4330 EXAM 4 Flashcards by Cassidy Arredondo

The study of patterns and structure of genetic diveristy within interbreeding populations

population genetics

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ALDH2

Asian flush/glow gene asian people get when they consume alcohol

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Presence of two or more allels

Polymorphism

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Variation of a gene

Allele

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Combinations of alleles at multiple loci transmitted together

Haplotype

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AA or aa

two identical allelels

Homozygous

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two different alleles

Heterozygous

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Random mating, no mutations, infinite population size, no natural selection, no migration, diploid sexaully reproducing 2 alleles

Five factors that need to be in effect for a population to be at HW equilbrium

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one allele is favored therefore shifting the frequency towards the allele

Directional selection

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Heterozygous genotypes (Aa) have a higher fitness and are favored over homozygotes (aa or AA)

maintains both alleles in population

Stabilizing selection

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Heterozygous geneotypes have a lower fitness than homozygous genotypes

pushes pop to genetic divergence , two extremes

Diversifying selection

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The random change in allele frequencies from one generation to the next, caused by chance events rather than natural selection.

Genetic Drift

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Small populations → genetic drift dominates, causing random fluctuations in allele frequences

Why small population sizes create a population that is not HW equilibrium

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having two different versions (alleles) of the same gene, one from each parent

(Sample many individuals across populations to estimte it accurately)

Heterozygosity

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The number of individuals contributing genes to the next generation

(smaller than N)

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Actual headcount of individuals in the population

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Inhertied biparentally and undergo recombination each generation

Autosomal loci

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Follow different ineritance patterns, the Y chromosome shows no recombination across most of its length

Sex chromosomes

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Inherited maternally only, with no recombination and effectively behaves as a single haploid

Mitochondrial DNA

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The estimate of genetic diveristy

THETA

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The variation at a single base pair in the genome, most common type of genetic polymorphism in humans

SNP (Single Nucleotide Polymorphism)

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85%

Percentage of genetic diversity in the human species spread evenly across the entire population

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Large structural variations in genome where sections of DNA are duplicated or deleted, leading to differences in gene dosgae

CNVs (Copy Number Variations)

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Short tandem repeat sequences that are highly variable among individuals and are commonly used to study fine-scale genetic diversity

Microsatellites

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F Statistic: measure of population structure FST: Compariosn of the heterzygosity of the total population compared to the subpopulation

Review fixation index

Shared physical traits define species

morphological

interbreeding groups reproductivly isolated from others

biological

smallest monophyletic group with shared dervied character

phylogenetic

- PSC works for all organisms - Testable and doesnt rely on reproductive isolation - One clear rule that applies to all taxa, making species classification consisten

Wheeler's arguments for PSC

Struggles with reticulate evoltuion (non-tree like processes such as hybridization and gene flow)

PSC struggles with

A small region of a chrosome duplicated

segmental duplication

a larger chromosome section containing many genes is duplicated

chromosomal duplication

An entire set of chromosomes duplicated

whole genome duplicaiton

- "back up" copy - one copy mutates, the other still peforms essential function - reduces the harmful impact of deleterious mutations

advantages of genetic redundancy

one gene evolves a completely new function while the other maintinas the originl function

neofunctionalization

- ancestral gene has multiple roles - after duplication each copy becomes speciales for part of the original function

subfuncitonalization

one gene perfomrs multiple functions

how pleiotrphy realtes to the concept of subfunctionalization

a group of related genes within a genome that originated from repeated duplication of an ancestral gene

gene family

many paralogs that all originated from a single ancestral gene

Hox genes

occurs because there is no selective pressure to maintan both fully functional copies one often degrades over time

Pseudogene

covalent bond between amino acids

peptide bond

determines aa chemical behavior

functional group

antibody protein, immune defense, contracticle messenger, structural storage, transport enzymes, gene expressions

protein roles in living organisms

destroys secondary and primary structures

denaturation

protein only interacts with one particular ligand or substrate

specific protein

proteins interacts with multiple different substrates

promiscuous

function is resiliant to mutations or environmental changes

robustness

De novo, gene duplication, exon shuffling, motif duplication are all examples of

where new genes come from

the full set of proteins an organism can produce

protein repetoire

- image forming camera type eyes (vertebrates) - compound eyes (arthorpods) - mirror/cup/pinhole type (mollusks)

the three major types of fully functioning eyes found in the metazoan

not structurally homologous, but they are deeply homologous at the genetic and developmental level.

