Human genetic variation

How do we categorise P in psychological research

• Biological

  • Age, developmental, reproductive stage 

  • Health, disability, addiction, physiological state 

  • Sex/gender, orientation  

  • Race/ethnicity

• Not Biological

  • Occupation, work status, leadership

  • Socio-economic status

  • Education, family

  • Political views, religion

Sex/gender binary

• historically aligned with sex chromosomes

•  XX or XY

• Defined sex at birth 

• egg/sperm parent 

• male/female

Challenges to traditional deterministic view of sexual differentiation in humans 

• Sex chromosome anomalies have various symptoms  

• Intersex individuals

• Wide individual variation in traits is not dimorphic 

• Gender/sex

Wide individual variation in traits is not dimorphic 

• different experiences during development & social/physical/pre-birth physiological environmental factors

• gender identity/sexual preferences & behaviours may not align with reproductive binary 

Sex chromosome anomalies have various symptoms  

• Klinefelter syndrome & Triple X syndrome (XXY & XXX)

• Turner syndrome individuals (X chromosome missing)

Intersex individuals

• mild-severe anomalies in the development of sexual organs in newborns with intact two sex chromosomes

Gender/sex binary & intelligence

• IQ tests devised 120 years ago & repeatedly revised

  • High statistical reliability → limited validity

  • Subjects can increase IQ scores with training

• Alternative theories

  • dynamic assessment testing proximal development of children

  • multiple intelligence theory

• IQ studies select a range of tasks

  • correlate scores to calculate “g” factor that is then correlated with binary gender/sex IV making inferences about biological processes in the brain or genes

why does understanding genetics accurately matters

• “Careless use of genetical concepts can go astray “

  Weiss & Lambert (2011)

Why nature-nurture is a wrong

• Nature-nurture debate is considered a fallacy

  • a conceptually deficient & biologically implausible dichotomy

  • oversimplifies the dynamics of behaviour and development

    • Honeycutt (2023)

  • done more harm than good

    • Goldhaber (2012)

Researcher bias & Ethics

• Categories of participants 

•  IV in planned comparisons

• DV in multivariate analysis, structural equation modelling, path analysis

• Demographic information to check for biases in selection of subjects, contextualization of findings or post-hoc comparisons

What is a genome

• Genes (2%)

  • protein-coding DNA sequence

  • Mutations in the genome

• Non-coding DNA (98%) 

  • Functionally important 

  • Contributes to complex genetic architectures in which genes are embedded

  • Physical and social environment, nutrients

• Genome is all of the DNA present in each cell of the body

  • Somatic cells

  • Germline cells

Somatic cells

• Gene-environment interactions

• determine all body and cell functions in every moment of an individual’s life

Germline cells

• Reproduction & inheritance of traits

• Gene-environment interactions influence the development of an individual’s offspring

• inheritance of traits

Genetic variation in individuals of the same species

• variation of an individual’s genome

• Measurements of DNA sequences to identify genome variations at different levels

• measuring genetic variation

Causes of variation of an individual’s genome

• Multiple variants occur in different frequencies within/between populations

• DNA is recombined during egg & sperm production (genetic reshuffling)

  • Over time parental DNA mutates

• Different environmental/diseases/genetic factors between populations change the distribution in population over time

Measurements of DNA sequences to identify genome variations at different levels:

• between individuals (individual variation)

• from all individuals in an area (within-population variation)

• from populations in different areas (between-population variation)

Measuring genetic variation 

• Biometry & quantitative genetics

  • measure observable traits (height, enzymes) 

• Genetics

  • differences between chromosomes & DNA sequences of selected genes 

• Genomics

  • Search for markers of genetic loci in DNA sequences

  • include both genes & non-coding DNA:

    • short sequences

    • repeated sequences

    • single base pairs (SNPs) that are sites of single-nucleotide polymorphisms

history of human genetic research

• 19th century → Theory of evolution, Mendel’s breeding experiments, biometry

• 20th century → Mendelian laws of inheritance and quantitative genetics, biometry, the emergence of molecular genetics

• 1980-21st century → PCR test, age of genomics, HGP

Human Genome Project (HGP 1984-2004)

• International research → aimed to map all the human genes completely  

• Full sequence in 2001-2004, cost $2.7 billion

• Established Bermuda Principles:

  • making all human genome sequences available in public databases within 24 hours

• Natural human sequences cannot be patented  

Ethical concerns of the human genome project

• indigenous populations are societally most disadvantaged

• stand the least to benefit from resulting novel scientific discoveries & healthcare improvements

  •  Silent Genomes Project (Canada) since 2018  

  • Aotearoa Variome Project (New Zealand) since 2018

initiatives focusing on genome diversity

• Human Genome Diversity Project also launched in the 1990s  

• HapMap Project since 2003  

• Genographic Project (National Geographic) since 2005  

• 1000 Genomes Project since 2008  

• The Cancer Genome Atlas (TCGA)

example of quantitative genetics & presumed simple morphological trait 

Human height

• heritable & polygenic trait

• Studied using biometry/quantitative genetics → genomic research = high complexity of genetic interactions & role of biologically relevant genes/non-coding DNA

shrinking body heights during the Industrial Revolution

• Discovery of cyclic changes in height during Industrial Revolution 

  • growing economies but sizes shrinking 

• Shortage of workers as labour intensified → economic incentives for research on the biological causes of height variations

