Ancient DNA is preserved in fish fossils from tropical lake sediments.

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.

A late-Quaternary perspective, on atmospheric pCO2, climate, and fire as drivers of C4-grass abundance.

Various environmental factors, including atmospheric CO2 (pCO2), regional climate, and fire, have been invoked as primary drivers of long-term variation in C4 grass abundance. Evaluating these hypotheses has been difficult because available paleorecords often lack information on past C4 grass abundance or potential environmental drivers. We analyzed carbon isotope ratios (delta13C) of individual grains of grass pollen in the sediments of two East African lakes to infer changes in the relative abundance of C3 vs. C4 grasses during the past 25 000 years. Results were compared with concurrent changes in pCO2, temperature, moisture balance, and fire activity. Our grass-pollen delta13C analysis reveals a dynamic history of grass-dominated vegetation in equatorial East Africa: C4 grasses have not consistently dominated lowland areas, and high-elevation grasses have not always been predominantly C3. On millennial timescales, C4 grass abundance does not correlate with charcoal influx at either site, suggesting that fire was not a major proximate control of the competitive balance between C3 and C4 grasses. Above the present-day treeline on Mt. Kenya, C4 grass abundance declined from an average of approximately 90% during the glacial period to less than approximately 60% throughout the Holocene, coincident with increases in pCO2 and temperature, and shifts in moisture balance. In the lowland savanna southeast of Mt. Kilimanjaro, C4 grass abundance showed no such directional trend, but fluctuated markedly in association with variation in rainfall amount and seasonal-drought severity. These results underscore spatiotemporal variability in the relative influence of pCO2 and climate on the interplay of C3 and C4 grasses and shed light on an emerging conceptual model regarding the expansion of C4-dominated grasslands in Earth's history. They also suggest that future changes in the C3/C4 composition of grass-dominated ecosystems will likely exhibit striking spatiotemporal variability as a result of varying combinations of environmental controls.

Half-precessional dynamics of monsoon rainfall near the East African Equator.

External climate forcings-such as long-term changes in solar insolation-generate different climate responses in tropical and high latitude regions. Documenting the spatial and temporal variability of past climates is therefore critical for understanding how such forcings are translated into regional climate variability. In contrast to the data-rich middle and high latitudes, high-quality climate-proxy records from equatorial regions are relatively few, especially from regions experiencing the bimodal seasonal rainfall distribution associated with twice-annual passage of the Intertropical Convergence Zone. Here we present a continuous and well-resolved climate-proxy record of hydrological variability during the past 25,000 years from equatorial East Africa. Our results, based on complementary evidence from seismic-reflection stratigraphy and organic biomarker molecules in the sediment record of Lake Challa near Mount Kilimanjaro, reveal that monsoon rainfall in this region varied at half-precessional ( approximately 11,500-year) intervals in phase with orbitally controlled insolation forcing. The southeasterly and northeasterly monsoons that advect moisture from the western Indian Ocean were strengthened in alternation when the inter-hemispheric insolation gradient was at a maximum; dry conditions prevailed when neither monsoon was intensified and modest local March or September insolation weakened the rain season that followed. On sub-millennial timescales, the temporal pattern of hydrological change on the East African Equator bears clear high-northern-latitude signatures, but on the orbital timescale it mainly responded to low-latitude insolation forcing. Predominance of low-latitude climate processes in this monsoon region can be attributed to the low-latitude position of its continental regions of surface air flow convergence, and its relative isolation from the Atlantic Ocean, where prominent meridional overturning circulation more tightly couples low-latitude climate regimes to high-latitude boundary conditions.

The contribution of intra- and interspecific tolerance variability to biodiversity changes along toxicity gradients.

