Table 2 Overview of the established BIOTA Observatories in Africa & Appendix

The international, interdisciplinary biodiversity research project BIOTA AFRICA initiated a standardized biodiversity monitoring network along climatic gradients across the African continent. Due to an identified lack of adequate monitoring designs, BIOTA AFRICA developed and implemented the standardized BIOTA Biodiversity Observatories, that meet the following criteria (a) enable long-term monitoring of biodiversity, potential driving factors, and relevant indicators with adequate spatial and temporal resolution, (b) facilitate comparability of data generated within different ecosystems, (c) allow integration of many disciplines, (d) allow spatial up-scaling, and (e) be applicable within a network approach. A BIOTA Observatory encompasses an area of 1 km2 and is subdivided into 100 1-ha plots. For meeting the needs of sampling of different organism groups, the hectare plot is again subdivided into standardized subplots, whose sizes follow a geometric series. To allow for different sampling intensities but at the same time to characterize the whole square kilometer, the number of hectare plots to be sampled depends on the requirements of the respective discipline. A hierarchical ranking of the hectare plots ensures that all disciplines monitor as many hectare plots jointly as possible. The BIOTA Observatory design assures repeated, multidisciplinary standardized inventories of biodiversity and its environmental drivers, including options for spatial up- and downscaling and different sampling intensities. BIOTA Observatories have been installed along climatic and landscape gradients in Morocco, West Africa, and southern Africa. In regions with varying land use, several BIOTA Observatories are situated close to each other to analyze management effects.

Geochemistry of Southern Ocean sediments

Reconstructing past detrital flux and provenance in the Southern Ocean provides information about changes in source regions associated with climate variations and transport pathways. We present a Last Glacial Maximum (LGM) to Holocene comparison of 230Th normalised fluxes combined with sediment provenance data (Pb, Nd and Sr isotopes) from a latitudinal core transect in the eastern Atlantic sector of the Southern Ocean (ODP Leg 177 cores). We compare the radiogenic isotopic composition (IC) of detritus in these cores to that of cores proximal to potential source areas. We observe a well-defined latitudinal Holocene gradient in both detrital flux and provenance of sediment. High detrital fluxes in the north are associated with terrigenous material derived from southern Africa, while low detrital fluxes in the south are associated with supply from southern South America, West Antarctica and the South Sandwich Islands. The data suggest that this well-defined Holocene gradient in detrital flux and sediment provenance is controlled by the flow of the Antarctic Circumpolar Current (ACC) and the position of its frontal zones. The LGM is characterised by 2 to 6 times higher than modern detrital fluxes at most ODP Leg 177 sites. The LGM detrital fluxes do not show a latitudinal trend and suggest a greater supply of glaciogenic detritus sourced from southern South America. Glacial Patagonian outwash sediments (< 5 µm fraction) were analysed and compared to the bulk compositions of the marine sediments. The Pb IC of the Patagonian sediments is very similar to the glacial IC of sediments in the Scotia Sea and at ~ 49° S latitude in the eastern Atlantic sector. We propose that the glacial IC of sediments is controlled by increased delivery of Patagonian detritus initially supplied by glaciers and then transported at depth via the ACC.

Model simulation output data (CCSM3) related to uplift of Africa and Himalaya/Tibet Plateau and the influence on tropical African vegetation

Hominid evolution in the late Miocene has long been hypothesized to be linked to the retreat of the tropical rainforest in Africa. One cause for the climatic and vegetation change often considered was uplift of Africa, but also uplift of the Himalaya and the Tibetan Plateau was suggested to have impacted rainfall distribution over Africa. Recent proxy data suggest that in East Africa open grassland habitats were available to the common ancestors of hominins and apes long before their divergence and do not find evidence for a closed rainforest in the late Miocene. We used the coupled global general circulation model CCSM3 including an interactively coupled dynamic vegetation module to investigate the impact of topography on African hydro-climate and vegetation. We performed sensitivity experiments altering elevations of the Himalaya and the Tibetan Plateau as well as of East and Southern Africa. The simulations confirm the dominant impact of African topography for climate and vegetation development of the African tropics. Only a weak influence of prescribed Asian uplift on African climate could be detected. The model simulations show that rainforest coverage of Central Africa is strongly determined by the presence of elevated African topography. In East Africa, despite wetter conditions with lowered African topography, the conditions were not favorable enough to maintain a closed rainforest. A discussion of the results with respect to other model studies indicates a minor importance of vegetation-atmosphere or ocean-atmosphere feedbacks and a large dependence of the simulated vegetation response on the land surface/vegetation model.

