Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

Mountains are reservoirs for a tremendous biodiversity which was fostered by a suite of factors acting in concert throughout evolutionary times. These factors can be climatic, geological, or biotic, but the way they combine through time to generate diversity remains unknown. Here, we investigate these factors as correlates of diversification of three closely related sections of Gentiana in the European Alpine System. Based upon phylogenetic approaches coupled with divergence dating and ancestral state reconstructions, we attempted to identify the role of bedrock preferences, chromosome numbers coupled with relative genome sizes estimates, as well as morphological features through time. We also investigated extant climatic preferences using a heavily curated set of occurrence records individually selected for superior precision, and quantified rates of climatic niche evolution in each section. We found that a number of phylogenetic incongruences derail the identification of correlates of diversification, yet a number of patterns persist regardless of the topology considered. All the studied correlates are likely to have contributed to the diversification of Gentiana in Europe, however, their respective importance varied through time and across clades. Chromosomal variation and divergence of climatic preferences appear to correlate with diversification throughout the evolution of European Gentiana (Oligocene to present), whereas shifts in bedrock preferences appear to have been more defining during recent diversification (Pliocene). Overall, a complex interaction among climatic, geological and biotic attributes appear to have supported the diversification of Gentiana across the mountains of Europe, which based upon phylogenetic as well as other evidence, was probably also bolstered by hybridization.

Environmental DNA simultaneously informs hydrological and biodiversity characterization of an Alpine catchment

Alpine streams are particularly valuable for downstream water resources and of high ecological relevance; however, a detailed understanding of water storage and release in such heterogeneous environments is often still lacking. Observations of naturally occurring tracers, such as stable isotopes of water or electrical conductivity, are frequently used to track and explain hydrologic patterns and processes. Importantly, some of these hydrologic processes also create microhabitat variations in Alpine aquatic systems, each inhabited by characteristic organismal communities. The inclusion of such ecological diversity in a hydrologic assessment of an Alpine system may improve our understanding of hydrologic flows while also delivering biological information. Recently, the application of environmental DNA (eDNA) to assess biological diversity in water and connected habitats has gained popularity in the field of aquatic ecology. A few of these studies have started to link aquatic diversity with hydrologic processes but hitherto never in an Alpine system. Here, we collected water from an Alpine catchment in Switzerland and compared the genetic information of eukaryotic organisms conveyed by eDNA with the hydrologic information conveyed by naturally occurring hydrologic tracers. Between March and September 2017, we sampled water at multiple time points at 10 sites distributed over the 13.4 km2 Vallon de Nant catchment (Switzerland). The sites corresponded to three different water types and habitats, namely low-flow or ephemeral tributaries, groundwater-fed springs, and the main channel receiving water from both previous mentioned water types. Accompanying observations of typical physicochemical hydrologic characteristics with eDNA revealed that in the main channel and in the tributaries, the biological richness increases according to the change in streamflow, dq/dt, whereas, in contrast, the richness in springs increased in correlation with electrical conductivity. At the catchment scale, our results suggest that transport of additional, and probably terrestrial, DNA into water storage or flow compartments occurs with increasing streamflow. Such processes include overbank flow, stream network expansion, and hyporheic exchange. In general, our results highlight the importance of considering the at-site sampling habitat in combination with upstream connected habitats to understand how streams integrate eDNA over a catchment and to interpret spatially distributed eDNA samples, both for hydrologic and biodiversity assessments. At the intersection of two disciplines, our study provides complementary knowledge gains and identifies the next steps to be addressed for using eDNA to achieve complementary insights into Alpine water sources. Finally, we provide recommendations for future observation of eDNA in Alpine stream ecosystems.

Environmental DNA simultaneously informs hydrological and biodiversity characterization of an Alpine catchment

Alpine streams are particularly valuable for downstream water resources and of high ecological relevance, however a detailed understanding of water storage and release in such heterogeneous environments is still often lacking. Observations of naturally occurring tracers, such as stable isotopes of water or electrical conductivity, are frequently used to track and explain hydrological patterns and processes. Importantly, some of these hydrological processes also create microhabitat variations in Alpine aquatic systems, each inhabited by characteristic organismal communities. The inclusion of such ecological diversity in a hydrologic assessment of an Alpine system may improve our understanding of hydrologic flows while also delivering biological information. Recently, the application of environmental DNA (eDNA) to assess biological diversity in water and connected habitats has gained popularity in the field of aquatic ecology. A few of these studies have started to link aquatic diversity with hydrologic processes, but hitherto never in an Alpine system. Here, we collected water from an Alpine catchment in Switzerland and compared the genetic information of eukaryotic organisms conveyed by eDNA with the hydrologic information conveyed by naturally-occurring, hydrologic tracers. Between March and September 2017, we sampled water at multiple time points at 10 sites distributed over the 13.4 km2 Vallon de Nant catchment (Switzerland). The sites corresponded to three different water types and habitats, namely low flow or ephemeral tributaries, groundwater fed springs, and the main channel receiving water from both previous mentioned water types. Accompanying observations of typical physico-chemical hydrologic characteristics with eDNA revealed that in the main channel and in the tributaries the biological richness increases according to change in streamflow, dq/dt. Whereas, in contrast, the richness in springs increased in correlation with electrical conductivity. At the catchment scale, our results suggest that transport of additional, and probably terrestrial, DNA into water storage or flow compartments occurs with increasing streamflow. Such processes include overbank flow, stream network expansion, and hyporheic exchange. In general, our results highlight the importance of considering the at-site sampling habitat in combination with upstream connected habitats to understand how streams integrate eDNA over a catchment and to interpret spatially distributed eDNA samples, both for hydrologic and biodiversity assessments. At the intersection of two disciplines, our study provides complementary knowledge gains and identifies the next steps to be addressed for using eDNA to achieve complementary insights into Alpine water sources. Finally, we provide recommendations for future observation of eDNA in Alpine stream ecosystems.