Human Var Exam 1 Flashcards
Approaches to studying Human Variation
Two persistent themes are classification vs adaptation and types vs variation
Classification
Naming and description of discrete groups, types of questions that are asked is the relationship between groups (evolutionary/biological, historical, geographical)
Carleton Coon defined 18 races of humans, sometimes with and sometimes without justification
Adaptation
Looks at correlations between human variation and the environment, types of questions asked are do physical variations correlate with the environment and can adaptive traits be separated from neutral ones. Also looks at patterns of variation and dynamics that are responsible for it (could be evolutionary or from population)
It can sometimes reject classification but it also commonly accepts rigid classifications and uses them as markers for groups/human populations
Types
Connected to the Platonic ideal of essentialism where the world is viewed as a series of types that have a universal validity. Types can be seen as real or ideal and some anthropologists posit that ideal ‘types’ can be created through a process of weeding out variation. Variations can be seen as imperfect degenerations of a given type
Variation
All entities exist within ranges of variation that can be continuous (within a normal or Gaussian curve) or discrete (a binomial or polynomial distribution)
Groups are sometimes categorized and evaluated differently before it is established that separating two groups is valid or justified
Perspectives on race studies
Primarily European, scales of division are continental, national, and ethnic groups within a nation
From the late middle ages to renaissance, there was a monogenesis camp where there was one human creation and subsequent variation due to differentiation. Connected to the essentialist idea of “types” where those who don’t fit that type (indigenous groups, Africans, etc) are “lost tribes” or “lesser”
There was also a polygenesis camp where each “race” was a separate creation. Since the Bible only mentioned one “divine race” this led to hierarchical rankings of races. Polygenesis was later reinterpreted as different races being descended from different past human species or apes
In both of these viewpoints there was a recognition that all humans come from a European ideal and bred racist thinking
Carolus Linnaeus
Included 4 subspecies of Homo sapiens based on skin color, hair color, hair texture, and eye color. Linnaeus was concerned with classification which was determined by a combination of geography, physical appearance, culture economics, psychology (often inferred), reflects prejudice of his time
Georges Louis Leclerc
Attempted to describe and explain the diversity of living humanity by attempting to historically relate people based on resemblances and differences and also relate differences to general environmental characteristics
Johann Freidrich Blumenbach
First large scale attempt to categorize people, emphasized observable physical characteristics but there was still racial prejudice in characterizing personalities
Anthropometry
Study of measurements and proportions of the human body. This attempted to quantify differences between human groups and allow for the identification of “deviant” forms of humans
Led to phrenology which was the study of the shape and size of cranium as an indication of character and mental abilities, criminology, and psychology
Samuel Morton
Amassed a large collection of skulls mostly around the US and focused on how race correlates with cranial capacity and how that correlates with other traits, produced a rank order of brain size and race
There were problems with the rank order, some accused him of faking the data, used small sample sizes, did not account for body size which scales with brain size
Anders Retzius
came up with cephalic index (length/width ratio) and tied it into the racial history of European ethnic groups
Paul Broca
Identified Broca’s area of the brain and used a microscope for pathology. Also made attempts to describe human physical differences systematically and concluded that males have larger brains than females which led to a delay in female education, founder of physical anthropology
19th Century Evolutionary Anthropology
Associated with Lewis Henry Morgan, represented a commonly held view that all societies progress through a series of stages (savagery, barbarism, civilization), some societies make faster progress and others make less progress, existing social variation can be used to document the past, and societies at “higher” levels have a responsibility to help the others “catch up”
Commonly held view that differences between people is the result of different abilities and that the human population can be improved through directed or controlled breeding
Eventually there was a desire to document every aspect of variation (anatomy, blood groups), but little was known as to how to analyze variation so many statistics were rejected/ignored and a typological framework was used
Francis Galton
Developed eugenicist thinking and founded a laboratory to document the heredity of behavioral traits and physiques
Cesare Lombroso
Criminologist who posited criminality was associated with “primitive” groups of people with “ape-like” features
Alphonse Bertillon
Police officer who used anthropometrics for personal identification and rejected the idea that certain populations have a predisposition to crime
Franz Boas
Developed the distinction between Race-Language-Culture where a clear separation between biology and culture was identified. Emphasized the plasticity of the human biological form (due to factors such as health and nutrition) and rejected the idea of progress. Instead posited that “progress” is accompanied by trade-offs or regressions in other areas
Dr. William Montague Cobb
First Black American to earn a Ph.D. in physical and biological anthropology. Used skull craniometry to demonstrate that there were no anatomical differences between Black and Caucasian athletes, common belief that Black people were physically superior
What were some of the effects of racial eugenics?
