| 1. |
- Ellegren, Hans, et al.
(författare)
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The genomic landscape of species divergence in Ficedula flycatchers
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7426, s. 756-760
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Tidskriftsartikel (refereegranskat)abstract
- Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre-as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.
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| 2. |
- Künstner, Axel, et al.
(författare)
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Gene content and patterns of gene expression in the flycatcher genome
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Phenotypic evolution may be driven by changes in the sequence of protein-coding genes or by the way (when, where, at what level) proteins are expressed. Generally, our knowledge about the evolution of gene expression is relatively limited, and this is particularly so for wild populations. Collared flycatcher (Ficedula albicollis) and pied flycatcher (F. hypoleuca) are two recently diverged passerine birds, which have been subject to extensive ecological research, including aspects of speciation. We obtained RNA-seq data with Illumina technology from 10 adult individuals per species (five females and five males) using brain, kidney, liver, lung, muscle, skin, ovary, and testis tissue (plus eight embryos of each species). A total of more than 1 billion sequencing reads were assembled into >15.000 gene models for each species. The proportion of differentially expressed genes between species ranged from 8% to 18% per adult tissue. Very few GO categories were found to be overrepresented among differentially expressed genes, which at least in part might reflect that orphan and not yet annotated genes are prone to evolve more rapidly in gene expression level. However, in testis, the category olfactory receptor activity was significantly overrepresented among differentially expressed genes and it is of interest to note that this category of genes is involved in sperm-egg communication and thereby potentially may contribute to reproductive incompatibility between the two species. Genes with a high degree of differentiation in gene expression between species tended to have high rates of sequence evolution (high dN/dS). Overall, this study illustrates both the feasibility and usefulness of deep transcriptome sequencing in non-model organisms.
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| 3. |
- Uebbing, Severin, et al.
(författare)
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Divergence in gene expression within and between two closely related flycatcher species
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Compared to DNA sequence evolution, relatively little is known about the character of gene expression evolution as species diverge. For example, it is unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or from neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression patterns, we sequenced and compared the transcriptomes of multiple tissues from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), a species pair which diverged less than one million years ago. Tissues resolved into separate clusters in non-metric multidimensional scaling ordination analysis and samples from the two species generally clustered by tissue rather than by species. Tissues differed in the degrees of expression variance within species and divergence between species. Variance was positively correlated with expression breadth and negatively correlated with protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression QST approach, we identified genes differentially expressed between species. We also identified 10 genes uniquely expressed in one of the species. For one such gene (DPP7, uniquely expressed in collared flycatcher), the absence of expression in pied flycatchers could be associated with a fixed ≈ 20 kb deletion including 11 out of 13 exons in this species. This study conducted in a young vertebrate speciation model system expands our knowledge of how gene expression evolves in natural populations.
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| 4. |
- Uebbing, Severin, et al.
(författare)
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Divergence in gene expression within and between two closely related flycatcher species
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:9, s. 2015-2028
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Tidskriftsartikel (refereegranskat)abstract
- Relatively little is known about the character of gene expression evolution as species diverge. It is for instance unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression, we sequenced and compared the transcriptomes of multiple organs from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), two species which diverged less than one million years ago. Ordination analysis separated samples by organ rather than by species. Organs differed in their degrees of expression variance within species and expression divergence between species. Variance was negatively correlated with expression breadth and protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression PST approach, we identified genes differentially expressed between species and found 16 genes uniquely expressed in one of the species. For one of these, DPP7, uniquely expressed in collared flycatcher, the absence of expression in pied flycatcher could be associated with a ≈ 20 kb deletion including 11 out of 13 exons. This study of a young vertebrate speciation model system expands our knowledge of how gene expression evolves as natural populations become reproductively isolated.
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| 5. |
- Uebbing, Severin, et al.
(författare)
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Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 32:10, s. 2716-2725
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Tidskriftsartikel (refereegranskat)abstract
- There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography–tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.
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