human genetic variation complete

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Week of 5/4 - last Discussion Tues 5/12 - Exam #4

- we will try to get all your scores up (exams, Discussion, clickers, HW) so you can choose if you want to take the nal - previous nal curves are posted in BB

Tues 5/19 - Final Exam (cumulaKve) 1 3 pm here

- exam period is over Weds 5/21 - I will automaKcally drop the lowest score of your 5 exams

- Discussion secKon grades may be normalized to class average

Lectures 24 and 25

The Human Genome Human Gene1c Varia1on

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understanding the human genome

- one goal of modern biology has been to understand the human organism

- at the molecular level, we would like to understand the human genome

- how many genes does it encode? - what do those genes do? - how does our genome compare to that of other primates, mammals, animals, eukaryotes?

- how dierent is the genome between any two people, or between dierent ethnic groups of humans?

- do dierences in the genome explain dierent behaviors, propensiKes to disease, etc?

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whole genome shotgun sequencing

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the library is kept in thousands of plates, each well In the plate holds one cloned plasmid

automated dideoxy sequencing of all clones

computer assembly

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What did we learn from the human genome sequence?

- almost half of our DNA is relics of ancient transposable elements and viruses, and may not do much

What did we learn from the human genome sequence?

- we dont have as many genes as we always thought we did - we have about as many as other complex animals and plants

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BLAST site at NCBI Basic Local Alignment Search Tool - searches your DNA sequence of interest against all known sequences - builds on what is already known to find genes that look like your gene and therefore might perform a similar function

What types of proteins does the human genome encode?

broad categories of of human proteins largest categories - genes encoding factors involved in cell signaling

- genes involved in regulaKng gene expression - most genes encode proteins of unknown funcKon

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How similar is our genome to that of other organisms?

- we can now compare the human genome to the genomes of other species that have been sequenced, and ask what makes us the same or dierent from other species

Percentage of DNA in human in common with: Neanderthal 99% last common ancestor 400,000 years ago chimpanzee 96% last common ancestor 7-13 million years ago cat 90% cow 80% mouse 75% last common ancestor 75 million years ago fruit y 60% last common ancestor 600 million years ago nematode worm 50% banana 50% last common ancestor 1.5 billion years ago

the human genome, now

- initially we wanted to know what the human genome looked like

- now we want to know what individual human genomes look like and how they are the same or different

human genetic variation

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the human genome, now

1) there has been a worldwide effort to determine more human DNA sequences, and from different ethnic groups, and to find out how much genetic diversity, and what kind, exists in the human population - 2007 - the personal genomes of Jim Watson and Craig Venter were sequenced - 2008 - genomes of anonymous Han Chinese and Nigerians were sequenced

- the Thousand Genome project

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- there are about 3 billion (3 x 109) base pairs in the human genome

- no two humans have idenKcal genomes

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human geneKc variaKon

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- no two humans have idenKcal genomes - not even idenKcal twins, since mutaKons arise during normal development

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- no two humans have idenKcal genomes - not even idenKcal twins, since mutaKons arise during normal development

- children have an average of 70 new mutaKons not present in their parents genomes due to new mutaKons arising during development

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- on average, two human genomes dier from each other at about 1 nucleoKde in every 1000 = 0.1%

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- on average, two human genomes dier from each other at about 1 nucleoKde in every 1000 = 0.1%

- on one hand, this means that any two humans share 99.9% of their DNA sequence in common

- this is why we all look, func3on and behave similarly

- on the hand, this means that two humans have, on average, 3 million base pair changes between them

- this is why we all look, func3on and behave dierently, get dierent diseases, respond to drugs dierently, etc

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- small DNA differences between people may have no effect on the organism

- or they could affect the expression of some gene, or the function of some protein, causing a disease, or variation in some phenotype

- the hope is that we will be able to identify genetic variations

that explain differences in human behaviors, traits, susceptibility to diseases, etc

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1) how can we determine if a given person (or animal,

or plant or any kind of cell) carries a particular DNA polymorphism?

2) what can we do with information about the genetic

variation in a specific individual?

3) what can we learn with information about the

genetic variation in our species?