It was universal in Western Europe and North America and it directly affected immigration laws, marriage laws, segregation, forced sterilizations, etc. Nazi’s actively referred to American laws/writings to justify actions
What were some differences between how race was studied before and after WWII?
DNA was identified to be genetic material so genetics was merged with Darwin’s theory of natural selection/evolution. Race and geographical classification was therefore no longer deemed as an appropriate subject of study
Carleton Coon
proposed human races reach a Homo sapiens stage at different times which explains differences
Richard Lewontin
founded population genetics and posited ~85% of total human genetic variation is found within any given population and only 15% reflects allele frequency differences between populations
Nuclear vs Mitochondrial genome
Mitochondrial genome has 37 genes that encode 13 proteins and 24 that encode RNA’s, made up of 0.0005% of the nuclear genome
One mitochondrion contains multiple copies of mitochondrial genome and numerous mitochondria, so cells can contain several thousand copies of a mitochondrial genome but only 1 copy of a nuclear genome
Nuclear DNA is inherited such that each parents provides 1 chromosome, mitochondrial DNA inherited from egg donor
Organizational features and functions of DNA
Proteins encoded by genes may be structural, enzymatic, regulatory, or contain several of these functions. These products from multiple genes can combine to form a protein molecule
Genes contain an exon/intron structure along with intergenic regions
Haplotype
everything inherited together on the same chromosome (either the entire chromosome or a portion of the chromosome)
Aneuploidy
Abnormal number of chromosomes, almost always occurs in egg rather than sperm, commonly due to nondisjunction
Balanced translocation
even exchange of material between two chromosomes with no genetic information extra or missing, this generally means full functionality occurs but sometimes the coding sequence is disrupted, regulatory regions are separated from the transcription unit, or genes are fused together. This involves different chromosomes meaning no recombination between homologous chromosomes occurs
Unbalanced translocation
occurs when the exchange of chromosomal material is unequal which results in extra or missing genes, this often results in a miscarriage but can be variable
What are some functions of intergenic regions and introns (“junk” DNA)?
“Junk” DNA can allow new variability to emerge. VNTR (Variable number tandem repeats) which are highly variable and classified based on size and number of repeats or level of variability (Microsatellites are short tandem repeats 1-6, minisatellites are 8-100 nucleotides, satellites are 1000-10,000 nucleotides)
Also may contain transposable element insertions such as SINE (short interspersed nuclear elements) and LINE
May contain promoter or enhancer regions
These regions may also encode for non-coding RNA molecules which can affect the gene regulatory process
~10-15% of the noncoding human genome can be regulatory elements such as promoters or enhancers
Promoter
usually 100-1,000 bp upstream from transcription start site and other proteins bind to turn transcription “on” or “off”
Enhancer
can be further away and can upregulate or downregulate transcription, sometimes proteins that bind to an enhancer region can bind to proteins that bind to the promoter region since DNA wraps and has tertiary structure. Tertiary structure means distant elements can come into closer proximity with the gene that is being regulated
How are non-coding RNA molecules significant to gene regulation?
microRNAs or siRNAs can block mRNA translation and bind closer to the start of mRNA in order to respond to environmental cues more readily, small RNAs can modify target RNAs and allow for the synthesis of telomeric DNA, alter chromosome structure medium and large RNAs can cause X chromosome inactivation, promote gene transcription, promote synthesis of microRNAs or small RNAs
What kinds of mutations can cause a significant alteration of phenotype?
