Abstracts (first author)

Talk 

The rapid life cycle of Drosophila orphans

Author(s): Schlötterer C, Palmieri N, Nolte V, Kosiol C

Summary:

Orphans are genes restricted to a single phylogenetic lineage. They emerge at high rates and frequently provide a selective advantage or even essential functions to their host. While these features predict an accumulation of genes, the gene number has remained remarably constant through evolution. This paradox of a stable gene number in the presence of a high rate of gene birth has not been resolved. Because orphan genes were mainly analyzed over large evolutionary time scales, orphan loss, a key factor of orphan evolution, remained unexplored. Here, we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but they are also rapidly lost. The pattern of orphan loss is clearly non-random: young orphans are more likely to be lost than orphans, which originated earlier. Furthermore, highly expressed orphan genes with a strong male-bias are more likely to be retained. Since lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that intron loss is not driven by different evolutionary rates, but lineage specific functional requirements.



Abstracts (coauthor)

Summary:

How adaptation effects segregating variation at the population genomic level in sexually reproducing diploids remains a poorly understood yet fundamental biological question. However, recent advances in sequencing technology in combination with experimental evolution have promised to reveal the temporal patterns of genomic adaptation down to individual SNP resolution. Here I discuss results from 15 generations of experimental evolution in replicated populations of D. melanogaster maintained in two separate thermal environments, which mimic either heat and cold stress. When taking the top candidate SNPs from each base-evolved population comparison, we find an enrichment of hot candidate SNPs in genes associated with heat tolerance, and likewise for cold candidate SNPs in cold tolerance genes, but not vice versa. Furthermore, we find that the rising allele (i.e. that most likely to be under selection) tends to start at either low or intermediate frequencies in the hot and cold treatments, respectively. Hence, it appears that thermal selection is involved in driving changes between the two treatments and is deferentially dependent on the starting allele frequency. The possible causes behind these intriguing patterns are discussed with respect to our emerging understanding of thermal adaption in D. melanogaster.

Polymorphisms-aware phylogenetic models

Author(s): DeMaio, N, Schlötterer C, Kosiol C

Summary:

Comparative analysis of genomes of related species, and of different individuals of the same species, can reveal adaptive trends in the history of the considered taxa, as well as show intensity and genomic variation of evolutionary patterns. However, these intra and interspecific data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms.

We propose a new POlymorphisms-aware phylogenetic MOdel (PoMo) that relaxes the assumption of instantaneous substitutions of standard phylogenetic approaches. A substitution is hereby modeled through a mutational event followed by a gradual fixation. Our model utilizes both divergence and polymorphism data from different species/populations. By allowing polymorphisms at internal phylogenetic nodes, it also naturally accounts for incomplete lineage sorting and shared ancestral polymorphisms. PoMo can accurately and time-efficiently estimate phylogenetic trees of any shape and dimension, e.g. species trees, population trees, or any combination of those. It can also disentangle the contributions of mutations and fixation biases in substitution patterns.

We analyzed synonymous sites in genome-wide alignments of human, chimpanzee, and two orangutan species. Using PoMo, we obtained accurate estimates of mutation rates and GC-biased gene conversion (gBGC) in great apes. We found that both mutation rates and gBGC vary with GC content, determining the well-known differences in substitution rates. Our results are consistent with the presence of directional selection in synonymous sites regarding exonic splicing enhancers.

Lastly, we show with simulations that PoMo accurately estimates phylogenetic branch lengths, whereas standard substitutions models present large biases due to ancestral polymorphisms. Furthermore, our methods are more computationally efficient than coalescent-based approaches.

Summary:

Experimental evolution in combination with whole genome resequencing is a promising approach to investigate evolutionary responses to direct selective treatments or novel environments. In particular D. melanogaster has been used as a model for a sexually reproducing diploid organism. Using Pool-Seq to identify putative targets of selection, all studies identified a vast number of putatively selected loci. Hence, it appears likely that the distinction of true and false positives is a problem common to these studies. Most important, false positives do not necessarily appear only in close proximity to the targets of selection, but appear to be distributed throughout the entire genome. Reasoning that more detailed information about dynamics of the underlying haplotype structure will be highly instrumental to distinguish true and false positives, we analyzed the patterns of linkage disequilibrium in an experimental evolution study with D. melanogaster adapting to a novel temperature regime. We will show how the information about whole chromosome linkage pattern changes during experimental evolution and to what extent this linkage pattern provides the basis of an improved strategy to distinguish between true and false positives in Pool-Seq data from experimental evolution studies.

