Human Var Exam 1

Question 1

Approaches to studying Human Variation

Answer 1

Two persistent themes are classification vs adaptation and types vs variation

Question 2

Classification

Answer 2

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

Question 3

Adaptation

Answer 3

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

Question 4

Types

Answer 4

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

Question 5

Variation

Answer 5

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

Question 6

Perspectives on race studies

Answer 6

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

Question 7

Carolus Linnaeus

Answer 7

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

Question 8

Georges Louis Leclerc

Answer 8

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

Question 9

Johann Freidrich Blumenbach

Answer 9

First large scale attempt to categorize people, emphasized observable physical characteristics but there was still racial prejudice in characterizing personalities

Question 10

Anthropometry

Answer 10

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

Question 11

Samuel Morton

Answer 11

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

Question 12

Anders Retzius

Answer 12

came up with cephalic index (length/width ratio) and tied it into the racial history of European ethnic groups

Question 13

Paul Broca

Answer 13

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

Question 14

19th Century Evolutionary Anthropology

Answer 14

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

Question 15

Francis Galton

Answer 15

Developed eugenicist thinking and founded a laboratory to document the heredity of behavioral traits and physiques

Question 16

Cesare Lombroso

Answer 16

Criminologist who posited criminality was associated with “primitive” groups of people with “ape-like” features

Question 17

Alphonse Bertillon

Answer 17

Police officer who used anthropometrics for personal identification and rejected the idea that certain populations have a predisposition to crime

Question 18

Franz Boas

Answer 18

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

Question 19

Dr. William Montague Cobb

Answer 19

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

Question 20

What were some of the effects of racial eugenics?

Answer 20

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

Question 21

What were some differences between how race was studied before and after WWII?

Answer 21

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

Question 22

Carleton Coon

Answer 22

proposed human races reach a Homo sapiens stage at different times which explains differences

Question 23

Richard Lewontin

Answer 23

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

Question 24

Nuclear vs Mitochondrial genome

Answer 24

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

Question 25

Organizational features and functions of DNA

Answer 25

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

Question 26

Haplotype

Answer 26

everything inherited together on the same chromosome (either the entire chromosome or a portion of the chromosome)

Question 27

Aneuploidy

Answer 27

Abnormal number of chromosomes, almost always occurs in egg rather than sperm, commonly due to nondisjunction

Question 28

Balanced translocation

Answer 28

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

Question 29

Unbalanced translocation

Answer 29

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

Question 30

What are some functions of intergenic regions and introns (“junk” DNA)?

Answer 30

“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

Question 31

Promoter

Answer 31

usually 100-1,000 bp upstream from transcription start site and other proteins bind to turn transcription “on” or “off”

Question 32

Enhancer

Answer 32

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

Question 33

How are non-coding RNA molecules significant to gene regulation?

Answer 33

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

Question 34

What kinds of mutations can cause a significant alteration of phenotype?

Answer 34

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)

Question 35

Ankylosing spondylitis

Answer 35

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

Question 36

Lactase persistence

Answer 36

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

Question 37

Alternative splicing

Answer 37

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

Question 38

Huntington’s Disease

Answer 38

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

Question 39

Simple trait

Answer 39

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)

Question 40

Additive traits

Answer 40

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)

Question 41

Codominance

Answer 41

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

Question 42

Complex traits

Answer 42

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

Question 43

Polygenic trait

Answer 43

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)

Question 44

Epigenetics

Answer 44

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

Question 45

How can variation occur between DNA, mRNA, and Proteins?

Answer 45

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

Question 46

Species

Answer 46

Group of organisms that can breed in nature, hybrids can occur in species both naturally (baboons) and also artificially (ligers/tigons)

Question 47

What are common causes of speciation?

Answer 47

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,

Question 48

How do we know which group a species belongs to?

Answer 48

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

Question 49

Homology

Answer 49

Traits that are similar in superficial appearance and reflect common ancestry

Question 50

Homoplasy

Answer 50

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

Question 51

Phylogeny

Answer 51

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

Question 52

What are the mechanisms of microevolution?

Answer 52

Mutations, Gene flow, Genetic drift, Natural selection

Question 53

Mutations

Answer 53

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

Question 54

Gene flow/migration

Answer 54

movement of genes from one population to another via migration and the subsequent introduction of new genes to a population

Question 55

Genetic drift

Answer 55

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)

Question 56

Natural selection

Answer 56

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

Question 57

Sources of genetic variation

Answer 57

Mutation, recombination, sexual reproduction. Phenotypic variation often reflects genotypic variation

Question 58

Fitness

Answer 58

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

Question 59

Sexual Selection

Answer 59

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

Question 60

Positive selection

Answer 60

when the frequency of advantageous alleles increases

Question 61

Negative selection

Answer 61

when the frequency of harmful/deleterious alleles decreases

Question 62

Balancing selection

Answer 62

favoring of multiple alleles, this often occurs due to heterozygotes having greater fitness of homozygotes

Question 63

What are some lines of evidence for evolution?

Answer 63

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

Question 64

What are some key factors of evolution to keep in mind?

Answer 64

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

Question 65

What are some differences between anatomically modern humans and earlier Neanderthals?

Answer 65

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

Question 66

How were differences between modern and early humans uncovered?

Answer 66

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

Question 67

What is the debate on single vs multiregional origins of H. Sapiens?

Answer 67

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

Question 68

Pleistocene

Answer 68

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

Question 69

Hominin

Answer 69

group that consists of modern humans, extinct human species, all other immediate ancestors (includes members of genus Homo, Australopithecus, Paranthropus, Ardipithecus)

Question 70

What was some evidence that H. sapiens originated in Africa?

Answer 70

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

Question 71

SNPs

Answer 71

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

Question 72

What are some problems with haplotype trees and their construction of populations/diversity?

Answer 72

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

Question 73

Gene flow

Answer 73

smaller scale migration between populations

Question 74

Admixture

Answer 74

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

Question 75

Introgression

Answer 75

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

Question 76

EDAR gene and incisors

Answer 76

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

Question 77

How can recent admixture between human populations be detected in an individual?

Answer 77

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

Question 78

What factors are important to consider when sampling individuals from populations in order to generate the most accurate population data?

Answer 78

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

Question 79

Genetic data on variation that can be collected/quantified

Answer 79

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

Question 80

Physiological data on variation that can be collected/quantified

Answer 80

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

Question 81

What are examples of discrete anatomical traits that can be measured and why are they significant?

Answer 81

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

Question 82

What are examples of continuous anatomical traits that can be measured and why are they significant?

Answer 82

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

Question 83

Analysis using Hypothesis testing

Answer 83

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

Question 84

Effect size

Answer 84

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

Question 85

What is Fst and how can it be calculated?

Answer 85

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)

Question 86

What is heterozygosity, what are two types, and how can they be measured?

Answer 86

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

Question 87

Isolation by distance

Answer 87

where populations further apart have a greater genetic distance and differentiation

Question 88

GWAS Manhattan Plots

Answer 88

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

Question 89

Dendograms

Answer 89

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

Question 90

Cladogram

Answer 90

Tree diagram made up of clades that are hypotheses about evolutionary history and where branch lengths do not represent evolutionary time

Question 91

Phylogram

Answer 91

Tree diagram made up of clades that do represent actual evolutionary history where branch lengths represent evolutionary time

Question 92

What assumptions are made when constructing trees?

Answer 92

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

Question 93

Principle Components Analysis

Answer 93

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