VL 12 Molecular dating Flashcards
What is the aim of molecular dating?
The aim of molecular dating is to infer species or lineage divergence ages based on molecular sequence data and external information such as generation time, sampling dates, and fossil records.
What is the molecular clock hypothesis?
The molecular clock hypothesis, proposed by Pauling and Zuckerkandl, suggests that the rate of evolution for a given protein or DNA sequence is approximately constant over time across different lineages. This allows for the use of molecular data to estimate divergence times.
What are the basics of the molecular clock?
- Assumed: constant mutation rate over time
- Expected number of nucleotide differences: Depends on the mutation rate and the number of generations since the split between two lineages.
- Mathematical formula:
E(d)=2μt, where
μ is the mutation rate and
t is the time (generations) since divergence.
What are the problems with the molecular clock?
- Variation in mutation rates over time.
- Substitutions can occur due to processes other than drift.
- Substitutions might not be neutral.
- Variation in generation times among species.
What is the relative rate test?
The relative rate test compares the number of substitutions in two taxa to an outgroup. If the evolutionary rates are equal, the number of substitutions to the outgroup should be the same for both taxa.
What is Felsenstein’s Likelihood Ratio Test?
Felsenstein’s Likelihood Ratio Test assesses whether the evolutionary rate is homogeneous across all branches of a phylogeny by comparing the likelihood of a clock-like tree (null hypothesis) to a non-clock-like tree.
What are the limitations of molecular clock tests?
- Typically evaluate if tips are equally distant from the root.
- Cannot distinguish a constant rate from an average variable rate within a lineage.
- Do not test whether the rate is constant over time.
What are the different clock models?
- Global Clock Model: Assumes a strict constant rate for all taxa and over time.
- Non-Clock Model: Assigns separate rates for every branch, leading to a high number of parameters.
- Relaxed Clock Model: Allows variation in the clock rate following a global distribution, typically treating branch rates as uncorrelated.
- Local Clock Model: Different strict clocks for different parts of the phylogeny.
- Autocorrelated Rates Model: Clock rate variation follows a variable distribution centered on the ancestral branch rate, with closely related lineages sharing similar rates.
What is tip dating?
tip dating informs the molecular clock by the temporal &
genetic differences among samples.
- Heterochronous Samples: Genetic data from different time points.
- Temporal + Genetic Differences: Among samples inform the molecular clock rate.
- Examples: Serial sampling (e.g., SARS-CoV-2 emergence, influenza strains) and ancient tips (e.g., Stone Age Yersinia pestis genomes).
What is node dating?
node dating integrates information of absolute node age from
fossils, geological events or previous studies.
- Assigns Temporal Information: To nodes in the phylogeny.
- Sources: Fossil occurrences, geological events, and previous results (secondary calibrations).
- Probability Distributions: Temporal information is modeled as probability distributions with hard and soft bounds.
What is Bayesian clock dating?
Bayesian clock dating enable complex, parameter rich analyses
and the integration of prior information
Concept: Combines prior knowledge with the likelihood distribution of the data to produce a posterior distribution.
Outcome: Provides a distribution of estimated divergence times rather than a single value.
Components:
* Prior: Knowledge or guess on the distribution of data before analysis.
* Likelihood: Distribution of data given a substitution model.
* Posterior: Product of prior probability distribution and likelihood distribution.
What is the impact of clock model choice?
Choice Affects Results: The selected clock model can significantly impact the estimated divergence times.
Evaluation: Best-fitting clock models are often evaluated using likelihood ratio tests (LRTs) and other statistical methods.
Examples: Studies on parasitic plant clades, Hawaiian silverswords, and placental mammal radiation illustrate the impact of different clock models on divergence date analyse
