The Future of the Past DNA DNA DNA studies can uncover new relationships and disprove the ones you thought you had. chromosome pair chromosome pair In color with clickable links at http://udel.edu/~tdoherty/DNAweb11s.pdf DNA, Chromosomes and Genes DNA (DeoxyriboNucleic Acid): in most all body cells - Very long twisted double helix structure, composed of a sugar (deoxyribose), a phosphate and two base pairs - Organized into chromosome pairs: 23 in nucleus of cell plus mitrochondrial-DNA outside cell nucleus - Your DNA, stretched end to end, goes to moon and back Chromosome pairs: 23 strung along our DNA chain DNA -- Dog: 39 chromosome pairs, cat 19, mosquito 3, rice 12 - One sex chromosome pair: XX=female, XY=male chromosome - plus 22 autosomes (non-sex) chromosome pairs pair Genes: an estimated 25,000 genes on our 23 chromosomes - Genes are groups of base pairs along a chromosome chain. - How base pairs are grouped into genes at fixed positions on the chromosome chain define us as unique human beings. © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 1 Cell Structure Nucleus contains 23 chromosome pairs (½ from each parent) Y-chromosome from father only to his sons X-chromosome from father only to his daughters DNA chromosome pair Mitochondria, DNA to all children from mother; only outside the nucleus Chromosomes are threadlike “packages” of genes and other DNA cell drawing ©2004 Pearson Education, Inc. in Tortora, Funke & Case, “Microbiology An Introduction” 8th edition Mitochondrion mitochondria: ~1,000 (1K)/cell ~16K base pairs /mitochondrion none in nucleus where energy is generated for cell metabolism contains mtDNA only from mother only changed by rare mutation not thought to carry much genetic code drawing ©2004 Pearson Education, Inc. in Tortora, Funke & Case, “Microbiology An Introduction” 8th edition © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 2 Human Chromosomes DNA chromosome pair graphics from http://www.smgf.org/education/animations/four_types.jspx The Structure of DeoxyriboNucleic Acid (DNA) DNA looks like a twisted ladder Has sugar-phosphate backbone Base pairs form rungs of ladder Has only 4 bases, only 2 base pairs: 1. adenine-thymine (A-T) ( - ) 2. cytosine-guanine (C-G) ( - ) Four configurations: A-T, T-A, C-G, G-C Weak Hydrogen Bonds Between Bases Sugar-Phosphate Backbone mtDNA: has ~16 thousand base pairs Y-chromosome: ~50 million base pairs for more: http://blairdna.com/dna101.html © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 3 Chemical Structure of Bases DNA: 4 bases, 2 base pairs: 1. adenine-thymine (A-T) ( - ) 2. cytosine-guanine (C-G) ( - ) For those who really had to know Weak Hydrogen Bonds Between Bases DNA Each base pair: 3 double-bond rings Each DNA “rung” is relatively flat Testing Your DNA 1. adenine-thymine (A-T) ( - ) 2. cytosine-guanine (C-G) ( - ) Sequence, esp. repeat units, of these base pairs (bp) determines your genetic code of 50M base pairs, Y-DNA focus is on Weak Hydrogen Bonds Between Bases a few “markers” markers contain ~2-5 bp (e.g. ATCG) repeated head-to-tail numerous times mutation: delete or add repeat unit repeated head-to-tail numerous times improve odds of finding relationships: - normally a cheek swab is taken - recruit more participants - test 37 or more markers/participant for more: http://blairdna.com/dna101.html © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 4 Why Are My 25,000 Genes Unique? Genes are groupings of base pairs on a chromosome chain. - Human DNA is 99.9% the same; we study 0.1% difference - Geneticists have identified specific locations on chains to study base pair groupings (genes), called “markers” Markers are assigned a specific identifying code. - Y-DNA markers have a DYS# code, e.g. 393, 464a, CDY b - Some markers, not all, have been connected to a genetic trait. Gene mutation rates: vary markedly among genes, e.g. - Both Y-DNA and mtDNA pass “unchanged” from parents - Y-DNA mutates 0.002 times/marker/generation - mtDNA mutates less than 0.0002 times/marker/generation Recombination: mixing of each parent’s 22 autosomes - each parent contributes ½ part of each of their 22 autosomes the recombined ½ parts (called gametes) join at conception Testing your DNA: - Was blood sample, now cheek swab (better for queasy men). - Widespread autosomal DNA testing first offered 2010 Random Infrequent Mutations are measured in ““markers” markers” Test markers known to mutate more often