The worldwide distribution of toxicants is an important yet understudied driver of biodiversity, and the mechanisms relating toxicity to diversity have not been adequately explored. Here, we present a community model integrating demography, dispersal and toxicant-induced effects on reproduction driven by intraspecific and interspecific variability in toxicity tolerance. We compare model predictions to 458 species abundance distributions (SADs) observed along concentration gradients of toxicants to show that the best predictions occur when intraspecific variability is five and ten times higher than interspecific variability. At high concentrations, lower settings of intraspecific variability resulted in predictions of community extinction that were not supported by the observed SADs. Subtle but significant species losses at low concentrations were predicted only when intraspecific variability dominated over interspecific variability. Our results propose intraspecific variability as a key driver for biodiversity sustenance in ecosystems challenged by environmental change.

Contrasting long-term records of biomass burning in wet and dry savannas of equatorial East Africa.

Rainfall controls fire in tropical savanna ecosystems through impacting both the amount and flammability of plant biomass, and consequently, predicted changes in tropical precipitation over the next century are likely to have contrasting effects on the fire regimes of wet and dry savannas. We reconstructed the long-term dynamics of biomass burning in equatorial East Africa, using fossil charcoal particles from two well-dated lake-sediment records in western Uganda and central Kenya. We compared these high-resolution (5 years/sample) time series of biomass burning, spanning the last 3800 and 1200 years, with independent data on past hydroclimatic variability and vegetation dynamics. In western Uganda, a rapid (<100 years) and permanent increase in burning occurred around 2170 years ago, when climatic drying replaced semideciduous forest by wooded grassland. At the century time scale, biomass burning was inversely related to moisture balance for much of the next two millennia until ca. 1750 ad, when burning increased strongly despite regional climate becoming wetter. A sustained decrease in burning since the mid20th century reflects the intensified modern-day landscape conversion into cropland and plantations. In contrast, in semiarid central Kenya, biomass burning peaked at intermediate moisture-balance levels, whereas it was lower both during the wettest and driest multidecadal periods of the last 1200 years. Here, burning steadily increased since the mid20th century, presumably due to more frequent deliberate ignitions for bush clearing and cattle ranching. Both the observed historical trends and regional contrasts in biomass burning are consistent with spatial variability in fire regimes across the African savanna biome today. They demonstrate the strong dependence of East African fire regimes on both climatic moisture balance and vegetation, and the extent to which this dependence is now being overridden by anthropogenic activity.

Linking isoprenoidal GDGT membrane lipid distributions with gene abundances of ammonia-oxidizing Thaumarchaeota and uncultured crenarchaeotal groups in the water column of a tropical lake (Lake Challa, East Africa).

Stratified lakes are important reservoirs of microbial diversity and provide habitats for niche differentiation of Archaea. In this study, we used a lipid biomarker/DNA-based approach to reveal the diversity and abundance of Archaea in the water column of Lake Challa (East Africa). Concentrations of intact polar lipid (IPL) crenarchaeol, a specific biomarker of Thaumarchaeota, were enhanced (1 ng l(-1) ) at the oxycline/nitrocline. The predominance of the more labile IPL hexose-phosphohexose crenarchaeol indicated the presence of an actively living community of Thaumarchaeota. Archaeal 16S rRNA clone libraries revealed the presence of thaumarchaeotal groups 1.1a and 1.1b at and above the oxycline. In the anoxic deep water, amoA gene abundance was an order of magnitude lower than at the oxycline and high abundance (∼90 ng l(-1) ) of an IPL with the acyclic glycerol dialkyl glycerol tetraether (GDGT-0) was evident. The predominance of archaeal 16S rRNA sequences affiliated to the uncultured crenarchaeota groups 1.2 and miscellaneous crenarchaeotic group (MCG) points to an origin of GDGT-0 from uncultured crenarchaeota. This study demonstrates the importance of thermal stratification and nutrient availability in the distribution of archaeal groups in lakes, which is relevant to constrain and validate temperature proxies based on archaeal GDGTs (i.e. TEX86 ).

Checklist of the diatoms (Bacillariophyta) from Lake Naivasha, Kenya, with some historical notes.

