genetic Ancestors Selective Sweeps

  7. Human History Levels: Physical, Cultural & Genealogical The physical population size, N(t), and the efficient population size, Ne(t) are separate concepts. i. N(t)can mainly be studied by historical/archeological means, ii. Ne(t)can be studied genealogically, for instance by tracing the ancestries of DNA sequences. Main departures from simplest Population Genetical Models: A. Long epochs of exponential growth at increasing rates B. Bottlenecks & small populations. C. Migrations & Geographical subdivisions

  8. Our relationship to the great Apes. From Nei,2003 13 Myr 7 Myr 5.5 Myr 1 Myr Chimp Pygmee Chimp Orangutan Gorilla Humans

  9. Ancestral Population of Human and Chimp 7 Myr G H 5 Myr C Now Human Chimp Gorilla Example: Chen & Li (2001) 53 triads: 31 (H,C), 10 (H,G) & 11 (C,G)

  10. Out-of-Africa and different degrees of replacements Total replacement No replacement Partial replacement 1-1.2 Myr 1-1.2 Myr 1-1.2 Myr 80-130 Kyr 80-130 Kyr 80-130 Kyr Europe Africa Asia Africa Europe Asia Africa Europe Asia Example: Takahata (2001) found data could be explained by total replacement.

  11. Allele Frequencies and Principal Components Cavalli-Sforza,2001 • Allele frequencies for different localities are subjected to a smoothing procedure. • Principle Components are found and projected on geographical maps. • Strongly criticized (Sokal et al.): even no geographical structure will “look like” geographical structure, no timing of gradients,... Agriculture 6-10 Kyr Greek Colonisation 3 Kyr Retraction of the Basques Uralic People Horse domestication

  12. Time slices All positions have found a common ancestors on one sequence All positions have found a common ancestors Time 1 2 1 2 1 2 1 2 1 2 N 1 Population

  13. Number of genetic ancestors to the Human Genome Sr– number of Segments E(Sr) = 1 + r time C C C R R R sequence Simulations Statements about number of ancestors are much harder to make. Wiuf conjectured ~r/ln(r)

  14. Applications to Human Genome (Wiuf and Hein,97) 0 260 Mb 0 52.000 *35 0 7.5 Mb 6890 8360 *250 30kb 0 Parameters used 4Ne 20.000 Chromos. 1: 263 Mb. 263 cM Chromosome 1: Segments 52.000 Ancestors 6.800 All chromosomes Ancestors 86.000 Physical Population. 1.3-5.0 Mill. A randomly picked ancestor: (ancestral material comes in batteries!)

  15. Many sampled alleles relative to Ne Wakeley03, Pitman, Schweinberg 1. Simultaneous Events 2. Multifurcations. 3. Underestimation of Coalescent Rates

  16. Cystic Fibrosis • (Wiuf 2000) • F508 – possibly maintained by heterosis (1.023)- higher resistance to Salmonella infections. • Data: 1. Frequency of F508-allele - .022. • 2. Inter variability in 1.705 individuals 46 variable positions. • 3. Model of human demography. • Model parameters: mutation rate, heterosis advantage and an exponential growth model of human population expansion. Estimated age of F508 is estimated to be *

  17. Pedigree Issues Chinese http://demography.anu.edu.au/People/Staff/zhongwei.html Burke’s British Peerage http://www.burkes-peerage.net/sites/wars/sitepages/home.asp Mormons http://genealogy-mormons.com/ Quebec French Heyer and Tremblay, 1998 PNAS Icelandic http://www.decode.com + Helgason, A. et al. (2003 June) “A population-wide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: Evidence for a faster evolutionary rate of mtDNA lineages than Y-chromosomes” American Journal Human Genetics. i. Icelandic Pedigree Theoretical Models

  18. Icelandic Genealogies Helgason, 2003 Total Genealogy Males only Females only Of (June 2002) 276,00 Icelanders 131,060 born after 1972 was traced back.

  19. Icelandic Genealogies Helgason, 2003 Ancestors to 1972 cohort Backtracable

  20. Icelandic GenealogiesHelgason, 2003 Variation in annual offspring number greater for females in males, due to shorter generation time. Positive correlation in fertility between parent-offspring.

  21. Finding Ancestral Individuals. Joe Chang 1999 Dec. Adv. Appl. Prob. 11 10 9 8 7 Finding (Great)k Grand Parents. 6 5 4 3 2 1 NOW 0 Let T be the time, when somebody was everybody’s ancestor. Changs’ result: lim T*/log2(N) =1 prob. 1

  22. Combining Ancestral Individuals and the Coalescent Wiuf & Hein, 2000. Finding Common Ancestors. NOW Unify the two processes: Sample more individuals Let each have p parents. ( p – possibly stochastic >= 1). Result: A discontinuity at 1. For p>1 change log2logp Comment:Genetic Ancestors is a vanishing set within Genealogical Ancestors.

