Ecological niche and geographic distribution of human monkeypox in Africa

Monkeypox virus, a zoonotic member of the genus Orthopoxviridae, can cause a severe, smallpox-like illness in humans. Monkeypox virus is thought to be endemic to forested areas of western and Central Africa. Considerably more is known about human monkeypox disease occurrence than about natural sylvatic cycles of this virus in non-human animal hosts. We use human monkeypox case data from Africa for 1970-2003 in an ecological niche modeling framework to construct predictive models of the ecological requirements and geographic distribution of monkeypox virus across West and Central Africa. Tests of internal predictive ability using different subsets of input data show the model to be highly robust and suggest that the distinct phylogenetic lineages of monkeypox in West Africa and Central Africa occupy similar ecological niches. High mean annual precipitation and low elevations were shown to be highly correlated with human monkeypox disease occurrence. The synthetic picture of the potential geographic distribution of human monkeypox in Africa resulting from this study should support ongoing epidemiologic and ecological studies, as well as help to guide public health intervention strategies to areas at highest risk for human monkeypox.     

Ecology and geography of plague transmission areas in northeastern Brazil

Plague in Brazil is poorly known and now rarely seen, so studies of its ecology are difficult. We used ecological niche models of historical (1966-present) records of human plague cases across northeastern Brazil to assess hypotheses regarding environmental correlates of plague occurrences across the region. Results indicate that the apparently focal distribution of plague in northeastern Brazil is indeed discontinuous, and that the causes of the discontinuity are not necessarily only related to elevation-rather, a diversity of environmental dimensions correlate to presence of plague foci in the region. Perhaps most interesting is that suitable areas for plague show marked seasonal variation in photosynthetic mass, with peaks in April and May, suggesting links to particular land cover types. Next steps in this line of research will require more detailed and specific examination of reservoir ecology and natural history.     

Ecology of cobras from southern Africa

Large slender-bodied snakes that forage actively for a generalized array of small vertebrates are conspicuous elements of the terrestrial snake fauna of most continents; the venomous elapid species fill this role in much of Asia, Africa and Australia. Our dissections of eight species of cobras from southern Africa Aspidelaps, Hemachatus, Naja; Serpentes and Elapidae (total of 1290 specimens) provide extensive data on sexual dimorphism, reproductive biology and food habits. Females grow larger than males in Aspidelaps lubricus and Naja nigricincta , but (perhaps reflecting selection on male body size due to male–male combat) males grow as large as females in Naja anchietae, Naja melanoleuca, Naja mossambica, Naja nivea and Hemachatus haemachatus , and males grow larger than females in Naja annulifera . Overall, the degree of male size superiority is higher in species with a larger absolute mean adult body size. Male cobras typically have larger heads and longer tails than conspecific females. Fecundity increases with maternal body size, and is higher in the viviparous rhinkals H. haemachatus than in the oviparous Naja species studied. Diets are broad in all eight species, comprising a wide variety of amphibians, reptiles, mammals and (less often) birds. Ontogenetic (size-related) shifts in dietary composition (amphibian to reptile to mammal) are significant within some taxa ( N. annulifera, N. nigricincta ) but absent in others (notably N. nivea , the most arid-adapted species). Overall, despite substantial interspecific variation among the eight study species, strong parallels are evident between the cobras of southern Africa and their ecological counterparts in other continents.     

