The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene

Abstract Background Little is known about the diversity, phylogenetic relationships, and biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids. Methods Small Subunit rRNA (SSU rRNA) and glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) genes were employed for phylogenetic inferences. Trypanosomes from crocodilians were obtained by haemoculturing. Growth behaviour, morphology, and ultrastructural features complement the molecular description of two new species strongly supported by phylogenetic analyses. Results The inferred phylogenies disclosed a strongly supported crocodilian-restricted clade comprising three subclades. The subclade T. grayi comprised the African Trypanosoma grayi from Crocodylus niloticus and tsetse flies. The subclade T. ralphi comprised alligatorid trypanosomes represented by Trypanosoma ralphi n. sp. from Melanosuchus niger, Caiman crocodilus and Caiman yacare from Brazilian river basins. T. grayi and T. ralphi were sister subclades. The basal subclade T. terena comprised alligatorid trypanosomes represented by Trypanosoma terena n. sp. from Ca. yacare sharing hosts and basins with the distantly genetic related T. ralphi. This subclade also included the trypanosome from Ca. crocodilus from the Orinoco basin in Venezuela and, unexpectedly, a trypanosome from the African crocodilian Osteolaemus tetraspis. Conclusion The close relationship between South American and African trypanosomes is consistent with paleontological evidence of recent transoceanic dispersal of Crocodylus at the Miocene/Pliocene boundaries (4–5 mya), and host-switching of trypanosomes throughout the geological configuration of South American hydrographical basins shaping the evolutionary histories of the crocodilians and their trypanosomes.

The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene

Background: Little is known about the diversity, phylogenetic relationships, and biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids. Methods: Small Subunit rRNA (SSU rRNA) and glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) genes were employed for phylogenetic inferences. Trypanosomes from crocodilians were obtained by haemoculturing. Growth behaviour, morphology, and ultrastructural features complement the molecular description of two new species strongly supported by phylogenetic analyses. Results: The inferred phylogenies disclosed a strongly supported crocodilian-restricted clade comprising three subclades. The subclade T. grayi comprised the African Trypanosoma grayi from Crocodylus niloticus and tsetse flies. The subclade T. ralphi comprised alligatorid trypanosomes represented by Trypanosoma ralphi n. sp. From Melanosuchus niger, Caiman crocodilus and Caiman yacare from Brazilian river basins. T. grayi and T. ralphi were sister subclades. The basal subclade T. terena comprised alligatorid trypanosomes represented by Trypanosoma terena n. sp. from Ca. yacare sharing hosts and basins with the distantly genetic related T. ralphi. This subclade also included the trypanosome from Ca. crocodilus from the Orinoco basin in Venezuela and, unexpectedly, a trypanosome from the African crocodilian Osteolaemus tetraspis. Conclusion: The close relationship between South American and African trypanosomes is consistent with paleontological evidence of recent transoceanic dispersal of Crocodylus at the Miocene/Pliocene boundaries (4–5 mya), and host-switching of trypanosomes throughout the geological configuration of South American hydrographical basins shaping the evolutionary histories of the crocodilians and their trypanosomes.

A river runs through it - ancient DNA data on the neolithic populations of the Great Hungarian Plain