Frameshift mutations and mutations on exon regions tend to have a larger phenotypic effect. Mutations earlier in the gene sequence also tend to have a larger phenotypic effect especially with frameshift mutations, so location matters
Where a mutation occurs on a protein also matters, whether it occurs in a critical region such as the active/functional site of an enzyme or a less critical region
What kind of amino acid change that occurs is also significant. A non-conservative change where the property/charge of the amino acid changes also tends to cause more phenotypic effects
Mutations in promoter or enhancer regions that regulate gene activity can cause an upregulation or downregulation of gene expression
Mutations can affect gene copy number where duplication leads to too much of a protein and deletion leads to too little of a protein, leads to potentially adaptive variation. Gene copy number can be linked to diet/environmental factors (higher starch diet associated with higher amylase production)
Ankylosing spondylitis
chronic inflammatory arthritis that affects the spine, differs by a single amino acid change in a critical region of the molecule. Amino acid change is also non-conservative where there is a mutation from aspartic acid (- charge) to histidine (+ charge), so binding profile of molecule changes
Lactase persistence
Lactase allows for digestion of lactose, lactase is highly expressed during lactating phase of development but generally drop after weaning, but some humans retain high levels of lactase expression into adulthood
Promoter variant can be “turned off” due to a mutation
Alternative splicing
a process of rearranging exons to alter proteins and create splice variants, occurs under “normal” conditions. Mutations nearby the splice site can affect the binding of splicing factors along with proper splicing
Alternative splicing of sp140 associated with arthritis since mutation prevents one exon from being part of protein
Huntington’s Disease
Neurodegenerative genetic disorder that results from excess CAG repeats that causes protein misfolding. Misfolded proteins accumulate around neurons and interfere with function. Age of onset is quantitative since an earlier age of onset is associated with a larger number of repeats
Simple trait
Trait encoded by one gene that tends to have a Mendelian inheritance pattern (dominant, recessive, additive) where a trait can be predicted by a single locus genotype model, tends to have a low environmental influence and also tends to be qualitative/discrete (either/or)
Additive traits
Two alleles are expressed and the effects combine to create an intermediate phenotype (classic example is flower color where heterozygotes are an intermediate phenotype, white, pink, red)
Codominance
Can occur with sickle cell where heterozygotes can be anemic and contain some regular red blood cells and sickle cells. Heterozygotes are also more sensitive to high stress conditions
Complex traits
Tend to be heritable but not readily predictable from a pedigree, contains the involvement of many genes (polygenic), has a high environmental influence, and often has quantitative or non-discrete traits. Distributions tend to fall along a typical Gaussian bell curve
Human height is a classic example, around 180 genes and SNPs explain around 10% of the variation in height and there are >3000 loci that are statistically significantly associated with the trait
Polygenic trait
When a human trait is influenced by one or more genes, some traits that were previously considered to be Mendelian have now been identified to be polygenic (earlobes)
Epigenetics
Changes to gene function that do not involve changes to the DNA sequence. Epigenetic patterns can be inherited and can take many forms (they can involve how DNA is folded, DNA methylation, etc)
Heterochromatin DNA is tightly wrapped around histones which makes transcription and gene regulation more difficult, euchromatin DNA is loosely wrapped and tends to be nearby transcriptionally active genes
Twins are mostly identical in DNA but not always in methylation and expression, epigenetic variation allows human body to change in response to new environmental conditions in a flexible and reversible way, it also occurs since we do not need different DNA content per cell to get different cell types
How can variation occur between DNA, mRNA, and Proteins?
Variation can occur between mutants/allelic variants in DNA
Amount of mRNA produced can lead to variation and mRNA can regulate gene transcription
mRNA splicing and microRNAs can affect protein translation and final product
Species
Group of organisms that can breed in nature, hybrids can occur in species both naturally (baboons) and also artificially (ligers/tigons)
What are common causes of speciation?
Speciation is a lineage splitting event that produces two or more species, can be caused by geographical barriers, changes in behaviors leading to reproductive isolation,
How do we know which group a species belongs to?
Evolutionary systematics is a system of classification focusing on overall similarity and relationship between species. Used to be based on homology but now is usually genetic
Cladistics is a system of classification that focuses on evolutionary relationships. These are generally shared derived novel traits and tend to be character-based and representing hypothesized relationships
Homology
Traits that are similar in superficial appearance and reflect common ancestry
Homoplasy
Traits that are similar in superficial appearance due to the adaptation for a certain function that arrived via independent evolution
Convergence occurs when this phenomenon occurs in distantly related species, parallelism is the independent evolution of similar traits in closely related species
Phylogeny
Old phylogeny was based on homology or morphological characteristics and was shaped by biases where it was posited that humans were the “pinnacle of evolution.” DNA analysis and genomics called these biases into question since humans were compared to other species in a non-value laden way and similarities and differences were highlighted from sequence data. Genomics also gave stronger evidence for our close relationships between chimpanzees and bonobos
What are the mechanisms of microevolution?
