New genes contribute to genetic and phenotypic novelties in human evolution

Abstract

New genes in human genomes have been found relevant in evolution and biology of humans. It was conservatively estimated that the human genome encodes more than 300 human-specific genes and 1000 primate-specific genes. These new arrivals appear to be implicated in brain function and male reproduction. Surprisingly, increasing evidence indicates that they may also bring negative pleiotropic effects, while assuming various possible biological functions as sources of phenotypic novelties, suggesting a non-progressive route for functional evolution. Similar to these fixed new genes, polymorphic new genes were found to contribute to functional evolution within species, for example, with respect to digestion or disease resistance, revealing that new genes can acquire new or diverged functions in its initial stage as prototypic genes. These progresses have provided new opportunities to explore the genetic basis of human biology and human evolutionary history in a new dimension.

Figure 1

Distribution of new genes with CT expression with respect to their evolutionary ages. For the X chromosome, the proportion is defined as the number of CT-X genes divided by the number of all X-linked genes in the same age group. It was analogously defined for autosomes. The age class was computationally generated on Ensembl v69 by using the pipelines developed in [10] with the time information in TimeTree [44], while the CT gene list was downloaded from CTpedia database in July 2014 [40]. We fitted the observed frequencies of CT-Xs in various stages of human genome evolution to an exponential decay formula (f(t) ^~ e^rt). We mark the time with a blue triangle when the mammalian X chromosome was originated, i.e., before the split of human and opossum [10,45].