Lake Naivasha is one of only two large freshwater lakes in the Eastern Rift Valley of Kenya, East Africa. Together with its satellite lakes Crescent Island Crater, Oloidien and Sonachi, it comprises a great variety of pelagic and benthic habitats for aquatic biota, and its sediment record represents a unique archive of past climate change and long-term ecosystem dynamics in equatorial East Africa. This is particularly so because local paleoenvironmental reconstructions can be checked against historical data on the composition of aquatic fauna and flora collected in Lake Naivasha since the early 20th century. Some of the most prominent biological proxies for reconstructing past changes in lakes are diatoms (Bacillariophyta), a group of unicellular autotrophic eukaryotes of which the siliceous skeletons (valves) preserve well in lake sediments and are good indicators for, among others, climate-driven changes in salinity. However, diatom taxonomy and species concepts have changed a lot in recent decades, making it sometimes difficult for non-taxonomists to know which species are concerned in different published studies. This paper provides the currently accepted taxonomic names of the 310 specific and infraspecific diatom taxa reported from Lake Naivasha and its satellite lakes to date, together with their synonyms used in literature concerning these lakes as well as other, commonly used synonyms. Further, a short overview is given of the history of diatom research conducted on materials from Lake Naivasha and its satellite lakes. The present checklist may facilitate the identification and interpretation aspects of future diatom studies on the wider Lake Naivasha ecosystem and on other East African lakes that are less well studied.

Long-term variability and rainfall control of savanna fire regimes in equatorial East Africa.

Fires burning the vast grasslands and savannas of Africa significantly influence the global carbon cycle. Projecting the impacts of future climate change on fire-mediated biogeochemical processes in these dry tropical ecosystems requires understanding of how various climate factors influence regional fire regimes. To examine climate-vegetation-fire linkages in dry savanna, we conducted macroscopic and microscopic charcoal analysis on the sediments of the past 25 000 years from Lake Challa, a deep crater lake in equatorial East Africa. The charcoal-inferred shifts in local and regional fire regimes were compared with previously published reconstructions of temperature, rainfall, seasonal drought severity, and vegetation dynamics to evaluate millennial-scale drivers of fire occurrence. Our charcoal data indicate that fire in the dry lowland savanna of southeastern Kenya was not fuel-limited during the Last Glacial Maximum (LGM) and Late Glacial, in contrast to many other regions throughout the world. Fire activity remained high at Lake Challa probably because the relatively high mean-annual temperature (~22 °C) allowed productive C4 grasses with high water-use efficiency to dominate the landscape. From the LGM through the middle Holocene, the relative importance of savanna burning in the region varied primarily in response to changes in rainfall and dry-season length, which were controlled by orbital insolation forcing of tropical monsoon dynamics. The fuel limitation that characterizes the region's fire regime today appears to have begun around 5000-6000 years ago, when warmer interglacial conditions coincided with prolonged seasonal drought. Thus, insolation-driven variation in the amount and seasonality of rainfall during the past 25 000 years altered the immediate controls on fire occurrence in the grass-dominated savannas of eastern equatorial Africa. These results show that climatic impacts on dry-savanna burning are heterogeneous through time, with important implications for efforts to anticipate future shifts in fire-mediated ecosystem processes.

Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing.

Several methodological issues currently hamper the study of entire trematode communities within populations of their intermediate snail hosts. Here we develop a new workflow using high-throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. We designed primers to amplify four snail and five trematode markers in a single multiplex PCR. While also applicable to other genera, we focused on medically and economically important snail genera within the superorder Hygrophila and targeted a broad taxonomic range of parasites within the class Trematoda. We tested the workflow using 417 Biomphalaria glabrata specimens experimentally infected with Schistosoma rodhaini, two strains of Schistosoma mansoni and combinations thereof. We evaluated the reliability of infection diagnostics, the robustness of the workflow, its specificity related to host and parasite identification, and the sensitivity to detect co-infections, immature infections and changes of parasite biomass during the infection process. Finally, we investigated its applicability in wild-caught snails of other genera naturally infected with a diverse range of trematodes. After stringent quality control the workflow allows the identification of snails to species level, and of trematodes to taxonomic levels ranging from family to strain. It is sensitive to detect immature infections and changes in parasite biomass described in previous experimental studies. Co-infections were successfully identified, opening the possibility to examine parasite-parasite interactions such as interspecific competition. Together, these results demonstrate that our workflow provides a powerful tool to analyse the processes shaping trematode communities within natural snail populations.