This thesis was part of a multidisciplinary research project funded by the German Research Foundation (“Bevölkerungsgeschichte des Karpatenbeckens in der Jungsteinzeit und ihr Einfluss auf die Besiedlung Mitteleuropas”, grant no. Al 287/10-1) aimed at elucidating the population history of the Carpathian Basin during the Neolithic. The Carpathian Basin was an important waypoint on the spread of the Neolithic from southeastern to central Europe. On the Great Hungarian Plain (Alföld), the first farming communities appeared around 6000 cal BC. They belonged to the Körös culture, which derived from the Starčevo-Körös-Criş complex in the northern Balkans. Around 5600 cal BC the Alföld-Linearbandkeramik (ALBK), so called due to its stylistic similarities with the Transdanubian and central European LBK, emerged in the northwestern Alföld. Following a short “classical phase”, the ALBK split into several regional subgroups during its later stages, but did not expand beyond the Great Hungarian Plain. Marking the beginning of the late Neolithic period, the Tisza culture first appeared in the southern Alföld around 5000 cal BC and subsequently spread into the central and northern Alföld. Together with the Herpály and Csőszhalom groups it was an integral part of the late Neolithic cultural landscape of the Alföld. Up until now, the Neolithic cultural succession on the Alföld has been almost exclusively studied from an archaeological point of view, while very little is known about the population genetic processes during this time period. The aim of this thesis was to perform ancient DNA (aDNA) analyses on human samples from the Alföld Neolithic and analyse the resulting mitochondrial population data to address the following questions: is there population continuity between the Central European Mesolithic hunter-gatherer metapopulation and the first farming communities on the Alföld? Is there genetic continuity from the early to the late Neolithic? Are there genetic as well as cultural differences between the regional groups of the ALBK? Additionally, the relationships between the Alföld and the neighbouring Transdanubian Neolithic as well as other European early farming communities were evaluated to gain insights into the genetic affinities of the Alföld Neolithic in a larger geographic context. 320 individuals were analysed for this study; reproducible mitochondrial haplogroup information (HVS-I and/or SNP data) could be obtained from 242 Neolithic individuals. According to the analyses, population continuity between hunter-gatherers and the Neolithic cultures of the Alföld can be excluded at any stage of the Neolithic. In contrast, there is strong evidence for population continuity from the early to the late Neolithic. All cultural groups on the Alföld were heavily shaped by the genetic substrate introduced into the Carpathian Basin during the early Neolithic by the Körös and Starčevo cultures. Accordingly, genetic differentiation between regional groups of the ALBK is not very pronounced. The Alföld cultures are furthermore genetically highly similar to the Transdanubian Neolithic cultures, probably due to common ancestry. In the wider European context, the Alföld Neolithic cultures also highly similar to the central European LBK, while they differ markedly from contemporaneous populations of the Iberian Peninsula and the Ukraine. Thus, the Körös culture, the ALBK and the Tisza culture can be regarded as part of a “genetic continuum” that links the Neolithic Carpathian Basin to central Europe and likely has its roots in the Starčevo -Körös-Criş complex of the northern Balkans.

Miocene basin development and volcanism along a strike-slip to flat-slab subduction transition: Stratigraphy, geochemistry, and geochronology of the central Wrangell volcanic belt, Yakutat-North America collision zone

New geochronologic, geochemical, sedimentologic, and compositional data from the central Wrangell volcanic belt (WVB) document basin development and volcanism linked to subduction of overthickened oceanic crust to the northern Pacific plate margin. The Frederika Formation and overlying Wrangell Lavas comprise >3 km of sedimentary and volcanic strata exposed in the Wrangell Mountains of south-central Alaska (United States). Measured stratigraphic sections and lithofacies analyses document lithofacies associations that reflect deposition in alluvial-fluvial-lacustrine environments routinely influenced by volcanic eruptions. Expansion of intrabasinal volcanic centers prompted progradation of vent-proximal volcanic aprons across basinal environments. Coal deposits, lacustrine strata, and vertical juxtaposition of basinal to proximal lithofacies indicate active basin subsidence that is attributable to heat flow associated with intrabasinal volcanic centers and extension along intrabasinal normal faults. The orientation of intrabasinal normal faults is consistent with transtensional deformation along the Totschunda-Fairweather fault system. Paleocurrents, compositional provenance, and detrital geochronologic ages link sediment accumulation to erosion of active intrabasinal volcanoes and to a lesser extent Mesozoic igneous sources. Geochemical compositions of interbedded lavas are dominantly calc-alkaline, range from basaltic andesite to rhyolite in composition, and share geochemical characteristics with Pliocene-Quaternary phases of the western WVB linked to subduction-related magmatism. The U/Pb ages of tuffs and Ar-40/Ar-39 ages of lavas indicate that basin development and volcanism commenced by 12.5-11.0 Ma and persisted until at least ca. 5.3 Ma. Eastern sections yield older ages (12.5-9.3 Ma) than western sections (9.6-8.3 Ma). Samples from two western sections yield even younger ages of 5.3 Ma. Integration of new and published stratigraphic, geochronologic, and geochemical data from the entire WVB permits a comprehensive interpretation of basin development and volcanism within a regional tectonic context. We propose a model in which diachronous volcanism and transtensional basin development reflect progressive insertion of a thickened oceanic crustal slab of the Yakutat microplate into the arcuate continental margin of southern Alaska coeval with reported changes in plate motions. Oblique northwestward subduction of a thickened oceanic crustal slab during Oligocene to Middle Miocene time produced transtensional basins and volcanism along the eastern edge of the slab along the Duke River fault in Canada and subduction-related volcanism along the northern edge of the slab near the Yukon-Alaska border. Volcanism and basin development migrated progressively northwestward into eastern Alaska during Middle Miocene through Holocene time, concomitant with a northwestward shift in plate convergence direction and subduction collision of progressively thicker crust against the syntaxial plate margin.