Compound specific stable isotopes, BIT, pollen and spores of Miocene to Pliocene sediments of ODP Hole 175-1085A

Pollen and stable carbon (d13C) and hydrogen (dD) isotope ratios of terrestrial plant wax from the South Atlantic sediment core, ODP Site 1085, is used to reconstruct Miocene to Pliocene changes of vegetation and rainfall regime of western southern Africa. Our results reveal changes in the relative amount of precipitation and indicate a shift of the main moisture source from the Atlantic to the Indian Ocean during the onset of a major aridification 8 Ma ago. We emphasise the importance of declining precipitation during the expansion of C4 and CAM (mainly succulent) vegetation in South Africa. We suggest that the C4 plant expansion resulted from an increased equator-pole temperature gradient caused by the initiation of strong Atlantic Meridional Overturning Circulation following the shoaling of the Central American Seaway during the Late Miocene.

Biomarkers, stable carbon isotope record and pollen distribution of the soutwest African continental margin

This is part 2 of a study examining southwest African continental margin sediments from nine sites on a north-south transect from the Congo Fan (4°S) to the Cape Basin (30°S) representing two glacial (MIS 2 and 6a) and two interglacial stages (MIS 1 and 5e). Contents, distribution patterns, and molecular stable carbon isotope signatures of long-chain n-alkanes (C27-C33) and n-alkanols (C22-C32) as indicators of land plant vegetation of different biosynthetic types were correlated with concentrations and distributions of pollen taxa in sediments of the same time horizons. Selected single pollen type data reveal details of vegetation changes, but the overall picture is best illustrated by summing pollen known to predominantly derive from C4 plants or C4 plus CAM plants. The C4 plant signals in the biomarkers are recorded in the delta13C data and in the abundances of C31 and C33 n-alkanes, and the C32 n-alkanol. Calculated clusters of wind trajectories for austral summer and winter situations for the Holocene and the Last Glacial Maximum afford information on the source areas for the lipids and pollen and their transport pathways to the ocean. This multidisciplinary approach provides clear evidence of latitudinal differences in leaf wax lipid and pollen composition, with the Holocene sedimentary data paralleling the current major phytogeographic zonations. The northern sites (Congo Fan area and northern Angola Basin) get most of their terrestrial material from the Congo Basin and the Angolan highlands dominated by C3 plants. Airborne particulates derived from the western and central South African hinterland dominated by deserts, semideserts, and savannah regions are rich in organic matter from C4 plants. As can be expected from the present and glacial positions of the phytogeographic zones, the carbon isotopic signatures of n-alkanes and n-alkanols both become isotopically more enriched in 13C from north to south. In the northern part of the transect the relative importance of C4 plant indicators is higher during the glacials than in the interglacials, indicating a northward extension of arid zones favoring grass vegetation. In the south, where grass-rich vegetation merges into semidesert and desert, the difference in C4 plant indicators is small.

Middle Miocene to recent sedimentological record of ODP sites 177-1088 and 177-1092

During Leg 177 of the Ocean Drilling Program (ODP), well-preserved Middle Miocene to Pleistocene carbonate-rich sediment records were recovered on a north-south transect through the south-eastern Atlantic sector of the Southern Ocean at Site 1088 on the Agulhas Ridge and Site 1092 on Meteor Rise. Both sites were dominated by the deposition of calcareous nannofossil oozes through the Miocene, indicating low biological productivity in warm to temperate surface waters. A continuous increase in the proportions of foraminifera since the latest Miocene (6.5 Ma) points to enhanced nutrient supply, possibly related to the global 'biogenic bloom' event across the Miocene-Pliocene boundary. Since the Late Pliocene, different styles of biological productivity developed between the sites. Enhanced deposition of biosiliceous constituents at the southern Site 1092, particularly in the Early Pleistocene, is consistent with the formation of the Circum-Antarctic Opal Belt since 2.5 Ma in a setting near the Polar Front, whereas carbonate deposition still prevailed at the northern Site 1088 situated near the Subtropical Front. Clay-mineral tracers of water-mass advection together with the pattern of sedimentation rates and hiatuses reflect distinct pulses in the development of regional ocean circulation between 14 and 12 Ma, around 8 Ma and since 2.8 Ma. These pulses can be related to Antarctic ice-sheet extension that mediates the production and flow of southern source water, and stepwise increases in North Atlantic Deep Water production that drives global conveyor circulation. At Site 1088, illite chemistry and silt/clay ratios of the terrigenous sediment fraction reflect the history of terrestrial climate in southern Africa, with humid conditions prior to the Early Late Miocene (9.7 Ma), followed by a dry episode until 7.7 Ma. The latest Miocene and Early Pliocene were characterized by a humid episode until modern aridity was established in the Late Pliocene between 4.0 and 2.8 Ma. These climate changes were related to the latitudinal migration of climate belts in response to tectonically caused reorganizations in atmospheric and ocean circulation.

