Evidence of neofunctionalization after the duplication of the highly conserved Polycomb group gene Caf1-55 in the obscura group of Drosophila

Drosophila CAF1-55 protein is a subunit of the Polycomb repressive complex PRC2 and other protein complexes. It is a multifunctional and evolutionarily conserved protein that participates in nucleosome assembly and remodelling, as well as in the epigenetic regulation of a large set of target genes. Here, we describe and analyze the duplication of Caf1-55 in the obscura group of Drosophila. Paralogs exhibited a strong asymmetry in evolutionary rates, which suggests that they have evolved according to a neofunctionalization process. During this process, the ancestral copy has been kept under steady purifying selection to retain the ancestral function and the derived copy (Caf1-55dup) that originated via a DNA-mediated duplication event ~18 Mya, has been under clear episodic selection. Different maximum likelihood approaches confirmed the action of positive selection, in contrast to relaxed selection, on Caf1-55dup after the duplication. This adaptive process has also taken place more recently during the divergence of D. subobscura and D. guanche. The possible association of this duplication with a previously detected acceleration in the evolutionary rate of three CAF1-55 partners in PRC2 complexes is discussed. Finally, the timing and functional consequences of the Caf1-55 duplication is compared to other duplications of Polycomb genes

Molecular population genetics of the Polycomb genes in Drosophila subobscura

Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. Herein, we have studied the nucleotide polymorphism of PcG genes in a natural population of D. subobscura to detect whether natural selection has also modulated the evolution of these important regulatory genes in a more recent time scale. Results show that most genes are under the action of purifying selection and present a level and pattern of polymorphism consistent with predictions of the neutral model, the exceptions being Su(z)12 and Pho. MK tests indicate an accumulation of adaptive changes in the SU(Z)12 protein during the divergence of D. subobscura and D. guanche. In contrast, the HKA test shows a deficit of polymorphism at Pho. The most likely explanation for this reduced variation is the location of this gene in the dot-like chromosome and would indicate that this chromosome also has null or very low recombination in D. subobscura, as reported in D. melanogaster

A hands-on genetics teaching approach at university level.

Teaching general Genetics is a cornerstone of a large number of university degrees. Being a scientific topic, laboratory classes are an essential element in student-centered learning. Here, we present our experience in implementing new material for teaching hands-on genetics, a subject of interest for other academic professionals in the field of Genetics. Our students carry out a genetic analysis of the su (sense ulls) mutation of Drosophila melanogaster, which produces a drastic eye reduction. The complete strain description can be found in Mestres et al. (2016a). The aim of the course is to give students the appropriate genetics tools to answer the three following questions: 1) Is the su mutation dominant or recessive? 2) In which chromosome is su located? 3) Can we identify in which gene the su mutation is

Descritpion of a double mutant strain of Drosophila melanogaster useful for genetic laboratory courses.

Many years ago, individuals showing drastically reduced eyes arose in our laboratory e (ebony) strain (Bridges and Morgan, 1923). We selected those flies presenting both traits and constituted a new double mutant strain e su (e, ebony; su, 'sense ulls', eyes drastically reduced). Both mutations were linked and located in the chromosome III. We used this strain in linkage analyses with our undergraduate students. [...

Evidence of neofunctionalization after the duplication of the highly conserved Polycomb group gene Caf1-55 in the obscura group of Drosophila

Drosophila CAF1-55 protein is a subunit of the Polycomb repressive complex PRC2 and other protein complexes. It is a multifunctional and evolutionarily conserved protein that participates in nucleosome assembly and remodelling, as well as in the epigenetic regulation of a large set of target genes. Here, we describe and analyze the duplication of Caf1-55 in the obscura group of Drosophila. Paralogs exhibited a strong asymmetry in evolutionary rates, which suggests that they have evolved according to a neofunctionalization process. During this process, the ancestral copy has been kept under steady purifying selection to retain the ancestral function and the derived copy (Caf1-55dup) that originated via a DNA-mediated duplication event ~18 Mya, has been under clear episodic selection. Different maximum likelihood approaches confirmed the action of positive selection, in contrast to relaxed selection, on Caf1-55dup after the duplication. This adaptive process has also taken place more recently during the divergence of D. subobscura and D. guanche. The possible association of this duplication with a previously detected acceleration in the evolutionary rate of three CAF1-55 partners in PRC2 complexes is discussed. Finally, the timing and functional consequences of the Caf1-55 duplication is compared to other duplications of Polycomb genes

Molecular population genetics of the Polycomb genes in Drosophila subobscura

Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. Herein, we have studied the nucleotide polymorphism of PcG genes in a natural population of D. subobscura to detect whether natural selection has also modulated the evolution of these important regulatory genes in a more recent time scale. Results show that most genes are under the action of purifying selection and present a level and pattern of polymorphism consistent with predictions of the neutral model, the exceptions being Su(z)12 and Pho. MK tests indicate an accumulation of adaptive changes in the SU(Z)12 protein during the divergence of D. subobscura and D. guanche. In contrast, the HKA test shows a deficit of polymorphism at Pho. The most likely explanation for this reduced variation is the location of this gene in the dot-like chromosome and would indicate that this chromosome also has null or very low recombination in D. subobscura, as reported in D. melanogaster

Location of the PcG genes on the <i>D</i>. <i>subobscura</i> chromosomes.

<p>The location of the sixteen studied PcG genes is indicated on the polytene chromosomes of <i>D</i>. <i>subobscura</i> (<i>ch cu</i> strain) by arrowheads. All chromosomes have the standard arrangement shown in the cytological map of the species [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185005#pone.0185005.ref027" target="_blank">27</a>] except the O chromosome that has the O₃₊₄ arrangement that includes the overlapping inversions O₃ and O₄. Chromosomes are identified by capital letters (A, J, U, E and O) at the distal end. The dot-like chromosome is also indicated (Dot).</p

Summary of synonymous and nonsynonymous polymorphism and divergence with <i>D</i>. <i>guanche</i> in the PcG genes.

<p>Summary of synonymous and nonsynonymous polymorphism and divergence with <i>D</i>. <i>guanche</i> in the PcG genes.</p