Ecology of small rodents in Africa

This account considers progress in research on small rodent ecology since about 1970. While some ecological survey has been undertaken throughout much of the continent, the main research thrust has involved the detailed examination of population processes in a range of habitats from deserts to tropical rain forests. The deserts and semi-arid regions support a range of species with some better adapted to these harsh conditions than others. The adaptations manifest themselves in different life history strategies e.g., opportunistic with high turnover species, or low turnover-low reproduction species, in their physiology e.g., adaption to water retention, and in their behaviour e.g., avoiding heat of day. Long term studies show large numerical fluctuations with a quick response by some species to favourable conditions caused by relatively high precipitation. In the savanna and grasslands, studies have centred on population dynamics, the relationship between food and breeding, reproductive and life history strategies and the determination of niche. These have been approached through the study of groups of species in particular localities as well as by the examination of individual species. In these habitats populations are more stable and less erratic than in semi-arid regions. Perturbations, particularly fire, can have various effects on the numbers and species composition of the disturbed area. In the tropical rain forest population fluctuations are modest and may take up to 2–3 years to pass from a peak to a trough and back again. Breeding typically extends over much of the year with, apparently, the greatest number of rodents occurring on the ground surface. Bush and temporary farms derived as a result of forest modification support more animals (and often more species) than forest. The niches occupied by forest rodents are poorly understood and very little is known of the ecology within the canopy. In most localities a small number of species are abundant and the remainder much less frequent.     

Mid-Holocene and glacial-maximum vegetation geography of the northern continents and Africa

BIOME 6000 is an international project to map vegetation globally at mid‐Holocene (6000 ¹⁴C yr bp ) and last glacial maximum (LGM, 18,000 ¹⁴C yr bp ), with a view to evaluating coupled climate‐biosphere model results. Primary palaeoecological data are assigned to biomes using an explicit algorithm based on plant functional types. This paper introduces the second Special Feature on BIOME 6000. Site‐based global biome maps are shown with data from North America, Eurasia (except South and Southeast Asia) and Africa at both time periods. A map based on surface samples shows the method’s skill in reconstructing present‐day biomes. Cold and dry conditions at LGM favoured extensive tundra and steppe. These biomes intergraded in northern Eurasia. Northern hemisphere forest biomes were displaced southward. Boreal evergreen forests (taiga) and temperate deciduous forests were fragmented, while European and East Asian steppes were greatly extended. Tropical moist forests (i.e. tropical rain forest and tropical seasonal forest) in Africa were reduced. In south‐western North America, desert and steppe were replaced by open conifer woodland, opposite to the general arid trend but consistent with modelled southward displacement of the jet stream. The Arctic forest limit was shifted slighly north at 6000 ¹⁴C yr bp in some sectors, but not in all. Northern temperate forest zones were generally shifted greater distances north. Warmer winters as well as summers in several regions are required to explain these shifts. Temperate deciduous forests in Europe were greatly extended, into the Mediterranean region as well as to the north. Steppe encroached on forest biomes in interior North America, but not in central Asia. Enhanced monsoons extended forest biomes in China inland and Sahelian vegetation into the Sahara while the African tropical rain forest was also reduced, consistent with a modelled northward shift of the ITCZ and a more seasonal climate in the equatorial zone. Palaeobiome maps show the outcome of separate, independent migrations of plant taxa in response to climate change. The average composition of biomes at LGM was often markedly different from today. Refugia for the temperate deciduous and tropical rain forest biomes may have existed offshore at LGM, but their characteristic taxa also persisted as components of other biomes. Examples include temperate deciduous trees that survived in cool mixed forest in eastern Europe, and tropical evergreen trees that survived in tropical seasonal forest in Africa. The sequence of biome shifts during a glacial‐interglacial cycle may help account for some disjunct distributions of plant taxa. For example, the now‐arid Saharan mountains may have linked Mediterranean and African tropical montane floras during enhanced monsoon regimes. Major changes in physical land‐surface conditions, shown by the palaeobiome data, have implications for the global climate. The data can be used directly to evaluate the output of coupled atmosphere‐biosphere models. The data could also be objectively generalized to yield realistic gridded land‐surface maps, for use in sensitivity experiments with atmospheric models. Recent analyses of vegetation‐climate feedbacks have focused on the hypothesized positive feedback effects of climate‐induced vegetation changes in the Sahara/Sahel region and the Arctic during the mid‐Holocene. However, a far wider spectrum of interactions potentially exists and could be investigated, using these data, both for 6000 ¹⁴C yr bp and for the LGM.     

