High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afadé and B237.

Members of the Mycoplasma mycoides cluster' represent important livestock pathogens worldwide. Mycoplasma mycoides subsp. mycoides is the etiologic agent of contagious bovine pleuropneumonia (CBPP), which is still endemic in many parts of Africa. We report the genome sequences and annotation of two frequently used challenge strains of Mycoplasma mycoides subsp. mycoides, Afadé and B237. The information provided will enable downstream 'omics' applications such as proteomics, transcriptomics and reverse vaccinology approaches. Despite the absence of Mycoplasma pneumoniae like cyto-adhesion encoding genes, the two strains showed the presence of protrusions. This phenotype is likely encoded by another set of genes.

Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

The Out-of-Africa (OOA) dispersal ∼50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

Global patterns of DNA polymorphism in noncoding regions in human populations

DNA sequence variation is currently a major source of data for studying human origins, evolution, and demographic history, and for detecting linkage association of complex diseases. In this dissertation, I investigated DNA variation in worldwide populations from two ∼10 kb autosomal regions on 22q11.2 (noncoding) and 1q24 (introns). A total of 75 variant sites were found among 128 human sequences in the 22q11.2 region, yielding an estimate of 0.088% for nucleotide diversity (π), and a total of 52 variant sites were found among 122 human sequences in the 1q24 region with an estimated π value of 0.057%. The data from these two regions and a 10 kb noncoding region on Xq13.3 all show a strong excess of low-frequency variants in comparison to that expected from an equilibrium population, indicating a relatively recent population expansion. The effective population sizes estimated from the three regions were 11,000, 12,700, and 8,600, respectively, which are close to the commonly used value of 10,000. In each of the two autosomal regions, the age of the most recent common ancestor (MRCA) was estimated to be older than 1 million years among all the sequences and ∼600,000 years among non-African sequences, providing first evidence from autosomal noncoding or intronic regions for a genetic history of humans much more ancient than the emergence of modern humans. The ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck. This study strongly suggests that both the “out of Africa” and the multiregional models are too simple for explaining the evolution of modern humans. A compilation of genome-wide data revealed that nucleotide diversity is highest in autosomal regions, intermediate in X-linked regions, and lowest in Y-linked regions. The data suggest the existence of background selection or selective sweep on Y-linked loci. In general, the nucleotide diversity in humans is low compared to that in chimpanzee and Drosophila populations. ^

(Table 1) Distribution of copper porphyrins and other pigments in deep-sea sediments

Copper porphyrins have been isolated from deep-sea sediments collected during six legs of the Deep Sea Drilling Project-International Program of Ocean Drilling. These pigments are present in depositional areas receiving high inputs of terrestrially derived oxidized organic matter. Such areas include the Black Sea, the Bay of Biscay, the Blake-Bahama Basin, and slumped Miocene deposits off Cape Bojador on the west coast of Africa.

Late Quaternary planktonic foraminifera of ODP Hole 175-1087A

Planktonic foraminiferal assemblages from the upper Pleistocene part of Hole 1087A (0 to 12.1 meters below seafloor) are investigated to assess the role of global and local climate changes on surface circulation in the southern Benguela region. The benthic stable isotope record indicates that the studied interval is representative of the last four climatic cycles, that is, down to marine isotope Stage (MIS) 12. The species assemblages bear a clear transitional to subpolar character, with Neogloboquadrina pachyderma (d), Globorotalia inflata, and Globigerina bulloides, in order of decreasing abundance, as the dominant taxa. This species association presently characterizes the mixing domain of old upwelled and open ocean waters, seaward of the Benguela upwelling cells. Abundance variation of the dominant foraminiferal species roughly follows a glacial-interglacial pattern down to MIS 8, suggesting an alternation of upwelling strength and associated seaward extension of the belt of upwelled water as a response to global climate changes. This pattern is interrupted from ~250 ka down to MIS 12, where the phase relationship with global climate is ill defined and might be interpreted as a local response of the southern Benguela region to the mid-Brunhes event. Of particular interest is a single pulse of newly upwelled waters at the location of Site 1087 during early MIS 9 as indicated by a peak abundance of sinistral N. pachyderma (s). Variable input of warm, salty Indian Ocean thermocline waters into the southeast Atlantic, a key component of the Atlantic heat conveyor, is indicated by abundance changes of the tropical taxon Globorotalia menardii. From this tracer, we suggest that interocean exchange was hardly interrupted throughout the last 460 k.y., but was most effective at glacial terminations, particularly during Terminations I and II, as well as during the upper part of MIS 12. This maximum input of Indian Ocean waters around the southern tip of Africa is associated with the reseeding of G. menardii in the tropical Atlantic.

