BIOL 3010 Exam 4

Single Sequence Repeat (SSR)

Genomic locus that consists of one or a few bases repeated in tandem up to 100 times. Different alleles have different repeat numbers

Single Nucleotide Polymorphism (SNP)

Single nucleotide locus with two naturally existing alleles defined by a single base-pair substitution

Microarray

How SNP chips are able to identify what SNPs an individual’s DNA contains based on how they stick to the probes after heating

Drift

Random fluctuation in allele frequency due to finite population size

Quantitative Trait Locus (QTL)

Chromosomal regions that are statistically associated with variation in phenotype

Backcross

Crossing the progeny of two parents with one of the parents

Ex: P little tomato x big tomato

F1 medium tomato x big tomato

Intercross

Crossing two of the same progeny from the same parents with each other

Gene-environment Interaction (GxE)

When two different genotypes respond to environmental variation in different ways

Genome-wide Association Study (GWAS)

Looking for SNPs that are in certain groups of the population but not others

THE SNP IS NOT CAUSATIVE; we’re only looking for the associated regions of the genome

Linkage Disequilibrium (LD)

Define the statistical correlation between SNPs

The allele is not randomly segregating in the population if it is in LD

Chi Squared Test

To find the odds ratio/probability of getting vs not getting a trait, disease, etc.

Polygenic Risk Score

Metrics that predict an individual’s phenotype from their genotype and GWAS results

Principle Components

Take correlated data and identify numerical values that describe variation within the dataset

Used to predict place of origin

Site-frequency Spectrum

Graph that represents the proportion of SNPs in the genome that are found at that that frequency in a population

Ancestry Painting

Relies on subtle differences in haplotype frequencies around the world to place ancestry

Ex: 23&me, Ancestry

How do we observe an individual’s diploid genome?

PCR, Sanger Sequencing, SNP Chips

How can we infer timing of migration events?

Subtle shifts in allele frequency

How do new mutations enter the genome?

Mutation

How are mutations removed from the genome?

Drift and Selection

Germline Mutation Rate

Enter species with each new generation

Most are lost instantly, but some remain

Standing Mutation Rate

The amount of mutations that have accumulated in a population over time

Fixation

Process whereby a single allele of a locus becomes the only one in a population

Negative Selection

Removes deleterious mutations

Positive Selection (Adaptation)

When one allele increases in fitness

Goes to fixation very quickly

Locally Adapted

When beneficial mutations are only beneficial in certain environments

Ex: differently colored mice

Balancing Selection

When mutations are good in some situations (e.g. environments, genetic backgrounds) but not others

Which has the most impact? drift, positive selection, negative selection

Drift because most standing genetic variation is likely neutral

Molecular Clock

The average rate at which a species' genome accumulates mutations

McDonald-Kreitman Test

To test whether neutral evolution is occurring at a gene

What causes phenotypic variation?

Environmental or genetic variation

Broad-sense Heretability

Vg/Vp

Additive Genetic Variation

The phenotypic effects of each allele are added together, and the
allelic effects are the same no matter what environment or genetic
background

Ex: height, skin color

Dominance Genetic Variation

The phenotypic effects of each allele are dependent on the
genotype at that gene

Ex: dominant vs recessive genes

Interaction (Epistatic)

The phenotypic effects of each allele are dependent on the
genotype at another gene.

Narrow-sense Heritability

Va/Vp

Estimating Additive Variation

Mean Parent - Mean Offspring Method

Ex: the progeny of the parents will most likely be somewhere in between the parent’s height and the average population height

Heritability

The proportion of phenotypic variation in a population due to genetics

Measuring Heritability

Parent Offspring Regression

Twin Studies

QTL Mapping

Approach to identify genetic regions of interest to determine continuous traits

Marker

A mutation (SNP, SSR) that you know is a fixed difference between strains

Human Genome Diversity Cell Line Panel

Composed of “immortal” cell lines collected from people around the world

How do genetic differences compare between and within populations?

Genetic differences between populations are small compared to the amount of diversity within populations

Fst

Quantifies population differentiation

Genetic Determinism

Belief that genetic variation has a disproportionately large effect on phenotypic variation

Genomic Relatedness Matrix

Heritability estimated by comparing phenotypic similarity to genetic similarity among pairs of individuals

Vastly overestimate heritability

Polygenic Index

Takes the effects of all of the SNPs and adds them up to predict phenotype

Phasing

separating maternally and paternally inherited copies of each chromosome into haplotypes to get a complete picture of genetic variation

Dynastic Effects

Genetic nurture effects

Occur when the expression of parental genotype in the parents' phenotype directly affects their offspring's outcomes

Ex: If your parents went to college, you will go to college

Assortative Mating

Occurs if the mated pairs in a population are composed of individuals with the same phenotype

Population Stratification

Occurs when each subgroup has different SNP allele frequencies

Ex: A lot of Asian people use chopsticks, but it was not genetically inherited