The natural sciences during the industrial revolution in europe

• 1785: Hutton 

• 1798: Malthus 

• 1809: Lamarck

• 1831: Darwin’s voyage on the Beagle 

• 1833: Lyell 

• 1854: Humboldt 

• 1859: Darwin’s On the Origin of Species 

• 1866: Mendel (rediscovered in 1900)

Quantitative genetics - Measuring correlation between traits

• Measuring body/differences

• Anthropometry - measuring variations in body, head, face 

• Correlation with racial categories, behavioural/psychological traits

• Galton (1888) correlated head size vs degree results → claimed strong relationship & proposed later the concept of generalized mental ability

Quantitative genetics - Using pedigrees to trace heritability of traits

• Broad population surveys & case studies

  • Trace differences in mental, personality/behavioural traits through IQ tests, genealogy or surveys of mental illnesses

• Galton → eugenics→ concluded the pedigrees of rich families with superior intelligence/abilities are heritable

  • Supported beliefs of racial segregation & Study of “defective”

  • Pedigree chart → misuse in professional sphere to general popular culture

Misuse of Darwin’s theory of evolution

• Darwin’s theory of evolution - diversity of species on Earth & how species with different adaptations appear and disappear

• Misplaced morality and Social Darwinism - evolution is not the ”survival of the fittest”

• Misconception of selective (human-driven, artificial) breeding as evolution 

• Natural selection is not 

  • Goal-oriented

  • optimise traits & results in progress

  • remove variation/prevent individuals from reproducing

Scientific racism in theory and action formally denounced only after WW2

• Scientific racism→ deep impact on society

  • Nazi Germany - concentration camps, forced sterilisations, ethnic cleansing & holocaust 

  • First compulsory sterilization laws (1907-1927) in USA

• Crimes against humanity & genocide deploy simplified wrong claims about natural selection/biological “superiority”

• Pseudoscience → seemingly objective justification for colonisation, slavery & social policies that control/limit opportunities & rights of those considered “inferior”

Long-lasting impact of half a century of eugenics and race science

• Opposition to eugenics & race science amongst scientists/society disputing the theoretical claims + generated disproving evidence 

• Numbers & visibility of opponents amongst scientists started to increase after 1925

• Supremacy ideas persist → claim to show modern evidence or confirmation of data from eugenic studies

Race categories have no biological basis

• Inheritance is not simply blending the characteristics of egg & sperm

• Variation in skin pigmentation is highest on the african continent → paucity of studies in Africa

• Race is real but a social construct

Inheritance is not simply blending the characteristics of egg and sperm

• Genomics → Most trait variations are polygenic

• Skin is the largest organ → colour highly variable & complex trait

  • Complex relationship between genes determining polygenic inheritance

• variation due to

  • genes regulating amount of melanin in the melanocytes of the skin → limited to only some variations

  • biological sex, changes in different environments, during disease or pregnancy

Variation in skin pigmentation is highest on the african continent 

• Correlation between UV-levels and adaptive selection for lighter skin

• Studies on genetics of skin pigmentation in European populations

• Research on skin color variation in Africans identifying novel pigmentation genes

• Spectrophotometry for accurate melanin level determination

• San people of South Africa with lightly pigmented skin and oldest genetic lineages

lack of studies in Africa

• Earliest humans in Africa 200 000 years ago → time to accumulate largest genetic diversity 

• Overdue to study much more human genetic diversity of populations on the African continent

Race is real but it a social construct

• Race = social & cultural construct

• not a biological category

  • scientifically evidenced that ‘biologically distinct’ races are obsolete

• Genetic variability primarily due to differences among individuals within populations

• Differences between populations account for a small part of genetic variability

• Genomics research use of term ‘race’ in relationship to genetic variation is:

  • unnecessary & dangerous = racism

    • used to establish social hierarchies & slavery

Ancestral genetic variation, migration and selection pressures in human population

• mTDNA tests

• ancestry

• homosapeins

mTDNA tests

• Whole-genome sequencing is expensive

• Mitochondrial DNA (mtDNA) sequencing is cost-effective

• Share very similar mtDNA with close relatives → Inherited from egg (maternal inheritance)

• is an important genetic marker in human research

Nuclear genome

• 3.3 billion DNA base pairs (93% non-coding DNA)

Mitochondrial genome

• 16,569 DNA base pairs (3% non-coding).

benefits of mtDNA sequencing:

• No recombination  

• High mutation rate  

• High number of copies in a cell

Ancestry - long story of migration of modern humans & genetic admixtures

• Genetic variation provides information on population’s ancestors, whether modern humans interbred with other human species

• DNA analysed:

  • Mitochondrial DNA

  • Y-chromosome 

  • SNP mapping

homo sapiens

• a migratory species compromising of several interlinked populations in Africa (connectivity changing over time)

• Early human species dispersed/migrated overcoming geographical isolation

• no physiological reproductive barriers that prevent admixture

• Mixed diet, cognitive functions & cultural innovations enabled humans to survive in many different environments/change them

Immunological changes in the genomes of human population

• Migration exposes groups of humans to new environments & diseases 

  • 60% mortality amongst Dutch colonists → typhoid

• Infectious diseases killed individuals in 59 indigenous communities of Amazonia in the past 200 years

  • mortality rate decayed over time due to genetic adaptation

• HIV transmission from apes to humans in 1920s

  • Spread out of Africa from 1960s

  • Mutation found in 14% of European populations

  • Mutation not found elsewhere