Outbreaks of human monkeypox after cessation of smallpox vaccination

The recent observation of a surge in human monkeypox in the Democratic Republic of the Congo (DRC) prompts the question of whether cessation of smallpox vaccination is driving the phenomenon, and if so, why is re-emergence not universal throughout the historic geographic range of the virus? Research addressing the virus's mechanisms for immune evasion and induction, as well as that directed at elucidating the genes involved in pathogenesis in different viral lineages (West African vs Congo Basin), provide insights to help explain why emergence appears to be geographically limited. Novel vaccines offer one solution to curtail the spread of this disease.     

Political Ecology across Spaces, Scales, and Social Groups

Political Ecology across Spaces, Scales, and Social Groups. Susan Paulson and Lisa Gezon, eds. New Brunswick, NJ: Rutgers University Press, 2005. 289 pp.     

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions.

Orthopoxviruses are among the largest and most complex of the animal viruses. In response to the recent emergence of monkeypox in Africa and the threat of smallpox bioterrorism, two orthopoxviruses with different pathogenic potentials, human monkeypox virus and vaccinia virus, were proteomically compared with the goal of identifying proteins required for pathogenesis. Orthopoxviruses were grown in HeLa cells to two different viral forms (intracellular mature virus and extracellular enveloped virus), purified by sucrose gradient ultracentrifugation, denatured using RapiGest surfactant, and digested with trypsin. Unfractionated samples and strong cation exchange HPLC fractions were analyzed by high-resolution reversed-phase nano-LC-MS/MS, and analyses of the MS/MS spectra using SEQUEST and X! Tandem resulted in the confident identification of hundreds of monkeypox, vaccinia, and copurified host-cell proteins. The unfractionated samples were additionally analyzed by LC-MS using an LTQ-Orbitrap, and the accurate mass and elution time tag approach was used to perform quantitative comparisons. Possible pathophysiological roles of differentially abundant Orthopoxvirus proteins are discussed. Data, processed results, and protocols are available at http://www.proteomicsresource.org/.     

The Origins and Maintenance of Female Genital Modification across Africa

We present formal evolutionary models for the origins and persistence of the practice of Female Genital Modification (FGMo). We then test the implications of these models using normative cross-cultural data on FGMo in Africa and Bayesian phylogenetic methods that explicitly model adaptive evolution. Empirical evidence provides some support for the findings of our evolutionary models that the de novo origins of the FGMo practice should be associated with social stratification, and that social stratification should place selective pressures on the adoption of FGMo; these results, however, are tempered by the finding that FGMo has arisen in many cultures that have no social stratification, and that forces operating orthogonally to stratification appear to play a more important role in the cross-cultural distribution of FGMo. To explain these cases, one must consider cultural evolutionary explanations in conjunction with behavioral ecological ones. We conclude with a discussion of the implications of our study for policies designed to end the practice of FGMo.     

