LECTURE 25 - Variation in contemporary humans

Question 1

What is species and what is race?

Answer 1

• Species
  
  • members of the same species can mate and produce viable offspring
  • All humans (Homo sapiens) belong to the same species
• Race
  
  • member of the same species that are “distinctive” in some way
  • Racial classifications are often arbitrary and non-functional

Question 2

Is considering race as a taxonomic level appropriate?

Answer 2

• The classification of animal and plant species into races has often been an ill-defined and idiosyncratic practice

Question 3

What Blumenbach’s racial classifications (1795)?

Answer 3

• “Scientific” approach
• Based on “coherence” traits
• Originally included both cultural and biological traits
• BUT different “racial” traits are RARELY coherent in the same way

Question 4

How are race and ethnicity defined?

Answer 4

• “Folk categories” (those used in everyday life) often conflate race and ethnicity (i.e., they use biological characteristics and cultural characteristics at the same time)
• e.g., Barack Obama was the first “black” president of the USA, but some people question if he is “really black”; not because of biological reasons but rather because of culture (the schools he went to, the way he talks, etc.)

Question 5

Why is race not a scientifically useful scheme for categorizing human diversity?

Answer 5

• Phenotypic traits do not cohere enough to make race useful
• Typical use of race is as a set of social and cultural categories
• This is not to say that different groups of humans do not show discontinuities in trait variation, but most traits do not cohere enough to make race useful
• So, when talking about variation in humans, it is often more useful to think about specific traits, e.g., resistance to malaria, colour blindness, perfect pitch, height, cheek dimples, eye colours, etc.

Question 6

How much variation is there in humans relative to other species?

Answer 6

• A randomly chosen pair of humans is likely to be about as different as a different randomly chosen pair of eastern chimpanzees, but substantially less than a random pair of central chimps, western chimps, bonobos, or gorillas

Question 7

What are the variations within versus between human populations?

Answer 7

• The majority of genetic variation in human populations is WITHIN them (~85%), as opposed to BETWEEN them (~15%)
• This amount of subdivision is very low relative to other primates (approximately 1/3 what is observed in most species)
• Thus, despite occupying a much broader geographic area, not only do humans show low genetic variation overall, but we are also distributed into populations that are highly-related to each other

Question 8

How are founder effects caused?

Answer 8

• Founder effects are caused by random sampling of large populations that start new smaller populations

Question 9

Where is genetic drift more powerful?

Answer 9

• In small populations

Question 10

What does loss of allelic diversity occur?

Answer 10

• During sharp reductions in population size (i.e., “bottlenecks”)
• Rare alleles are the most likely to be lost in a bottleneck event

Question 11

What is a population?

Answer 11

• “A potentially interbreeding group of individuals that belong to the same species and live within a restricted geographical area”
• Seemingly straightforward, but populations often represent a continuum of differentiation
• Isolation can reduce the exchange of genes between populations (gene flow), which allows them to evolve somewhat independently, resulting in “population structure”

Question 12

What is population structure?

Answer 12

• With a complete isolation, over time, some alleles will increase in frequency through random chance and “fix” (reach 100% in the population)
• Because different alleles may fix in different populations, they will diverge through time
• Migration between populations allows “gene flow” of alleles between populations, which will reduce differentiation of populations by preventing “fixation” of alleles
• Because migration tends to be higher between populations that are geographically close to each other, isolation correlates with distance (i.e., :isolation by distance”)

Question 13

Describe ‘isolation by distance’ in humans

Answer 13

• Genetic variance between these populations is patterned in geographical space, and can be described as clinal
• There is a strong relationship between geography and various measures of genetic diversity at the worldwide scale

Question 14

What does human population structure provide strong evidence on?

Answer 14

• Human population structure provides strong evidence that a small number of founders from Africa dispersed to colonize the whole planet (OUT OF AFRICA)
• Geographic distances from Africa show a high negative correlation with measures of population-level genetic diversity
• Genetic differences between randomly chosen African individuals are greater than between European and Asian individuals
• Genetic difference between African populations are on average greater than between African and Eurasian populations
• Alleles found outside Africa are often a subset of the African allele pool
• Continent-specific alleles are rare in general, but are far more common in Africa than any other continent
• A combination of genetic data suggests that migration out of Africa occurred multiple times
• All present-day non-African people are descended from H. sapiens ancestors who left Africa within the last few hundred thousand years

Question 15

Are there distinct genetic “groups” of humans?

Answer 15

• 10% of variation exists between continental populations
• The program STRUCTURE can be used to assign individual genotypes to an arbitrary number of groups
• In recent genome-wide analysis, seven groups were distinguished, largely corresponding to continent or subcontinents
• Although, many studies have been able to distinguish discrete groups of humans, the same groups are not always observed when different genes are used

Question 16

How does culture complicate geographic signals?