Eolian accumulation rates of ODP Leg 121 holes

The late Cenozoic history of eolian sedimentation in the eastern Indian Ocean was developed from samples recovered during drilling of Sites 752, 754, and 756. Temporal changes in the mass accumulation rate of eolian material reflect major climatic shifts in the southern African source region. A significant drop in dust mass flux values occurs near the end of the lower Oligocene. Younger sediments are characterized by a gradual reduction in dust accumulation rates until the middle Miocene after which values remain consistently low throughout the late Cenozoic, although a slight increase in eolian accumulation rate occurs near 2.5 Ma. This pattern of dust mass flux appears related to the supply of dust-sized particles in the source region and represents a shift in the climatic regime of southern Africa to increasingly more arid conditions throughout the late Cenozoic.

Raster maps for 29 environmental variables in three geographical regions

Aim: Greater understanding of the processes underlying biological invasions is required to determine and predict invasion risk. Two subspecies of olive (Olea europaea subsp. europaea and Olea europaea subsp. cuspidata) have been introduced into Australia from the Mediterranean Basin and southern Africa during the 19th century. Our aim was to determine to what extent the native environmental niches of these two olive subspecies explain the current spatial segregation of the subspecies in their non-native range. We also assessed whether niche shifts had occurred in the non-native range, and examined whether invasion was associated with increased or decreased occupancy of niche space in the non-native range relative to the native range. Location: South-eastern Australia, Mediterranean Basin and southern Africa. Methods: Ecological niche models (ENMs) were used to quantify the similarity of native and non-native realized niches. Niche shifts were characterized by the relative contribution of niche expansion, stability and contraction based on the relative occupancy of environmental space by the native and non-native populations. Results: Native ENMs indicated that the spatial segregation of the two subspecies in their non-native range was partly determined by differences in their native niches. However, we found that environmentally suitable niches were less occupied in the non-native range relative to the native range, indicating that niche shifts had occurred through a contraction of the native niches after invasion, for both subspecies. Main conclusions: The mapping of environmental factors associated with niche expansion, stability or contraction allowed us to identify areas of greater invasion risk. This study provides an example of successful invasions that are associated with niche shifts, illustrating that introduced plant species are sometimes readily able to establish in novel environments. In these situations the assumption of niche stasis during invasion, which is implicitly assumed by ENMs, may be unreasonable.

Microcharcoal concentration and elongation, and age model of sediment core MD96-2098

Although grassland and savanna occupy only a quarter of the world's vegetation, burning in these ecosystems accounts for roughly half the global carbon emissions from fire. However, the processes that govern changes in grassland burning are poorly understood, particularly on time scales beyond satellite records. We analyzed microcharcoal, sediments, and geochemistry in a high-resolution marine sediment core off Namibia to identify the processes that have controlled biomass burning in southern African grassland ecosystems under large, multimillennial-scale climate changes. Six fire cycles occurred during the past 170,000 y in southern Africa that correspond both in timing and magnitude to the precessional forcing of north-south shifts in the Intertropical Convergence Zone. Contrary to the conventional expectation that fire increases with higher temperatures and increased drought, we found that wetter and cooler climates cause increased burning in the study region, owing to a shift in rainfall amount and seasonality (and thus vegetation flammability). We also show that charcoal morphology (i.e., the particle's length-to-width ratio) can be used to reconstruct changes in fire activity as well as biome shifts over time. Our results provide essential context for understanding current and future grassland-fire dynamics and their associated carbon emissions.

