Evolutionary New Genes in a Growing Paradigm

Betrán, Esther; Long, Manyuan

doi:10.3390/genes13091605

Cited by 3 publications

(5 citation statements)

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“…Over the past decades, the significance of evolutionary new genes has been increasingly recognized, shaping a new paradigm in evolutionary biology (Betrán and Long 2022). Empirical evidence has highlighted the essential and innovative roles of evolutionary new genes in biological systems (Chen, et al 2013; Heinen, et al 2009; Long and Langley 1993; Long, et al 2013; Tautz 2014; Xia, et al 2021; Xie, et al 2019a; Xie, et al 2019b; Zhuang, et al 2019).…”

Section: Discussionmentioning

confidence: 99%

One million years of solitude: the rapid evolution of de novo protein structure and complex

Chen,

Li,

Xia

et al. 2023

Preprint

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Recent studies have established that de novo genes, evolving from non-coding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their structural evolution over time remain unclear. Here, we addressed these issues within a short evolutionary timeframe (∼1 million years for 97% of rice de novo genes). We found that de novo genes evolve faster than gene duplicates in the intrinsic disordered regions (IDRs, such as random coils), secondary structural elements (such as α-helix and β-strand), hydrophobicity, and molecular recognition features (MoRFs). Specifically, we observed an 8-14% decay in random coils and IDR lengths per million years per protein, and a 2.3-6.5% increase in structured elements, hydrophobicity, and MoRFs. These patterns of structural evolution align with changes in amino acid composition over time. We also revealed significantly higher positive charges but smaller molecular weights for de novo proteins than duplicates. Tertiary structure predictions demonstrated that most de novo proteins, though not typically well-folded on their own, readily form low-energy and compact complexes with extensive residue contacts and conformational flexibility, suggesting “a faster-binding” scenario in de novo proteins to promote interaction. Our findings illuminate the rapid evolution of protein structure in the early life of de novo proteins in rice genome, originating from noncoding sequences, highlighting their quick transformation into active, complex-forming components within a remarkably short evolutionary timeframe.

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Section: Discussionmentioning

confidence: 99%

One million years of solitude: the rapid evolution of de novo protein structure and complex

Chen,

Li,

Xia

et al. 2023

Preprint

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“…Evolutionarily new genes -such as de novo genes, chimeric genes, and gene duplicates -have been continually emerging and integrating into the human genome throughout the macroevolutionary process of human lineage [9][10][11][12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

“…Evolutionarily new genes – such as de novo genes, chimeric genes, and gene duplicates – have been continually emerging and integrating into the human genome throughout the macroevolutionary process of human lineage (Brosius 1991; Kaessmann et al 2002; Conrad and Antonarakis 2007; Baertsch et al 2008; Wu et al 2011; Long et al 2013; Van Oss and Carvunis 2019; Betrán and Long 2022; Zhang et al 2022). Decades of genetic studies in non-human systems have provided extensive evidence contradicting this intuitive argument.…”

Section: Introductionmentioning

confidence: 99%

“…Evolutionarily new genes -such as de novo genes and gene duplicates -have been continually emerging and integrating into the human genome throughout the macroevolutionary process of human lineage [9][10][11][12][13][14][15]. Previous reports revealed that human disease genes tend to be primarily ancient, with many tracing back to the last common ancestor of eukaryotes [16].…”

Section: Introductionmentioning

confidence: 99%

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Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

Chen,

Landback,

Arsala

et al. 2023

Preprint

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New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impacts on humans, however, remain elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (∼0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures shaped by different gene ages. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a “pleiotropy-barrier” model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.

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Section: Introductionmentioning

confidence: 99%

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

chen

2023

Preprint

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New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impact on humans, however, remains elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals that new genes associated with disease phenotypes steadily integrate into the human genome at a rate of ~ 0.07% every million years over macroevolutionary timescales. Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures between young and old genes. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, bipedal locomotion, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a “pleiotropy-barrier” model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.

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Evolutionary New Genes in a Growing Paradigm

Abstract: How new genes evolve has become an interesting problem in biology, particularly in evolutionary biology [...]

Cited by 3 publications

References 35 publications

One million years of solitude: the rapid evolution of de novo protein structure and complex

One million years of solitude: the rapid evolution of de novo protein structure and complex

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

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