Y-DNA mutates .002 times/marker/generation - 25, 37, 67 “markers” commonly tested - now best way to find common recent ancestors - if female, you must recruit a male relative mtDNA mutates <.0002 times/marker/generation - mtDNA: hypervariable (HVR) regions I and II - too few differences to detect recent [1000 yr] descent - but can determine ancestral heritage - our mtDNA differs, depending on which cell it’s in © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 5 Are We Part Neandertal ? Neandertal? Draft results* - Neandertals 99.84% identical to humans - Used SNP markers: mutate only once in human history - Europeans/Asians share 1-4% DNA with Neandertals/Neanderthals - Africans share no DNA with Neandertals Very small sampling - Three 38,000 year old female Neandertals from Croatia region - Not many samples available: ice age glacier damage *R.Green, A Draft Sequence of the Neandertal Genome, Science v.328, #5979, p.710 (7 May 2010) Also see: http://www.sciencemag.org/special/neandertal/feature/index.html (graphic) Markers DNA Each marker has a different mutation rate. Mutations occur often during recombination. from http://www.smgf.org/education/animations/mutation.jspx © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 6 Markers Commonly Tested compared to Cambridge Reference Standard Test Regions of more recent mutation - some markers of known genetic traits, others “junk” area - Y-DNA: 37($119-169), 67 ($269); autosomal ($293) - mtDNA: hypervariable (HVR) regions I and II Large samplings needed for best results Testing Companies: see http://genetealogy.com - http://www.familytreedna.com 90% of family projects - http://dnaancestry.com (dnagroups) – with ancestry.com -- from http://www.relativegenetics.com/relativegenetics/index.jsp -- Sorenson is partner: http://sorensongenomics.com Nat’l Geographic Genographic Project (deep ancestry): - see https://www3.nationalgeographic.com/genographic Sampling process: http://davedorsey.com/dna.html Y -Chromosome Inheritance Y-Chromosome Father passes Y-chromosome unchanged* to every son and to none of his daughters The Y-DNA of my great-grandfather (Thomas F. Doherty) dies with me. only one of his sons had a son (my dad). Genetically, I was an only child. I have no sons. Where was my great-grandfather born? born 15 May 1850 [Bible] in “Ireland” [many sources] st Child’s birth record: father b “Co Clare, Ireland” 1st 1880s Boston photo of family: “brother James Doherty” 1881 Photo: man of Limerick; same as man in Boston? My 67 markers:part of Doherty project at FamilyTreeDNA * a random mutation (.002/marker/generation) © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 7 Y -Chromosome Inheritance Y-Chromosome Are these people related? 1881 Limerick 1875-90? Boston My My great-grandfather great-grandfather (Thomas (Thomas F. F. Doherty) Doherty) born born 15 15 May May 1850 1850 Co.Clare Co.Clare Ireland Ireland d.1904 d.1904 Chicago Chicago my my grandfather grandfather >> >> (Edward (Edward James James Doherty) Doherty) My My Dad Dad >> >> (Maynard (Maynard Thomas Thomas Doherty) Doherty) (2 (2 photos) photos) Me Me >> >> (2 (2 photos) photos) 1880s 1880s Boston Boston “brother “brother James James Doherty” Doherty” and and family family [Generations to] Most Recent Common Ancestor [[MRCA: MRCA: 50% likely that two individuals are related related]] Note: 36/37 means 36 markers match out of 37 tested – could be higher certainty than 15/15. Some markers of known genetic traits, others in ““junk” junk” junk” area. chart from http://www.relativegenetics.com (Y-DNA) © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 8 Sample Y-DNA Results from FamilyTreeDNA.com http://www.familytreedna.com/myhttp://www.familytreedna.com/my-ftdna/yftdna/y-dnadna-dys.aspx Locus = marker [I had 67 tested] DYS# = ID# of locus: chosen because alleles differ often, but not too often Alleles = # of repeating base pairs at that marker If your # of alleles differs from someone else, mutation(s) have occurred between your MCRA (Most Recent Common Ancestor) and either one or both of you. Matching Results: [groups of cousins] >> [Generations to] Most Recent Common Ancestor [[MRCA: MRCA: 50% likelihood that two individuals are related related]] Number of Generations to 50% likelihood of a common ancestor Some markers are of known genetic traits, but most in ““junk” junk” junk” area 17 generations goes back to 15th or 16th century, near the limit of most paper