Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia

Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment. © 2013 Blackwell Publishing Ltd.

Climate change and decadal to centennial-scale periodicities recorded in a late Holocene NE Pacific marine record: Examining the role of solar forcing

We present a decadal-scale late Holocene climate record based on diatoms, biogenic silica, and grain size from a 12-m sediment core (VEC02A04) obtained from Frederick Sound in the Seymour-Belize Inlet Complex of British Columbia, Canada. Sediments are characterized by graded, massive, and laminated intervals. Laminated intervals are most common between c. 2948–2708 cal. yr BP and c. 1992–1727 cal. yr BP. Increased preservation of laminated sediments and diatom assemblage changes at this time suggest that cli- mate became moderately drier and cooler relative to the preceding and succeeding intervals. Spectral and wavelet analyses are used to test for statistically significant periodicities in time series of proxies of primary production (total diatom abundance, biogenic silica) and hydrology (grain size) preserved in the Frederick Sound record. Periodicities of c. 42–53, 60–70, 82–89, 241–243, and 380 yrs are present. Results are com- pared to reconstructed sunspot number data of Solanki et al. (2004) using cross wavelet transform to evalu- ate the role of solar forcing on NE Pacific climate. Significant common power of periodicities between c. 42– 60, 70–89, 241–243, and of 380 yrs occur, suggesting that celestial forcing impacted late Holocene climate at Frederick Sound. Replication of the c. 241–243 yr periodicity in sunspot time series is most pronounced be- tween c. 2900 cal. yr BP and c. 2000 cal. yr BP, broadly correlative to the timing of maximum preservation of laminated sedimentary successions and diatom assemblage changes. High solar activity at the Suess/de Vries band may have been manifested as a prolonged westward shift and/or weakening of the Aleutian Low in the mid-late Holocene, which would have diverted fewer North Pacific storms and resulted in the relatively dry conditions reconstructed for the Seymour-Belize Inlet Complex.

A high resolution 15,600-year pollen and microcharcoal record from the Cederberg Mountains, South Africa

The Cederberg Mountains (Western Cape Province, South Africa) are located within the Fynbos Biome, which exhibits some of the highest levels of species richness and endemism in the world. The region's post-glacial vegetation history, however, remains largely unknown. Presented here are high resolution pollen and microcharcoal records spanning the last 15,600 years obtained from the De Rif rock hyrax midden from the Driehoek Valley of the central Cederberg. In this region, previous pollen studies have shown muted variability in vegetation community composition during periods of globally marked climatic variability (e.g. the last glacial-interglacial transition). In our record, however, significant changes in vegetation composition are apparent. Most notably, they indicate a shift from ericaceous/restioid fynbos (present from 15,600 to 13,300 cal yr BP) to a brief, but prominent, development of proteoid fynbos at the beginning of the Holocene around 11,200 cal yr BP. This vegetation shift is associated with increased moisture at the site, and coincides with reduced fire frequency as indicated by the microcharcoal record. At 10,400 cal yr BP, there is a marked reduction in Protea-type pollen, which is replaced by thicket, characterised by Dodonaea, which became the dominant arboreal pollen type. This shift was likely the result of a long relatively fire-free period coupled with warmer and wetter climates spanning much of the early Holocene. A brief but marked decrease in water availability around 8500-8000 cal yr BP resulted in the strong decrease of Dodonaea pollen. The vegetation of the mid- to late Holocene is characterised by the increased occurrence of Asteraceae and succulent taxa, suggesting substantially drier conditions. These data give unprecedented insight into the vegetation dynamics across a period of substantial, rapid climate change, and while they confirm the presence of fynbos elements throughout the last 15,600 years, the results highlight significant fluctuations in the vegetation that were triggered by changes in both climate and fire regimes. (C) 2013 Elsevier B.V. All rights reserved.

Geochemical records of palaeoenvironmental controls on peat forming processes in the Mfabeni peatland, Kwazulu Natal, South Africa since the Late Pleistocene

