Asian genotypes of JC virus in Native Americans and in a Pacific Island population: Markers of viral evolution and human migration

The human polyomavirus JC (JCV) causes the central nervous system demyelinating disease progressive multifocal leukoencephalopathy. Previously, we showed that 40% of Caucasians in the United States excrete JCV in the urine as detected by PCR. We have now studied 68 Navaho from New Mexico, 25 Flathead from Montana, and 29 Chamorro from Guam. By using PCR amplification of a fragment of the VP1 gene, JCV DNA was detected in the urine of 45 (66%) Navaho, 14 (56%) Flathead, and 20 (69%) Chamorro. Genotyping of viral DNAs in these cohorts by cycle sequencing showed predominantly type 2 (Asian), rather than type 1 (European). Type 1 is the major type in the United States and Hungary. Type 2 can be further subdivided into 2A, 2B, and 2C. Type 2A is found in China and Japan. Type 2B is a subtype related to the East Asian type, and is now found in Europe and the United States. The large majority (56–89%) of strains excreted by Native Americans and Pacific Islanders were the type 2A subtype, consistent with the origin of these strains in Asia. These findings indicate that JCV infection of Native Americans predates contact with Europeans, and likely predates migration of Amerind ancestors across the Bering land bridge around 12,000–30,000 years ago. If JCV had already differentiated into stable modern genotypes and subtypes prior to first settlement, the origin of JCV in humans may date from 50,000 to 100,000 years ago or more. We conclude that JCV may have coevolved with the human species, and that it provides a convenient marker for human migrations in both prehistoric and modern times.

Ancient single origin for Malagasy primates.

We report new evidence that bears decisively on a long-standing controversy in primate systematics. DNA sequence data for the complete cytochrome b gene, combined with an expanded morphological data set, confirm the results of a previous study and again indicate that all extant Malagasy lemurs originated from a single common ancestor. These results, as well as those from other genetic studies, call for a revision of primate classifications in which the dwarf and mouse lemurs are placed within the Afro-Asian lorisiforms. The phylogenetic results, in agreement with paleocontinental data, indicate an African origin for the common ancestor of lemurs and lorises (the Strepsirrhini). The molecular data further suggest the surprising conclusion that lemurs began evolving independently by the early Eocene at the latest. This indicates that the Malagasy primate lineage is more ancient than generally thought and places the split between the two strepsirrhine lineages well before the appearance of known Eocene fossil primates. We conclude that primate origins were marked by rapid speciation and diversification sometime before the late Paleocene.

Genetics and the origin of European languages.

A new set of European genetic data has been analyzed to dissect independent patterns of geographic variation. The most important cause of European genetic variation has been confirmed to correspond to the migration of Neolithic farmers from the area of origin of agriculture in the Middle East. The next most important component of genetic variation is apparently associated with a north-south gradient possibly due to adaptation to cold climates but also to the differentiation of the Uralic and the Indo-European language-speaking people; however, the relevant correlations are not significantly different from zero after elimination of the spatial autocorrelation. The third component is highly correlated with the infiltration of the Yamna ("Kurgan") people, nomadic pastoralists who domesticated the horse and who have been claimed to have spread Indo-European languages to Europe; this association, which is statistically significant even when taking spatial autocorrelations into account, does not completely exclude the hypothesis of Indo-European as the language of Neolithic farmers. It is possible that both expansions were responsible for the spread of different subfamilies of Indo-European languages, but our genetic data cannot resolve their relative importance.

Emergence of a new epidemic/epizootic Venezuelan equine encephalitis virus in South America.

One of the most important questions in arbovirology concerns the origin of epidemic Venezuelan equine encephalitis (VEE) viruses; these viruses caused periodic, extensive epidemics/epizootics in the Americas from 1938-1973 (reaching the United States in 1971) but had recently been presumed extinct. We have documented the 1992 emergence of a new epidemic/epizootic VEE virus in Venezuela. Phylogenetic analysis of strains isolated during two outbreaks indicated that the new epidemic/epizootic virus(es) evolved recently from an enzootic VEE virus in northern South America. These results suggest continued emergence of epizootic VEE viruses; surveillance of enzootic viruses and routine vaccination of equines should therefore be resumed.

Isolation and molecular characterization of a human T-cell lymphotropic virus type II (HTLV-II), subtype B, from a healthy Pygmy living in a remote area of Cameroon: an ancient origin for HTLV-II in Africa.

