Survivor bias drives overestimation of stability in reconstructed ancestral proteins

Abstract

Ancestral sequence reconstruction has been broadly employed over the past two decades to probe the evolutionary history of life. Many ancestral sequences are thermostable, supporting the "hot-start" hypothesis for lifes origin. Recent studies have observed thermostable ancient proteins that evolved in moderate temperatures. These effects were ascribed to "consensus bias". Here, we propose that "survivor bias" provides a complementary rationalisation for ancestral protein stability in alignment-based methods. As thermodynamically unstable proteins will be selected against, ancestral or consensus sequences derived from extant sequences are selected from a dataset biased towards the more stabilising amino acids in each position. We thoroughly explore the presence of survivor bias using a highly parameterizable in silico model of protein evolution that tracks stability at the population, protein, and amino acid levels. We show that ancestors and consensus sequences derived from populations evolved under selective pressure for stability throughout their history are significantly biased toward thermostability. Our work proposes a complementary explanation of the origin of thermostability in the burgeoning engineering tools of ancestral sequence reconstruction and consensuses. It provides guidance for the thorough derivation of conclusions from future ancestral sequence reconstruction work.