Klausurfragen

Question 1

Homologous genes,
2 types

Answer 1

(Analogos: evolved independently through convergent evolution)

Homologos: originate in a common ancestor

1) Orthologous genes: Orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. -> Orthology is strictly defined in terms of ancestry. e.g. haemoglobin in human and mouse
2) Paralogous genes: Genes that resulted from a gene duplication event, building a gene family in the same organism. Can gain different funtions over time. E.g. haemoglobin and myoglobin

Question 2

Mendel: Bialelic locus, discontinous trait and next generation.

Answer 2

Biallelic Locus: A1A1
Discontinous trait: no intermediate exist between categories + often controlled by a single gene

Question 3

wie heisst das phenomen wenn man random sampled dann bekommt man verschiedene allele und hängt das von initial alllel frequency oder intial population frequncy abhängign

Answer 3

Genetic drift. depends on initial allele frequency as well as on initial population size.

Question 4

RHO beispiel. wann sind die lang? Pseudohalotypen assembly. welche drei charakteristiken von einem genom kommen da nicht zum tragen

Answer 4

RHO. Long runs of homozygosity are due to inbreeding. This happens when the poulation sizes are small and closely related individuals mate.
If the RHOs are quite long, it suggets that the inbreeding event was not long ago, so recombination did not have enought time o braek them up.

Through pseudohaplotype assembly, important charackteristics of the genome get lost. Information about the genotypes, like Heterozygosity and Phasing, and information about recombination events are getting lost, because the chromosomes are not viewed at seperately.

Question 5

wie testet man auf positivie selection und neutrality wenn man den gene locus kennt. nennen und beschreiben

Answer 5

If the locus is known: Tajimas D, to detect deviation from neutrality. under infinite site model.
* E (𝛑) = 𝛳 (average number of nt diferences between sequence pairs)
* E (s) = a𝛳 (number of segregating sites, scled by number of sampled sequences)

-> the two estimates should give the same result

D = (𝛑-s/a) / √ V (𝛑-s/a)
* D = 0 Population is evolving neutrally/ Natural evolution (𝛑 and s in agreement)
* D > 0 fewer rare variants/ lower frequency of polymorphisms than expected
-> balancing selection or population decline (𝛑 is higer than s)
* D < 0 more rare variantsthan expected due to
-> positive selection or population expansion (𝛑 is lower than s)

Selection and demography can result in similar values for Tajimas D.

Question 6

wie testet man auf positivie selection und neutrality wenn man den gene locus nicht kennt. nennen und beschreiben

Answer 6

If there is no candidate locus for a geotype: GENOME SCANS
1) Sliding window approach: for each window you can compute Fst, Tajimas D, SNP density and nucleotide diversity (𝛑) -> calculate fro each window to find and identify region of interest. * choosing a fitting windw size (that reflect recombination rate and decay of LD) and stepsize is crucial. If the windows are non-overlapping: more independent data
2) Haplotype test: EHH (exzended haplotype homozygosity) measures decay of homozygosity for a particular haplotype while moving away from a focal allele, by identifying long streches. High EHH suggests strong recent positive seletion, due to strong and recnet selective sweep. e.g lactose intolerance

Question 7

haplotypen netzwerk von zwei linien mit 20 individuen und zwei sind miteinander connected

Question 8

linkigae disequilibrium und heritabillity definieren und auswirkungen auf GWAS und QTL

Answer 8

Linkage Disequlibrium: A non-random associatopn between alleles at different loci in a population in which certin haplotypes are statistically overrepresented.
* strong LD is the key in QTL to identifying genomic architekture, but because there is just one generation of recombination, LD is not sufficiently broken down enough to identify specific candidate genes.
* LD plays a crucial role in how GWAS identifies associations with traits, but it also introduces challenges in pinpointing the causal variants due to the correlation among SNPs in LD blocks.

Heritability:
1. Describes the proportion of variation in a trait within a population that is due to genetic differences, as opposed to environmental factors.

2. The propoiton of the total variance in a trait that is due to additive variance in a population.
   Additive variance refers to the deviation from the mean phenotype due to additive genetic effects.

• In GWAS there is the missing heritability problem, where the heritability of traits is often overestimated.
• The success of QTL mapping is influenced by the heritability of the trait: higher heritability generally leads to better identification of QTLs, while lower heritability makes it more challenging to detect significant loci.

Question 9

genetic drift, population size and allele frequency

Answer 9

Genetic drift: Random changes in allele frequencies in a population.

• The average time to fixation increases with population size. (4N generations)
• The probability of fixation depends on the initial allele frequency (1/2N)
• In the absence of selection, the probability of fixation for a mutation depends on its initial allele frequency.
• Fixation of such mutations is more rapid in small populations.
• Smaller populations carry more deleterious mutations.

(Smaller populations are more susceptible to genetic drift, leading to faster changes in allele frequencies, including possible fixation or loss of alleles.
Alleles at low frequency are more vulnerable to loss due to genetic drift, especially in small populations. Conversely, high-frequency alleles are more likely to become fixed due to drift in small populations.)

Question 10

JBS aussage und hamilton gefragt

Answer 10

Kin seletion: Selection that favours the prdoctivity of family groups even at the expanse of indvidual survival or reproductive success.
-> trys to explain alturism

Hamiltons rule has to be fulfilled, where the benefit times the reatedness has to be higher than the cost, so that an alruistic allele gets fixed in a population. BUT, it is not that easy, because the altriustic allele would not be able to spread, if the individual carrying that allel would not reproduce.

r*B > C

r- relatedness
B- Benefit
C- Cost

” I would lay down my life for two brothers or 8 cousins.” JBS Haldane.

Famous example are eusocial insects like Bees and ants. (But there are also theories, that they are one superorganism).

Question 11

evolutionary fitness definieren und 2 dinge die beeinflussen.
5 abiotische und biotische faktoren

Answer 11

Evolutionary fitness has two components: Survial and Reproduction

Question 12

polyploid hybridisation selection

Question 13

divergence time and with what meseaurement

Question 14

museum. warum magere ausbeute und beide methoden beschreiben