The Mfabeni peatland is the only known sub-tropical coastal fen that transcends the Last Glacial Maximum (LGM). This ca. 10m thick peat sequence provides a continuous sedimentation record spanning from the late Pleistocene to present (basal age c. 47kcalyr BP). We investigated the paleaeoenvironmental controls on peat formation and organic matter source input at the Mfabeni fen by: 1) exploring geochemical records (mass accumulation rate, total organic carbon, carbon accumulation rate, δC, δN and C/N ratio) to delineate primary production, organic matter source input, preservation and diagenetic processes, and 2) employ these geochemical signatures to reconstruct the palaeoenvironmental conditions and prevailing climate that drove carbon accumulation in the peatland. We established that the Mfabeni peat sediments have undergone minimal diagenetic alteration. The peat sequence was divided into 5 linear sedimentation rate (LSR) stages indicating distinct changes in climate and hydrological conditions: LSR stage 1 (c. 47 to c. 32.2kcalyr BP): predominantly cool and wet climate with C4 plant assemblages, interrupted by two short warming events. LSR stage 2 (c. 32.2 to c. 27.6kcalyr BP): dry and windy climate followed by a brief warm and wet period with increased C4 sedge swamp vegetation. LSR stage 3 (c. 27.6 to c. 20.3kcalyr BP): initial cool and wet period with prevailing C4 sedge plant assemblage until c. 23kcalyr BP; then an abrupt change to dry and cool glacial conditions and steady increases in C3 grasses. LSR stage 4 (c. 20.3 to c. 10.4kcalyr BP): continuation of cool and dry conditions and strong C3 grassland signature until c. 15kcalyr BP, after which precipitation increases. LSR stage 5 (c. 10.4kcalyr BP to present): characterised by extreme fluctuations between pervasive wet and warm to cool interglacial conditions with intermittent abrupt millennial-scale cooling/drying events and oscillations between C3 and C4 plant assemblages. In this study we reconstructed a high-resolution record of local hydrology, bulk plant assemblage and inferred climate since the Late Pleistocene, which suggest an anti-phase link between Southern African and the Northern Hemisphere, most notably during Heinrich (5 to 2) and Younger Dryas events. © 2013 Elsevier B.V.

Evaluating the use of testate amoebae for palaeohydrological reconstruction in permafrost peatlands

The melting of high-latitude permafrost peatlands is a major concern due to a potential positive feedback on global climate change. We examine the ecology of testate amoebae in permafrost peatlands, based on sites in Sweden (~ 200 km north of the Arctic Circle). Multivariate statistical analysis confirms that water-table depth and moisture content are the dominant controls on the distribution of testate amoebae, corroborating the results from studies in mid-latitude peatlands. We present a new testate amoeba-based water table transfer function and thoroughly test it for the effects of spatial autocorrelation, clustered sampling design and uneven sampling gradients. We find that the transfer function has good predictive power; the best-performing model is based on tolerance-downweighted weighted averaging with inverse deshrinking (performance statistics with leave-one-out cross validation: R2 = 0.87, RMSEP = 5.25 cm). The new transfer function was applied to a short core from Stordalen mire, and reveals a major shift in peatland ecohydrology coincident with the onset of the Little Ice Age (c. AD 1400). We also applied the model to an independent contemporary dataset from Stordalen and find that it outperforms predictions based on other published transfer functions. The new transfer function will enable palaeohydrological reconstruction from permafrost peatlands in Northern Europe, thereby permitting greatly improved understanding of the long-term ecohydrological dynamics of these important carbon stores as well as their responses to recent climate change.

How subtle are the biases that shape the fidelity of the fossil record? A test using marine molluscs

Biases in preservation shape the fossil record, and therefore impact on our reconstructions of past environments and biodiversity. Given the intensive recent research in the general fields of taphonomy and exceptional preservation, surprisingly, fundamental questions remain unanswered about species-level variation in skeletal preservation potential at low taxonomic levels (e.g. between genera from the same family, or between taxa from related families) across myriad groups with multi-element skeletons. Polyplacophoran molluscs (chitons sensu lato) are known from the late Cambrian to Recent, and possess a distinctive articulated scleritome consisting of eight overlapping calcareous valves. The apparent uniformity of living chitons presents an ideal model to test the potential for taphonomic biases at the alpha-taxon level. The vast majority of fossil chitons are preserved as single valves; few exhibit body preservation or even an articulated shell series. An experimental taphonomic programme was conducted using the Recent polyplacophorans Lepidochitona cinerea and Tonicella marmorea (suborder Chitonina) and Acanthochitona crinita (Acanthochitonina). Experiments in a rock tumbler on disarticulated valves found differential resistance to abrasion between taxa; in one experiment 53.8-61.5% of Lepidochitona valves were recovered but 92% of those from Tonicella and 100% of elements from Acanthochitona. Chiton valves and even partly decayed carcasses are more resistant to transportation than their limited fossil record implies. Different species of living chitons have distinctly different preservation potential. This, problematically, does not correlate with obvious differences in gross valve morphology; some, but not all, of the differences correlate with phylogeny. Decay alone is sufficient to exacerbate differences in preservation potential of multi-element skeletons; some, but not all, of the variation that results is due to specimen size and the fidelity of the fossil record will thus vary intra-specifically (e.g. between ontogenetic stages) as well as inter-specifically. 