Trematode infection affects shell shape and size in Bulinus tropicus.

Trematodes can increase intraspecific variation in the phenotype of their intermediate snail host. However, the extent of such phenotypic changes remains unclear. We investigated the influence of trematode infection on the shell morphology of Bulinus tropicus, a common host of medically important trematodes. We focused on a snail population from crater lake Kasenda (Uganda). We sampled a single homogeneous littoral habitat to minimize the influence of environmental variation on shell phenotype, and barcoded snails to document snail genotypic variation. Among the 257 adult snails analysed, 99 tested positive for trematode infection using rapid-diagnostic PCRs. Subsequently we used high-throughput amplicon sequencing to identify the trematode (co-)infections. For 86 out of the 99 positive samples trematode species delineation could discriminate among combinations of (co-)infection by 11 trematode species. To avoid confounding effects, we focused on four prevalent trematode species. We performed landmark-based geometric morphometrics to characterize shell phenotype and used regressions to examine whether shell size and shape were affected by trematode infection and the developmental stage of infection (as inferred from read counts). Snails infected by Petasiger sp. 5, Echinoparyphium sp. or Austrodiplostomum sp. 2 had larger shells than uninfected snails or than those infected by Plagiorchiida sp. Moreover, the shell shape of snails infected solely by Petasiger sp. 5 differed significantly from that of uninfected snails and snails infected with other trematodes, except from Austrodiplostomum sp. 2. Shape changes included a more protuberant apex, an inward-folded outer apertural lip and a more adapically positioned umbilicus. Size differences were more pronounced in snails with 'late' infections (>25 days) compared to earlier-stage infections. No phenotypic differences were found between snails infected by a single trematode species and those harbouring co-infections. Further work is required to assess the complex causal links between trematode infections and shell morphological alterations of snail hosts.

A predominantly tropical influence on late Holocene hydroclimate variation in the hyperarid central Sahara.

The climate history of the Sahara desert during recent millennia is obscured by the near absence of natural climate archives, hampering insight in the relative importance of southerly (tropical) and northerly (midlatitude) weather systems at submillennial time scales. A new lake sediment record from Ounianga Serir oasis in northern Chad, spanning the Late Holocene without interruption, confirms that immediately before ca 4200 years ago, the Sahara experienced an episode of hyperaridity even more extreme than today's desert climate. The hypersaline terminal lake which formed afterwards never desiccated during the late Holocene due to continuous inflow of fossil groundwater, yet its water balance was sensitive to temporal variation in local rainfall and lake surface evaporation. Our in-lake geochemical proxies show that, during the last 3000 years, century-scale hydroclimate variation in the central Sahara primarily tracked the intensity of the tropical West African monsoon, modulated at shorter time scales by weather patterns linked to shifts in midlatitude Atlantic Ocean circulation.

Priority effects and species sorting in a long paleoecological record of repeated community assembly through time.

We studied the relative roles of environmental species sorting and priority effects in the assembly of ecological communities on long time scales, by analyzing community turnover of water fleas (Daphnia) in response to strong and recurrent environmental change in a fluctuating tropical lake. During the past 1800 years, Lake Naivasha (Kenya) repeatedly fluctuated between a small saline pond habitat during lowstands and a large freshwater lake habitat during highstands. Starting from a paleoecological reconstruction, we estimated the role of priority effects in Daphnia community assembly across 16 of these habitat turnovers and compared this with the response of the community to reconstructed changes in three environmental variables important for species sorting. Our results indicate that the best predictor of Daphnia community composition during highstands was the community composition just prior to the transition from lowstands to highstands. This reflects a long-lasting priority effect of late lowstand communities on highstand communities, arising when remnant lowstand populations fill newly available ecological space in the rapidly expanding lake habitat. Species sorting and priority effects had a comparable but relatively small influence on community composition during the lowstands. Moreover, these priority effects decayed rapidly with time as Daphnia communities responded to environmental change, in contrast with the highstand communities where priority effects lasted for several decades.