trails (Y-DNA) about 3 generations for 67 markers chart from http://nitro.biosci.arizona.edu/ftDNA/TMRCA.html © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 9 The The Determination Determination of of aa Boy, Boy, Age Age 15 15 A A Possible Possible Con Con of of Testing Testing Your Your DNA DNA Warning for anyone who has fathered a child and wants that fact to remain a secret © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 10 Haplotype: Y -DNA & mtDNA Y-DNA Haplotype: DNA inherited unchanged Haplogroup Haplogroup:: collection of similar haplotypes New haplotype from mutation: random time/place Y-DNA min. mutations .002/marker/generation: - for combined mutations in 10 generations: -- 12 markers tested: .24; 37 markers: .74 -- 2 unique paper trails to 10 gen: 1.5 mismatches -- 2 unique paper trails to 5 gen: 0.5 mismatch magnitude fewer mtDNA mutations: < .0002/m/g - only 2 markers measured routinely - maybe only 100-200 European mtDNA halotypes - can confirm only a few paper trails Mutation occurs frequently during recombination My Mitochondrial DNA Line 1. Ruth Green m Thomas Whittier c1645 Newbury MA and had 2. Susanna Whittier m Jacob Morrill 1674 Salisbury MA and had 3. Susanna Morrill m Israel Webster 1714 Salisbury MA and had 4. Ruth Webster m Thomas Bagley 1747 Salisbury MA and had 5. Dolly Bagley m John Morrill c1781 Salisbury MA and had 6. Dolly Morrill m Richard Currier 1806 Amesbury MA and had 7. Dolly Currier m William Cushing Binney 1848 Amesbury MA = 8. Anna Sophia Binney m Charles W. Melcher 1881 St Louis MO = 9. Alice F. Melcher m Harold St.Clair MacMillan 1907 Hinsdale IL= 10. Mary A. MacMillan m Maynard T. Doherty 1931 Kankakee IL = 11. Me I have my mother’s mitochondrial DNA, but I cannot pass it on. There are a few rare mtDNA types; but mine is not rare. © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 11 Mitochondrial DNA Inheritance Mother passes mtDNA unchanged* to every son and daughter purple circles (female) * a very rare mutation (perhaps 1 per ~5000 generations), but father passes none of his mtDNA to offspring Hold the Presses: A new study shows several variations of mtDNA in every human [Bert Vogelstein, Johns Hopkins University School of Medicine, Nature (March 4, 2010)] Deep Ancestry Migration Studies http://www.testsymptomsathome.com/gti71_halogroups.asp (mt/Y-DNA) http://www.dna-worldwide.com/ancestry-testing/female-ancestry (mtDNA) https://genographic.nationalgeographic.com/genographic/index.html UD UD Life Life Long Long Learning: Learning: Rise Rise and and Spread Spread of of Humans Humans (Frank (Frank Gay): Gay): 9am 9am Fridays, Fridays, Fall Fall 2010 2010 © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 12 The Future of the Past Use DNA studies to confirm suspected evidence of ancestry Current work is mostly limited to descent through Y-chromosome mitochondrial DNA green boxes (male) 16 purple circles (female) great-great-grandparents 8 4 2 you > you > Y-DNA mtDNA If male, only 6.25% of your 2-greats-grandparents has your Y-DNA. Only 6.25% have mtDNA The Rest of your DNA Story Only 1/32 (3.12%) of your great-great-great-grandparents has your mtDNA. If male, only 1/32 (3.12%) of 3-greats-grandparents has your Y-DNA. What about the other 22 chromosome pairs? Autosomal DNA Testing All 32 of your great-great-great-grandparents have contributed to those 22 chromosome pairs. ... but it is much more complicated! Both males and females participate equally!! © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 13 Tom’ Tom’s 3gr3gr-grandfathe The Rest of your DNA Story If male, only 1/16 of 2g -grandparents has 2g-grandparents your mtDNA or Y -DNA; Y-DNA; If male, only 1/32 of 3g -grandparents has 3g-grandparents your mtDNA or Y -DNA Y-DNA not Tom’ Tom’s YY-DNA not Tom’ Tom’s YY-DNA Tom’ Tom’s grgr-grandfather not Tom’ Tom’s YY-DNA Tom’ Tom’s maternal grandmother Tom’ Tom’s mtDNA What about the other 22 chromosome pairs? Autosomal DNA Testing Tom’ Tom’s grgr-grandmother Tom’ Tom’s mtDNA ^^^ Tom’’s mtDNA Harold St Clair MacMillan Tom husband of Alice Frances Melcher Tom’ Tom’s mtDNA Autosomal DNA Testing Autosomal DNA testing scans 22 chromosome pairs Intergenerational DNA shuffle (recombination) occurs - Except for occasional mutations, only Y-DNA and mtDNA pass unchanged from father or mother - Autosomes from each parent randomly recombine before they combine during conception Now good for relationships back to great-great