Sedimentology, Depositional Age, and Provenance of Sedimentary and Volcanic Rocks Exposed Along Willow Creek, Eastern Susitna Basin, South-Central Alaska: Implications for Modification of a Forearc Basin by Spreading Ridge Subduction

This is the first detailed study of the westernmost portion of the outcrop belt, which extends along the western flank of the Talkeetna Mountains and includes thick, well-exposed outcrops along Willow Creek in the eastern Susitna basin. New sedimentologic, compositional, and geochronologic data were obtained from stratigraphic sections within Arkose Ridge Formation strata at Willow Creek. This data combined with new geologic mapping and geochronologic data from Willow Bench and Kashwitna River Bluff (north of Willow Creek), and from the Government Peak area (east of Willow Creek), help constrain depositional processes and source terranes that provided detritus to the westernmost Arkose Ridge Formation strata.

Ground Water in the Lake Basin Field and Adjacent Area

This thesis consists of studying the stratigraphic and structural features of the Lake Basin Field and an adjacent area with special emphasis upon the ground water conditions present.

Reading Our Land Use Legacy in Groundwater: Nitrate Dynamics in the Judith River Watershed

Elevated nitrate in groundwater is common is agricultural areas where fertilizer has been added at high rates for decades. Within the Judith River Wastershed, high native soil fertility allowed for dryland wheat production without N fertilization until the 1980s, yet elevated nitrate levels were frequently observed in shallow aquifers. Dr. Stephanie Ewing presents results for soil, groundwater and surface water analyses from a hydrologically isolated strath terrace near Moccasin, MT. In context of this uniquely well constrained field setting, these observed data, along with land use history and a simple mass balance model, revel the long term development and perturbation of native soil fertility with cultivation.

Lateral sediment sources and knickzones as controls on spatio-temporal variations of sediment transport in an Alpine river

Modern mixed alluvial-bedrock channels in mountainous areas provide natural laboratories for understanding the time scales at which coarse-grained material has been entrained and transported from their sources to the adjacent sedimentary sink, where these deposits are preserved as conglomerates. This article assesses the shear stress conditions needed for the entrainment of the coarse-bed particles in the Glogn River that drains the 400 km2 Val Lumnezia basin, eastern Swiss Alps. In addition, quantitative data are presented on sediment transport patterns in this stream. The longitudinal stream profile of this river is characterized by three ca 500 m long knickzones where channel gradients range from 0·02 to 0·2 m m−1, and where the valley bottom confined into a <10 m wide gorge. Downstream of these knickzones, the stream is flat with gradients <0·01 m m−1 and widths ≥30 m. Measurements of the grain-size distribution along the trunk stream yield a mean D84 value of ca 270 mm, whereas the mean D50 is ca 100 mm. The consequences of the channel morphology and the grain-size distribution for the time scales of sediment transport were explored by using a one-dimensional step-backwater hydraulic model (Hydrologic Engineering Centre – River Analysis System). The results reveal that, along the entire trunk stream, a two to 10 year return period flood event is capable of mobilizing both the D50 and D84 fractions where the Shields stress exceeds the critical Shields stress for the initiation of particle motion. These return periods, however, varied substantially depending on the channel geometry and the pebble/boulder size distribution of the supplied material. Accordingly, the stream exhibits a highly dynamic boulder cover behaviour. It is likely that these time scales might also have been at work when coarse-grained conglomerates were constructed in the geological past.

