Ch6: Population Structure Flashcards
Describe the molecular clock, how are they calibrated?
Uses average RATE changes that occur in a given gene or protein to gauge the time of DIVERGENCE
They are calibrated using fossil records (known time of divergence) or biogeographic dates (time for separation of continents)
What are phylogenies constructed based on? (Hint: 3 things)
1) Protein folds
2) RNA sequences
3) DNA sequences
Where do homologous characters come from? Explain why this is needed for the construction of a phylogeny.
A common ancestor; this is needed for phylogenies because they are based around relatedness, and thus traits tested all need to stem from a common ancestor.
How do we check characters are homologous? Which option do we choose?
Sequence and align data: the alignment with the fewest number of changes (parsimonious)
Why are nucleic acids good for making phylogenies? (Hint: 2 reasons)
1) Because we get a better estimation of evolutionary events.
2) All entities are biological, and thus all entities can be compared based off of them
How do we check the accuracy of phylogenies?
Run DNA to see if divergence time matches
What are the 3 types of phylogenies, define each option:
See Doc, 6a:
1) Cladogram:
- Only shows the topology (BRANCHING PATTERN)
- Length of branches means nothing
- All branches = evenly spread
2) Phylogram:
- branch length represents the proportion of (inferred) accumulated changes a species has undergone before branching
3) Ultrametric Tree:
- Scales the divergence of species (TIME axis)
- Terminal nodes align ( the present day)
Define a speciation gene
a gene that contributes to the splitting of two lineages by reducing the amount of gene flow between them
Define transposable elements, what do they affect?
A segment of DNA that can move to new locations in the genome, or give rise to new copies that insert into another location in the genome.
This may effect translation of proteins, and whether a gene functions or not. They also increase recombination rate and crossover rate in chromosome
When will transposable elements be selected for
When they create a gene that is beneficial
Define population structure, how does it arise?
Arises when demographic processes produce systematic difference in allele frequencies between subsets of a larger population.
Typically arise from ISOLATION or other factors causing non-random mating (agents of change)
Define polymorphic sites, what do they allow for
When there are variants in a gene amongst individuals of a population (can be as small as single nucleotide variants). They are differentiated based on frequency.
They allow for blocking and grouping, based on similarities and understanding of divergence
Describe what a structure plot is
Plots that show different groups of traits (each with a unique colour) of individuals (each has own column)
If an individual has multiple traits their column has multiple colours (ancestry of 2 or more populations)
Do indigenous populations have high or low levels of population structure? What is this due to?
High levels; due to divergence of populations occurring a long time ago AND low, but stable effective populations sizes
What else does genetic structure reflect?
It shares similarities with linguistic groups (linguistic structure)
