# Divergence dating clock rate

### Index

- How can I calculate divergence time in Beast?
- What is the most accurate way to estimate divergences?
- Where do substitution rates come from for clock estimations?
- Do tip-calibrated analyses yield more accurate divergence-time estimates than node-calibration?
- How to estimate the divergence time?
- Can We Date species divergences with Beast?
- What are tree priors for divergence time estimation in Beast?
- How to estimate the age of lineage divergence?
- How to estimate substitution rates from time-structured sequence data?
- Is rate variation associated with incongruence across the rate estimates?
- What is the rate of substitution in the human mitochondrial genome?
- What is the most accurate method of rate estimation?
- Do tip-calibrated analyses yield more accurate divergence-time estimates than node-calibration?
- What is the most accurate way to estimate divergences?
- Does tip-calibration yield older clade ages?
- What is Tiptip-calibration?

### How can I calculate divergence time in Beast?

Alternatively, you can calculate (with DNAsp or other software) the divergence between sequences, and calibrate it with paleo/geological data (if available). This procedure will give you an estimation of the clock that you can use as input for dIvergence time analysis in BEAST.

### What is the most accurate way to estimate divergences?

Divergence-time estimates based on node-calibration are the most precise in all but four of the component clades ( Figure 1 ). In line with almost all previous TED studies, tip-calibration yields clade ages that are older, in general, than like-for-like estimates based on node-calibration, the only exceptions being divergences outside Hymenoptera.

### Where do substitution rates come from for clock estimations?

clock estimations (e.g., Nei 1987, Li and Graur 1991), today these substitution rates are typically derived from phylogenies or from sequence data in conjunction with tree topologies (Rutschmann 2006). for this application the software Mega4 can help you.

### Do tip-calibrated analyses yield more accurate divergence-time estimates than node-calibration?

Our analyses show that when fossil age uncertainty is properly accounted for, tip-calibrated analyses do not necessarily yield divergence-time estimates that are more precise than those derived using node-calibration.

### How to estimate the divergence time?

Divergence time estimation requires a model of among-lineage substitution rate variation to tease apart rate and time Branch lengths = TIME Fossils and other geological dates can be used to calibrate divergence time analyses and produce estimates of node ages in absolute time.

### Can We Date species divergences with Beast?

Divergence Time Estimation using BEAST v2.2.0 Dating Species Divergences with the Fossilized Birth-Death Process Central among the questions explored in biology are those that seek to understand the timing and rates of evolutionary processes.

### What are tree priors for divergence time estimation in Beast?

BEAST v2.0 Tutorial In BEAST, the available tree priors for divergence time estimation using inter-species sequences are variants of the birth-death prior.

### How to estimate the age of lineage divergence?

When applied in methods for divergence time estimation, the resulting trees have branch lengths that are proportional to time. External node age estimates from the fossil record or other sources are necessary for inferring the real-time (or absolute) ages of lineage divergences (Figure 1). Branch lengths = SUUBSTITION RATE X TIME

### Do tip-calibrated analyses yield more accurate divergence-time estimates than node-calibration?

Our analyses show that when fossil age uncertainty is properly accounted for, tip-calibrated analyses do not necessarily yield divergence-time estimates that are more precise than those derived using node-calibration.

### What is the most accurate way to estimate divergences?

Divergence-time estimates based on node-calibration are the most precise in all but four of the component clades ( Figure 1 ). In line with almost all previous TED studies, tip-calibration yields clade ages that are older, in general, than like-for-like estimates based on node-calibration, the only exceptions being divergences outside Hymenoptera.

### Does tip-calibration yield older clade ages?

In line with almost all previous TED studies, tip-calibration yields clade ages that are older, in general, than like-for-like estimates based on node-calibration, the only exceptions being divergences outside Hymenoptera.

### What is Tiptip-calibration?

Tip-calibration was originally introduced based on empirical divergence-time analyses of insects [19] and amphibians [18], and it has since been applied to mammals 21, 22, 23, 24, 25, 26, teleost fishes 27, 28, 29, 30, 31, arachnid spiders 32, 33, flies [34], and plants [35].