Developing a methodology for carbon isotope analysis of lacustrine diatoms.

Stable isotope analysis of sedimentary carbon in lakes can help reveal changes in terrestrial and aquatic carbon cycles. A method based on a single, photosynthetic organism, where host effects are minimised, should offer more precision than carbon isotope studies of bulk lake sediments. Here we report the development of a systematic method for use on fossil lacustrine diatom frustules, adapted from previous studies in marine environments. A step-wise cleaning experiment on diatomaceous lake sediments from Lake Challa, near Mount Kilimanjaro, was made to demonstrate the necessary treatment stages to remove external sedimentary carbon. Changes in soluble carbon compounds during these cleaning experiments were measured using gas chromatography/mass spectrometry (GC/MS). The mass spectrometry methods were refined to measure the small percentage of carbon in these samples and details of these methods are presented. Samples of cleaned diatoms containing <1% carbon yielded robust results. Carbon isotope analyses of diatom samples containing different species mixtures were performed and suggested that differences existed, although the effects lay within current experimental error and require further work. Unlike what was found in work on oxygen and silicon isotopes from diatom frustules, mineral contamination had no discernible impact on the diatom carbon isotope ratios from these sediments. The range of values found in the lakes investigated thus far can be interpreted with reference to the supply and nature of carbon from the catchment as well as to the demand generated from lake primary productivity.

Population collapse in Congo rainforest from 400 CE urges reassessment of the Bantu Expansion.

The present-day distribution of Bantu languages is commonly thought to reflect the early stages of the Bantu Expansion, the greatest migration event in African prehistory. Using 1149 radiocarbon dates linked to 115 pottery styles recovered from 726 sites throughout the Congo rainforest and adjacent areas, we show that this is not the case. Two periods of more intense human activity, each consisting of an expansion phase with widespread pottery styles and a regionalization phase with many more local pottery styles, are separated by a widespread population collapse between 400 and 600 CE followed by major resettlement centuries later. Coinciding with wetter climatic conditions, the collapse was possibly promoted by a prolonged epidemic. Comparison of our data with genetic and linguistic evidence further supports a spread-over-spread model for the dispersal of Bantu speakers and their languages.

Extinction, recolonization, and dispersal through time in a planktonic crustacean.

Dormant propagule banks are important reservoirs of biological and genetic diversity of local communities and populations and provide buffering mechanisms against extinction. Although dormant stages of various plant and animal species are known to remain viable for decades and even centuries, little is known about the effective influence of recolonization from such old sources on the genetic continuity of intermittent populations under natural conditions. Using recent and old dormant eggs recovered from a dated lake sediment core in Kenya, we traced the genetic composition of a local population of the planktonic crustacean Daphnia barbata through a sequence of extinction and recolonization events. This was combined with a phylogeographic and population-genetic survey of regional populations. Four successive populations, fully separated in time, inhabited Lake Naivasha from ca. 1330 to 1570 AD, from ca. 1610 to 1720 AD, from ca. 1840 to 1940 AD, and from 1995 to the present (2001 AD). Our results strongly indicate genetic continuity between the 1840-1940 and 1995-2001 populations, which are separated in time by at least 50 years, and close genetic relatedness of them both to the 1330-1580 population. A software tool (Colonize) was developed to find the most likely source population of the refounded 1995-2001 population and to test the number of colonists involved in the recolonization event. The results confirmed that the 1995-2001 population most probably developed out of a limited number of surviving local dormant eggs from the previous population, rather than out of individuals from regional (central and southern Kenya) or more distant (Ethiopia, Zimbabwe) populations that may have immigrated to Lake Naivasha through passive dispersal. These results emphasize the importance of prolonged dormancy for the natural long-term dynamics of crustacean zooplankton in fluctuating environments and suggest an important role of old local dormant egg banks in aquatic habitat restoration.