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DNA polymorphisms

- the human genome has many polymorphic sites - meaning many forms

- a site is considered polymorphic if there are two or more alleles at that site, each found in more than 1% of the populaKon

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DNA polymorphisms - SNPS

- the most common type of genomic variaKon is called a single nucleoKde polymorphism or SNP

- a SNP is a single base pair change in DNA between 2 people

example - G-C is found in 65% of people

- A-T is found in 35% of people

- there are two alleles at that site, the GC form and the AT form

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DNA polymorphisms - SNPS

- the most common type of genomic variaKon is called a single nucleoKde polymorphism or SNP

- SNPs account for 80% of the variaKon between human genomes

(the other 20% is inserKons, deleKons, variaKons in repeats)

- we now know > 7 million SNPs present at 5% or more in humans

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a) restriction enzyme digestion of the genomic DNA

b) polymerase chain reaction (PCR) analysis of the genomic DNA c) SNP analysis on the genomic DNA with microarrays

Techniques for idenKfying DNA polymorphisms

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when we treat DNA with a restricKon enzyme, we do a restricKon digest, and produce restricKon fragments that we can separate by running them on an agarose gel

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Restriction Fragment Length Polymorphism - RFLP

- a change in the recogniKon sequence of a restricKon enzyme between two dierent DNA samples can lead to dierences in cugng at that site

- the resulKng dierence in fragments seen on the gel is called a restricKon fragment length polymorphism or RFLP

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SNP identification by RFLP analysis

we can distinguish between two different homozygous and the heterozygous state using RFLPs and a gel

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an RFLP in the beta-globin gene in sickle cell anemia

DdeI site CTNAG GANTC

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sickle cell status determination by RFLP analysis

can identify carriers for sickle cell disease

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Chapter 10 Animation

Testable Genetic Mutations

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b) polymerase chain reaction (PCR) analysis of the genomic DNA c) SNP analysis on the genomic DNA with microarrays


- STRs are abundant in the human genome (one every 2 kb) - they are very polymorphic (many alleles in the populaKon)

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simple tandem repeats - STRs

- an STR is a site where a small number of base pairs is repeated

also called SSRs simple sequence repeats

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Simple Tandem Repeat Polymorphism (STRPs)

STR variants can be disKnguished by PCR amplicaKon of the repeated region using primers that hybridize outside the repeated region. More repeats lead to a larger PCR product on an agarose gel.

10 alleles in the populaKon 33

individuals are often heterozygous at an STR locus

can distinguish between two homozygotes and heterozygote

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b) polymerase chain reaction (PCR) analysis of the genomic DNA c) SNP analysis on the genomic DNA with microarrays (SNP chip)


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- a SNPchip contains millions of short single stranded pieces of DNA that will each hybridize to one alleles for one SNP

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- current SNP chips can analyze >500,000 SNPs at once 37

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- a persons genomic DNA is randomly broken up into small fragments, and all of the fragments are labeled at one end with a fluorescent molecule

- the labeled genomic fragment are then hybridized with the SNPchip

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Heating of DNA leads to the separation of 2 strands (denaturation)

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Cooling of DNA leads to the pairing of 2 strands (reannealing or hybridization)

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G allele hybridizes

C allele doesnt

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- a laser is shined on the chip and the fluorescent pattern is recorded and analyzed by a computer to find which SNP variants are present in the persons DNA

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b) polymerase chain reaction (PCR) analysis of the genomic DNA c) SNP analysis on the genomic DNA with microarrays (SNP chip) - in the near future you will be able to sequence an individual persons genome for ~$1,000. At that point it will be as cheap as other routine tests prescribed by doctors, and everyone might know their own genetic variations



- what can we do with this kind of personal geneKc informaKon?