Lithogeochemical and isotope (Rb-Sr, Sm-Nd, Pb-Pb whole rock and Lu-Hf zircon) composition of samples from the Shackleton Range, East Antarctica

Three distinct, spatially separated crustal terranes have been recognised in the Shackleton Range, East Antarctica: the Southern, Eastern and Northern Terranes. Mafic gneisses from the Southern Terrane provide geochemical evidence for a within-plate, probably back-arc origin of their protoliths. A plume-distal ridge origin in an incipient ocean basin is the favoured interpretation for the emplacement site of these rocks at c. 1850 Ma, which, together with a few ocean island basalts, were subsequently incorporated into an accretionary continental arc/supra-subduction zone tectonic setting. Magmatic underplating resulted in partial melting of the lower crust, which caused high-temperature granulite-facies metamorphism in the Southern Terrane at c. 1710-1680 Ma. Mafic and felsic gneisses there are characterised by isotopically depleted, positive Nd and Hf initials and model ages between 2100 and 2000 Ma. They may be explained as juvenile additions to the crust towards the end of the Palaeoproterozoic. These juvenile rocks occur in a narrow, c. 150 km long E-W trending belt, inferred to trace a suture that is associated with a large Palaeoproterozoic accretionary orogenic system. The Southern Terrane contains many features that are similar to the Australo-Antarctic Mawson Continent and may be its furthermost extension into East Antarctica. The Eastern Terrane is characterised by metagranitoids that formed in a continental volcanic arc setting during a late Mesoproterozoic orogeny at c. 1060 Ma. Subsequently, the rocks experienced high-temperature metamorphism during Pan-African collisional tectonics at 600 Ma. Isotopically depleted zircon grains yielded Hf model ages of 1600-1400 Ma, which are identical to Nd model ages obtained from juvenile metagranitoids. Most likely, these rocks trace the suture related to the amalgamation of the Indo-Antarctic and West Gondwana continental blocks at ~600 Ma. The Eastern Terrane is interpreted as the southernmost extension of the Pan-African Mozambique/Maud Belt in East Antarctica and, based on Hf isotope data, may also represent a link to the Ellsworth-Whitmore Mountains block in West Antarctica and the Namaqua-Natal Province of southern Africa. Geochemical evidence indicates that the majority of the protoliths of the mafic gneisses in the Northern Terrane formed as oceanic island basalts in a within-plate setting. Subsequently the rocks were incorporated into a subduction zone environment and, finally, accreted to a continental margin during Pan-African collisional tectonics. Felsic gneisses there provide evidence for a within-plate and volcanic arc/collisional origin. Emplacement of granitoids occurred at c. 530 Ma and high-temperature, high-pressure metamorphism took place at 510-500 Ma. Enriched Hf and Nd initials and Palaeoproterozoic model ages for most samples indicate that no juvenile material was added to the crust of the Northern Terrane during the Pan-African Orogeny but recycling of older crust or mixing of crustal components of different age must have occurred. Isotopically depleted mafic gneisses, which are spatially associated with eclogite-facies pyroxenites, yielded late Mesoproterozoic Nd model ages. These rocks occur in a narrow, at least 100 km long, E-W trending belt that separates alkaline ocean island metabasalts and within-plate metagranitoids from volcanic arc metabasalts and volcanic arc/syn-collisional metagranitoids in the Northern Terrane. This belt is interpreted to trace the late Neoproterozoic/early Cambrian Pan-African collisional suture between the Australo-Antarctic and the combined Indo-Antarctic/West Gondwana continental blocks that formed during the final amalgamation of Gondwana.

Sea surface temperature reconstruction of ODP Site 175-1087

Successful application of the alkenone palaeothermometer, the UK'37 index, relies upon the assumption that fossil alkenone synthesisers responded to growth-temperature changes in a similar manner to the modern producers, chiefly the coccolithophores Emiliania huxleyi and Gephyrocapsa oceanica. We compare coccolith and UK'37 data from ODP Site 1087 in the south-east Atlantic between 1500 and 500 ka, and show that evolutionary events and changes in species dominance within the coccolithophore populations had little impact on the UK'37 record. The relative abundances of the C37 and C38 alkenones also closely resembled those found in modern populations, and suggest a similar temperature sensitivity of UK'37 during the early and mid-Pleistocene to that found at present. These results support the application of the UK'37 index to reconstruct sea-surface temperatures (SSTs) throughout the Quaternary. The UK'37 record at ODP Site 1087 contains an SST signal that documents the emergence of the 100-kyr cycles that characterise the late Quaternary ice volume records. This is preceded by significant cooling at ODP Site 1087, marked by a negative shift in SSTs and a positive shift in the planktonic delta18O some 250-kyr earlier, at ca 1150-1000 ka. This results in a permanent fall in average SSTs of around 1.5 °C. The predicted increase in aridity onshore as a result of this cooling can be identified in a number of published records from southern Africa, and may have played a role in some important evolutionary events of the mid-Pleistocene.