Ecology and fish catches in natural lakes of Benin,West Africa

Synopsis A preliminary study of the ecology and commercial fish catches was carried out in the Toho-Todougba, Ahouangan and Dati lakes (1500 ha) in southern Benin (West Africa) over a period of 18 consecutive months. Water quality, species richness, and the reproductive biology of the dominant species, Sarotherodon galilaeus, were examined. Unlike Lagoon Toho-Todougba, lakes Ahouangan and Dati are less favourable for fish production because of their high total iron content and their relative low pH. The study revealed the existence of 19 species belonging to eleven (11) families: 16 species in Lagoon Toho-Todougba,12 in Lake Ahouangan, and 7 in Lake Dati. Lakes Ahouangan and Dati had a relatively high faunal similarity whereas Lagoon Toho-Todougba exhibited a relatively low faunal similarity with the former systems. In Lagoon Toho-Todougba, six cichlid species were the most important component of the fishery: Sarotherodon galilaeus, Tilapia guineensis, T. zillii, T. mariae, Chromidotilapia guntheri, Hemichromis fasciatus. Three catfish species Chrysichthys auratus, Clarias agboyiensis, and Clarias lazera were harvested in low abundances. Some other fish, such as Polypterus senegalus senegalus, Protopterus annectens and Heterotis niloticus were captured sporadically, with H. niloticus appearing more consistently in catches than the others. Although not abundant, Gymnarchus niloticus and the African pike, Hepsetus odoe, were almost always present in the catches. Ctenopoma kingsleyae appeared only in Ahouangan. Some predatory species, such as Notopterus afer and Xenomystus nigri, are encountered only in lakes Ahouangan and Dati. In Lagoon Toho-Todougba, Sarotherodon galilaeus had a sex ratio (: ) of 0.49:1, and size at maturation was estimated as 12.3 cm TL. The spawning period extended from May to September with the peak occurring in July. Fecundity was correlated to log-body length (r = 0.74) and log-body weight (r = 0.76). Fish catches were estimated at 389 kg ha^–1 year^–1; about 73% of which was Sarotherodon galilaeus. The overexploitation of juvenile fish and the use of this lagoon for the irrigation of palm tree plantations have reduced fish recruitment and mean size.     

Ecology and zoogeography of aquatic Hemiptera from temporary pools in Central Africa

Summary 35 species of aquatic and semi-aquatic Hemiptera taken in ephemeral pools and pans at 21 collecting sites in 2 regions of Southern Rhodesia are recorded. Ecological conclusions on the habitat preferences of some of these species are described and comparisons are made with collections from equivalent habitats in South Africa, East Africa, Abyssinia and Arabia. Differences in alkalinity, pH and acidity have no detectable effect on the occurrence of species, but the physical conditions of the habitat appear to be critical (e.g. size, depth of pool, temperature, etc.). The majority of the aquatic Hemiptera from these temporary pools and pans are widespread Ethiopian species, e.g. Anisops pellucens, A. varia, A. debilis (Some occur also in Arabia), or are Ethiopian-Oriental species, e.g. Anisops sardea, Laccotrephes brachialis, Mesovelia vittigera and the remainder of the fauna consists of a few endemic (regionally abundant) species. Such endemics are for instance Anisops convexonota in Arabia, A. worthingtoni in Kenya, A. hancocki and A. jaczewski in East and Central Africa, A. aglaia in the Transvaal and Cape Province. It is suggested that the widespread Ethiopian species may show more complete adaptation and versatility to life in pans than regionally occurring species, and that the zoogeographic spread of Ethiopian species may be restricted in part by climatic change (e.g. temprature) and in part by the restriction of pans themselves to certain climatic regions. It would be extremely difficult to differentiate between such effects. These results are discussed in relation to recent zoogeographic studies in Africa.University College of Rhodesia and Nyasaland     

Timing of C4 grass expansion across sub-Saharan Africa

The emergence of C(4) grass biomes is believed to have first taken place in the upper Miocene, when a series of events modified global climate with long-lasting impacts on continental biotas. Changes included major shifts in floral composition-characterized in Africa by shrinking of forests and emergence of C(4) grasses and more open landscapes-followed by large-scale evolutionary shifts in faunal communities. The timing of the emergence of C(4) grasses, and the subsequent global expansion of C(4) grass-dominated biomes, however, is disputed, leading to contrasting views of the patterns of environmental changes and their links to faunal shifts, including those of early hominins. Here we evaluate the existing isotopic evidence available for central, eastern, and southern Africa, and review interpretations in light of these data. Pedogenic and biomineral carbonate delta(13)C data suggest that clear evidence for C(4) biomass in low latitudes exists only from 7-8 Ma. This likely postdates the emergence of C(4) plants, whose physiology is adapted to low atmospheric carbon dioxide concentrations. Biomes with C(4) grasses appeared later in mid-latitude sites. Moreover, C(4) grasses apparently remained a relatively minor component of most environments until the late Pliocene and early Pleistocene. Hence establishment of C(4) grasses, even as minor components of African biomes, precedes the very earliest evidence for bipedalism by two million years, and the more abundant and secure evidence by some three to four million years. This may suggest a protracted process of hominin adaptation to these emerging, more open landscapes.     