1) mapping human disease genes

2) determining a persons suscepKbility to disease based on their genes

3) forensics

4) understanding human evoluKon

5) understanding migraKon and ancestry

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GATTACA (1997) 45

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3) forensics



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Disease genes can be mapped using DNA markers

GWAS - genome-wide association studies - use DNA microarrays (SNPchips) to catalog the polymorphisms that are present in a population

- use DNA from thousands of people, with and without a disease or condition, and examine 100,000s of SNPs (500,000 routinely done)

- find SNPs statistically correlated with the disease

- SNPs may not cause the disease, they are just genetically associated with it

- but we dont care if they cause the disease - they can identify people at increased risk for the disease

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Disease genes can be mapped using DNA markers

- this technique can map disease susceptibility to many loci, each of which may make a small contribution to the trait

- cannot predict or guarantee you will get the disease

- can say things like:

- if you have this combination of polymorphisms, you have an X% increased chance of developing this disease

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recent genome-wide association studies (in last 5 years)

- have identified SNPs associated with the many diseases or conditions:

heart disease breast cancer restless leg syndrome (!)` atrial fibrillation glaucoma colon cancer amyotrophic lateral sclerosis type 2 diabetes multiple sclerosis rheumatoid arthritis bipolar disorder slow onset of AIDS

18 SNPs correlated with type 2 diabetes

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Direct To Consumer geneKc tesKng services

deCODE decodeme.com Navigenics navigenics.com 23andme 23andme.com

For $600 - $2500 and a sample of saliva, they will report back to you your SNP pattern for 500,000 SNPs (out of maybe 4 million) 23andme reports on SNPs for 150 traits/conditions/diseases (for 54 of them, they) give you information about conditions and traits for which there are genetic associations supported by multiple, large, peer-reviewed studies. Those associations must also have a substantial influence on a person's chances of developing the disease or having the trait. Because these associations are widely regarded as reliable, we use them to develop quantitative estimates and definitive explanations of what they mean for you.

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Age-related Macular Degenera1on Alcohol Flush Reac1on Alpha-1 An1trypsin Deciency BRCA Cancer Muta1ons (Selected) BiOer Taste Percep1on Bloom's Syndrome Celiac Disease Crohn's Disease Cys1c Fibrosis (Delta F508 muta1on) Earwax Type Eye Color G6PD Deciency Glycogen Storage Disease Type 1a Hemochromatosis Lactose Intolerance Malaria Resistance (Duy An1gen) Muscle Performance Non-ABO Blood Groups Norovirus Resistance Parkinson's Disease Prostate Cancer Psoriasis Resistance to HIV/AIDS Rheumatoid Arthri1s Sickle Cell Anemia & Malaria Resistance Type 1 Diabetes Type 2 Diabetes Venous Thromboembolism

Abdominal Aor1c Aneurysm Alcohol Dependence Ankylosing Spondyli1s An1depressant Response Asthma Atrial Fibrilla1on AOen1on-Decit Hyperac1vity Disorder Avoidance of Errors Back Pain Baldness Beta-Blocker Response Bipolar Disorder Birth Weight Bladder Cancer Blood Glucose Brain Aneurysm Breast Cancer Breast Cancer Risk Modiers Breas`eeding and IQ C-reac1ve Protein Level Caeine Metabolism Celiac Disease: Preliminary Research Chronic Lymphocy1c Leukemia Clec Lip and Clec Palate Cluster Headaches Colorectal Cancer Creutzfeldt-Jakob Disease Developmental Dyslexia Endometriosis Esophageal Cancer Eye Color Food Preference Freckling Gallstones

Gesta1onal Diabetes Glaucoma Gout HDL Cholesterol Level HIV Progression Hair Color Hair Thickness Heart AOack Height Heroin Addic1on High Blood Pressure (Hypertension) Intrahepa1c Cholestasis of Pregnancy Kidney Disease Larynx Cancer Longevity Lou Gehrig's Disease (ALS) Lung Cancer Lupus (Systemic Lupus Erythematosus) Male Infer1lity Measures of Intelligence Memory Mul1ple Sclerosis Neuroblastoma Nico1ne Dependence Obesity Obesity: Preliminary Research Obsessive-Compulsive Disorder Odor Detec1on Oral and Throat Cancer Osteoarthri1s Pain Sensi1vity Parkinson's Disease: Preliminary Research Peripheral Arterial Disease Persistent Fetal Hemoglobin Placental Abrup1on Preeclampsia 51