Literature review of elasmobranch bycatch and retention rate

To address growing concern over the effects of fisheries non-target catch on elasmobranchs worldwide, the accurate reporting of elasmobranch catch is essential. This requires data on a combination of measures, including reported landings, retained and discarded non-target catch, and post-discard survival. Identification of the factors influencing discard vs. retention is needed to improve catch estimates and to determine wasteful fishing practices. To do this we compared retention rates of elasmobranch non-target catch in a broad subset of fisheries throughout the world by taxon, fishing country, and gear. A regression tree and random forest analysis indicated that taxon was the most important determinant of retention in this dataset, but all three factors together explained 59% of the variance. Estimates of total elasmobranch removals were calculated by dividing the FAO global elasmobranch landings by average retention rates and suggest that total elasmobranch removals may exceed FAO reported landings by as much as 400%. This analysis is the first effort to directly characterize global drivers of discards for elasmobranch non-target catch. Our results highlight the importance of accurate quantification of retention and discard rates to improve assessments of the potential impacts of fisheries on these species.

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.

Pollen distribution in marine sediment samples along the south-western African coast

The distribution of pollen in marine sediments is used to reconstruct pathways of terrigenous input to the oceans and provides a record of vegetation change on adjacent continents. The wind transport routes of aeolian pollen is comprehensively illustrated by clusters of trajectories. Isobaric, 4-day backward trajectories are calculated using the modelled wind-field of ECHAM3, and are clustered on a seasonal basis to estimate the main pathways of aeolian particles to sites of marine cores in the south-eastern Atlantic. Trajectories and clusters based on the modelled wind-field of the Last Glacial Maximum hardly differ from those of the present-day. Trajectory clusters show three regional, and two seasonal patterns, determining the pathways of aeolian pollen transport into the south-eastern Atlantic ocean. Mainly, transport out of the continent occurs during austral fall and winter, when easterly and south-easterly winds prevail. South of 25°S, winds blow mostly from the west and southwest, and aeolian terrestrial input is very low. Generally, a good latitudinal correspondence exists between the distribution patterns of pollen in marine surface sediments and the occurrence of the source plants on the adjacent continent. The northern Angola Basin receives pollen and spores from the Congolian and Zambezian forests mainly through river discharge. The Zambezian vegetation zone is the main source area for wind-blown pollen in sediments of the Angola Basin, while the semi-desert and desert areas are the main sources for pollen in sediments of the Walvis Basin and on the Walvis Ridge. A transect of six marine pollen records along the south-western African coast indicates considerable changes in the vegetation of southern Africa between glacial and interglacial periods. Important changes in the vegetation are the decline of forests in equatorial Africa and the north of southern Africa and a northward shift of winter rain vegetation along the western escarpment.

Pollen analysis of sediment cores from the mouth of the river Congo to Walvis Bay and Lüderitz

The distribution of pollen in marine sediments is used to record vegetation changes over the past 30,000 years on the adjacent continent. A transect of marine pollen sequences from the mouth of the river Congo (~5°S) to Walvis Bay and Lüderitz (~25°S) shows vegetation changes in Congo, Angola and Namibia from the last glacial period into the Holocene. The comparison of pollen records from different latitudes provides information about the latitudinal shift of open forest and savannahs (Poaceae pollen), the extension of lowland forest (rain forest pollen) and Afromontane forest (Podocarpus pollen), and the position of the desert fringe (pollen of Caryophyllaceae, Chenopodiaceae and Amaranthaceae). High Cyperaceae pollen percentages in sediments from the last glacial period off the mouth of the river Congo suggest the presence of open swamps rather than savannah vegetation in the Congo Basin. Pollen from Restionaceae in combination with Stoebe-type pollen (probably from Elytropappus) indicates a possible northwards extension of winter rain vegetation during the last glacial period. The record of Rhizophora (mangrove) pollen is linked to erosion of the continental shelf and sea-level rise. Pollen influx is highest off river mouths (10-2000 grains year**-1 cm**-2), close to the coast (300-6000 grains year**-1 cm**-2), but is an order of magnitude lower at sites situated far from the continent (<10 grains year**-1 cm**-2).