Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline

Peak and persistent excess of genetic diversity following an abrupt migration increase

Séverine Vuilleumier Varisco

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.

2013

Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS

Stéphane Laurent Escrig, Anders Meibom

Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N-2 and 002 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake water with N-15(2) and (CO2)-C-13 under in situ conditions with and without NH4+. Subsequently, we used flow cell sorting with auto-fluorescence gating based on a pure culture isolate to concentrate C. phaeobacteroides from its natural abundance of 0.2% to now 26.5% of total bacteria. C. phaeobacteroides cells were identified using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting the 16S rRNA in the sorted population with a species-specific probe. In a last step, we used nanometer-scale secondary ion mass spectrometry to measure the incorporation N-15 and 130 stable isotopes in more than 252 cells. We found that C. phaeobacteroides fixes N-2 in the absence of NH4+, but not in the presence of NH4+ as has previously been suggested. N-2 and 002 fixation were heterogeneous among cells and positively correlated indicating that N-2 and CO2 fixation activity interact and positively facilitate each other in individual cells. However, because CARD-FISH identification cannot detect genetic variability among cells of the same species, we cannot exclude genetic variability as a source for phenotypic heterogeneity in this natural population. Our study demonstrates the technical feasibility of measuring phenotypic heterogeneity in a rare bacterial species in its natural habitat, thus opening the door to study the occurrence and relevance of phenotypic heterogeneity in nature.

Frontiers Research Foundation2015

Experimental Study on Bedload Transport and Bedforms: Behaviour and Interplay in Steep Turbulent Streams

Ivan Pascal

In mountain regions, steep streams play an important role in water and sediment connectivity. In these highly dynamic systems, water flow features, sediment fluxes and stream morphologies are tightly interlinked over a broad range of temporal and spatial scales. Understanding their interactions is key to forecast, prevent and mitigate the impacts of stream-related hazards on human population and facilities as well as to manage the resources connected to the rivers. Sediment clasts at rest on the bed surface may be eroded, transported and deposited by the water flow. Grains that move in rolling and saltation regimes close to the bed compose the 'bedload', which is considered the main mode of sediment transport when studying morphodynamics of mountain rivers. The fate of these particles is of primary interest for river scientists and engineers as bedload predominantly drives the river morphology evolution and responds to it in a complex manner. Therefore, measuring and predicting bedload transport rates are fundamental concerns for many works of research and applications. Bedload transport rates may exhibit large non-Gaussian fluctuations, even under steady-state conditions, especially when bedload transport intensity is weak. These fluctuations may originate from different phenomena and affect the accuracy of bedload transport rate estimates. Particles transported by the water flow can destabilise other particles at rest on the bed surface. Under weak bedload transport conditions, this positive feedback can lead to large bedload pulses. When grains settle, they often organise in small clusters or larger bedforms. Bedform migration has been identified as one of the potential causes of bedload transport fluctuations. Trains of upstream-migrating antidunes may develop in steep coarse-bedded streams when the water discharge is sufficiently high to ensure fully supercritical flow conditions. In this dissertation, I present an experimental investigation on the behaviour of bedload transport fluctuations and antidunes in steep supercritical flows. The experiments were conducted in narrow flumes under well-controlled conditions with high-resolution image-based bedload transport and bed topography monitoring. The dependence of mean bedload transport rate uncertainty on the averaging time interval was analysed. Furthermore, I performed experimental runs with increasing transport intensity and a nearly constant mean bed slope angle to study how antidune sequences composed by bedforms of variable shape typically responded to the mean bedload flux imposed under steady-state conditions. Spectral analysis of the bed elevation perturbation in time and space allowed us to quantify the variability ranges of antidune shape and celerity. Scaling the spectra with opportune reference scales made it possible to identify a consistent dimensionless relationship between antidune geometry and migration celerity, which includes the dependencies on flow and sediment supply forcings. I studied how the bedload transport rate fluctuates in presence of migrating bedforms. The effects on the bedload transport rate periodicity due to non-uniformities in the antidune migration period and to deviations from the steady-state transport conditions were also investigated. This work is a further step on the way towards a complete understanding of the interplay between bedload transport fluctuations and bedforms in mountain streams.