Mutations, Gene flow, Genetic drift, Natural selection
Mutations
copy errors when DNA replicates in preparation for cell division, can also be caused by factors such as environmental damage (UV/other kinds of radiation). Germline mutations can be passed down and non-germ line mutations can become cancers/cause other complications
Gene flow/migration
movement of genes from one population to another via migration and the subsequent introduction of new genes to a population
Genetic drift
when allele frequencies shift in a population across generations due to chance rather than increased fitness. Many different factors may alter reproductive success independent of the fitness of a gene causing some variants to be more present in a population
Founder and bottleneck effects may also lead to this where a segment of a population is cut off allowing some alleles to have increased and decreased frequencies compared to original populations
Afrikaners have an increased frequency of Huntingtons due to founding population of Dutch settlers with a high frequency of the allele, also occurred in Lake Maribo and Tristan da Cunha (colonizers had increased frequency of retinitis pigmentosa so 47% of population has asthma from 3 founders)
Natural selection
when variation is present, variants can be inherited, competition is present where environment cannot support all offspring, and differential selection results causing allele frequency changes over generations
Natural selection acts on different traits as an environment changes, drought was a strong selective event for birds and caused a microevolutionary shift where beak size increased over time since a larger beak size was favored
Sources of genetic variation
Mutation, recombination, sexual reproduction. Phenotypic variation often reflects genotypic variation
Fitness
Determined by the environment an organism lives in, can be measured as the average number of surviving offspring compared to alternative phenotypes. Selection acts on a phenotype which then has associated genotypic effects, in order for it to be inherited fitness must reflect underlying genotype and must be visible as a phenotype
Sexual Selection
Can occur via male competition (often more intrasexual) where males compete with one another for females and this can occur via physical confrontations, intimidation, sperm competition, etc
Can also occur via female choice (often more intersexual) where females decide which males to mate with based on characteristics that indicate health which can provide selective pressure for certain traits
Sometimes sexual selection can have trade-offs with other traits such as being more subject to predation or a physical fitness advantage
Positive selection
when the frequency of advantageous alleles increases
Negative selection
when the frequency of harmful/deleterious alleles decreases
Balancing selection
favoring of multiple alleles, this often occurs due to heterozygotes having greater fitness of homozygotes
What are some lines of evidence for evolution?
Genetic evidence of “immortal genes” shared across lineages, also evidence of a molecular clock showing well established mutation rates
Development anatomy showing shared features, shared histories, a common ancestor, shared phylogeny
Fossil evidence showing extinct species and intermediate forms
Biogeography showing a distribution of species and traits
Lab experimentation and direct observation in nature
What are some key factors of evolution to keep in mind?
Evolution is constrained and must work with what is already in place
Evolution does not have a direction and “lower” species do not progress to “higher” species
Every trait is not an adaptation
Mutations are random, but selection is not random
Natural selection is not the only mechanism of evolution
Humans can adapt morphologically, physiologically, and via behavior and culture
What are some differences between anatomically modern humans and earlier Neanderthals?
The skeleton has a lighter build compared to earlier humans, brains are very large and the average size is 1300 cubic cm, the skull is thin-walled, high-vaulted, and has a flat and near vertical forehead, faces have less heavy brow ridges and prognathism of other early humans, and jaws are also less heavily developed with smaller teeth
How were differences between modern and early humans uncovered?
Fossilization where buried bodies (usually how experienced a rapid burial) were identified and timed via radiocarbon dating, use of a molecular clock since stretches of DNA can mutate at a steady/reliable rate which can be estimated, and argon
Fossil evidence that modern humans originated in Africa and migrated to populate rest of world
What is the debate on single vs multiregional origins of H. Sapiens?