Deglacial mesophotic reef demise on the Great Barrier Reef

Submerged reefs are important recorders of palaeo-environments and sea-level change, and provide a substrate for modern mesophotic (deep-water, light-dependent) coral communities. Mesophotic reefs are rarely, if ever, described from the fossil record and nothing is known of their long-term record on Great Barrier Reef (GBR). Sedimentological and palaeo-ecological analyses coupled with 67 14C AMS and U–Th radiometric dates from dredged coral, algae and bryozoan specimens, recovered from depths of 45 to 130 m, reveal two distinct generations of fossil mesophotic coral community development on the submerged shelf edge reefs of the GBR. They occurred from 13 to 10 ka and 8 ka to present. We identified eleven sedimentary facies representing both autochthonous (in situ) and allochthonous (detrital) genesis, and their palaeo-environmental settings have been interpreted based on their sedimentological characteristics, biological assemblages, and the distribution of similar modern biota within the dredges. Facies on the shelf edge represent deep sedimentary environments, primarily forereef slope and open platform settings in palaeo-water depths of 45–95 m. Two coral–algal assemblages and one non-coral encruster assemblage were identified: 1) Massive and tabular corals including Porites, Montipora and faviids associated with Lithophylloids and minor Mastophoroids, 2) platy and encrusting corals including Porites, Montipora and Pachyseris associated with melobesioids and Sporolithon, and 3) Melobesiods and Sporolithon with acervulinids (foraminifera) and bryozoans. Based on their modern occurrence on the GBR and Coral Sea and modern specimens collected in dredges, these are interpreted as representing palaeo-water depths of < 60 m, < 80–100 m and > 100 m respectively. The first mesophotic generation developed at modern depths of 85–130 m from 13 to 10.2 ka and exhibit a deepening succession of < 60 to > 100 m palaeo-water depth through time. The second generation developed at depths of 45–70 m on the shelf edge from 7.8 ka to present and exhibit stable environmental conditions through time. The apparent hiatus that interrupted the mesophotic coral communities coincided with the timing of modern reef initiation on the GBR as well as a wide-spread flux of siliciclastic sediments from the shelf to the basin. For the first time we have observed the response of mesophotic reef communities to millennial scale environmental perturbations, within the context of global sea-level rise and environmental changes.

Combining environmental and medical datasets to explore potential associations between environmental factors and health: Policy implications for human health risk assessments

This review paper discusses the use of Tellus and Tellus Border soil and stream geochemistry data to investigate the relationship between medical data and naturally occurring background levels of potentially toxic elements (PTEs) such as heavy metals in soils and water. The research hypothesis is that long-term low level oral exposure of PTEs via soil and water may result in cumulative exposures that may act as risk factors for progressive diseases including cancer and chronic kidney disease. A number of public policy implications for regional human health risk assessments, public health policy and education are also explored alongside the argument for better integration of multiple data sets to enhance ongoing medical and social research. This work presents a partnership between the School of Geography, Archaeology and Palaeoecology, Northern Ireland Cancer Registry, Queen’s University Belfast, and the nephrology (kidney medicine) research group.

50,000-years of vegetation and climate change in the southern Namib Desert, Pella, South Africa

This paper presents the first continuous pollen record from the southern Namib Desert spanning the last 50,000 years. Obtained from rock hyrax middens found near the town of Pella, South Africa, these data are used to reconstruct vegetation change and quantitative estimates of temperature and aridity. Results indicate that the last glacial period was characterised by increased water availability at the site relative to the Holocene. Changes in temperature and potential evapotranspiration appear to have played a significant role in determining the hydrologic balance. The record can be considered in two sections: 1) the last glacial period, when low temperatures favoured the development of more mesic Nama-Karoo vegetation at the site, with periods of increased humidity concurrent with increased coastal upwelling, both responding to lower global/regional temperatures; and 2) the Holocene, during which time high temperatures and potential evapotranspiration resulted in increased aridity and an expansion of the Desert Biome. During this latter
period, increases in upwelling intensity created drier conditions at the site.
Considered in the context of discussions of forcing mechanisms of regional climate change and environmental dynamics, the results from Pella stand in clear contrast with many inferences of terrestrial environmental change derived from regional marine records. Observations of a strong precessional signal and interpretations of increased humidity during phases of high local summer insolation in the marine records are not consistent with the data from Pella. Similarly, while high percentages of Restionaceae pollen has been observed in marine sediments during the last glacial period, they do not exceed 1% of the assemblage from Pella, indicating that no significant expansion of the Fynbos Biome has occurred during the last 50,000 years. These findings pose interesting questions regarding the nature of environmental change in southwestern Africa, and the significance of the diverse records that have been obtained from the region.