A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

TLDR

Identifying genomic changes underlying phenotypic adaptations, such as gene loss, remains a key challenge in evolutionary biology and genomics. The study develops a genomics approach to accurately detect gene losses and assess their role in mammalian adaptive evolution. The authors use a comparative genomics pipeline to detect gene losses across mammalian genomes and evaluate their contribution to adaptation. The study identifies numerous gene losses that likely contributed to morphological, physiological, and metabolic adaptations in aquatic and flying mammals, demonstrates that relaxed selection following adaptation can reveal species biology, and suggests gene loss is a widespread evolutionary mechanism for adaptation.

Abstract

Abstract Identifying the genomic changes that underlie phenotypic adaptations is a key challenge in evolutionary biology and genomics. Loss of protein-coding genes is one type of genomic change with the potential to affect phenotypic evolution. Here, we develop a genomics approach to accurately detect gene losses and investigate their importance for adaptive evolution in mammals. We discover a number of gene losses that likely contributed to morphological, physiological, and metabolic adaptations in aquatic and flying mammals. These gene losses shed light on possible molecular and cellular mechanisms that underlie these adaptive phenotypes. In addition, we show that gene loss events that occur as a consequence of relaxed selection following adaptation provide novel insights into species’ biology. Our results suggest that gene loss is an evolutionary mechanism for adaptation that may be more widespread than previously anticipated. Hence, investigating gene losses has great potential to reveal the genomic basis underlying macroevolutionary changes.