Answer 16

• Investigation of structure in South India found that tribal and caste populations could be distinguished independently of geographic differentiation
• Thus, cultural, religious, language, or social boundaries can contribute to maintenance of genetic variation
• Geographic proximity is only a proxy for gene flow

Question 17

What would be an ideal sample of the human species?

Answer 17

• Imagine we want to collect a sample of 1000 human genomes for a multi-purpose description of human diversity - what would be the ideal composition of this sample?
• Some possible strategies
  
  • superimpose an evenly spaced grid on the Earth’s surface and sample one individual at each node
  • sample relatively isolated populations
  • Sample proportionally to population density
  • intensively sample individuals from a relatively small number of populations
• Unclear which strategy is best - it depends on the goal of the study

Question 18

Does any of this have any bearing for our treatment of human diseases?

Answer 18

• Some genetic disorders are more common in certain ancestral populations
• But a focus on race based on certain phenotypic characteristics can lead to incorrect inferences about ancestry
• Many common disorders are caused by alleles of multiple genes
• To identify them one must compare the allelic state of many genes in affected vs. control individuals
• Population structure is important to consider when choosing a control population

Question 19

Are contemporary humans evolving due to selection?

Answer 19

• For a population of contemporary humans to be evolving through selection, they would need to satisfy three requirements: variation for a trait, heritability of that trait, and differences in fitness (survival and reproductive success) that are due to variation in the trait

Question 20

Could selection cause the evolution of HIV resistance in humans?

Answer 20

• Is there variation in the population?
  
  • the d32 allele has a frequency of ~10% in many European countries, but is almost absent in Asia and Africa
• Is the trait heritable?
  
  • Immunity conferred by d32 is inherited as a simple Mendelian trait
• Does variation in the trait affect the ability to survive and reproduce?
  
  • Homozygosity at d32 confers a high level of resistance to HIV infection
  • Given that HIV infection can result in death, d 32 could experience positive selection
  • HIV infection in humans is too recent to have had a strong effect on the frequency of d32, but there is evidence that the reason it is at relatively high frequency in Europeans is that it experienced positive selection because it confers some resistance to smallpox and bubonic plague

Question 21

Could selection promote height?

Answer 21

• Is there a variation in the population?
  
  • Human height is variable, with almost all populations showing a normal distribution
  • In industrialized countries, average adult height has increased by ~10 cm in the last 50 years
• Is the trait heritable?
  
  • Height is a quantitative trait that is controlled by many genes of small effect
  • At east 20 genes have been found that contribute 0.2-0.6 cm to height per allele, but these genes only explain about 3% of the variation in human height
  • After birth, monozygotic (identical) twins grow to be more similar in height then dizygotic (fraternal) twins
  • Monozygotic twins reared apart are more different in height than monozygotic twins reared together, but are still more similar than dizygotic twins who grew up together
• Does variation in the trait affect the ability to survive or reproduce?
  
  • Several studies have shown a positive relationship between height and reproductive success (in particular for men), although the effect sizes are low

Question 22

What are the environmental effects on human height?

Answer 22

• Human height may be evolving via selection, but most of the increase in height over the last century is likely due to environmental effects
• Height is strongly affected by nutrition and health care
  
  • Differences in nutrition between North Korea and South Korea are thought to explain the ~4-10 cm lower average adult male height in the North
  • Height increased in the Japanese population in the generation after World War II following changes in diet

Question 23

Can selection in contemporary humans affect heart health?

Answer 23

• Is there variation in the population?
  
  • There was significant quantitative variation in all traits measured
• Are the traits heritable?
  
  • Heritability of traits ranged from 0.34 to 0.84 based on parent-offspring regression
• Does variation in the traits affect survival or reproductive success?
  
  • Detected weak but significant selection for women to be shorter, with lower values of total cholesterol and systolic blood pressure, to have their first child earlier, and to reach menopause later
  • Thus, it appears that natural selection is acting slowly and gradually on traits of medical important in this population

Question 24

SUMMARY (variation in contemporary humans lecture)

Answer 24

• Humans possess relatively little genetic diversity compared with other primates
• Although genetic differences among human groups are small, these differences can still be used to assign individuals to broad, geographically based groupings
• Groups are highly unstable and dependent on which genes are used for identification; no consensus has been reached on their number or definition
• For humans to be divided into systematic groups we would require ‘coherence’ between sets of genes (or traits), but this does not occur
• As a consequence of a mixture of processes including isolation, selection, drift, and migration, our genomes appear to be mosaics with ancestry from many parts of the globe, but nested within the diversity present in our African ancestors