Dataset Information

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.

ABSTRACT: De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between database updates due to the fluctuating annotation of these genes. Nonetheless we identified 35 de novo genes: 16 human-specific; 5 human and chimpanzee specific; and 14 that originated prior to the divergence of human, chimpanzee, and gorilla and are found in all three genomes. The taxonomically restricted distribution of these genes cannot be explained by loss in other lineages. Each gene is supported by an open reading frame-creating mutation that occurred within the primate lineage, and which is not polymorphic in any species. Similarly to previous studies we find that the de novo genes identified are short and frequently located near pre-existing genes. Also, they may be associated with Alu elements and prior transcription and RNA-splicing at the locus. Additionally, we report the first case of apparent independent lineage sorting of a de novo gene. The gene is present in human and gorilla, whereas chimpanzee has the ancestral noncoding sequence. This indicates a long period of polymorphism prior to fixation and thus supports a model where de novo genes may, at least initially, have a neutral effect on fitness.

SUBMITTER: Guerzoni D

PROVIDER: S-EPMC4860702 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.

Guerzoni Daniele D McLysaght Aoife A

Genome biology and evolution 20160425 4

De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between databas ...[more]

PMID: 27056411

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Project description:BACKGROUND: Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification. The six species within the Rhinella crucifer group of toads were defined under morphological criteria alone. Previous data suggest limited correspondence of these species to mitochondrial lineages, and morphological intergradation at transitions between forms suggests hybridization. Here we extensively sampled populations throughout the geographic distribution of the group and analyzed mitochondrial and nuclear sequence data to delimit genetic units using tree-based and allele frequency-based approaches. RESULTS: These approaches yielded complementary results, with allele frequency-based methods performing unexpectedly well given the limited number of loci examined. Both mitochondrial and nuclear markers supported a genetic structure of five units within the group, with three of the inferred units distributed within its main range, while two other units occur in separate isolates. The inferred units are mostly discordant with currently described forms: unequivocal association exists for only two of the six species in the group. Genetic evidence for hybridization exists for two pairs of units, with clear cyto-nuclear allele mixing observed in one case. CONCLUSIONS: Our results confirmed that current taxonomy does not represent evolutionary units in the Rhinella crucifer group. Correspondence between genetically distinguishable units and the currently recognized species is only possible for Rhinella henseli and R. inopina. The recognition of other species relies on the reassessment of the geographic range of R. crucifer, the examination of the type series of R. ornata for hybrids, and on the use of additional markers to verify the genetic distinctiveness of R. abei. We state that R. pombali should not remain a valid species since its description appears to be based on hybrids, and that the name R. pombali should be considered a synonym of both R. crucifer and R. ornata. The fifth inferred but undescribed genetic unit may represent a new species. Our results underscore the potential of the R. crucifer species group to contribute to a better understanding of diversification processes and hybridization patterns in the Neotropics, and provide the basis for future evolutionary and taxonomic studies.

Project description:Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific community at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/.

Dataset Information

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.

Publications

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.

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