In many species, selection pressures and fitness optima differ between the sexes. Heterogamy will facilitate this effect since sex chromosomes can harbor sexually antagonistic alleles. On evolving sex chromosomes, lack of recombination results in degeneration of the Y (or W) and may affect the speed at which beneficial alleles accumulate (faster X (or Z)). Recent evidence has demonstrated that chromosome XIX in threespine stickleback (G. aculeatus) is actually the nascent sex chromosome pair. The sex determining locus maps to this group and the Y contains various physical differences, including deletions, inversions and accumulation of repetitive DNA, indicating that the Y has started to degenerate. In order to determine the impact of degeneration on the function of genes residing on the Y, and hence a potential mechanism for the evolution of sex-specific traits, we examined genomic DNA and RNA transcriptomes from several individuals from two distinct lineages with independent Y chromosome populations since the last ice age. Since sex chromosomes and autosomes are presumed to evolve at different rates, we can examine the selective forces specific to the evolving Y chromosome. We used sequence capture and transcriptome sequencing to obtain sequence from the majority of the sex chromosomes as well as portions of several autosomes to predict the effects of Y degeneration on gene function in two geographically distinct populations: Alaska and Finland. When comparing the capture data with transcriptomes, over 68 000 variants were determined to be Y-specific. Many of the expressed genes from XIX in male are affected by nonsense and missense mutations or by mutations affecting splice sites. Despite the large amount of mutations, a large number of genes have a transcript from both X and Y, although incomplete splicing is also evident from the Y. If Y-mutations produce functional protein products, this could be a potential source of novel male-beneficial alleles.
Author(s): Gohli, J, Johnsen A, Popp M, Leder E, Lifjeld J
Resolving species trees for island populations is challenging due to high complexity of demographic factors. We have analysed RAD tag SNPs from African Blue Tit (Cyanistes teneriffae) populations on the Canary Islands and from the mainland Blue Tit (Cyanistes caeruleus), applying only tools that do not rely on concatenation of loci. Our data provide resolution where earlier reports have been unsuccessful, and strongly indicate that the population on La Palma (C. t. palmensis) represent a recent colonization from mainland Europe while the other Canary Islands were colonized from Morocco, which seems to be the oldest population in our system. Sperm collected from these birds was used to test the hypothesis that divergence in sperm length mirrors genetic divergence, which held true against both SNPs and the mitochondrial COI marker. Our sperm data supports the phylogenetic division between C. caeruleus and C. teneriffae, and also C. t. palmensis as sister to mainland Europe. We conclude that recent advances in analytical tools make short-read sequencing technology a powerful option for phylogenetic analyses. Lastly we suggest that the taxonomy of C. t. palmensis be revised.
Author(s): Primmer, CR, Papakostas S, Leder EH, Davis MJ, Ragan MA
Recent advances in molecular technologies have opened up unprecedented opportunities for evolutionary biologists and ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. In my poster, I will highlight how the Gene Ontology (GO) database can be of use in meeting this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species neutral, the GO is well suited for cross-species use i.e. functional annotation derived from model organisms can be transferred to inferred orthologs in newly sequenced species. In other words, the GO can provide gene annotation information for species with non-annotated genomes. I will highlight the both the strengths and the current weaknesses of using GO for enhancing the understanding of molecular function in ecologically relevant species and present some examples of its use for evolutionary contexts
Author(s): Pritchard, VL, Merilä J, Nikinmaa M, Primmer C, Sävilammi T, Viitaniemi H, Leder E
Ongoing climate change will expose populations to altered thermal regimens, which are likely to include more frequent and higher temperature maxima. Whether and how a resident population can withstand or adapt to these new conditions will depend on the genetic architecture underlying responses to temperature changes. This includes both coding genes and the regulatory regions that govern expression of these genes. Recent advances enabling the quantification of transcription levels for a large number of genes and the genotyping of many thousands of genetic markers throughout the genome, together with novel statistical methods, are facilitating the identification of such regulatory regions via expression quantitative trait locus (eQTL) analysis.
The threespine stickleback (Gasterosteus aculeatus) is an important model organism in evolutionary biology. The species occurs as resident populations in a wide range of habitats with different thermal profiles. We used sticklebacks derived from the Baltic coast of Finland to identify and localize eQTLs underlying changes in gene expression in response to thermal stress. Experimental subjects comprised 600 individuals in 30 sib–halfsib families, half of which were subject to a thermal challenge immediately prior to tissue collection. Liver mRNA expression was subsequently quantified using Agilent custom microarrays. Over 2000 genes were found to be differentially expressed between control and treatment groups. Genotyping of the families by sequencing on the Illumina platform, in combination with the existing G. aculeatus genome, was used to generate a linkage map that included over 10,000 SNPs. This enabled us to characterize and explore the regulatory networks underlying these changes in gene expression.
The establishment of non-recombining regions is a critical early step in the evolution of sex chromosomes. To compensate for the resulting difference in the expression of X-linked genes the heterogametic sex will increase the expression of X-linked genes or the homogametic sex will shut down one of the X chromosomes. This process is known as dosage compensation. It has recently been suggested that incomplete or imperfect dosage compensation may have a stronger influence on sex-biased expression than previously thought. We use the threespine stickleback (Gasterosteus aculeatus) as a model system to study the role of dosage compensation in the evolution and maintenance of sex-biased gene expression. Threespine sticklebacks constitute a particular interesting system in this respect because its chromosome group 19 are nascent sex chromosomes: Whereas there is still recombination between sexes in the region spanning the first 3 million bases on the chromosome, recombination is significantly reduced in the region from 3-12 million bases. The last 6 million bases are mostly deleted from the male Y-chromosome. We collected five specimens of each sex from a benthic and a limnetic population in four Alaskan lakes, respectively, and utilized deep RNA sequencing of brain tissue to study gene and transcript isoform expression differences between the sexes. Preliminary results from expression of genes corresponding to the missing region of the X chromosome suggest no dosage compensation as the expression pattern is indicative of a copy number variation biased towards females. In other areas of the genome, there is more varied sex-biased expression.