grandparents and anthropological origins (1,000s of yrs ago) Much more complicated Need larger samplings (that is, more participants) Genealogical research, analysis and database building to confirm relationships: 6 generations is commercial. © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 14 Recombination During sexual reproduction, the mothers’ chromosome pairs and the father’s autosome pairs (male XY is not a pair!) undergo a recombination process. Each parent contributes ½ part of each recombined chromosome (called a gamete) - mother’s and father’s gametes join at conception to form a unique child Animations http://www.smgf.org/education/animations/four_types.jspx http://www.smgf.org/education/animations/autosomal.jspx http://www.smgf.org/education/animations/y_chromosome.jspx http://www.smgf.org/education/animations/x_chromosome.jspx http://www.smgf.org/education/animations/mitochondrial.jspx Autosomal DNA Graphic above is for one chromosome pair for one child; each chromosome pair and each recombination is different, so we are unique. from http://www.smgf.org/education/animations/autosomal.jspx © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 15 DNA Study Warnings Can disprove genealogical descent Early results say that about 5-10% of births are “non-paternity events”* *births where genetic father’s identity was a surprise: http://www.childsupportanalysis.co.uk/analysis_and_opinion/choices_and_behaviours/misattributed_paternity.htm Genetic father may be surprised Found a young girl, who suited him nice Went to his papa to ask his advice His papa said son, “I have to say ‘No’ That girl is your sister, but your mama don't know...” Went to his mama who his papa had wed And told his mama, what his papa had said His mama she laughed, she says, “go son go Your daddy ain't your daddy, paraphrased paraphrased from: from: but your daddy don't know...” "Shame "Shame and and Scandal", Scandal", traditional, traditional, lead lead vocalvocalPeter Peter Tosh Tosh (1965) (1965) produced produced by by Coxone Coxone Dodd Dodd The The Autosomal Autosomal Testing Testing Companies Companies Relative Finder (23 and Me): https://www.23andme.com - Geared toward health, then ancestry: $399 or $99 +1 yr HGS@$9/mo Family Finder (FamilytreeDNA): http://www.familytreedna.com - Geared toward ancestry (not medical): $289 to participate - Measures data point pairs: single nucleotide polymorphisms (SNPs) - Measures 710,000 SNPs on 22 autosomal chromosomes - If >500 SNPs in series match, cousins named “identical by descent” - Doesn’t use sex chromosomes test data (e.g.Y-DNA): separate study - Doesn’t use mtDNA test results: separate study - Population Finder %: Assigns closeness to world population groups Both “Finder” results uncover relationships for 5 generations: Share grandparents greatgreat-grandparents 2-greatgreat-grandparents 3-greatgreat-grandparents chart from: http://www.familytreedna.com/faq/answers/default.aspx?faqid=17#628 © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 16 Autosomal Autosomal Testing Testing Results Results Avg. percentage of common ancestors’ DNA shared with cousin: Sibling 50% 1st cousin 12.5% 2nd cousin 3.125% 3rd cousin 0.781% 3rd cousin 2X removed 0.781% 4th cousin 0.195% 5th cousin 0.049% 66h cousin 0.012% 76h cousin 0.003% 86h cousin 0.001% chart from: http://www.familytreedna.com/img/familyfinder/whatpercentage.jpg Another Possible Con of Testing Your DNA Dear Dear Abby Abby by by Jeanne Jeanne Phillips Phillips January January 20, 20, 2010 2010 A question of paternity DEAR DEAR ABBY: ABBY: My My parents parents divorced divorced when when my my older older brother brother and and II were were small. small. Mom Mom remarried, remarried, and and II was was adopted adopted by by the the wonderful wonderful man man who who raised raised me me as as his his beloved beloved daughter. daughter. II had had limited limited contact contact with with my my biological biological father, father, "Nate," "Nate," which which seemed seemed to to please please everyone. everyone. After After my my adopted adopted dad dad passed, passed, Nate Nate came came back back into into my my life. life. II have have not not seen seen much much of of him him but but he he was was present present at at my my second second marriage marriage five five years years ago, ago, traveling traveling across across country country to to be be there. there. Last month he called to tell