Genes and Genomes Unit 3

what are linked genes

genes that are located on the same chromosome and each chromosome can carry many linked genes (they disrupt Mendel’s predicted outcomes)

what are recombinant chromosomes

chromosomes that have a different combination of alleles from its parents after crossing over

what info do recombinant chromosomes provide 

a map of the locations of genes in the genome or map based on recombination

what info do genetic maps provide

1. structure and organization of a genome

2. can be used to predict how often certain traits will be inherited together

3. find genes from a mutant genotype

what is a genetic/recombination map

linear representation of gene order and relative distance on chromosome

what is the max distance between two mutant

50 cM

what does a lower recombination frequency indicate

more closely the genes are physically linked

what indicates that two genes are linked using a test cross

if test cross with F1 heterozygote with recessive alleles for two different genes do not result in equal numbers of four phenotypes in the F2 generation

what is a rare situation when no crossing over occurs between two genes

two genes are very close together on the same chromosome

what are balancer chromosomes

crossover suppressors

what is a physical map

provide the location of a gene in terms of base pairs of DNA within a sequence of interest, which can be obtained through sequencing

what is a cytological map

they are based on the physical structure of chromosomes and rely on banding patterns 

how can you obtain a cytological map

fluorescence in situ hybridization (FISH)

what is an X-linked gene

gene that is located on the X-chromosome, but not the Y-chromosome

examples of X-linked genes in humans

color blindness, hemophilia, and muscular dystrophy

what happens when females are heterozygous for x-linked diseases

they are typically carriers and will pass on their carrier status to half of their daughters and half of their sons will get the disease. recessive x linked traits appear more frequently in males that females

what happens when a female is homozygous for a recessive x linked trait

the trait will be passed on to 100% of her offspring

what determines the sex in C. elegans and Drosphila melanogaster

number of X chromosomes (C. elegans lacks a Y chromosome)

what is the SRY

the Sex-determining Region Y is a gene in the Y chromosome that encodes a protein called testis determining factor (TDF)

what does TDF do

triggers testis differentiation in immature gonads of developing embryo

what does the testis produce

testosterone, which stimulates cascade of differentiation that produces males 

what do aneuploid eggs like XXY correspond to

klinefelter syndrome in males, and X0/turner syndrome in females

what is dosage compensation

ensures that somatic cells of either sex express equal levels of x linked gene products 

how does dosage compensation work in drosophila

hyper transcription of x linked genes

how does dosage compensation work in c. elegans

both x chromosomes are active, but repress transcript levels from each chromosome by half

how does dosage compensation work in homosapiens

occurs via inactivation of x chromosomes. females randomly inactivate one x chromosome in a process by x-inactive specific transcript (Xist)

what is responsible for dosage compensation

dosage compensation complex (DCC)

what is mosaicism

mosaic cells that are a result of x inactivation

what approaches were used for the first draft of the human genome

hierarchical shotgun sequencing (HS) and whole-genome shotgun sequencing (WGS)

what is the difference between HS and WGS

HS has a cloning step

what is a complex trait

trait that is inherited but its phenotype is affected by multiple genes and environmental factors 

what is the most widely used method for genetic mapping in humans

GWAS, genome wide association study

what is GWAS (genome wide association study)

the use of linkage analysis/gene mapping to find the causative genes for many diseases and complex traits

what does GWAS do

tests SNPs between affected and unaffected people and looks for alleles that are shared among affected people

what are polymorphisms

variation in the dna sequences

what polymorphisms are most used for mapping and GWAS

SNPs located in noncoding regions or intergenic

what can be used to read several SNPs

microarrays

what are the steps of microarray

1. sample collection

2. isolation of DNA

3. design/prepare probes

4. hybridization

5. scanning and analysis

what do microarrays tell us

different genotypes or mutations

what are population genetics

the study of changes in allele frequency over multiple generations in a given population

what are the evolutionary forces

genetic drift, gene flow, mutations, natural selection

what is an allele

variant form of a gene

how are new alleles created

when gene changes contribute to a new phenotype in a given population

what is an effective population

any group of organisms occupying a specific place at a specific time that are capable of genetic exchange/reproduction

what is genetic structure

composition of alleles or haplotypes

how to calculate frequency of an allele

number of that allele/total number of all alleles

what is the equation for genotype frequency

p²+2pq+q²=1

what is HW equilibrium

when allele frequencies remain stable through generations over time, and there are no evolutionary influences acting upon them

what happens when migration between two populations is prevented

the populations will diverge

what happens when migration between two populations is allowed

the populations will become similar

what is genetic drift

change in allele frequencies in a population over time due to random chance (strongly impacts smaller populations)

what is the bottleneck effect

large portion of the genome is wiped out typically through natural disasters

what is the founder effect

when a new population (small size) is started by a few members of the original population. new population may have reduced genetic variaiton and non-random sample of the genes from the original population

what is natural selection

more prolific reproduction of individuals with favorable traits that survive environmental changes bc of those traits

what does nat selection favor

the fittest

what does fittest mean

best suited to a specific environment based on the survival and reproductive rate

what is fitness

measure of total reproductive output of an organism with a particular genotype

what is survival rate

percentage of individuals that survive to reproductive age

what is reproductive rate

average number of offspring born per individual

four principles of natural selection/ Darwin’s four postulates

variation exists among organisms that make up a population

what mechanisms lead to variation or genetic diversity

mutation and sexual reproduction

what does natural selection lead to

descent with modification and adaptive evolution

what is descent with modfication

offspring and parent don’t have the same phenotype

what is adaptive evolution

greater adaptation of the population to its local environment

what does jukes cantor method tell us

if selection has/is occurring for a particular locus

what jukes cantor method tells there is neutral selection

dN/dS = 1

what jukes cantor method tells there is negative selection

dN/dS < 1

what jukes cantor method tells there is positive selection

dN/dS > 1