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ASV
- amplicon sequence variants
- (ASV) is any one of the inferred single DNA sequences recovered from a high-throughput analysis of marker genes.
- Because these analyses, also called "amplicon reads," are created
- following the removal of erroneous sequences generated during PCR and sequencing, using ASVs makes it possible to distinguish sequence variation by a single nucleotide change.
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OTU
- operational taxonomic unit
- OTUs are employed in microbial community DNA sequencing research to
- delineate species-level distinctions among organisms and represent the
- most frequently utilized unit for measuring microbial diversity
- In other words, OTUs are pragmatic proxies for "species" (microbial or metazoan) at different taxonomic levels, in the absence of traditional systems of biological classificationas are available for macroscopic organisms.
- For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes[5]) marker gene sequence datasets.
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Transitions vs. Transversions
What are they, and which is more likely to occur, over time, evolutionary?
- Transitions occur more frequently than transversions
- Transitions are interchanges of purines (A-G) or pyrimdines (C-T), which involve bases of similar shape.
- Transversions are interchanges between purine and pyrmidine bases, which involve exchange of one-ring and two-ring structures
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Transitions
- Transitions are interchanges of purines (A-G) or pyrimdines (C-T), which involve bases of similar shape.
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Transversion
- Transversions are interchanges between purine and pyrmidine bases, which involve exchange of one-ring and two-ring structures
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bifurcation
branching pattern typical in phylogenies
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reticulation
- when species recombine and create a net like pattern in phylogenies
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what are different modes of reproduction seen in phylogenies?
- asexual (clonal)
- sexual (recombination)
- combination of the two
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Method for inferring structure and process in populations:
Non-genealogical (frequency-based)
- Classical Wright’s FST statistics
- Neutrality tests (Tajima, Fu)
- Genetic Diversity measures (Nei)
- Population subdivision (Hudson)
- Population parameter estimators (θ)
- Compatibility methods (Le Quesne)
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Method for inferring structure and process in populations:
Genealogical (single tree)
- Wright’s FST estimators (Slatkin)
- Neutrality tests (Fu and Li)
- Haplotype phenotype association testing
- Phylogeography
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Method for inferring structure and process in populations:
Genealogical (random trees)
- Coalescent approaches (parameter estimation: θ , recombination, migration rates) (Beerli and Felsenstein)
- Bayesian approaches (Hey and Nielsen)
- Probability distributions of mutations for different phenotypic categories (Griffiths and Tavaré)
- Equilibrium and non-equilibrium models
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Method for inferring structure and process in populations; give an example of each:
Non-parametric
mixed
Parametric
- Non-parametric: Hardy-Weinberg (simple model)
- mixed: Wright-Fisher
- Parametric: coalescence (complex model)
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Which category of inferring structure/process in populations is this:
Classical Wright's FST statistics
Non-genealogical (frequency based)
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Which category of inferring structure/process in populations is this:
Neutrality tests (Tajima, Fu)
Non-genealogical (frequency based)
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Which category of inferring structure/process in populations is this:
Genetic Diversity measures (Nei)
Non-genealogical (frequency based)
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Which category of inferring structure/process in populations is this:
Population subdivision (Hudson)
Non-genealogical (frequency based)
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Which category of inferring structure/process in populations is this:
Population parameter estimators (θ)
Non-genealogical (frequency based)
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Which category of inferring structure/process in populations is this:
Compatibility methods (Le Quesne)
Non-genealogical (frequency based)
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Which category of inferring structure/process in populations is this:
Wright's Fst estimators (Slatkin)
Genealogical (single tree)
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Which category of inferring structure/process in populations is this:
Neutrality tests (Fu and Li)
Genealogical (single tree)
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Which category of inferring structure/process in populations is this:
Haplotype phenotype association testing
Genealogical (single tree)
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Which category of inferring structure/process in populations is this:
phylogeography
Genealogical (single tree)
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Which category of inferring structure/process in populations is this:
Coalescent approaches (parameter estimation: θ, recombination, migration rates)- Beerli and Felsenstein
Genealogical (random trees)
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Which category of inferring structure/process in populations is this:
Bayesian approaches (Hey and Nielsen)
Genealogical (random trees)
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Which category of inferring structure/process in populations is this:
Probability distributions for mutations for different phenotypic categories (Griffiths and Tavare)
Genealogical (random trees)
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Which category of inferring structure/process in populations is this:
Equilibrium and non-equilibrium models
Genealogical (random trees)
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Neutral mutation rate (μ)
the number of neutral mutations arising in an individual per nucleotide site (10^9) or per gene per unit time
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Effective population size (Ne)
the number of interbreeding individuals in a population having the same magnitude of random genetic drift as the actual population, but never exceeding the actual population size
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Define the population neutral mutation rate (θ) for diploids
- θ = 4Ne µ
- Some properties of θ = 4Ne µ
- If we assume a neutral mutation rate of 2 x 10-9 mutations per site per year, then Ne can be estimated from θ
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What are assumptions of Tajima's D?
D=X/(√var(x))
X = k – (s / (1 + 1/2 + 1/3 + ... + 1/n-1))
- Constant population size (i.e. equilibrium)
- Infinite-sites compatible, no recombination, no migration
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