My BeauKful Genome Lone Frank 2011

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- current studies show that most doctors dont know enough about geneKcs

to adequately advise their paKents about the results of geneKc tests

issue with Direct To Consumer geneKc tesKng services

- Time magazine called the retail DNA test the InvenKon of the Year in 2008

- in the same year the New England Journal of Medicine warned there is limle clinical value in them the diseases that strike the general populaKon the most diabetes, cardiovascular disease, cancer are complex and mulKcausal and we already know how to reduce our risk for these diseases!

issues with Direct To Consumer geneKc tesKng services

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- some people worry about the use of providing people informaKon about

their DNA for condiKons for which there is no treatment (Alzheimers)

- also studies are looking at behavior and genes - the aggression gene, indelity gene, gay gene, anxiety gene,

depression gene, etc - interesKngly no intelligence gene yet extensive studies have found limle evidence for major geneKc genes inuencing intelligence


- some people worry about the use of providing people informaKon about

their DNA for condiKons for which there is no treatment (Alzheimers)

- DNA is not desKny

- phenotype = your DNA (geneKcs) + your environment and your mothers environment (epigeneKcs) + your lifestyle


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Direct To Consumer geneKc tesKng services


For $600 - $2500 and a sample of saliva, they will report back to you your SNP pattern for 500,000 SNPs (out of maybe 4 million) 23andme reports on SNPs for 150 traits/conditions/diseases (for 54 of them, they) give you information about conditions and traits for which there are genetic associations supported by multiple, large, peer-reviewed studies. Those associations must also have a substantial influence on a person's chances of developing the disease or having the trait. Because these associations are widely regarded as reliable, we use them to develop quantitative estimates and definitive explanations of what they mean for you.

57 2014 FDA stops these companies from giving out medical test results

Pharmacogenomics

- idenKfying SNPs that correlate with bemer or worse responses to certain drugs will allow bemer prescribing by physicians

- example - codeine is converted to morphine in the liver by the enzyme cytochrome P450 CYP2D6 - 10% of people have a mutaKon that abolishes enzyme funcKon - codeine is of no benet to these people

- your physician can prescribe drugs that will be more eecKve for you if he/she knows your genome informaKon

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3) forensics



- no two human genomes are likely to be exactly identical The variation in a persons genome can be used to:

- identify potential suspects whose DNA may match evidence left at crime scenes

- exclude potential suspects whose DNA does not match evidence - exonerate persons wrongly accused of crimes - identify crime and catastrophe victims - establish paternity and other family relationships

Human geneKc variaKon: forensics

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- the FBI uses a set of 13 STRs to genotype individuals and crime scene samples

- they know the number and frequency of the alleles at these 13 sites in Caucasian, African-American, Hispanic and Asian populations in the US

- obtain crime scene sample - semen, blood, hair cell, skin cells

- do PCR on each of the 13 loci from the sample and suspects

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- at one of the real sites used, people have between 5 and 16 repeats of GATA - so 12 alleles and 78 genotypes (homozygous and heterozygous) 62

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WA

15, 16 18, 19

15, 16

FGA

23, 27 21, 23

23, 27

3S1358

15, 17 17, 17

15, 17

3S1358

15, 17 17, 17

15, 17

D21S11

28, 30 27, 30.2

28, 30

D18S51

12, 18 14, 18

12, 18

D5S818

13, 13 9, 12

13, 13

D13S317

12, 12 12, 12

12, 12

D7S820

10, 11 9, 10

10, 11

CSF1PO

8, 11 11, 12

8, 11

TPOX

7, 8 8, 8

7, 8

THO1

9.3, 9.3 6, 9.3

9.3, 9.3

D16S539

9, 13 11, 12

9, 13

SSR Crime sample Suspect A Suspect B

Frequency of Suspect 0.13 0.22 0.31 0.34 0.06 0.11 0.29 0.21 0.26 0.18 0.30 0.38 0.10 Bs genotype

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WA

15, 16 18, 19

15, 16

FGA

23, 27 21, 23

23, 27

3S1358

15, 17 17, 17

15, 17

3S1358

15, 17 17, 17

15, 17

D21S11

28, 30 27, 30.2

28, 30

D18S51

12, 18 14, 18

12, 18

D5S818

13, 13 9, 12

13, 13

D13S317

12, 12 12, 12

12, 12

D7S820

10, 11 9, 10

10, 11

CSF1PO

8, 11 11, 12

8, 11

TPOX

7, 8 8, 8

7, 8

THO1

9.3, 9.3 6, 9.3

9.3, 9.3

D16S539

9, 13 11, 12

9, 13



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- can you conclude that suspect A did or did not commit the crime?

