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Adaptation by Natural Selection

Natural Selection

• Darwinian natural selection is a two-stepprocess:

– The production of new genetic variationthrough the process of mutation

– The differential reproduction of favorablevariants through the process of selection

Selection

• Selection causes changes in allele andgenotype frequencies from one generation tothe next due to differential net reproductivesuccess of individuals with differentgenotypes

– If individuals with genotype AA consistentlyhave twice as many offspring as individuals withAB and BB genotypes, the frequency of the Aallele will increase through time and eventually,everyone will have the AA genotype

Selection, 2

• There are two elements contributing to thedifferential reproductive success ofindividuals with differing genotypes

– Viability or survival: individuals must surviveto reproductive maturity in order to be able toreproduce

– Fertility: individuals must produce offspring inorder to pass on their genes on to the nextgeneration of the population

Modeling Selection

• Selection operates by reducing the completedfertility of individuals with a certainphenotype, relative to other phenotypes withina population

– Fitness (1.0 < w < 0.0) is the completed fertility fora given genotype, relative to the genotype with thehighest completed fertility

– The selection coefficient (1.0 < s < 0.0) measuresthe relative reduction in fertility for a genotype

• s = 1 - w

Modes of Somatic Selection

Autosomal Inheritance GenotypesSelection Against: AA AB BBComplete Dominance

Dominant (Huntington’s Disease) sAA sAA

Recessive (PKU, Tay Sachs) sBB

Incomplete Dominance/CodominanceHeterozygote sAB

One homozygote, heterozygote sAA sAB

Both homozygotes (sickle cell) sAA sBB

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Modes of Sex-linked Selection

Traits on X Chromosome Females MalesSelection Against: AA AB BB A BComplete Dominance

Dominant sAA sAA sAA

Recessive (Hemophilia A) sBB sBB

Incomplete DominanceHeterozygote sAB

1 homozygote, heterozygote sAA sAB sAA

Both homozygotes (G6PD) sAA sBB sAA sBB

Traits on Y ChromosomeAny allele (A) sAA

Selection against a recessive

AA AB BBHardy-Weinberg Freq: p

22pq q

2

Fitness (w) 1.0 1.0 1 – s(BB)

Frequency after selection p2 (1) 2pq (1) q

2 (1-s)

New Total Frequency ( ) = p2

+ 2pq + q2

- q2s = 1 - q

2s

Relative frequency afterselection

(p2)

(1 - q2s)

(2pq)(1 - q

2s)

(q2

– q2s)

(1 - q2s)

w

Frequency of B in next generation = freq (BB) + ½ freq (AB)

(q – q2s)q1 = —————

(1 - q2s)

Selection against a recessive

0

0.1

0.2

0.3

0.4

0.5

0 2 4 6 8 10 12 14 16 18 20 22 24

Generations of Selection

All

ele

Fre

qu

ency

s = 0.2

s = 0.5

s = 1

OverdominanceAA AB BB

Hardy-Weinberg Freq: p2 2pq q2

Fitness (w) 1-sAA 1.0 1 – sBB

Frequency after selection p2 (1-sAA) 2pq (1) q2 (1-sBB)New Total Frequency ( ) = 1 - p2sAA - q2sBB

Relative frequency afterselection

(p2 - p2sAA)( )

(2pq)( )

(q2 – q2sBB)( )

w

Frequency of B in next generation = freq (BB) + ½ freq (AB)

q1 = (q – q2sBB) (1 - p2sAA - q2sBB)

Equilibrium is attained if q = 0;

q = q1 - q0 = [(q – q2sBB) (1 - p2sAA - q2sBB)] - q

= [pq (psAA – qsBB)] (1 - p2sAA - q2sBB)sAAq = 0 if psAA – qsBB = 0; that is, if q = —————

(sAA + sBB)

w w w

Sickle Cell Hemoglobin andMalaria

Natural Selection in HumanPopulations

Structure of Hemoglobin• 4 polypeptides (globins) and 4 iron-based

oxygen-binding heme molecules

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Genetics of Hemoglobin

• The alpha and beta globin genes aretransmitted separately, as parts of the 16thand 11th chromosome pair, respectively

– Transmission follows Mendel’s Law ofIndependent Assortment for genes located ondifferent homologous chromosome pairs

– Each individual has two alpha globin genes andtwo beta globin genes inheriting one gene ofeach pair from the mother and one from father

Function of Hemoglobin

• Hemoglobin is the primary protein constituent ofred blood cells

– Transports oxygen by binding with it tightly as thered blood cells pass through the capillaries of thelungs

– As oxygenated red blood cells circulate through theheart and to the other body tissues, hemoglobinloosens its hold on the oxygen so that it can passreadily out of the red cells and be made available toperipheral cells for respiration

