Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

TL;DR

This study reveals that large molecular phylogenies can falsely suggest early bursts of speciation due to sampling bias, especially in large clades, and highlights the limitations of current methods in detecting true diversification rate changes.

Contribution

It demonstrates how sampling bias in large clades can lead to false inference of early bursts and evaluates the performance of common methods under various extinction scenarios.

Findings

Large clades often show false early burst signals due to sampling bias.

Common methods are susceptible to detecting false early bursts, especially with low extinction.

Some models can detect true early bursts under higher extinction but are prone to bias.

Abstract

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the gamma-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.