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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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Inferring speciation and extinction rates under different sampling schemes.

Sebastian Höhna¹, Tanja Stadler, Fredrik Ronquist

¹Department of Mathematics, Stockholm University, Stockholm, Sweden. hoehna@math.su.se

Molecular Biology and Evolution

|April 13, 2011

Summary

This summary is machine-generated.

The birth-death process in phylogenetics is sensitive to lineage sampling. Diversified sampling (DS) is often a better fit than random sampling, and mismodeling it can severely bias extinction rate estimates.

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Area of Science:

Phylogenetics
Evolutionary Biology
Computational Biology

Background:

The birth-death process is a cornerstone for modeling speciation and extinction rates in phylogenetics.
Inferred rates are known to be sensitive to assumptions about lineage sampling probabilities.
Previous studies often assumed random sampling (RS), potentially overlooking biases.

Purpose of the Study:

To investigate the impact of different lineage sampling strategies on inferred birth-death process rates.
To compare the effects of random sampling (RS), diversified sampling (DS), and cluster sampling (CS).
To assess how mismodeling sampling strategies affects extinction rate estimations.

Main Methods:

Simulations were used to model phylogenetic data under different sampling schemes.
Empirical phylogenetic data sets were analyzed to test various sampling models.
Bayesian model testing was employed across 18 empirical data sets to evaluate model fit.

Main Results:

Inferred rates, particularly extinction rates, can be heavily biased if the sampling strategy is not accurately modeled.
Diversified sampling (DS) is often a better fit to empirical data than RS or cluster sampling (CS).
Treating diversified samples as random or complete samples leads to severe underestimation of extinction rates, often near zero.

Conclusions:

Accurate modeling of lineage sampling strategies is crucial for reliable phylogenetic rate estimation.
Diversified sampling (DS) is a common sampling method in practice and should be explicitly modeled.
Anomalous phylogenetic rate variations previously attributed to temporal changes may be artifacts of mismodeling sampling strategies.