HIV-1 diversity among young women in rural South Africa: HPTN 068

Background South Africa has one of the highest rates of HIV-1 (HIV) infection world-wide, with the highest rates among young women. We analyzed the molecular epidemiology and evolutionary history of HIV in young women attending high school in rural South Africa. Methods Samples were obtained from the HPTN 068 randomized controlled trial, which evaluated the effect of cash transfers for school attendance on HIV incidence in women aged 13–20 years (Mpumalanga province, 2011–2015). Plasma samples from HIV-infected participants were analyzed using the ViroSeq HIV-1 Genotyping assay. Phylogenetic analysis was performed using 200 pol gene study sequences and 2,294 subtype C reference sequences from South Africa. Transmission clusters were identified using Cluster Picker and HIV-TRACE, and were characterized using demographic and other epidemiological data. Phylodynamic analyses were performed using the BEAST software. Results The study enrolled 2,533 young women who were followed through their expected high school graduation date (main study); some participants had a post-study assessment (follow-up study). Two-hundred-twelve of 2,533 enrolled young women had HIV infection. HIV pol sequences were obtained for 94% (n = 201/212) of the HIV-infected participants. All but one of the sequences were HIV-1 subtype C; the non-C subtype sequence was excluded from further analysis. Median pairwise genetic distance between the subtype C sequences was 6.4% (IQR: 5.6–7.2). Overall, 26% of study sequences fell into 21 phylogenetic clusters with 2–6 women per cluster. Thirteen (62%) clusters included women who were HIV-infected at enrollment. Clustering was not associated with study arm, demographic or other epidemiological factors. The estimated date of origin of HIV subtype C in the study population was 1958 (95% highest posterior density [HPD]: 1931–1980), and the median estimated substitution rate among study pol sequences was 1.98x10-3 (95% HPD: 1.15x10-3–2.81x10-3) per site per year. Conclusions Phylogenetic analysis suggests that multiple HIV subtype C sublineages circulate among school age girls in South Africa. There were no substantive differences in the molecular epidemiology of HIV between control and intervention arms in the HPTN 068 trial

Macrofossils associated with the fossil fern spore Cyatheacidites annulatus and their significance for Southern hemisphere biogeography

Copyright © 2001 Elsevier B.V.Oligocene - Early Miocene macrofossils of parts of a fertile frond are assigned to the extant South American species Lophosoria quadripinnata (Gmel.)C.Chr. These macrofossils bear the dispersed spore species Cyatheacidites annulatus Cookson ex Potonié, which has an extensive recorded history in the Southern hemisphere, only recently retracting to its current range. This history suggests major episodes of expansion and extinction, with a double extinction occurring in Australia and the Falkland Plateau and Cenozoic introductions to the Kerguelen Islands and the Falkland Plateau that probably involved transoceanic dispersal. Cretaceous Lophosoria records may or may not include L. quadripinnata, but they probably included several related species, especially in the southern South America - Antarctic Peninsula region, where other dispersed spore species of Cyatheacidites and the macrofossil species L. cupulatus are recognised. This species diversity probably collapsed during the Cretaceous, possibly due to angiosperm radiation. The Cenozoic record of C. annulatus in Australia appears to represent a radiation of L. quadripinnata, probably from South America and possibly involving long distance dispersal via West Antarctica. © 2001 Elsevier Science B.V. All rights reserved.R. S. Hill, M. K. Macphail and G. J. Jordanhttp://www.elsevier.com/wps/find/journaldescription.cws_home/503359/description#descriptio

A stratigraphic evaluation of Ettingshausen's New England Tertiary plant localities

Published online: 09 May 2007Recent work on Australian Tertiary macrofloras has highlighted the importance of the writings of early workers such as Ettingshausen and Deane; placing their localities in a modern stratigraphic context is an important preliminary to further work. The setting of these localities in New England is examined, and age constraints obtained from palynological and isotope studies are used to provide controls on the stratigraphy. A correlation table of Tertiary volcanic stratigraphy in the most significant areas is provided.J. W. Pickett, N. Smithb, P. M. Bishop, R. S. Hill, M. K. Macphail and W. B. K. Holme

The past is a guide to the future? Comparing Middle Pliocene vegetation with predicted biome distributions for the twenty-first century

During the Middle Pliocene, the Earth experienced greater global warmth compared with today, coupled with higher atmospheric CO2 concentrations. To determine the extent to which the Middle Pliocene can be used as a ‘test bed’ for future warming, we compare data and model-based Middle Pliocene vegetation with simulated global biome distributions for the mid- and late twenty-first century. The best agreement is found when a Middle Pliocene biome reconstruction is compared with a future scenario using 560ppmv atmospheric CO2. In accordance with palaeobotanical data, all model simulations indicate a generally warmer and wetter climate, resulting in a northward shift of the taiga–tundra boundary and a spread of tropical savannahs and woodland in Africa and Australia at the expense of deserts. Our data–model comparison reveals differences in the distribution of polar vegetation, which indicate that the high latitudes during the Middle Pliocene were still warmer than its predicted modern analogue by several degrees. However, our future scenarios do not consider multipliers associated with ‘long-term’ climate sensitivity. Changes in global temperature, and thus biome distributions, at higher atmospheric CO2 levels will not have reached an equilibrium state (as is the case for the Middle Pliocene) by the end of this century