- can you conclude that suspect B did or did not commit the crime?

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WA

15, 16 18, 19

15, 16

FGA

23, 27 21, 23

23, 27

3S1358

15, 17 17, 17

15, 17

3S1358

15, 17 17, 17

15, 17

D21S11

28, 30 27, 30.2

28, 30

D18S51

12, 18 14, 18

12, 18

D5S818

13, 13 9, 12

13, 13

D13S317

12, 12 12, 12

12, 12

D7S820

10, 11 9, 10

10, 11

CSF1PO

8, 11 11, 12

8, 11

TPOX

7, 8 8, 8

7, 8

THO1

9.3, 9.3 6, 9.3

9.3, 9.3

D16S539

9, 13 11, 12

9, 13



Conclusion:

- suspect A is ruled out as the source of the crime scene sample - the chance that the sample came from some other random person of Suspect Bs ethnicity

= product of all the frequencies = about 1 in 1.5 billion 65



- CODIS - FBIs database - Combined DNA Index System

- as of February 2007 it had data from 67,000 crime scenes and 1.5 million individuals convicted of felonies or arrested for felonies (more recently) - CODIS has made more than 45,000 hits

- first case and Snowball case

Abraham Lincolns DNA by Philip Reilly (2000) The Strongest Boy in the World by Philip Reilly (2006) Tears of the Cheetah by Stephen OBrien (2003) Genetic Rounds by Robert Marion (2010) When a Gene Makes You Smell Like a Fish by Lisa Seachrist Chiu (2006)

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Human geneKc variaKon: paternity

- similar types of analyses are used in paternity cases

- analysis for one STR shown

- A = accused males DNA - C = childs DNA - M = mothers DNA - A=C = mixture of A and C

case 1 case 2

A A + C

C M A A + C

C M

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Human geneKc variaKon: forensics - can also do this to identify body remains

- 911 victims - Russian Romanov family (last czar)

- in this case, you use DNA from relatives as the match

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3) forensics



Human geneKc variaKon: human evoluKon

- following human evolution, migration and history via: - changes in mitochondrial DNA sequence

- changes in human Y chromosome sequence

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human evoluKon and mitochondrial DNA

- mitochondria are self-replicaKng organelles that contain their own DNA - supercoiled circles of DNA

- mammalian mtDNA is only 16,500 bp (16.5 kb)

- about 40 genes encode proteins used in mitochondria, such as the DNA polymerase for replicaKng mtDNA and a few proteins used in respiraKon

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- human eggs and sperm both contain mitochondria

- aqer ferKlizaKon, when the sperm and egg fuse, the mitochondria from the sperm are destroyed, so that all the mitochondria in the ospring are inherited from the mother

- so genes in the mitochondrial DNA show non-Mendelian inheritance pamerns - uniparental inheritance - also called extranuclear inheritance or cytoplasmic inheritance

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- so human mitochondrial DNA

- is passed only through the maternal side - does not undergo recombinaKon

- therefore, in the absence of new mutaKons, your mitochondrial DNA is exactly the same as your mothers, grandmothers, etc

- if you went back six generaKons in your own family tree, you'd see that your nuclear DNA could come from 32 men and 32 women

- your mtDNA, on the other hand, would have come from only one of those 32 women, on your mothers side.

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- so human mitochondrial DNA

- is passed only through the maternal side - does not undergo recombinaKon

- therefore, in the absence of new mutaKons, your mitochondrial DNA is exactly the same as your mothers, grandmothers, etc

- if you went back six generaKons in your own family tree, you'd see that your nuclear DNA could come from 32 men and 32 women

- your mtDNA, on the other hand, would have come from only one of those 32 women, on your mothers side

- but there is mutaKon in mtDNA, from errors during DNA replicaKon and from environmental causes

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- starKng with all the dierent types of mitochondrial DNA variants present around the world today, we can work backwards to nd a most recent common ancestor (MRCA)

- the mtDNA molecule that was mutated to give rise to all exisKng mtDNA molecules around today

