BackgroundPhylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction.ResultsBayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia.ConclusionWe describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.
We present a kinematic model for the Himalayan thrust belt that satisfies structural and metamorphic data and explains recently reported late Miocene-Pliocene geochronologic and thermochronologic ages from rocks in the Main Central thrust zone in central Nepal. At its current exposure level, the Main Central thrust juxtaposes a hanging-wall flat in Greater Himalayan rocks with a footwall flat in Lesser Himalayan rocks of the Ramgarh thrust sheet, which is the roof thrust of a large Lesser Himalayan duplex. Sequential emplacement of the Main Central (early Miocene) and Ramgarh (middle Miocene) thrust sheets was followed by insertion of thrust sheets within the Lesser Himalayan duplex and folding of the Main Central and Ramgarh thrusts during late Miocene-Pliocene time. Thorium-lead (Th-Pb) ages of monazite inclusions in garnets from central Nepal record the timing of coeval, progressive metamorphism of Lesser Himalayan rocks in the footwall of the Main Central thrust. Although this model does not rule out minor, late-stage reactivation of the Main Central thrust, major late Miocene reactivation is not required.
The Ramgarh thrust is one of the major fault systems of the Himalayan thrust belt in Nepal and northern India. The Ramgarh thrust sheet is ∼0.2–2.0 km thick and can be traced along strike the entire length of the Himalaya in Nepal. The fault generally places the oldest Paleoproterozoic rocks in the Lesser Himalayan series upon younger Lesser Himalayan rocks or lower Miocene foreland basin deposits. Regional balanced cross sections suggest that the Ramgarh thrust had at least ∼120 km of initial south vergent displacement. Subsequently, the frontal part of the thrust experienced further slip as the roof thrust for a large duplex in underlying Lesser Himalayan rocks. Ramgarh hanging wall strata are greenschist‐grade phyllite, quartzite, and augen gneiss, all of which locally exhibit phyllonitic and mylonitic fabrics that indicate a top‐to‐the‐south sense of shear. Structural fabrics in the Ramgarh thrust sheet are generally parallel to the fabrics in rocks above and below the thrust sheet. Regional and local mapping of the Ramgarh thrust in Nepal demonstrates that the fault always places a hanging wall flat upon a footwall flat, except where local lateral ramps complicate its geometry. Similarly, the structurally overlying Main Central thrust always places a hanging wall flat in Greater Himalayan series rocks upon the regionally flat Ramgarh thrust sheet. These geometric relationships preclude kinematic and thermal models that elevate Greater Himalayan and lower Lesser Himalayan rocks along high‐angle thrust ramps in the vicinity of the present traces of the Ramgarh and Main Central thrust faults. Instead, the corresponding footwall ramps for these thrusts must be located more than 100 km north of the current trace of the Main Central thrust. The present steep dips of the Ramgarh and Main Central thrust sheets can be attributed to tilting during emplacement of structurally lower thrust sheets within a large antiformal duplex that occupies most of the Lesser Himalayan zone. The Ramgarh thrust sheet overlaps a bed length of at least 100 km in lower Miocene foreland basin deposits, indicating that a significant amount of displacement on the thrust must have occurred after ∼15 Ma. Growth of the Lesser Himalayan duplex and additional slip on the frontal part of the Ramgarh thrust occurred from ∼12 to 5 Ma. The presence of a major greenschist‐grade metasedimentary thrust sheet composed of Lesser Himalayan rocks directly below the Main Central thrust suggests that the famous “inverted metamorphism” in this region is a result of structural inversion. Similarly, the concept of a broad zone of intense shear strain related exclusively to emplacement of the Main Central thrust sheet is probably invalid in Nepal.
For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade.
Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean resources of 8.5 billion barrels of oil and 66 trillion cubic feet of gas in continuous accumulations in the Upper Cretaceous Eagle Ford Group and associated Cenomanian-Turonian strata in onshore lands of the U.S. Gulf Coast region, Texas.
Sequence analyses and subtyping of Bacillus anthracis strains from Georgia reveal a single distinct lineage (Aust94) that is ecologically established. Phylogeographic analysis and comparisons to a global collection reveals a clade that is mostly restricted to Georgia. Within this clade, many groups are found around the country, however at least one subclade is only found in the eastern part. This pattern suggests that dispersal into and out of Georgia has been rare and despite historical dispersion within the country, for at least for one lineage, current spread is limited.
South-vergent channel flow from beneath the Tibetan Plateau may have played an important role in forming the Himalaya. The possibility that Greater Himalayan rocks currently exposed in the Himalayan Fold-Thrust Belt flowed at mid-crustal depths before being exhumed is intriguing, and may suggest a natural link between orogenic processes operating under the Tibetan Plateau and in the fold-thrust belt. Conceptual and numeric models for the Himalayan-Tibetan Orogen currently reported in the literature do an admirable job of replicating many of the observable primary geological features and relationships. However, detailed observations from Greater Himalayan rocks exposed in the fold-thrust belt’s external klippen, and from Lesser Himalayan rocks in the proximal footwall of the Main Central Thrust, suggest that since Early Miocene time, it may be more appropriate to model the evolution of the fold-thrust belt using the critical taper paradigm. This does not exclude the possibility that channel flow and linked extrusion of Greater Himalayan rocks may have occurred, but it places important boundaries on a permissible time frame during which these processes may have operated.
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