Function of Hemoglobin 2

• Deoxygenated hemoglobin molecules inperipheral capillaries bind loosely with carbondioxide and help remove this waste product ofcellular respiration to the lungs for expiration

• The binding capacity of hemoglobin moleculesis a function of the partial pressure of oxygenin the blood

– high in the lungs, bind tightly

– low in peripheral capillaries, bind loosely

HbA

• “Wild”or most common form, found in allhuman populations

Beta Hemoglobin 6th 26th

DNA sequence C-T-C C-T-C

Amino Acids Glutamic Glutamic

Acid Acid

HbS

• Sub-Saharan Africa, Mediterranean, MiddleEast, South Asia

Beta Hemoglobin 6th 26th

DNA sequence C-A-C C-T-C

Amino Acids Valine GlutamicAcid

Sickled vs. Normal RBC

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289/100,000 isequivalent toapproximately 0.3%of the African-American populationhaving Sickle CellAnemia, or an Sallele frequency ofabout 5% for African-Americans

Sickle Cell Disease in the United States

HbC

• Predominantly West African populations

Beta Hemoglobin 6th 26th

DNA sequence T-T-C C-T-C

Amino Acids Lysine GlutamicAcid

HbE

• Southeast Asia

Beta Hemoglobin 6th 26th

DNA sequence C-T-C T-T-C

Amino Acids Glutamic LysineAcid

Genetics of Sickle Cell• Three genotypes can form from combinations

of the A and S alleles

– AA Homozygous Normal; “Normal”

– AS Heterozygote; “Sickle Cell Trait”

– SS Homozygous sickler; “Sickle Cell Anemia”

• Inheritance follows a Mendelian pattern for aco-dominant autosomal allele

– When two heterozygotes mate, ¼ of their offspringare predicted to be SS and have sickle cell anemia,¼ AA normal, and ½ AS, carrying the sickler allele

Sickling

• Red blood cells begin to sickle whenhemoglobin molecules have given up theiroxygen in the capillaries

• The S-hemoglobin molecules bind togetherinto long fibers, forming a complex helicalmolecule within the red blood cell

Sickling 2

• The formation of these fibers is dependenton the presence of valine at the -6 positionto bind one beta chain with the beta chain ofanother hemoglobin molecule

• For sickling of the red blood cell to occur ittakes from 0.1 to 1 second of extremedeoxygenation of the hemoglobin molecules

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Sickling 3

• The deoxygenation necessary for sicklingoccurs in the capillaries after oxygen hasbeen given off to the muscle cells andbefore the RBCs can return to the lungs

• Cells with higher concentrations ofhemoglobin S form fibers more rapidly andare therefore more likely to sickle

Sickling 4

• Hemoglobin S concentration is a function ofcell age, with the concentration increasingas the red blood cell ages

• Hence, the older the red blood cells, themore likely they are to sickle

• The result is a downward spiral ofcontinuous depletion of red blood cells,resulting in anemia

Symptoms of Sickle Cell Anemia

• As a result of sickling and the premature agingof red blood cells from sickling, there arefewer than normal red blood cells, the generalcondition referred to as anemia

• There is an increased risk of severe infections,especially bacterial infections--such as sepsis(a blood stream infection), meningitis, andpneumonia, especially in early childhood

– The risk of infection is increased because thespleen does not function normally

Symptoms 2

• Splenic sequestration crisis:

– The spleen is the organ that filters blood

– In children with sickle cell disease, the spleencan enlarge rapidly from trapped red blood cellscreating a situation that can be life-threatening.

• Stroke:

– This happens when blood vessels in the brainare blocked by sickled red blood cells

– Signs include seizure, weakness of the arms andlegs, speech problems, and loss ofconsciousness.

Symptoms 3

• Children with sickle cell anemia experienceslowed growth and delayed maturation,including puberty as a result of the anemia andinfections

• There are repeated, painful episodes, calledvaso-occlusive crises, associated withblockages of the circulatory system

– Frequently seen as swelling of extremities

• There is a progressive degeneration of organsfrom impaired circulation

Swollen Hands from Sickling

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Malaria

• Agent: The protozoan,Plasmodium falciparum, is themost deadly form

– Less virulent varieties include P.ovale, P. malariae, and P. vivax

• Vector: Female Anophelinemosquitoes

– Anopheles gambiae accounts for 75%of malaria infections in West Africa

Malaria

• Host: Man, although higher primates canalso may harbor P. malariae

– Monkeys harbor other plasmodium specieswhich can infect man

• Symptoms: Cyclic (sometimes) high fever,chills and sweating, headache, coagulationdefects, shock, anemia (inducing jaundice),kidney failure, acute encephalitis, coma