- by applying a molecular clock (1 change/3800 years) we can esKmate how long ago she lived

- the last female common ancestor of all people currently on the planet - named Mitochondrial Eve

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1987 - results from analysis of human mtDNA variaKon showed:

- there is twice as much mitochondrial diversity in Africa as in all the rest of the world (true for nuclear genes too - there is more diversity in Africa than all the rest of the world combined)

- 3 of 4 major mitochondrial lineages are found only in Africa,

- 1 mitochondrial lineage is found outside of Africa and it shares a most recent common ancestor with African lineages about 50,000 YA

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Figure 17.31: Phylogenetic tree of human mitochondrial DNA 78

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1987 - results from analysis of human mtDNA variaKon showed:

- there is twice as much mitochondrial diversity in Africa as in all the rest of the world, and 3 of 4 major mitochondrial lineages are found only in Africa

- a subset of mitochondrial mutaKons are found outside of Africa - these share a MRCA with African lineages about 50,000 YA

- supports the Out of Africa hypothesis put forward by paleontologists - believed to be when a small populaKon of humans (5,000?) migrated out of Africa to populate the rest of the world about 50 - 100,000 YA

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Figure 17.32: The dispersal of modern human populations

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Human geneKc variaKon: human evoluKon

- following human evolution, migration and history via: - changes in mitochondrial DNA sequence

- changes in human Y chromosome sequence

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human evoluKon and the Y chromosome

- the Y chromosome only contains small regions at either end that are homologous to the X chromosome (called the pseudoautosomal regions)

- other than this, the Y chromosome has very few genes

- most of the X and Y are not homologous and do not pair during meiosis

- it is assumed that the X and Y chromosomes were once a normal pair of homologous chromosomes, and that over time the Y has lost sequences present on the X chromosome

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human evoluKon and the Y chromosome

- so the Y chromosome is present only in males, and does not go through recombination along most of its length

- therefore mutations that arise in one male will be passed on to that males sons without changing

- there are ~30 simple sequence repeats (SSRs) along the Y chromosome that can be easily mapped

- as was done for females and mtDNA, using the variation in all of the Y chromosomes in the current human population, it was estimated that the last common ancestor of all human males lived 50,000 years ago

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Mapping human history with the Y chromosome

- Genghis Khan - founder of the Mongol Empire in the 13th century - stretched from China to Europe - he and his descendants were very prolific - his son had 40 sons, his grandson Kubilai Khan had 22 - mapping 32 Y chromosome markers from >2000 Asian men showed a common pattern - the most recent common ancestor of all the men with this pattern lived ~1000 years ago - assumed to be Genghis Khan

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- the Lemba are a Bantu-speaking tribe living in S. Africa and Zimbabwe

- they practice male circumcision, have dietary restrictions similar to those of Jewish people, and have an oral history that says their ancestors arrived by boat from N. Africa/Middle East

- mapping 12 Y chromosome markers in 136 Lemba men showed they have two common patterns of variation - one is similar to the Bantu pattern - the other is similar to the Cohanim pattern of Jewish people - the last common ancestor of these men lived 3,000-5,000 years ago, around the time that the Jews were exiled from Assyria

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- Roma - tribe of nomadic people arriving in Europe about 1000 years ago - widely persecuted - called Gypsy because of legend they came from Egypt, but they call themselves Roma - their language is similar to languages spoken on the Indian subcontinent

- 12 million Roma today, in many countries - Y chromosome analysis of men from 14 Roma populations around the world showed 45% of them had a related pattern of variation

- the most closely related haplotype is found on the Indian subcontinent, suggesting this as their site of origin

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geneKcs and human history and migraKon

- dierent groups of people, geographically isolated on the planet, have dierent pamerns of DNA changes (haplotypes) for their genomic DNA (SNPs), Y chromosomes and mitochondrial DNA

- therefore, you can tell what part of the planet a persons ancestors came from by examining their DNA and comparing it to samples from living populaKons on the planet

- geneKc ancestry tesKng - $100 - $900


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human genetic variation complete

Documents

human genome sequence

human population

human organism

genome project

human dna sequences

individual human genomes

genome shotgun sequencing

common ancestor