The largest floods in the High Rhine basin since 1268 assessed from documentary and instrumental evidence

The magnitudes of the largest known floods of the River Rhine in Basel since 1268 were assessed using a hydraulic model drawing on a set of pre-instrumental evidence and daily hydrological measurements from 1808. The pre-instrumental evidence, consisting of flood marks and documentary data describing extreme events with the customary reference to specific landmarks, was “calibrated” by comparing it with the instrumental series for the overlapping period between the two categories of evidence (1808–1900). Summer (JJA) floods were particularly frequent in the century between 1651–1750, when precipitation was also high. Severe winter (DJF) floods have not occurred since the late 19th century despite a significant increase in winter precipitation. Six catastrophic events involving a runoff greater than 6000 m 3 s-1 are documented prior to 1700. They were initiated by spells of torrential rainfall of up to 72 h (1480 event) and preceded by long periods of substantial precipitation that saturated the soils, and/or by abundant snowmelt. All except two (1999 and 2007) of the 43 identified severe events (SEs: defined as having runoff > 5000 and < 6000 m 3 s -1) occurred prior to 1877. Not a single SE is documented from 1877 to 1998. The intermediate 121-year-long “flood disaster gap” is unique over the period since 1268. The effect of river regulations (1714 for the River Kander; 1877 for the River Aare) and the building of reservoirs in the 20th century upon peak runoff were investigated using a one-dimensional hydraulic flood-routing model. Results show that anthropogenic effects only partially account for the “flood disaster gap” suggesting that variations in climate should also be taken into account in explaining these features.

The people, the river and the border

In the catchment basin of the Songwe River, the institutional order thwarts sustainable resource management. District borders obstruct coherent policy - and so does the national border between Malawi and Tanzania. Joint decision making will be necessary if matter are to improve.

Patterns of landscape form in the upper Rhône basin, Central Swiss Alps, predominantly show lithologic controls despite multiple glaciations and variations in rock uplift rates

The development of topography depends mainly on the interplay between uplift and erosion. These processes are controlled by various factors including climate, glaciers, lithology, seismic activity and short-term variables, such as anthropogenic impact. Many studies in orogens all over the world have shown how these controlling variables may affect the landscape's topography. In particular, it has been hypothesized that lithology exerts a dominant control on erosion rates and landscape morphology. However, clear demonstrations of this influence are rare and difficult to disentangle from the overprint of other signals such as climate or tectonics. In this study we focus on the upper Rhône Basin situated in the Central Swiss Alps in order to explore the relation between topography, possible controlling variables and lithology in particular. The Rhône Basin has been affected by spatially variable uplift, high orographically driven rainfalls and multiple glaciations. Furthermore, lithology and erodibility vary substantially within the basin. Thanks to high-resolution geological, climatic and topographic data, the Rhône Basin is a suitable laboratory to explore these complexities. Elevation, relief, slope and hypsometric data as well as river profile information from digital elevation models are used to characterize the landscape's topography of around 50 tributary basins. Additionally, uplift over different timescales, glacial inheritance, precipitation patterns and erodibility of the underlying bedrock are quantified for each basin. Results show that the chosen topographic and controlling variables vary remarkably between different tributary basins. We investigate the link between observed topographic differences and the possible controlling variables through statistical analyses. Variations of elevation, slope and relief seem to be linked to differences in long-term uplift rate, whereas elevation distributions (hypsometry) and river profile shapes may be related to glacial imprint. This confirms that the landscape of the Rhône Basin has been highly preconditioned by (past) uplift and glaciation. Linear discriminant analyses (LDAs), however, suggest a stronger link between observed topographic variations and differences in erodibility. We therefore conclude that despite evident glacial and tectonic conditioning, a lithologic control is still preserved and measurable in the landscape of the Rhône tributary basins.

Stable carbon and oxygen isotopes in tree rings show physiological responses of Pericopsis elata to precipitation in the Congo Basin

In equatorial regions, where tree rings are less distinct or even absent, the response of forests to high-frequency climate variability is poorly understood. We measured stable carbon and oxygen isotopes in anatomically distinct, annual growth rings of four Pericopsis elata trees from a plantation in the Congo Basin, to assess their sensitivity to recorded changes in precipitation over the last 50 y. Our results suggest that oxygen isotopes have high common signal strength (EPS = 0.74), and respond to multi-annual precipitation variability at the regional scale, with low δ18O values (28–29‰) during wetter conditions (1960–1970). Conversely, δ13C are mostly related to growth variation, which in a light-demanding species are driven by competition for light. Differences in δ13C values between fast- and slow-growing trees (c. 2‰), result in low common signal strength (EPS = 0.37) and are driven by micro-site conditions rather than by climate. This study highlights the potential for understanding the causes of growth variation in P. elata as well as past hydroclimatic changes, in a climatically complex region characterized by a bimodal distribution in precipitation.