The Malaria Cycle of Infection

Mosquitobites an

uninfectedperson

Sporozoite incubates inLiver Cells 5 - 10 days,

metamorphosizes tomerozoite

Host immune responsecauses Plasmodium tosexually differentiate

Merozoiteinfects RedBlood Cells

Mosquitobites infected

person

Plasmodium changes tosporozoite in intestine,

migrates to salivary glands

Sickle Cell and Malaria

• There are three lines of evidence suggestingan association between the sickle cell alleleand Malaria:

– Geographic correlations

– Epidemiological associations

– Biochemical studies

Geographic Correlations

• Clinal studies show a substantial overlapbetween the distribution of malaria in theand the frequency of the sickle cell allele

– The Malaria belt extends across the SouthernMediterranean, sub-Saharan Africa, the MiddleEast, India, Southeast and Island SoutheastAsia, and Northern Australia, the S alleleexceeds a frequency of 10% only in Africa

– In the Mediterranean thallasemia and G-6-PDare elevated, while in India and Southeast Asia,Hemoglobin E and thallasemia predominate

Geographic Distribution of Falciparum MalariaPrior to 1930

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Geographic Distribution of HbS

Epidemiological Correlations

• A comparison of Plasmodium falciparumparasites in blood samples from childrenof AA and AS genotypes in Nigeria to thatof children with AA genotypes showed:

– AS children had lower frequencies and lowerdensities of parasites than AA children

– Fertility did not differ between AA and AS,but 29% more AS individuals survived toadulthood

Biochemical studies• Plasmodium metabolism causes sickle cell

hemoglobin to form the fibers that results inred blood cell sickling

– The parasite significantly lowers cytoplasm pH(increases acidity) causing hemoglobin to releaseoxygen

– “Knobs” form on the cell wall of infected RBCsslowing transit through capillaries

– The result is an increase of sickling to about 40%of the RBCs in AS individuals

Biochemical studies 2

• The development of the Plasmodium isdisrupted by the sickling of the red bloodcells

– Sickling depletes cell reserves of potassiumwhich is required for the parasite to grow

• Plasmodium quickly dies in potassium depleted cells

– Additionally, infected sickled cells may beprematurely removed by the spleen

Biochemical studies 3

• Sickling of a significant proportion ofinfected cells increases malaria resistance,even if not all parasites die

– The subsequent reduction in the rate ofmultiplication of Plasmodium gives the immunesystem time to mount a serious counterattack

Why does sickle cell reach suchhigh frequencies in West Africa?

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Cultural Factors

• Spread of swidden agriculture into previousTropical Rainforest regions 2-3,000 yearsago

– The invasion of rainforest areas is facilitatedparticularly by the arrival of the MalaysianCrop Complex from Indonesia

• Carried by sailors from Borneo across the IndianOcean, contact established with Madagascar (nativelanguage is an Indonesian variety), then spreadacross forest and woodland areas of continentalAfrica

Cultural Factors, 2

• As the root (Dioscorea yams) and tree (Musabananas and plantains) crops spread,increasing amounts of tropical rainforest arecleared, supporting larger and larger humanpopulations

• Clearing of the forest and high levels ofrainfall erodes the soils which are lateriticand relatively impermeable, making forformation of pools of water

Cultural Factors, 3• During the rainy season pools of fresh water

form, exposed to sunlight because of the forestclearing, which along with high humiditycreates an ideal breeding habitat for Anophelesgambiae

– Best predictor of malaria infection is variousmeasures of rainfall, excess water, relative humidity

• Agricultural expansion supports more people,living in sedentary villages with huts that themosquitoes use

Rainfall and Vegetation of Africa

Humans arrive with or adoptswidden horticulture

Initial forest with fewmosquitoes and little malaria

Forest ecology changes

Sunlit pools of fresh water developLand is cleared

Mosquito population increases

Malaria increases

Increased selection for AS heterozygotes

Frequency of sickle cell allele increases

A balance is reached between selection against A and S alleles

A Yoruba ExampleGenotype Number of

Adults (obs.)Expected

FrequencyExpectedNumber of

Adults

Observed /Expected

RelativeFitness

SelectionCoefficient

HbAHb

A9,365 0.769 9,525.6 0.98 0.88 0.12

HbAHb

S2,993 0.216 2,675.6 1.12 1.00 0.00

HbSHb

S29 0.015 185.8 0.16 0.14 0.86

Total 12,387 1.000 12,387

The difference in selection coefficients between the the threegenotypes is based on the difference in mortality between thethree groups

Numerous studies have examined differential fertility andmortality based on Hb genotype and they have found mostcommonly that there are no fertility differentials, onlymortality differentials

