Genetic Geography and Population Structure Oscar Lao - - PowerPoint PPT Presentation

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Genetic Geography and Population Structure Oscar Lao - - PowerPoint PPT Presentation

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Genetic Geography and Population Structure Oscar Lao oscar.lao@cnag.crg.eu 15.11.2018 GENETIC SIMILARITY IN HUMANS All our social policies are based on the fact that their intelligence is the same as ours whereas all the testing says

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Genetic Geography and Population Structure Oscar Lao

  • scar.lao@cnag.crg.eu

15.11.2018

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“All our social policies are based on the fact that their intelligence is the same as

  • urs — whereas all the

testing says not really,”

GENETIC SIMILARITY IN HUMANS

(FROM A GENETIC POINT OF VI VIEW) GENETICALL CALLY Y SIMILAR AR

HUMANS MANS

HUMANS ANS

Some me scientists entists

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a) c) b) d)

GUESS THE GENETIC ANCESTRY

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a) c) b) d)

GUESS THE GENETIC ANCESTRY (and be wrong!)

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GUESS THE GENETIC ANCESTRY

EUROPEAN ANCESTRY

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Erased recent historical memory & Forensics

  • Colonization of Americas &

slavery

  • Romani Diaspora
  • Australian’s Stolen Children
  • Recent migrations
  • Bombing attacks
  • …

Tiger Woods calls himself "Cablinasian“

Caucasian, Black, American Indian, Asian

GUESS THE GENETIC ANCESTRY (if you dare!)

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  • Why is there population substructure?
  • How much population substructure in the human

genome? (Do races exist?)

  • Some examples of population substructure
  • Final conclusions & suggestions

TOPICS TO BE DISCUSSED

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WHY IS THERE POPULATION SUBSTRUCTURE

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Mutation Recombination Selection Genetic drift Migration/Isolation Evolutionary parameters Population Sample Stochastic Evolutionary process

ATGCATGGGCTATTGGACCT ATGGATGGGCTATTGCACCT ATGCATGGGCAATTGCACCT ATGCATGGGCAATTGGACCT ATGGATGGGCTATTGCACCT

Stochastic Sampling process Inference

“Demographic” processes

METASOURCES OF GENETIC VARIATION

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Van Oven and Lao International Encyclopedia of Social and Behavioral Sciences 2nd Edition

  • Physical factors
  • Distance
  • Barriers
  • …
  • Cultural factors
  • Language
  • Religion
  • …

DEMOGRAPHY & POPULATION HISTORY

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DEMOGRAPHY & POPULATION HISTORY

Nielsen et al 2017, Nature

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Scientific American 308, 66 - 71 (2013)

DEMOGRAPHY & POPULATION HISTORY

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Dolgova and Lao; Genes 2018, 9(7), 358; https://doi.org/10.3390/genes9070358

DEMOGRAPHY & POPULATION HISTORY

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Mondal, Bertranpetit* and Lao*, accepted for publication in Nature Communications Lorente-Galdos *, Lao * et al under review in Genome Biology

DEMOGRAPHY & POPULATION HISTORY

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  • Science. 2016 Feb 12;351(6274):737-41

Curr Biol. 2016;26(9):1241-7

DEMOGRAPHY & POPULATION HISTORY

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Mutation Recombination Selection Genetic drift Migration/Isolation Evolutionary parameters Population Sample Stochastic Evolutionary process

ATGCATGGGCTATTGGACCT ATGGATGGGCTATTGCACCT ATGCATGGGCAATTGCACCT ATGCATGGGCAATTGGACCT ATGGATGGGCTATTGCACCT

Stochastic Sampling process Inference

METASOURCES OF GENETIC VARIATION

“Selective” processes

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https://es.pinterest.com/ http://www.bbc.co.uk/bitesize/ks3/history/industrial_era/the_industrial_revolution/revision/2/

CULTURAL ADAPTATION IS THE MAIN FORCE OF OUR SUCCESS

SELECTION

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Fan et al 2016

SELECTION

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  • Humans are

mammals

  • We consume milk

when we are babies

  • This is done thanks to

the enzyme LACTASE (LCT)

  • Milk is a complete

source of energy and proteins + defense

LCT

SELECTION

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  • The capacity to

metabolize lactose disappears at adult age in almost all the mammal species

  • LCT gene is not

expressed anymore because there is no more maternal milk to drink

  • Or is it not?

LCT

SELECTION

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  • How to recognize if

you are lactose intolerant?

