Evolution of genetic and genomic features unique to the human lineage

O’Bleness, Majesta; Searles, Veronica B.; Varki, Ajit; Gagneux, Pascal; Sikela, James M.

doi:10.1038/nrg3336

Cited by 133 publications

(134 citation statements)

References 125 publications

(179 reference statements)

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“…With gene duplications being presumed to have a major impact on primate evolution (12), we looked more closely at fixed duplications affecting protein-coding genes (8,27) by analyzing the sequence depth of coverage for 18,571 orthologous genes [available in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database] (28) in chimpanzees, orang-utans, macaques, and humans (SI Appendix). We identified 1,963 fixed gene duplications affecting 1,078 orthologous genes, including whole (i.e., gene encompassing; 226 events) and partial (gene intersecting; 852 events) gene duplications (Dataset S4).…”

Section: Interspecies Gene Duplications Can Impact Gene Expression Andmentioning

confidence: 99%

“…The development of massively parallel sequencing (MPS) to characterize SVs (3)(4)(5) has enabled comprehensive analyses of origin and functional impact of SVs in humans (3,6). Although SVs are presumed to play a major role in primate evolution and phenotypic variation (7) as well, empirical evidence showing such a role remains scarce (8). Comparative analyses of reference genome assemblies of the chimpanzee (9), orang-utan (10), and rhesus macaque (11) have provided some initial insights into large-scale structural changes in primate genome evolution (12).…”

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confidence: 99%

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Primate genome architecture influences structural variation mechanisms and functional consequences

Gökçümen

Tischler

Tica

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Although nucleotide resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact of phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing, we constructed fine-resolution genomic structural variation maps in five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, which are comprised of thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques compared with great apes. By comparison, nonallelic homologous recombination is specifically active in the great apes, which is correlated with architectural differences between the genomes of great apes and macaque. Transcriptome analyses across nonhuman primates and humans revealed effects of species-specific whole-gene duplication on gene expression. We identified 13 gene duplications coinciding with the species-specific gain of tissue-specific gene expression in keeping with a role of gene duplication in the promotion of diversification and the acquisition of unique functions. Differences in the present day activity of SV formation mechanisms that our study revealed may contribute to ongoing diversification and adaptation of great ape and Old World monkey lineages. genome evolution | retrotransposons | neofunctionalization | copy-number variation G enomic structural variants (SVs), including copy number variants and balanced SV forms (such as inversions), are a major source of human genetic variation (1, 2). The development of massively parallel sequencing (MPS) to characterize SVs (3-5) has enabled comprehensive analyses of origin and functional impact of SVs in humans (3, 6). Although SVs are presumed to play a major role in primate evolution and phenotypic variation (7) as well, empirical evidence showing such a role remains scarce (8). Comparative analyses of reference genome assemblies of the chimpanzee (9), orang-utan (10), and rhesus macaque (11) have provided some initial insights into large-scale structural changes in primate genome evolution (12). Microarray technology-based surveys have provided additional glimpses of the abundance of polymorphic unbalanced SVs (i.e., copy number variants) in different primate species, enabling the construction of SV maps at a resolution of tens to hundreds of kilobases (13-16).Thus far, despite ongoing progress in assessing SNP variation in primates (10,(17)(18)(19), no study has leveraged MPS technology for ascertaining inter-and intraspecies SVs in different primates. We, therefore, performed MPS-based genome analyses in five individuals from each of these primate species, Pan troglodytes (chimpanzee), Pongo abelii (orang-utan), and Macaca mulatta (rhesus macaque), to construct comprehensive SV maps in these species. Our analyses have revealed marked differences in SV formation mechanism activities and further yielded a complex relationship between genomic copy number and gene expression patterns, with several gen...

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Section: Interspecies Gene Duplications Can Impact Gene Expression Andmentioning

confidence: 99%

mentioning

confidence: 99%

Primate genome architecture influences structural variation mechanisms and functional consequences

Gökçümen

Tischler

Tica

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Examples of collaboration that can go all the way to the fusion of knowledge and to synthetic results 85 , or of works that approach with all receptiveness and benevolence from a certain field, and become available to everyone (O'Bleness et al, 2012) are only beacons of hope, the vast 85 Illustrative in this respect is Fitch (2010), a work that does not belong to a linguist (the author is an evolutionary biologist and cognitive scientist), but is a biolinguistic study of the evolution of language, from a Darwinian perspective, with elements of general and comparative linguistics, psycholinguistics, molecular genetics and neurology, based on a bibliography that is substantial in the quality of the consulted works; it is a study that-apart from numerous branches of biology and linguisticscalls into play contributions from other domains (mathematics, sociology, musicology, psychology, physics, ethology, etc. ), which allows the author to articulate, in a coherent and organic manner, a complex image.…”

Section: The Organicity Of Reality and Of Science (Mathesis Universalis)mentioning

confidence: 99%

The organicity of science

Gafton¹

2015

Diacronia

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The systemic character of entities implies their being formed of discrete elements whose conjunction generates hierarchical structures, functions, forces, and roles. While the observation and study of entities entails their segregation with respect to certain sets of criteria, their understanding follows from their thorough comprehension, in plenary connection with the environment of which they are component, product, and factor.Having the profound role of bringing the human being in the state of knowing and understanding the Universe, science (including the methodology that invents and governs paths, and the apparatus that makes the entire endeavour operational) follows this model of specialized division. Starting from the initial common state, science develops its observations by identifying and describing the reality and its specialized components, in accordance with how they are structured and function, constantly tailoring its means of investigations to the genetic, structural, and functional peculiarities of those aspects.The completion and evolution of science are consequent to the assimilation of this approach beyond the interdisciplinary level, and arise from the conjunction of scientific knowledge, methods, and instruments, aimed at reflecting reality in its entirety and integrality. This outcome requires a recurrent reconsideration and revision of the organism of science.

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“…In non-human primates, selection has been generally ascribed to genes with reproductive and immunological functions [5]. In humans, most evolutionary changes have been ascribed to the post-translational, epigenetic regime [17].…”

Section: Introductionmentioning

confidence: 99%