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Diet and Sickle Cell

• Today the consumption of cassava (Manihotesculenta) may confer an adaptation to bothmalaria and sickling and thereby disrupt theprehistoric balance of selective pressures

• Cassava is a significant source of biologicallyactive cyanide compounds including cyanide(CN-), thiocyanate (SCN-), and cyanate(CNO-)

Diet and Sickle Cell, 2• At sublethal levels these compounds

carbamylate polypeptides such as -globin,Glucose-6-phosphate dehydrogenase, and otherprotein constituents by binding with the amine(NH) end of the peptide chain

– This carbamylation prevents the formation of thesickle threads in deoxygenated sickle cells

– Enhances likelihood of survival of individuals withsickle cell anemia but reduces the malarialresistance of heterozygotes

Diet and Sickle Cell, 3

• Carbamylation of Glucose-6-phosphatedehydrogenase reduces the activity of thatenzyme, emulating G-6-PD deficiency to theextent that the enzyme is carbamylated

• High circulating levels of cyanide metabolitesmay directly interact with Plasmodiumfalciparum to disrupt growth and reproductionof the parasite inside red blood cells

– Lower levels carbamylate sickle cell hemoglobin

Diet and Sickle Cell, 4

• Cassava cannot have played a role in theevolution of sickle cell frequencies since itwas introduced as a significant cultigen inWest Africa in 1620

• But Yams yield smaller amounts ofthiocyanate which may have played a rolehistorically in selection related to malariaand sickle cell hemoglobin

Malaria, Sickle Cell, andCyanates

AA AS SS

Fertility Normal Normal LowMortality High Low Very highMortality adddietarycyanates

Moderate Low High

Geographic Distribution in Africa

• There are several centers of high frequencyof the S allele in Central Africa and WestAfrica

– DNA sequencing of the non-coding areas of theBeta-globin locus show different sequences onthe mutated 16th chromosome of the HbS

carriers in the different regions

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Sickle Cell Mutations Distribution of theSickle Cell Allele in

Africa

CameroonBeninSenegal

Bantu

Mutations

Agricultural Zones of West Africa

Yam Zone Groups:thiocyanates may ameliorateseverity of symptoms in Beninhaplotype groups

Bantu haplotype: malariaselection must be severe tosustain this haplotype

Rice Zone: Senegalhaplotype shows leastsevere symptoms, riceis adequate

Haplotypes andselection

Nitric Oxide

• Recent work has demonstrated that thepain associated with sickle cell crises islinked to excess hemoglobin in theblood

– Pain has been described as akin to childbirth or terminal cancer

Sickle Cell Crisis

• When RBCs sickle membrane is destroyedreleasing contents into the blood stream

– The bulk of the contents is hemoglobin

– Hemoglobin in the blood has high affinity for nitricoxide (NO)

• Hemoglobin in blood binds 1000X greater than when in RBCs

– Free hemoglobin scours nitric oxide

• NO is a short-lived gas produced by cells lining blood vessels

– Serves to regulate blood flow: prevents aggregation of platelets(clotting), protects cell membranes, relaxes vessels

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Sickle Cell and Nitric Oxide

– Blood vessels constrict and become clot proneas a result of hemoglobin reducing NO in thecirculatory stystem

• Increases blood pressure in lungs, restrict flow ofoxygen, nutrients to vital tissues and organs

• Severe pain ensues

– Potential for treatment for sickling crises• Breathe higher doses of nitric oxide to neutralize

hemoglobin effect

• Administer supplemental supplies of haptoglobin,the protein in our blood which normally scavengeshemoglobin

A “New” Genetic Adaptation to Malaria

• Nitric oxide inhibits the growth ofPlasmodium in vitro

• Researchers searched for a variant of thegene that regulates NO

– NOS2: Nitric Oxide Synthetase 2,(chromosome 17 q arm near centromere)

– Examined 1291 children in Tanzania andKenya

• Those with a specific mutation of NOS2 were muchless likely to get severe malaria

NOS2

• Risk reduction of severe malaria was 88%for the Tanzanian children and 75% for theKenyan children

– Two different varieties of malaria involved

• Children with the mutation produce greateramounts of NO

Nitric Oxide and Malaria

RBC withplasmodium

BreakdownRBC

ReleaseHemoglobin

Decrease NO

Stick to intima ofblood vessels, clogging

blood flow to tissuesincluding brain Blood vessels

susceptible to damage

Mutation increasesNO reducing

susceptibility ofblood vessels,

reducing severity ofsymptoms

More Nitric Oxide and Malaria

• Alteration of the Anopheles gene analogueto human NOS2 affects the ability of themosquito to transmit malaria

– Plasmodium life cycle in the mosquito isinterrupted by increased NO