Sedimentology, foraminiferal assemblage, and isotope record of the Agulhas Bank region

The Agulhas Bank region, south of Africa, is an oceanographically important and complex area. The leakage of warm saline Indian Ocean water into the South Atlantic around the southern tip of Africa is a crucial factor in the global thermohaline circulation. Foraminiferal assemblage, stable isotope and sedimentological data from the top 10 m of core MD962080, recovered from the western Agulhas Bank Slope, are used to indicate changes in water mass circulation in the southeastern South Atlantic for the last 450 kyr. Sedimentological and planktonic foraminiferal data give clear signals of cold water intrusions. The benthic stable isotope record provides the stratigraphic framework and indicates that the last four climatic cycles are represented (i.e. down to marine isotope stage (MIS) 12). The planktonic foraminiferal assemblages bear a clear transitional to subantarctic character with Globorotalia inflata and Neogloboquadrina pachyderma (dextral) being the dominant taxa. Input of cold, subantarctic waters into the region by means of leakage through the Subtropical Convergence, as part of Agulhas ring shedding, and a general cooling of surface waters is suggested by increased occurrence of the subantarctic assemblage during glacial periods. Variable input of Indian Ocean waters via the Agulhas Current is indicated by the presence of tropical/subtropical planktonic foraminiferal species Globoquadrina dutertrei, Globigerinoides ruber (alba) and Globorotalia menardii with maximum leakage occurring at glacial terminations. The continuous presence of G. menardii throughout the core suggests that the exchange of water from the South Indian Ocean to the South Atlantic Ocean was never entirely obstructed in the last 450 kyr. The benthic carbon isotope record and sediment textural data reflect a change in bottom water masses over the core location from North Atlantic Deep Water to Upper Southern Component Water. Planktonic foraminiferal assemblages and sediment composition indicate a profound change in surface water conditions over the core site approximately 200-250 kyr BP, during MIS 7, from mixed subantarctic and transitional water masses to overall warmer surface water conditions.

Chemical and amino acid compositions of bottom sediments from the Canary upwelling

Amino acid composition of bottom sediments on the northwestern continental slope of Africa is determined. Correlation similar to that found earlier in Caspian sediments between type of amino acid spectra of Atlantic sediments and distribution of reduced forms of sulfur in them is found. These correlations result from geochemical activity of benthic biocoenosis, which transforms sulfur compounds.

Planktonic foraminiferas in bottom sediments and Late Quaternary paleotemperatures of surface waters in the North Tropical Atlantic

Distribution of planktonic foraminiferal tests was studied in 15 Upper Quaternary sediment cores from the continental slope of Africa, the Canary and Cape Verde basins, and slopes of the Mid-Atlantic Ridge. In all the cores substantial variations were found in relationship between foraminiferal planktonic species reflecting fluctuations of mean annual temperatures of surface waters. Temperature difference in temperatures between present time and that of the maximum of the stadial of the last continental glaciation glacial stadial (about 18,000 yrs ago) ranges from 8.5°C in the Canary upwelling region to minimum values of 2.0°C in the central part of the ocean, i.e. the southern part of the subtropical gyre. Temperature difference the Holocene optimum and 18,000 yrs ago ranges from 10°C to 3°C. Age estimates are supported by radiocarbon dates.

