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Adaptive constraints and the phylogenetic comparative method: a computer simulation test.

Emília P Martins¹, José Alexandre F Diniz-Filho, Elizabeth A Housworth

¹Department of Biology, Indiana University, Bloomington 47408, USA. emartins@indiana.edu

Evolution; International Journal of Organic Evolution

|March 27, 2002

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Phylogenetic comparative methods (PCMs) are robust even when evolutionary assumptions are violated. Most PCMs perform well, with Felsenstein

Area of Science:

Evolutionary Biology
Quantitative Genetics

Background:

Phylogenetic comparative methods (PCMs) are crucial for studying trait evolution.
PCMs often assume traits evolve via Brownian motion (BM), which may not reflect natural selection.
The utility of PCMs under realistic evolutionary scenarios is debated.

Purpose of the Study:

To assess the statistical performance of various PCMs under diverse evolutionary models.
To evaluate the accuracy of correlation coefficient estimation in PCMs.

Main Methods:

Computer simulations generated data under realistic evolutionary scenarios.
Multiple PCMs were tested, including Felsenstein's independent contrasts (FIC), phylogenetic generalized least squares (PGLS), phylogenetic mixed models (PMM), spatial autoregression (SPAR), and phylogenetic eigenvector regression (PVR).

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Correlation coefficients were estimated and compared across methods and models.

Main Results:

Non-phylogenetic correlation estimates were poor.
Most PCMs performed well even when their assumptions were violated.
FIC performed well but showed bias under strong opposing constraints.
PGLS, PMM, SPAR, and PVR demonstrated good statistical performance across models.

Conclusions:

PCMs are generally robust to violations of their assumptions.
The choice of PCM may depend on specific trait types and evolutionary processes.
FIC can be biased under strong directional selection opposing random drift.