Persistence of Artemisia steppe in the Tangra Yumco Basin, west-central Tibet, China: despite or in consequence of Holocene lake-level changes?

The closed Tangra Yumco Basin underwent the strongest Quaternary lake-level changes so far recorded on the Tibetan Plateau. It was hitherto unknown what effect this had on local Holocene vegetation development. A 3.6-m sediment core from a recessional lake terrace at 4,700 m a.s.l., 160 m above the present lake level of Tangra Yumco, was studied to reconstruct Holocene flooding phases (sedimentology and ostracod analyses), vegetation dynamics and human influence (palynology, charcoal and coprophilous fungi analyses). Peat at the base of the profile proves lake level was below 4,700 m a.s.l. during the Pleistocene/Holocene transition. A deep-lake phase started after 11 cal ka BP, but the ostracod record indicates the level was not higher than similar to 4,720 m a.s.l. (180 m above present) and decreased gradually after the early Holocene maximum. Additional sediment ages from the basin suggest recession of Tangra Yumco from the coring site after 2.6 cal ka BP, with a shallow local lake persisting at the site until similar to 1 cal ka BP. The final peat formation indicates drier conditions thereafter. Persistence of Artemisia steppe during the Holocene lake high-stand resembles palynological records from west Tibet that indicate early Holocene aridity, in spite of high lake levels that may have resulted from meltwater input. Yet pollen assemblages indicate humidity closer to that of present potential forest areas near Lhasa, with 500-600 mm annual precipitation. Thus, the early mid-Holocene humidity was sufficient to sustain at least juniper forest, but Artemisia dominance persisted as a consequence of a combination of environmental disturbances such as (1) strong early Holocene climate fluctuations, (2) inundation of habitats suitable for forest, (3) extensive water surfaces that served as barriers to terrestrial diaspore transport from refuge areas, (4) strong erosion that denuded the non-flooded upper slopes and (5) increasing human influence since the late glacial.

"Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis

Background Mycobacterium tuberculosis has a global population structure consisting of six main phylogenetic lineages associated with specific geographic regions and human populations. One particular M. tuberculosis genotype known as “Beijing” has repeatedly been associated with drug resistance and has been emerging in some parts of the world. “Beijing” strains are traditionally defined based on a characteristic spoligotyping pattern. We used three alternative genotyping techniques to revisit the phylogenetic classification of M. tuberculosis complex (MTBC) strains exhibiting the typical “Beijing” spoligotyping pattern. Methods and Findings MTBC strains were obtained from an ongoing molecular epidemiological study in Switzerland and Nepal. MTBC genotyping was performed based on SNPs, genomic deletions, and 24-loci MIRU-VNTR. We identified three MTBC strains from patients originating from Tibet, Portugal and Nepal which exhibited a spoligotyping patterns identical to the classical Beijing signature. However, based on three alternative molecular markers, these strains were assigned to Lineage 3 (also known as Delhi/CAS) rather than to Lineage 2 (also known as East-Asian lineage). Sequencing of the RD207 in one of these strains showed that the deletion responsible for this “Pseudo-Beijing” spoligotype was about 1,000 base pairs smaller than the usual deletion of RD207 in classical “Beijing” strains, which is consistent with an evolutionarily independent deletion event in the direct repeat (DR) region of MTBC. Conclusions We provide an example of convergent evolution in the DR locus of MTBC, and highlight the limitation of using spoligotypes for strain classification. Our results indicate that a proportion of “Beijing” strains may have been misclassified in the past. Markers that are more phylogenetically robust should be used when exploring strain-specific differences in experimental or clinical phenotypes.