Are metazoan eyes homologous? Explain

mollusks have the boradest variation of eye compleixty in a single phylum

diversity of mullusk eyes

a large family of membrane proteins that detect signals outside the cell and activate internal signaling pathways

GPCRS

protein responsible for light detection in nearly all animals

opsins

- c-opsisn (vertabrates) - r-opsins (arthorpods) - go-opsins (mollusks) - non visual opsins (metazoans)

four subgroups in the Opsin gene family

- convergent evolution - rooting challeneges - sequence saturation

Reasons phylogeny is difficult:

Opsins are highly labile, duplicated many times, and co-opted into new roles, explaining how very different photoreceptor systems evolved across metazoans.

Review the “take home” message for the evolution of opsins and how some arthropod groups are a good example of this pattern

secretion produced by a specialzed gland (bite or sting) into another organims where disrupts physology to help prey capture or defense

venom

the full set of proteins expressed by a cell, tissue, or organims

proteom

- opsisn trace back to one ancestral family - venome is built by many unrealted gene families

difference between venome and opsisn

- snakes are nested with lizards - venom origianted once in a CA and was reduced in different snales and lizard lineages

phylogentic relationships of snakes and lizards

salivary secretion delivered through simple posterior grooved teeth

ancestral venom delivery system in replites

digestive enzymes, coagulation factors, signaling peptides, and ion-channel-active hormones

proteins that migth be preadapted as venoms

when exisiting gene evolves new expression in the venome gland and becomes part of the venome

gene recruitment

selection on venom function is constrained because mutations that improve toxicity might damage its other essential roles

pleoiotrophy in gene recruitment

- gene duplication - regulatory chances that evolve seperate expression - alternative splicing

How might the constraint placed on a pleiotropic gene be reduced?

- no - much higher concentration - delivered directly into tissue or bloodstream - new ecological context

Does a protein acting as a venome need to take on a new function?

- diet and prey types - hunting strategy - predation/defense pressures - microhabitats and constraints

ecological factors that might increase the likelihood of convergence in the evolution of venoms in different species

*Which of the following best explains why there is not a single, objective species definition?* Species are not real entities, they are simply a human construct Speciation is a process not an event, and different species may have different processes that help to establish the separation of a population into different species The process of speciation, no matter how advanced, is always reversible Some species don't reproduce sexually and so cannot be separated into species.

Speciation is a process not an event, and different species may have different processes that help to establish the separation of a population into different species

Which of the following describes the process of defining species phylogenetically? Drawing species boundaries based on the smallest, definable monophyletic group Defining species by the boundaries of gene flow between different populations Defining species based on their morphological features Defining species boundaries based only on mitochondrial genomes

Drawing species boundaries based on the smallest, definable monophyletic group

The most widely used species concept is the ecological species concept. True False

False

What is the term for a distinct, self-contained structural and functional unit of a protein that can often fold and function independently? Domain Motif Quaternary structure Helix

Domain

Proteins are mostly used for energy storage in living cells True False

Flase

Which of the following best explains the presence of gene families in genomes? Horizontal gene transfer from very closely relates species Gene duplication events with diversification and neofunctionalization Fusion of mitochondrial and nuclear genomes Convergent evolution of genes that originated independently

Gene duplication events with diversification and neofunctionalization

Protein domains mostly correspond to _______. introns exons non-coding regions of the genome non-functional parts of a protein

Exons

When choosing an outgroup to study the diversity of opsin genes, which of the following genes would be best? A G-protein coupled receptor that is a chemoreceptor Insulin Any protein that also has a transmembrane domain A zinc finger protein

A G-protein coupled receptor that is a chemoreceptor

Although simple visual perception originated once in a common metazoan ancestor; complex, image forming eyes evolved three times independently. True False

True

4330 EXAM 4 Flashcards

(77 cards)