Genome-wide gene flow in the Daphnia longispina complex

In recent years, the role of hybridization, i.e. genetic exchange between species, has raised a lot of attention among evolutionary biologists. In particular the discovery, that our own, human, lineage has interbred with ancient humans such as Neandertals has stimulated a considerable amount of debate and research on the consequences of gene flow between species In this project, I will study the effects of environmental change on gene flow between species. I will study several waterflea species in the Daphnia longispina species complex. The species in this complex are adapted to different levels of food and fish predation and therefore the various species predominate in lakes with different trophic states. Eutrophication, i.e. increased input of nutrients, of peri-Alpine lakes in Europe has changed the trophic conditions in many lakes during the last century and brought the differentially adapted species into close contact again. This has resulted in increased interbreeding between the species. I propose to study the effects of this genetic exchange between species over time. Daphnia produce so-called resting eggs which are deposited and preserved in lake sediments over time and represent a continuous archive of the evolutionary history of these species. The unique features of this system and new sequencing methods enable me to sequence whole genomes, not only from recent populations but also from resting eggs and hatchlings over time. I will then use a set of statistical methods to assess how much genetic material has been exchanged among species, to what extent this exchange is linked to environmental change, how gene flow changes across the genome and which genes are involved in adaptation to different trophic conditions. This interdisciplinary project therefore combines speciation and population genomics, sedimentology and environmental sciences to directly study gene flow between species over time and during ecological changes. This unique window into the past will enable me to considerably increase our knowledge on speciation and adaptation in the face of gene flow and environmental change. Ultimately, this study will help to understand how species barriers arise and are maintained and to assess the consequences of environmental change for biodiversity.

In this project, we have studied gene flow among ecologically diverged water flea species in the Daphnia longispina species complex. The occurrence of hybrids as a result of crossings among the different species have repeatedly been described and studied with low-resolution genetic markers. In this project, we generate detailed data using high-resolution, genome-wide markers to assess whether crossing and backcrossing among species and hybrids has consequences on the integrity of species and whether there is evidence for gene flow among the species. For that purpose, we generated a dataset of genome data for about 10 individuals of the most important representatives of this species complex (D. longispina, D. galeata, D. cucullata, D. dentifera, D. mendota, D. curvirostris) each and conducted cluster and gene flow analyses. As hybridization has been associated with human-made environmental changes, for example eutrophication of water bodies, we also studied this with high-resolution time-series data. We, thus, extracted water flea resting eggs, chronologically deposited in lake sediments, from sediment cores collected from lakes that have experienced strong human impact. To study resting eggs from lake sediments, we developed a novel workflow allowing for cost-effective, direct sequencing resting egg genomes. Additionally, we sequenced hatchlings from resting eggs. With these approaches, we have generated genomic time-series spanning the period of increasing nutrients in lakes and the subsequent period of nutrient reduction as a consequence of sewage management and lake restoration. By analysing these data sets we showed that the parental species can still be delimited as distinct entities despite extensive hybridization. However, we find evidence for gene flow, which at least to some extent pre-dates the period of extensive hybridization during eutrophication, which is apparently not fully reflected by the genomic composition of the parental species yet. Our time series analysis reveals changes in taxon composition as well as known and so far unknown invasions of non-native Daphnia longispina complex species in the studied lakes. Moreover, our genomic data clearly show the extent of hybridization in the context of environmental change. In particular during phases of very rapid change in nutrient conditions a large number of hybrids and several generations of backcrossing. In addition, we find asymmetries in backcrossing among species and, through analysing mitochondrial genomes, in the contribution of the different sexes. Such patterns indicate incompatibilities and barriers to gene flow. The high resolution of our data also enables us to conduct detailed analysis and, for example, to identify regions that are either freely or never exchanged among species. In this project, we show in great detail how anthropogenic environmental change affects species integrity and gene flow among species and we reveal that such alterations are not necessarily reversible even when environmental conditions are restored.