The Politics of Ecology in South Africa on the Radical Left

The South African ecologist and political activist Edward Roux (1903–1966) used evolutionary biology to argue against racism. During the cold-war, he transformed his communist beliefs into advocacy for scientific rationalism, management, and protection of nature against advancing capitalism. These pleas for saving the environment served as a vehicle for questioning the more risky issue of evolution and racial order in society. The link between ecological and political order had long been an important theme among the country's ecologists and politicians alike. The statesman Jan Christian Smuts' holistic theory of evolution and racial order inspired the nation's ecologists to sanctify an ecologically informed racial policy. This idealist informed methodology stood in direct opposition to the materialist approach to ecology of Roux. These methodological debates reflected differing political support from within the Union Party and people on the radical left, respectively. Ecology was of concern to politicians because understandings of the order of nature had direct implications for the racial order of the South African society. This revised version was published online in July 2006 with corrections to the Cover Date.     

Independent evolution of monkeypox and variola viruses.

Smallpox was eradicated more than 10 years ago, but infection with another Orthopoxvirus, monkeypox virus, can result in a clinical picture resembling smallpox. Human infection with monkeypox virus is extremely rare, not easily transmitted, and confined to the rain forest belt of Africa (Z. Jezek and F. Fenner, p. 81-102, in Human Monkeypox, 1988). Evidence that variola virus, the causative agent of smallpox, might be readily derived from monkeypox virus was presented [S. S. Marennikova and E. M. Shelukhina, Nature (London) 276:291-292, 1978; S. S. Marennikova, E. M. Shelukhina, N. N. Maltseva, and G. R. Matsevich Intervirology 11:333-340, 1979], but this was not confirmed [K. R. Dumbell and L. C. Archard, Nature (London) 286:29-32, 1980] and was subsequently discounted (J. J. Esposito, J. H. Nakano, and J. F. Obijeski, Bull. W.H.O. 63:695-703, 1985). Although enough difference between the genomes of monkeypox and variola viruses to rule out a simple interconversion has been demonstrated [K. R. Dumbell and L. C. Archard, Nature (London) 286:29-32, 1980; J. J. Esposito and J. C. Knight, Virology 143:230-251, 1985; J. J. Esposito, J. H. Nakano, and J. F. Obijeski, Bull. W.H.O. 63:695-703, 1985; M. Mackett and L. C. Archard, J. Gen. Virol. 45:683-701, 1979], the possibility that monkeypox virus was a more remote ancestor of variola virus remained. We have now identified a sequence in monkeypox virus DNA which is a homolog of a 1,065-bp open reading frame in the conserved region of the variola virus genome but which has multiple deletions. This is strong evidence that monkeypox virus is not ancestral to variola virus and strengthens confidence in the long-term success of smallpox eradication.     

Ecology and conservation status of endemic freshwater crabs in Lake Tanganyika, Africa

Sedimentation resulting from riparian deforestation has a wide range of detrimental effects on aquatic biodiversity, but predicting the full consequences of such disturbances requires an understanding of the ecosystem’s key functional components. We investigated the ecology and response to sedimentation of the diverse, endemic freshwater crabs of Lake Tanganyika, which may occupy important positions in littoral foodwebs. Our surveys revealed crab distribution patterns to be patchy, and that crabs can be locally abundant (0–28 individuals m⁻²). Crab densities decreased with depth and the dry mass of crab assemblages ranged from 0.0 to 117.7 g m⁻². Comparisons among sites revealed significant effects of sedimentation on crab assemblage evenness, but provided no evidence that sedimentation has altered densities, incidence or species richness. The resilience of crabs to sedimentation might be related to their intraspecific dietary breadth. Stable isotope data (δ¹³C and δ¹⁵N) from crabs and their potential food resources indicated differences in trophic roles among endemic crab species. Overall, crabs occupy higher trophic positions than most other invertebrates, and they draw upon both benthic and planktonic energy pathways. The high biomass and top-predator status of some crab species suggests the potential for cascading effects on organisms lower in the food web.     