me he has been Last month he called to tell me he has been diagnosed diagnosed with with terminal terminal cancer cancer and and has has named named me me as as his his heir heir since since my my older older brother brother is is deceased. deceased. As As aa birthday birthday gift, gift, II presented presented him him with with aa box box from from aa company company that that does does genome genome sequencing. sequencing. It It allows allows people people to to see see their their DNA DNA and and learn learn about about their their ancestry ancestry as as well well as as any any healthhealthrelated related issues. issues. II enjoyed enjoyed learning learning about about genetics genetics and and thought thought Nate Nate would, would, too. too. Imagine Imagine how how stunned stunned II was was when when II learned learned that that Nate Nate is is NOT NOT my my father. father. The The company company has has assured assured me me there there is is little little chance chance the the test test is is wrong. wrong. II am am close close to to my my mother mother and and horrified horrified that that my my mother mother kept kept this this secret secret from from me me for for more more than than 50 50 years. years. II don't don't want want anyone anyone to to be be hurt, hurt, but but II need need the the truth. truth. What What do do II do? do? Questioning Questioning my my DNA DNA in in S.F. S.F. DEAR DEAR QUESTIONING: QUESTIONING: Have Have aa calm, calm, private private conversation conversation with with your your mother mother and and tell tell her her what what you you have have learned. learned. If If she she denies denies it, it, have have the the test test repeated. repeated. When When you you receive receive the the results, results, either either apologize apologize to to your your mother mother or or raise raise the the subject subject again. again. She She may may know know who who your your father father was, was, or or you you may may have have been been the the result result of of an an opening opening shot shot in in the the sexual sexual revolution, revolution, aa chapter chapter your your mother mother may may not not care care to to revisit. revisit. Also for health reasons, question mother for identity of real father. © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 17 Genealogy: Fall 2011 offerings Contact: Tom Doherty ([email protected] ([email protected])) Genealogy: Genealogy Your Family Roots (12-1:45pm Th) – Jack Worton Computer Workshops*(2-3:20pm Th): short weekly lecture - Room 202 PC: Joyce Bischoff, Tom Freeman - Room 214 PC: Carol Callaghan, Tom Doherty, Jane McKinstry, Suzanne Milazzo - Room 219 Mac: Dick Cook, Linda McMeniman, Susan Kirk Ryan - Catalog offers 2 workshops per room: 1. using LLL computers, 2. students with own laptops In reality, both workshops are in the same room with 2-4 teachers. - If you know someone who wants to take this course, encourage them to apply now for UDelNetID# and password, so have for summer/fall - Those using their own wireless laptops increase odds of taking course. - Class Web Site: http://udel.edu/~tdoherty - changes soon after this semester ends - Strongly recommend taking both lecture course and a workshop Genealogy Interest Group (3:20-4:20pm Th): Rm - Dick Burns, Linda McMeniman 4 Sep 2005 How Many Generations Back to Your Most Recent Common Ancestor with Chimps? - over 200,000 years ago! Humans share 96% DNA with Chimps but still 40 million genetic differences 99.9% of human DNA is identical.* identical.* migrated from Africa ~50,000 yrs ago * * not counting the sex chromosomes which are quite different! * http://news.nationalgeographic.com/news/2005/08/0831_050831_chimp_genes.html © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 18 Genealogy Computer Workshop Volunteers We are here to help you find your past – please ask! Rm 202 Teachers: Joyce Bischoff/Tom Freeman Volunteer Help: Joyce Kunkle Jack Worton Susan Noonan Rm 214 Teachers: Carol Callaghan/Tom Doherty Volunteer Help: Richard Chappel Suzanne Milazzo Jane McKinstry Colette Watson Rm 219 Teachers: Frank Czeiner/Linda McMeniman Volunteer Help: Dick Burns Roaming (laptop and John Dietz (first few weeks) ID/password needs) Tom Keane (first several weeks) Also: help thy neighbor! © Spring 2011 Thomas P. Doherty ALL Class site: http://udel.edu/~tdoherty/DNAweb11s.pdf for clickable links 19
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