– Can be asymptomatic – Gas production – Diarrhea – Related to diseases such as inflammatory bowel disease – Usually lactose intolerant people “don’t like milk”

LCT

SELECTION

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LCT

SELECTION

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Yang et al (2012) Nature Genetics

LCT

SELECTION

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LCT

SELECTION

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EVOLUTIONARY MEDICINE: USING EVOLUTION TO UNDERSTAND HUMAN DISEASE

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Conditions thought to be caused by mismatch Acid reflux/chronic heartburn Depression Inflammatory bowel disease Acne Diabetes (type 1) Lactose intolerance Alzheimer’s disease Diaper rash Lower back pain Anxiety Eating disorders Malocclusion Apnea Emphysema Metabolic syndrome Asthma Endometriosis Multiple sclerosis Athlete’s foot Fatty liver syndrome Myopia Attention deficit hyperactivity disorder Fibromyalgia Obsessive-compulsive disorder Bunions Flat feet Osteoporosis Cancers (only certain ones) Glaucoma Plantar fascitis Carpal tunnel syndrome Gout Polycystic ovarian syndrome Cavities Hammer toes Pre-eclampsia Chronic fatigue syndrome Hemorrhoids Rickets Cirrhosis High blood pressure (hypertension) Scurvy Constipation (chronic) Iodine deficiency (goiter/cretinism) Stomach ulcers Coronary heart disease Impacted wisdom teeth Crohn’s disease Imsomnia (chronic)

EVOLUTIONARY MEDICINE: USING EVOLUTION TO UNDERSTAND HUMAN DISEASE

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2) DO RACES EXIST?

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Barbujani, Current Genomics

Table 1. Lists of Human Races Author Races proposed

  • No. of races

Races proposed Linnaeus (1735) 6 Europaeus, Asiaticus, Afer, Americanus, Ferus, Monstruosus Buffon (1749) 6 Laplander, Tartar, South Asian, European, Ethiopian, American Blumenbach (1795) 5 Caucasian, Mongolian, Ethiopian, American, Malay Cuvier (1828) 3 Caucasoid, Negroid, Mongoloid Deniker (1900) 29 Weinert (1935) 17 Von Eickstedt (1937) 38 Biasutti (1959) 53 Coon (1962) 5 Congoid, Capoid, Caucasoid, Mongoloid, Australoid US Office of Management and Budget (1997) 5 African-American, White, American Indian or Alaska Native, Asian, Native Hawaiian or Pacific Islander Risch et al. (2002) Fig. 1 5 African, Caucasian, Pacific islanders, East Asian, Native American Risch et al. (2002) Table 3 5 African Americans, Caucasians, Hispanic Americans, East Asians, Native Americans

FACTS: TOO MANY CLASSIFICATIONS

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http://theadvancedapes.com/genetic-origins/

FACTS: NOT TOO MUCH VARIATION

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Pagani et al, 2016, Nature Mallick et al, 2016, Nature De Manuel et al, 2016 Science

FACTS: NOT TOO MUCH VARIATION

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Classifying individuals according to continental

  • rigin is not a good idea

Richard Lewontin

Lewontin, R "The Apportionment of Human Diversity," Evolutionary Biology, vol. 6 (1972) pp. 391-398

FACTS: NOT TOO MUCH VARIATION AMONG POPULATIONS

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Using data from G3 (Bethesda). 2013 May 20;3(5):891-907

FACTS: GENETIC VARIATION FOLLOWS A GRADIENT

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Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15942-7 Henn 2015

FACTS: GENETIC VARIATION FOLLOWS A GRADIENT

Using data from G3 (Bethesda). 2013 May 20;3(5):891-907

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3) SOME EXAMPLES

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Novembre et al 2007 Nature Lao et al 2007 Current Biology Yang et al (2012) Nature Genetics

EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

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SLIDE 36 Maceda-Porto*, Martin-Alvarez*, et al, Lao** and Moral**, in preparation

NGS 30 individuals at 30x

EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

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SLIDE 37 Maceda-Porto*, Martin-Alvarez*, et al, Lao** and Moral**, in preparation

Number of highly damaging variants

EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

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EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

Mendizabal and Lao et al, Current Biology 2012

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Philip IV

  • f

Spain, who declared that Romani did not exist (they are Spanish people who had made up an artificial language)

EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

Mendizabal and Lao et al, Current Biology 2012

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EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

Mendizabal and Lao et al, Current Biology 2012

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EXAMPLE I:POPULATION SUBSTRUCTURE IN EUROPE

Mendizabal and Lao et al, Current Biology 2012

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EXAMPLE II:POPULATION SUBSTRUCTURE IN ABORIGINAL AUSTRALIA

Sapfo-Malaspina et al, 2016 Nature

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EXAMPLE II:POPULATION SUBSTRUCTURE IN ABORIGINAL AUSTRALIA

Sapfo-Malaspina et al, 2016 Nature

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80 100 120 140 160 180 10 20 30 40 time since first contact with Europeans mean(generations since first contact) BDV CAI ENY NGA PIL RIV WCD WON WPA ”Australian” ”Europe” ”East Asian” ”Papuan”

EXAMPLE II:POPULATION SUBSTRUCTURE IN ABORIGINAL AUSTRALIA

Sapfo-Malaspina et al, 2016 Nature

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CONCLUSIONS

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  • Population substructure must be interpreted in

evolutionary terms

– Demographic – Selective

  • The amount of population substructure depends
  • n the genomic region we are considering

– Magnitude – Geographic distribution

  • The amount of population substructure we detect

depends

  • n

the assumptions we make

FINAL REMARKS

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  • The amount of population substructure must be

interpreted in the context of what we are studying

  • AVOID over-interpretation

FINAL REMARKS

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A “small” or “modest” amount of genetic diversity when compared with other species can be “big” when trying to detect extremely small effects

FINAL REMARKS

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Thank you very much!

  • scar.lao@cnag.crg.eu