  23. Derrida G +1 G Recursion: a individual, g ancestor in tree, w - weight probability that uni. random path leads to g. Initialization:

  24. Kammerle 89: Pair Moran Model A pair of children are born – they choose parents randomly. A pair is erased and the children pair take their place. A. The stationary distribution of number of ancestors to present population is hypergeometric: y 0

  25. Non-Contributing Ancestors Kevin Donnelly, 1983 TPB x …. 1 22 x x …. y 1 22 No Recombination: Recombination: Generation: Ancestors: 2k k 46 packets < ≈k*72 + 46 packets y 1 21 1 1 x 22 22 <≈72 + 46 packets 46 packets x x …. …. y 1 y 1 22 22 0 1 46 packets 46 packets

  26. Non-Contributing Ancestors Yun song- pers.comm., 2003 Kevin Donnelly, 1983 The probability of 1. Any non-contributing ancestor 2.That a randomly chosen ancestors is non-contributing 1 2 4 8 16 32 From Yun Song Back in Time 64 128 256 512

  27. Pedigree Inference Father Mother From Yun Song Prior on Pedigrees Three Processes • Choosing Parents • Recombination • The Mutational Process Probability of data given pedigree Posterior on Pedigrees Elston-Stewart (1971) -Temporal Peeling Algorithm Lander-Green (1987) - Genotype Scanning Algorithm

  28. Inheritable phenomena Genetic Material Sequences “Allele Frequencies” Language Culture Pathogens Pests Pets Morphological Characters

  29. Pathogen phylogeniesFalush 2003 Helicobacter pylori is transmitted from mother to child. Falush et al. sequenced 8 genes from 370 strains from 27 populations – 3850 nucletides each. 5 ancestral populations:East Asia, Euro1, Euro2, Afr1 Afr2 Structure assign each polymorphism to an ancestral population. American indians are grouped as asian showing that H.pylori infection is ancient. Diversity of H.pylori 50 times larger than humans. Much recombination – i.e. positions can be treated as independent • Maori is east asian. • Inuit is Euro1 + Euro2 • South African Afr2 • English

  30. Cavalli- Sforza: Language Trees Cavalli-Sforza (1997) Genes Peoples and Languages PNAS 94.7719-24 Principle of Comparison. Loss of cognates (“homologous” words) Syntax Comparison. Sound use. Reconstruction (dependent on interpretation) – stretches back 2-6.000 years dependent on criteria.

  31. Historical Linguistics William Jones 1776 observes similarities between Sanskrit, Greek & Latin Swadesh (1952) makes on of the first glottochronological studies Kruskal, Dyer & Black (1971) large successful investigation. Principles: Distance - Swadesh’ rule. 20% lost per millenium. Parsimony Compatibility Likelihood Criticisms: Word Loss is not clocklike Languages and merge and borrow giving non-tree like structure Not much research goes into this area.

  32. Khoisan Global Phylogeny Cavalli-Sforza,2001 Ruhlen, 1994 African Niger-Kordofanian Congo-Saharan Nilo-Saharan Afro-Asiatic Kartvelian Dravidian Indo-European Uralic Eurasiatic 20-10 Kyr Eurasion/American 40-20 Kyr Altaic Eskimo-Aleut Chukchi-Kamchatkan Home sapiens sapiens 100-70 Kyr Amerind Na-Dene Eurasian 60-40 Kyr Dene-Caucasian 40-20 Kyr Sino-Tibetan Caucasian/Basque/Burushaski Asian 70-50 Kyr Austronesian Daic Austro-Tai Miao-Yao Austric Austro-Asiatic Dene-Caucasian 40-20 Kyr Indo-Pacific Pacific Australian

  33. Afghan Baluchi Persian Osetic Bengali Hindi Punjabi Marathi Nepali Kashmiri Singhalese Breton Welch Irish Bulgarian Macedonian Serbo Croatian Belorussian Ukranian Polish Chech Russian Slovenian Latvian Lithuanian French Walloon Italian Ladin Portugese Spanish Sardinian Rumanian Danish Swedish Riksmaal Faraoese Icelandic Dutch German Frisian English Greek Armenian Albanian Indo-European Language Trees Dyen, Kruskal & Black, 1992 Piazza, Cavalli-Sforza, 2001 Celtic Slavic Romance Germanic 9000 8000 7000 6000 5000 4000 3000 2000 1000

  34. Germanic Language Trees From Embleton, 1986 Swedish 1540 Danish 1803 Norwegian 1051 Faraoese Icelandic 1842 English 194 Tok Pisin 1051 Frisian 246 Flanders 1239 Africaans 1668 1423 Dutch 1025 1051 1234 Yiddish 1476 Hamburg Lower Saxony Pennsylvanian German 1558 German TrS

  35. The Coalescent & Human Evolution(11.6.04) Human History Methodological Problems: Reconstucting haplotypes, defining haplotype blocks + HapMap. Relationship to the great Apes, Ancestral Population of Human/Chimp Ancestor, Out of Africa, The Neanderthal. Human Population Growth, Ancestral Population Structure, Selection, Migrations & Age of Alleles. SNPs Haplotypes, Recombination Hotspots & Haplotype Blocks. Individual Stories: Mitochondria, Y, autosomal chromosomes & alleles. Emperical Genealogies Iceland Other Genealogical Issues: Genealogical Ancestors, Genetic and Non-Contributing Ancestors Heritable Characters Languages Associated Animals, Plants & Pathogens Surnames Morphological Characters The Role of Coalescent Theory

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