Some anthropologists say we descended from one group, some say we evolved from ancestral hominins but in a more complex way over the continent and there is debate on that. Some hypotheses are African multiregionalism, the entirety of Africa instead of a single place/population gave rise to H. sapiens, a changing climate/environment brought the mixing of groups
Pleistocene
Occurred 12,000 years ago where in Africa there was a repeated oscillation in temperature/rainfall, forests expanded, Sahara expanded, grasslands expanded into lowland forests and there were intervals of increasing length/amplitude
This had major effects on the flora and fauna of a population, and large mammals with a large population size/structure emerged. Both directly due to drought related mortality and indirectly via vegetation changes
Evidence shows climate oscillations during Pleistocene period were likely drivers of human migration and that there was extensive diversity of Africa that was in no way homogenous
Hominin
group that consists of modern humans, extinct human species, all other immediate ancestors (includes members of genus Homo, Australopithecus, Paranthropus, Ardipithecus)
What was some evidence that H. sapiens originated in Africa?
Apidima Cave fossils provide earliest evidence of humans in Eurasia and Misliya Cave provides evidence for humans in Israel, both dated more recent than earliest African specimens
mtDNA also serves as genetic evidence since sequences were used to construct taxonomic trees where horizontal lines were branches that represented evolutionary lineages changing over time, branch length represent evolutionary time between two nodes quantified by substitutions at a given sequence site, vertical lines represented nodes or evolutionary splits and length as no bearing. In a 1980s study on mtDNA two primary branches were identified both of which originated from Africa
Y chromosome studies were also used to identify male lineages along with autosomal DNA via genome-wide data
SNPs
showed that populations are less diverse with increasing distance from Africa, this is consistent with the serial founder effect where successive migration with a small fraction of individuals associated with less diversity, proportional to physical distance
What are some problems with haplotype trees and their construction of populations/diversity?
They often mask and simplify information, do not account more movements and mixings, and some populations are not included
No single genetic variant contains that much information about ancestry and variation present at more than a few % is usually shared around many populations around the world
Gene flow
smaller scale migration between populations
Admixture
result of inbreeding between two or more previously isolated populations
Comparisons between mtDNA, Y chromosome, and autosomal genetic similarities between populations and ancestral populations can give insight into how admixture occurred
Introgression
movement of a gene from one species into the gene pool of another via the repeated backcrossing of an interspecific hybrid with one of its parent species
EDAR gene and incisors
EDAR gene encodes from ectodysplasin A receptor which is part of a signaling pathway that helps with development before birth, also critical for interactions between ectoderm and mesoderm which is essential for formation of ectoderm related structures (skin, hair, nails, teeth, sweat glands)
Histogram showing EDAR influence on incisor shoveling demonstrates additive nature of influence on incisor shoveling. This is a complex trait since there is a mixture of number of copies and degree of shoveling
How can recent admixture between human populations be detected in an individual?
The genetic information of an admixed individual can be compared to genomic information that represents two “parental” populations, this occurs since ancestry proportions can be estimated based on the percent similarity of genotypes of admixed individual to genomic information that represents a specific population
mtDNA and the Y chromosome cannot give researchers an accurate picture of overall ancestry, but it can give insight into population history and how admixture occurred
One example is that a sample of Mexican-Americans have high mtDNA contribution and low Y-chromosome contribution from to Native Americans and intermediate autosomal genomic patterns, indicates women were more commonly Native American in a mixed population
Another example is that African-Americans have a larger Y chromosome contribution from European genome and a lower mtDNA contribution, underscores history of how white male slaveholders forcibly raped female slaves
What factors are important to consider when sampling individuals from populations in order to generate the most accurate population data?
Samples should be independent from one another and not related, this is difficult in smaller populations where there are close family groups
Samples should also be representative of a population and should not be an “outlier” (not pathological, not a recent immigrant, etc.)
Samples should also be chosen randomly, but they are often chosen out of convenience which can lead to subtle biases
The larger the sample the better it will represent a population, the more it will capture diversity, and the greater confidence that it will represent the true distribution of a population
Genetic data on variation that can be collected/quantified
Genetics can be measured by allelic diversity and allelic richness which is the average number of alleles per gene
p distance which is the proportion of nucleotide sites where two sequences being compared are different and gives researchers a sense of how different the alleles are
heterozygosity where the fraction of individuals that are heterozygous for a particular gene are measured and can give insight into population history relative to one another
allele frequencies can be measured and can be informative especially if data is gathered across a large group of people
Physiological data on variation that can be collected/quantified
breast milk composition is one example and one researchers posited that milk fat are increased at a high altitude than a low altitude
hormones are also one example and researcher posited that humans at higher altitudes have less testosterone and cortisol (reduced production could be beneficial for higher energetic demands at a higher altitudes)
basal metabolic rate, blood pressure, muscle strength, aerobic power output are also measures
What are examples of discrete anatomical traits that can be measured and why are they significant?