The tropical lapse rate steepened during the Last Glacial Maximum.

The gradient of air temperature with elevation (the temperature lapse rate) in the tropics is predicted to become less steep during the coming century as surface temperature rises, enhancing the threat of warming in high-mountain environments. However, the sensitivity of the lapse rate to climate change is uncertain because of poor constraints on high-elevation temperature during past climate states. We present a 25,000-year temperature reconstruction from Mount Kenya, East Africa, which demonstrates that cooling during the Last Glacial Maximum was amplified with elevation and hence that the lapse rate was significantly steeper than today. Comparison of our data with paleoclimate simulations indicates that state-of-the-art models underestimate this lapse-rate change. Consequently, future high-elevation tropical warming may be even greater than predicted.

Invasion of an asexual American water flea clone throughout Africa and rapid displacement of a native sibling species.

The huge ecological and economic impact of biological invasions creates an urgent need for knowledge of traits that make invading species successful and factors helping indigenous populations to resist displacement by invading species or genotypes. High genetic diversity is generally considered to be advantageous in both processes. Combined with sex, it allows rapid evolution and adaptation to changing environments. We combined paleogenetic analysis with continent-wide survey of genetic diversity at nuclear and mitochondrial loci to reconstruct the invasion history of a single asexual American water flea clone (hybrid Daphnia pulexxDaphnia pulicaria) in Africa. Within 60 years of the original introduction of this invader, it displaced the genetically diverse, sexual population of native D. pulex in Lake Naivasha (Kenya), despite a formidable numerical advantage of the local population and continuous replenishment from a large dormant egg bank. Currently, the invading clone has spread throughout the range of native African D. pulex, where it appears to be the only occurring genotype. The absence of genetic variation did not hamper either the continent-wide establishment of this exotic lineage or the effective displacement of an indigenous and genetically diverse sibling species.

History and timing of human impact on Lake Victoria, East Africa.

Lake Victoria, the largest tropical lake in the world, suffers from severe eutrophication and the probable extinction of up to half of its 500+ species of endemic cichlid fishes. The continuing degradation of Lake Victoria's ecological functions has serious long-term consequences for the ecosystem services it provides, and may threaten social welfare in the countries bordering its shores. Evaluation of recent ecological changes in the context of aquatic food-web alterations, catchment disturbance and natural ecosystem variability has been hampered by the scarcity of historical monitoring data. Here, we present high-resolution palaeolimnological data, which show that increases in phytoplankton production developed from the 1930s onwards, which parallels human-population growth and agricultural activity in the Lake Victoria drainage basin. Dominance of bloom-forming cyanobacteria since the late 1980s coincided with a relative decline in diatom growth, which can be attributed to the seasonal depletion of dissolved silica resulting from 50 years of enhanced diatom growth and burial. Eutrophication-induced loss of deep-water oxygen started in the early 1960s, and may have contributed to the 1980s collapse of indigenous fish stocks by eliminating suitable habitat for certain deep-water cichlids. Conservation of Lake Victoria as a functioning ecosystem is contingent upon large-scale implementation of improved land-use practices.

Reduced interannual rainfall variability in East Africa during the last ice age.

Interannual rainfall variations in equatorial East Africa are tightly linked to the El Niño Southern Oscillation (ENSO), with more rain and flooding during El Niño and droughts in La Niña years, both having severe impacts on human habitation and food security. Here we report evidence from an annually laminated lake sediment record from southeastern Kenya for interannual to centennial-scale changes in ENSO-related rainfall variability during the last three millennia and for reductions in both the mean rate and the variability of rainfall in East Africa during the Last Glacial period. Climate model simulations support forward extrapolation from these lake sediment data that future warming will intensify the interannual variability of East Africa's rainfall.