Population distribution, settlement patterns and accessibility across Africa in 2010

The spatial distribution of populations and settlements across a country and their interconnectivity and accessibility from urban areas are important for delivering healthcare, distributing resources and economic development. However, existing spatially explicit population data across Africa are generally based on outdated, low resolution input demographic data, and provide insufficient detail to quantify rural settlement patterns and, thus, accurately measure population concentration and accessibility. Here we outline approaches to developing a new high resolution population distribution dataset for Africa and analyse rural accessibility to population centers. Contemporary population count data were combined with detailed satellite-derived settlement extents to map population distributions across Africa at a finer spatial resolution than ever before. Substantial heterogeneity in settlement patterns, population concentration and spatial accessibility to major population centres is exhibited across the continent. In Africa, 90% of the population is concentrated in less than 21% of the land surface and the average per-person travel time to settlements of more than 50,000 inhabitants is around 3.5 hours, with Central and East Africa displaying the longest average travel times. The analyses highlight large inequities in access, the isolation of many rural populations and the challenges that exist between countries and regions in providing access to services. The datasets presented are freely available as part of the AfriPop project, providing an evidence base for guiding strategic decisions.     

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles,geography and ethnicities

Structural profiling of healthy human gut microbiota across heterogeneous populations is necessary for benchmarking and characterizing the potential ecosystem services provided by particular gut symbionts for maintaining the health of their hosts. Here we performed a large structural survey of fecal microbiota in 314 healthy young adults, covering 20 rural and urban cohorts from 7 ethnic groups living in 9 provinces throughout China. Canonical analysis of unweighted UniFrac principal coordinates clustered the subjects mainly by their ethnicities/geography and less so by lifestyles. Nine predominant genera, all of which are known to contain short-chain fatty acid producers, co-occurred in all individuals and collectively represented nearly half of the total sequences. Interestingly, species-level compositional profiles within these nine genera still discriminated the subjects according to their ethnicities/geography and lifestyles. Therefore, a phylogenetically diverse core of gut microbiota at the genus level may be commonly shared by distinctive healthy populations as functionally indispensable ecosystem service providers for the hosts.     

The Ecology of Influenza A Viruses in Wild Birds in Southern Africa

Avian influenza viruses (AIVs) are pathogens of global concern, but there has been little previous research on avian influenza in southern Africa and almost nothing is known about the dynamics of AIVs in the region. We counted, captured and sampled birds regularly at five sites, two in South Africa (Barberspan and Strandfontein) and one in each of Botswana (Lake Ngami), Mozambique (Lake Chuali) and Zimbabwe (Lakes Manyame and Chivero) between March 2007 and May 2009. The South African and Zimbabwean sites were visited every 2 months and the sites in Botswana and Mozambique every 4 months. During each visit we undertook 5-7?days of standardised bird counts followed by 5-10?days of capturing and sampling water-associated birds. We sampled 4,977 birds of 165 different species and completed 2,503 half-hour point counts. We found 125 positive rRT-PCR cases of avian influenza across all sites. Two viruses (H1N8 and H3N8) were isolated and additional H5, H6 and H7 strains were identified. We did not positively identify any highly pathogenic H5N1. Overall viral prevalence (2.51%) was similar to the lower range of European values, considerable spatial and temporal variation occurred in viral prevalence, and there was no detectable influence of the annual influx of Palearctic migrants. Although waterbirds appear to be the primary viral carriers, passerines may link wild birds and poultry. While influenza cycles are probably driven by the bird movements that result from rainfall patterns, the epidemiology of avian influenza in wild birds in the subregion is complex and there appears to be the possibility for viral transmission throughout the year.