Discrete anatomical traits can be measured such as wisdom teeth, presence of skull bones
Two hypotheses for wisdom teeth are genetic drift/probable mutation causing there to be less selective pressure to retain large molars, another hypothesis is positive selection where there is a fitness advantage to losing molars if the loss reduces the risk of impaction and health complications
What are examples of continuous anatomical traits that can be measured and why are they significant?
linear measurements, angles, and also cartesian coordinates and a matrix of 3D points to get a more 3D picture, also size and shape
Femur neck shaft angle varies based on degree of activity (urban has wider angle, agriculture has mixed angle, foragers have smaller angle)
Tibia condyle retroversion angle is determined by quadriceps muscle force and knee joint reaction force, large angles are adaptive for high levels of joint reaction force and minimizes shearing of joints/bones
Quantitative measures of an anatomical form can also be calculated
Analysis using Hypothesis testing
Null hypothesis is H0, assumes samples of 2 or more are equivalent, alternative hypothesis is Ha, posits samples are not equivalent
To do a hypothesis test assume the H0, test using probability whether the data is consistent with H0, reject H0 if probability is sufficiently low, fail to reject H0 if probability is not sufficiently low, this means you have failed to detect a difference not that there is no difference
p < 0.05 assumes that there is less than a 5% chance that a difference arose by chance and is not a true difference
Effect size
refers to the magnitude of a phenomenon where you can have high confidence in a small but significant difference but any effect may end up being statistically significant if there are replicates or a large population size
What is Fst and how can it be calculated?
Wright’s Fst is an indicator of population differentiation or fixation index and it can be determined using genetic data or character states, this can give information on how mixed two subpopulations are with 0 indicating completely mixed and 1 indicating completely separated
Fst = (var between populations - var within populations)/(var between populations)
Fst can be measured using heterozygosity where the total heterozygosity and average heterozygosity across subpopulations are measured where Fst = (Ht - Hs)/(Ht)
What is heterozygosity, what are two types, and how can they be measured?
Average Hs (heterozygosity of a subpopulation) can be measured by taking the average of the heterozygosity between subpopulations (2pq for each population), average Ht (heterozygosity of a total population) can be measured by taking the average allele frequencies between populations and using 2pq to calculate
Isolation by distance
where populations further apart have a greater genetic distance and differentiation
GWAS Manhattan Plots
can be used to test for candidate genetic factors (specific SNPs, genes, regions, etc) contributing to variation between groups by comparing entire genomes. Generally the strongest associations have the smallest p values and highest negative logarithms, this was used to identify a variant in CREBRF
Dendograms
tree constructed using data about variation, can be constructed using morphological characteristics or molecular sequences
Branching determinations can be used to create different trees that are distance based, character based (maximum parsimony), and probabilistic (maximum likelihood)
Rooted trees are based on ancestry and often use an out-group to root the tree, unrooted trees illustrate relationships without any assumptions on common ancestry
Cladogram
Tree diagram made up of clades that are hypotheses about evolutionary history and where branch lengths do not represent evolutionary time
Phylogram
Tree diagram made up of clades that do represent actual evolutionary history where branch lengths represent evolutionary time
What assumptions are made when constructing trees?
Lineage integrity where the process of speciation consists of distinct lineages
Assumes there is no reticulate evolution where blending of lineages does not occur via gene flow
Assumes no homoplasy in cladistic trees and no convergent evolution in phylogenetic trees where there is an independent evolution of similar features in species not connected to a common ancestor
Assumes evolution is a series of bifurcations where two distinct species branch from a common ancestor, not tri or more
Assumes trees can be constructed using sample means (do not account for scatter around the mean) and/or specimens where there could be issues with sample size
Principle Components Analysis
technique that is used to emphasize variation and bring out patterns in a dataset. Part of this analysis means each point represents a central or average value for a sample and axes are rank ordered by the percent variation