We report characterization of a human T-cell lymphotropic virus type II (HTLV-II) isolated from an interleukin 2-dependent CD8 T-cell line derived from peripheral blood mononuclear cells of a healthy, HTLV-II-seropositive female Bakola Pygmy, aged 59, living in a remote equatorial forest area in south Cameroon. This HTLLV-II isolate, designated PYGCAM-1, reacted in an indirect immunofluorescence assay with HTLV-II and HTLV-I polyclonal antibodies and with an HTLV-I/II gp46 monoclonal antibody but not with HTLV-I gag p19 or p24 monoclonal antibodies. The cell line produced HTLV-I/II p24 core antigen and retroviral particles. The entire env gene (1462 bp) and most of the long terminal repeat (715 bp) of the PYGCAM-1 provirus were amplified by the polymerase chain reaction using HTLV-II-specific primers. Comparison with the long terminal repeat and envelope sequences of prototype HTLV-II strains indicated that PYGCAM-1 belongs to the subtype B group, as it has only 0.5-2% nucleotide divergence from HTLV-II B strains. The finding of antibodies to HTLV-II in sera taken from the father of the woman in 1984 and from three unrelated members of the same population strongly suggests that PYGCAM-1 is a genuine HTLV-II that has been present in this isolated population for a long time. The low genetic divergence of this African isolate from American isolates raises questions about the genetic variability over time and the origin and dissemination of HTLV-II, hitherto considered to be predominantly a New World virus.

A 300 kyr record of upwelling off Oman during the Late Quaternary: evidence of the Asian southwest monsoon

In the northwest Arabian Sea upwelling occurs each summer, driven by the strong SW monsoon winds. Upwelling results in high biological productivity and a distinctive assemblage of plankton species in the surface waters off Oman that are preserved in the sediments along the Oman continental margin, creating a geologic record of monsoon-driven upwelling. Sediments recovered from the Oman continental margin during Ocean Drilling Program leg 117 provide an opportunity to examine how upwelling has varied during the late Quaternary, spanning a longer interval than piston cores recovered prior to the ODP cruise. Variations in foraminifer shell accumulation and in the relative abundance of Globigerina bulloides indicate dominant cycles of variation at 1/100 kyr, the dominant frequency of glacial-interglacial variations, and at 1/23 kyr, the frequency of precessionally driven cycles in seasonal insolation. The strongest monsoon winds (indicated by increased upwelling) occurred during interglacial times when perihelion was aligned with the summer solstice, an orbital change that increased the insolation received during summer in the northern hemisphere. During glacial times upwelling was reduced, and although the precessional cycles were still present their amplitude was smaller. At both frequencies the upwelling cycles are in phase with minimum ice volume, evidence that glacial-interglacial climate changes also include changes to the climate system that influence the low-latitude monsoon. We attribute the decrease in the monsoon winds observed during glacial times to changes in bare land albedo over Asia and/or to changes in the areal extent and seasonal cycle in Asian snow cover that decrease the summer land-sea temperature contrast. Other mechanisms may also be involved. These new upwelling time series differ substantially from previous results, however the previous work relied on cores located farther offshore where upwelling is less intense and other physical mechanisms become important. Our results support the observations derived from atmospheric general circulation models of the atmosphere that indicate that both glacial boundary conditions, and the strength of summer insolation are important variables contributing to cycles in the monsoon winds during the late Quaternary.

Petrology and geochemistry of sideromelane glass shards from Pleistocene as layers north and south of Gran Canaria

Major elements, S, F, Cl concentrations and relative proportions of S6+ to total S were analyzed with electron microprobe in sideromelane glass shards from Pleistocene volcaniclastic sediments drilled during ODP Leg 157. Glasses are moderately to strongly evolved and represent a spectrum from alkali basalt, basanite and nephelinite through hawaiite, mugearite and tephrite to phonolitic tephrite. Measured S6+/SumS (0.03±0.98) and calculated Fe2+/Fe3+ (2.5±5.8) ratios in the melt yield preeruptive redox conditions ranging from NNO-1.4 to NNO+2.1. The morphology of the glass shards, variations of S and Cl concentrations (0.010±0.127 wt% S, 0.018±0.129 wt% Cl), calculated preeruptive temperatures (1030±1200 °C) and oxygen fugacities suggest that glasses deposited even within the same ash layers have diverse origin and may have resulted from both submarine and subaerial eruptions. Most vesicle-free glasses are characterized by high concentrations of S and represent undegassed or slightly degassed submarine lavas, whereas vesiculated glasses with low concentrations of S and Cl are strongly degassed and can be ascribed to the eruptions in shallow water or on land. Sideromelane glass shards at Sites 953 are thought to have resulted from submarine eruptions northeast of Gran Canaria, glasses at Site 954 represent mostly volcaniclastic material of shallow water submarine and subaerial eruptions on Gran Canaria and Tenerife, and glasses deposited at Site 956 resulted from submarine or explosive eruptions on Tenerife.