Summary:

Natural populations of Drosophila melanogaster carry different Wolbachia strains, but it is not clear whether these Wolbachia strains are functionally diverged. To address this question, we exposed a natural D. melanogaster population to two different environments (hot and cold) and traced the relative frequency of different Wolbachia haplotypes during the experiment. Our D. melanogaster population sample from Portugal contained a highly polymorphic Wolbachia population in which three of the six described clades were present. Using Pool-Seq, we found that in the hot environment the Wolbachia composition remained remarkably stable over 37 generations. In the cold environment, however, Wolbachia strains from two clades increased in frequency. To distinguish between host and Wolbachia mediated effects, we exposed flies that evolved for 37 generations in the hot environment to the cold environment. Interestingly, we observed a very similar pattern to the previous experiment, suggesting that Wolbachia from two clades have a fitness advantage in the cold environment.

Summary:

Because hosts and parasites exert strong selection pressure on each other, it is particularly relevant to study their interaction in an evolutionary context. Experimental Evolution permits the establishment of causality between evolutionary processes and adaptation patterns. Here we use experimental evolution of Drosophila melanogaster exposed to Drosophila C virus (DCV) to address the phenotypic and genotypic changes of hosts evolving in presence of parasites. Upon exposure to the virus, Drosophila survival increased from 33% to almost 90% after 35 generations of selection. This response carried no detectable costs in fitness in the absence of infection, and was not lost after 10 generations in the absence of selection. Cross-resistance was found for other viruses, such as CrPV and FHV, but not to bacterial pathogens. Whole genome sequencing of pooled samples of virus-selected populations and their matching controls at generation 20 uncovered two regions of significant differentiation between these groups of populations. The first corresponded to a region of 4 megabases(Mb) in the 3L chromosomal arm. This region’s peak of differentiation corresponded to a polymorphism in pastrel (pst), a gene recently associated with increased DCV resistance. The second was a pair of significantly differentiated SNPs in the X chromosome, in genes not previously associated with virus resistance. Results with a panel of deficiencies in the 3L chromosome confirmed that deficiencies which encompass pst are the ones with more influence on survival after DCV infection, in a region of approximately 2 Mb. There is ongoing work to confirm the involvement of other candidate genes in this region and of the genes in the X chromosome in resistance to DCV infection. Overall we show that selection for increased virus resistance I) is stable and bears little costs, II) is advantageous in the defense against other viral pathogens, and III) has a simple genetic basis.

Summary:

Paracentric inversions are very common structural variants in many species of the genus Drosophila. Despite a large body of literature, still very little is known about the genetic mechanisms underlying inversion polymorphisms. Recent advances in sequencing technology now allow studying the distribution of genetic variation on a genome-wide level, which has reignited interest in the genomic basis of inversion evolution. To extend previous efforts we have combined karyotyping of polytene chromosomes with whole-genome sequencing in order to identify polymorphic inversions and examine associated haplotype structure in populations derived from a laboratory natural selection experiment in D. melanogaster. In addition, we combined information from 110 D. melanogaster genomes of known karyotype from Africa, Europe and North America to investigate patterns and distribution of fixed differences linked to different inversions. We used this novel dataset to estimate inversion frequencies from pooled next generation sequencing data (“Pool-Seq”) in our selection experiment and in populations collected along the North American and Australian latitudinal cline. Among six polymorphic inversions segregating in the experimental populations, two rare cosmopolitan inversions, In(3R)C and In(3R)Mo, showed a frequency increase consistent with non-neutral evolution. Genetic variation in and around In(3R)Mo was strongly reduced, consistent with previous findings from North America, and we found evidence for gene flux between this inversion and the non-inverted standard arrangement. Moreover, we identified a previously unknown latitudinal cline for In(3R)Mo in our Pool-Seq data from the North America east coast. Our novel data highlight the impact of inversions on patterns genetic variation and underline the importance of considering structural variants when attempting to detect patterns of adaptation.

Contacts

Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028
email: mail@eseb2013.com

Address

XIV Congress of the European Society for Evolutionary Biology

Organization Team
Department of Animal Biology (DBA)
Faculty of Sciences of the University of Lisbon
P-1749-016 Lisbon
Portugal

Website

Computational Biology & Population Genomics Group 
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