March 19, 2019

A Combinatorial View on Speciation and Adaptive Radiation

Speciation is often thought of as a slow process due to the waiting times for mutations that cause incompatibilities, and permit ecological differentiation or assortative mating. Cases of rapid speciation and particularly cases of rapid adaptive radiation into multiple sympatric species have remained somewhat mysterious. We review recent findings from speciation genomics that reveal an emerging commonality among such cases: reassembly of old genetic variation into new combinations facilitating rapid speciation and adaptive radiation. The polymorphisms in old variants frequently originated from hybridization at some point in the past. We discuss why old variants are particularly good fuel for rapid speciation, and hypothesize that variation in access to such old variants might contribute to the large variation in speciation rates observed in nature.

publication originale

March 5, 2019

Ecological and Evolutionary Processes Shaping Viral Genetic Diversity

The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.

publication originale

20 décembre 2018
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication
This study provides a genome-scale (16,173 RAD loci) analysis of Alpine whitefish from lakes Walen and Zurich. Philine and Ole demonstrated the feasibility of dense marker sets to unambiguously distinguish sympatric whitefish species. This ability then allowed them to show that in each of the two lakes the population of a different, but ecologically similar, whitefish species declined following a recent period of eutrophication. They also detected genomic signatures consistent with hybridisation that are more pronounced in the more severely impacted lake, Lake Zurich. Finally, four genomic loci were identified that provide evidence of parallel divergent adaptation between the shallow benthic species and the two different more profundal species. The genomic analysis indicates the action of divergent natural selection between sympatric whitefish species in pre‐alpine lakes and reveals the vulnerability of these species to anthropogenic alterations of the environment.

publication originale

20 décembre 2018
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication
Rishi and Philine investigate the genetic basis of the spectacular whitefish radiation across Swiss lakes. To achieve that new genetic resources are essential. One such resource is the linkage map that they created and now published in G3. With this map, they identify how the structure of the whitefish genome might differ from that of other salmonid species by comparing it with the Atlantic Salmon genome. The linkage map suggests that whitefish and atlantic salmon have a very different genome structure an the whitefish genome is more similar to that of other salmonid species including rainbow trout. They further identified regions which have a unique structure in whitefish which they aim to investigate further in the future.

publication originale

13 septembre 2018
Une nouvelle espèce de poisson découverte dans l'Oberland bernois
Des biologistes de l'Eawag et de l'université de Berne ont découvert une nouvelle espèce de poisson dans le complexe des lacs de Thoune et de Brienz. La nouvelle espèce, provisoirement baptisée «Balchen 2», se distingue des cinq autres espèces de corégones répertoriées dans le lac de Thoune sur le plan morphologique, écologique et génétique. Il faut aller dans le lac russe d'Onega, 200 fois plus grand, pour rencontrer une plus grande diversité de corégones. En savoir plus

24 août 2018
The Genomic Basis of Quantum Speciation in Lake Victoria Cichlids
Ole Seehausen gave this year's Wilhelmine Key Distinguished Lecture at the American Genetics Association in Hawaii. His lecture was on "The Genomic Basis of Quantum Speciation in Lake Victoria Cichlids".

The talk inspired Elizabeth Pennisi to write a wonderful story about it in Science on how "Hybrids spawned Lake Victoria's rich fish diversity".

17 août 2018
The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes
La famille des cichlidés fait partie de celles qui comptent le plus d’espèces – et en engendre sans cesse de nouvelles. Cette lignée de poissons aux couleurs chatoyantes se développe à une telle vitesse que les chercheurs de l’Eawag ont pu suivre leur évolution pour ainsi dire de leurs propres yeux

11 juillet 2018
A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination
Genetic linkage maps are essential for comparative genomics. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P. sp. ‘red head’). This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ~1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sexdetermination gene (amh).

Publication