Pliocene-Pleistocene stack of globally distributed benthic stable oxygen isotope records

We present a 5.3-Myr stack (the ''LR04'' stack) of benthic d18O records from 57 globally distributed sites aligned by an automated graphic correlation algorithm. This is the first benthic delta18O stack composed of more than three records to extend beyond 850 ka, and we use its improved signal quality to identify 24 new marine isotope stages in the early Pliocene. We also present a new LR04 age model for the Pliocene-Pleistocene derived from tuning the delta18O stack to a simple ice model based on 21 June insolation at 65 N. Stacked sedimentation rates provide additional age model constraints to prevent overtuning. Despite a conservative tuning strategy, the LR04 benthic stack exhibits significant coherency with insolation in the obliquity band throughout the entire 5.3 Myr and in the precession band for more than half of the record. The LR04 stack contains significantly more variance in benthic delta18O than previously published stacks of the late Pleistocene as the result of higher resolution records, a better alignment technique, and a greater percentage of records from the Atlantic. Finally, the relative phases of the stack's 41- and 23-kyr components suggest that the precession component of delta18O from 2.7-1.6 Ma is primarily a deep-water temperature signal and that the phase of d18O precession response changed suddenly at 1.6 Ma.

Body condition indices of Asian green mussels, Perna viridis, from Indonesia

While part of a single country, the Indonesian archipelago covers several biogeographic regions, and the high levels of national shipping likely facilitate transfer of non-native organisms between the different regions. Two vessels of a domestic shipping line appear to have served as a transport vector for the Asian green mussel Perna viridis (Linnaeus, 1758) between regions. This species is indigenous in the western but not in the eastern part of the archipelago, separated historically by the Sunda Shelf. The green mussels collected from the hulls of the ferries when in eastern Indonesia showed a significantly lower body condition index than similar-sized individuals from three different western-Indonesian mussel populations. This was presumably due to reduced food supply during the ships' voyages. Although this transportinduced food shortage may initially limit the invasive potential (through reduced reproductive rates) of the translocated individuals, the risk that the species will extend its distributional range further into eastern Indonesia is high. If the species becomes widely established in eastern Indonesia, there will then be an increased risk of incursions to Australia, where the mussel is listed as a high-priority pest species.

Whole rock analytical techniques and glas analytical techniques of silicic magmas from the South East Rift, Manus Basin

There has been much recent interest in the origin of silicic magmas at spreading centres away from any possible influence of continental crust. Here we present major and trace element data for 29 glasses (and 55 whole-rocks) sampled from a 40 km segment of the South East Rift in the Manus Basin that span the full compositional continuum from basalt to rhyolite (50-75 wt % SiO2). The glass data are accompanied by Sr-Nd-Pb, O and U-Th-Ra isotope data for selected samples. These overlap the ranges for published data from this part of the Manus Basin. Limited increases in Cl/K ratios with increasing SiO2, La-SiO2 and Yb-SiO2 relationships, and the oxygen isotope data rule out models in which the more silicic lavas result from partial melting of altered oceanic crust or altered oceanic gabbros. Rather, the data form a coherent array that is suggestive of closed-system fractional crystallization and this is well simulated by MELTS models run at 0.2 GPa and QFM (quartz-fayalite-magnetite buffer) with 1 wt % H2O, using a parental magma chosen from the basaltic glasses. Although some assimilation of altered oceanic crust or gabbro cannot be completely ruled out, there is no evidence that this plays an important role in the origin of the silicic lavas. The U-series disequilibria are dominated by 238U and 226Ra excesses that limit the timescale of differentiation to less than a few millennia. Overall, the data point to rapid evolution in relatively small magma lenses located near the base of thick oceanic crust; we speculate that this was coupled with relatively low rates of basaltic recharge. A similar model may be applicable to the generation of silicic magmas elsewhere in the ocean basins.