Ostracoda fauna of surface sediments from the Persian Gulf

During the "Meteor"-Expedition to the Persian Gulf in March-May 1965, approximately 300 samples were collected. Most of them have been already studied by various authors in sedimentological as well as micropaleontological respects. 49 samples were selected for ostracode studies. These samples are arranged to form a long-axis section ("Laengsprofil"), and 4 shorter cross-profiles, perpendicular to the long-axis profile in the Persian Gulf and Gulf of Oman. 52 species of ostracodes in this area were specifically determined; 39 of them are described under open nomenclature. 13 species are already known from surrounding sea areas: 2 species from the Red Sea; 2 species from the east coast of Africa; 1 species from the Mediterranean Sea; and others from the Indian and Pacific Oceans. 12 species show close relationships to species from the Indopacific Ocean. The ostracode species found in the area can be grouped after the method of BRAUN-BLANQUT into 2 bioassociations. Association 1 with the following 4 characteristic species : Cytherella cf. pulchra, Loxoconcha sp. A, Neomonoceratina sp. A, Alocopocythere reticulata. Association 2 with 1 characteristic species: Ruggieria (Ruggieria) sp. B. The association 1 is widespread in the entire studied area of the Persian Gulf, where it is considered to characterize the shallow water region down to 200 m. The association 2 is restricted to the deeper water below 200 m of the inner part of the Oman Gulf. Only a few species known from the shallow water association of the Persian Gulf are present. Within the two ostracode associations mentioned above 4 zones from the total studied area could be related to the water depth. The zones A-D are characterized more or less readily by the relative abundance of certain species: Zone A : 7-30 m depth, on substrates of poorly coarse-grained clayey marl; Zone B: 30-94 m depth, on substrates of richly coarse-grained calcareous marl; Zone C: 94-1961208 m depth, on substrates of richly coarse-grained calcareous marl; Zone D: 196/208-500 m depth, on substrates of calcareous clay, poor in benthos. The regional and bathymetric distribution of the ostracode fauna in the area studied was compared in relation to 10 environmental factors: water depth, temperature, salinity, water density, O2-concentration, phosphate-silica contents, pH-values, stratification of the water body, water currents and type of sediments. The major environmental factors which appear to control the ostracode distribution are water depth (as a complex factor), O2-concentration and the type of sediment. At 3 stations (GIK01058, GIK01074 and GIK01204) species of the shallow water association were found together with a few bathyal species. These stations are situated at the outer Biaban shelf, in an area where the bottom water of the Persian Gulf flows down the slope towards the Oman Gulf. Several samples of the Zone B in the major part of the Persian Gulf show also a high species diversity containing a high percentage of subfossil ostracode carapaces. It is probable that the recent biocoenosis has been mixed with a late quarternary thanatocoenosis.

Model simulation output data (CCSM3) related to uplift of African topography and the intensification of upwelling in the Benguela region

The Benguela Current, located off the west coast of southern Africa, is tied to a highly productive upwelling system**1. Over the past 12 million years, the current has cooled, and upwelling has intensified**2, 3, 4. These changes have been variously linked to atmospheric and oceanic changes associated with the glaciation of Antarctica and global cooling**5, the closure of the Central American Seaway**1, 6 or the further restriction of the Indonesian Seaway**3. The upwelling intensification also occurred during a period of substantial uplift of the African continent**7, 8. Here we use a coupled ocean-atmosphere general circulation model to test the effect of African uplift on Benguela upwelling. In our simulations, uplift in the East African Rift system and in southern and southwestern Africa induces an intensification of coastal low-level winds, which leads to increased oceanic upwelling of cool subsurface waters. We compare the effect of African uplift with the simulated impact of the Central American Seaway closure9, Indonesian Throughflow restriction10 and Antarctic glaciation**11, and find that African uplift has at least an equally strong influence as each of the three other factors. We therefore conclude that African uplift was an important factor in driving the cooling and strengthening of the Benguela Current and coastal upwelling during the late Miocene and Pliocene epochs.

Age models of ODP Leg 175 holes

A multiproxy approach including the use of stable isotopes, magnetic characterization analyses, and organic geochemistry has been adopted to consider factors such as productivity and terrigenous input over the past 1.5 m.y. at two areas off the western coast of Africa. These factors can, in turn, be used to consider variability in ocean circulation and upwelling in addition to changes in climate on the African continent. In particular, studies focused on the influence of glacial-interglacial cycles and evidence for the mid-Pleistocene revolution (MPR), a complex change in climate that occurred at ~1 Ma. A comparison of the records from the two areas drilled during Ocean Drilling Program Leg 175, the Congo Basin, at a latitude of 5°S (Holes 1076A and 1077A), and the Walvis Ridge, at 17°S (Hole 1081A), demonstrates that these sites are affected by different localized factors. The sites in the Congo Basin are strongly influenced by freshwater and sediment from the Congo River, whereas the site at the Walvis Ridge is located in the center of oceanic upwelling and contains a more marine signal. Evidence also suggests that the two sites responded differently to both long- and short-term climatic variations. In particular, the response at the Walvis Ridge to the MPR occurred over an extended period, from 1.1 to 0.8 Ma, and was associated with a change in the dominant source of terrigenous input to the site in conjunction with a change in the productivity signal. In the Congo Basin, the response to the MPR was more rapid, occurring between 0.9 and 0.8 Ma. During this period, the influence of the Congo River became significant. However, productivity records only began to respond toward the end of this interval, at 0.8 Ma.