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.
Highlights
One of the most fascinating aspects of nature is the diversity of life
For a gene to be classified as lost, we require that a lineage, which descends from an ancestor with an intact gene, exhibits several gene-inactivating mutations that most likely result in a non-functional protein
By making use of existing gene knockouts in mouse or loss-of-function mutations in human individuals and by dating gene loss events, we discovered a number of previously unknown gene losses (Supplementary Fig. 13 and Supplementary Table 4), some of which may have contributed to morphological, physiological, and metabolic adaptations in mammals, while others are likely a consequence of adaptive evolution
Summary
One of the most fascinating aspects of nature is the diversity of life. Mammals, for example, live in many different habitats, including land, air, and water, and exhibit remarkable phenotypic adaptations to their environment. Laboratory selection experiments demonstrated that gene loss is a frequent cause of adaptations to various environmental conditions[21] It is largely unknown whether gene loss could play an important role for natural phenotypic adaptations in non-human mammals[11]. Using sequenced genomes of 62 placental mammals, we search for gene loss events that occurred in mammals that exhibit prominent morphological, physiological, or metabolic adaptations This reveals a number of previously unknown gene losses that are likely a consequence of adaptations or may contribute to adaptations that evolved in individual or even in multiple mammalian lineages. Our results suggest that gene loss is a mechanism that has likely contributed to adaptive evolution in several mammals
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