Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families

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Abstract
The evolution of new gene families subsequent to gene duplication may be coupled to the fluctuation of population and environment variables. Based upon that, we presented a systematic analysis of the animal transmembrane gene duplication events on a macroevolutionary scale by integrating the palaeontology repository. The age of duplication events was calculated by maximum likelihood method, and the age distribution was estimated by density histogram and normal kernel density estimation. We showed that the density of the duplicates displays a positive correlation with the estimates of maximum number of cell types of common ancestors, and the oxidation events played a key role in the major transitions of this density trace. Next, we focused on the Phanerozoic phase, during which more macroevolution data are available. The pulse mass extinction timepoints coincide with the local peaks of the age distribution, suggesting that the transmembrane gene duplicates fixed frequently when the environment changed dramatically. Moreover, a 61-million-year cycle is the most possible cycle in this phase by spectral analysis, which is consistent with the cycles recently detected in biodiversity. Our data thus elucidate a strong coupling of duplication events and macroevolution; furthermore, our method also provides a new way to address these questions. The interplay of information-processing life and force-driven environment has characterized Earth's evolutionary history since its beginning some 4 billion years ago. The study of macroevolution has seen a growing appreciation of this interplay. Previously, a large-scale effort was mounted to collect and analyze the paleontological and geochemical data. In the meantime, more and more genomes have been sequenced. The growing molecular sequence database with these paleontological data will provide important opportunities to investigate this interplay. Using the transmembrane proteins of 12 genomes, Ding and his colleagues have devised a sophisticated pipeline to date 1,651 duplication events grouped into 786 gene families, and have mapped the distribution of duplication events to the profile of macroevolution. They showed that the oxidation events played a key role in the major transitions of this density trace, and that the pulse mass extinction time points in the Phanerozoic phase coincide with the local peaks of the age distribution. Through some mathematical transformation of the density trace of the transmembrane gene duplicates during the Phanerozoic phase, they reported a potential cycle similar to the cycle detected by paleontologists. They concluded that a dramatically changed environment affected the evolution of life and left some imprint in the molecular level that can be detected.