Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant—Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type,plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.

Palinostratigraphy of glaciomarine and marine sedimentsof the Barents Sea

By combining the palynologic, lithologic and published geophysical data a stratigraphic division into three main sedimentary units representing major stages in the development of post-glacial sedimentary environments in the southeastern and central parts of the Barents Sea has been substantiated. Unit 3 presumably characterizes proglacial environments of the early deglaciation (tentatively older than 15 ka) and is represented by relatively fine-grained, dark grey sediment matrix with numerous coarse terrigenous clasts. The unit contains low in diversity and concentration pollen assemblage, which is dominated by reworked, mostly Mesozoic pollen and sparse dinocysts of a cryophylic species Islandinium var. minutum. Unit 2 represents later deglacial conditions (estimated ca 12-15 ka) and is composed of finely laminated, grey to brownish sandy/silty muds with coarse clasts interpreted as iceberg-rafted debris. It is characterized by pollen assemblage zone with a low concentration of plant remains, a significant proportion of reworked pre-Cenozoic microfossils and club mosses among spores as well as a high percentage of dwarfBetula, Poaceae and Artemisia Islandinium var. minutum dominates among the aquatic palynomorphs. Unit 1, younger than ca 12 ka, is composed of soft, olive-grey mud with traces of bioturbations and spots of hydrotroilite at the top or sandy-silty mud within the South-Novozemelskii Trough and sand with inclusions of pebbles and broken shells within the Kanin Plateau. Three pollen assemblage zones correspond to it. They are marked by a high percentage of birch and pine pollen, an increased share of pollen of spruce and alder, as well as Sphagnum mosses and ferns. Constant presence of sparse pollen of broad-leaved plants in combination with peak values of Operculodinium centrocarpum and Spiniferites sp. testify the enhancement of Atlantic water influence upon the studied regions.

Climate and human induced 2000-year vegetation diversity change in Yunnan, southwestern China

Understanding long-term vegetation diversity patterns and their potential responses to climate and/or human driven processes are important for ecosystem modeling and conservation. Late-Holocene fossil pollen assemblage and associated vegetation diversity estimates provide an opportunity to explore the interactions among vegetation, climate, and human activities. A continuous 2000-year palynological record was obtained from the Beihai Wetland, southwestern China, to represent regional vegetation history, particularly the vegetation diversity changes. The results indicate that regional vegetation was dominated by deciduous broadleaved forest components (e.g. Alnus, deciduous Quercus), which showed a gradual decrease accompanied by expansion of herbaceous taxa (mainly Poaceae) after AD 800. Such progressive decline of forest was attributed to regional deforestation driven by intensified human activities, which was further confirmed by the increasing non-pollen polymorph abundance, particularly an abrupt rise after AD 1350. Vegetation diversity based on the Hill numbers ( N0, N1, and N2) showed a dramatic decline between ca. AD 200–400, which was triggered by regional fire events as shown by increased charcoal abundance from a nearby lake. The vegetation diversity reduced gradually after AD 800, especially the vegetation richness reflected by N0, revealing the transitional process from climate-driven to human-dominated vegetation changes. Minor increases of vegetation diversity occurred during Chinese dynastical transitions, probably due to reduced human activities following war-induced population crises. On the multidecadal scale, variations in vegetation diversity correlated significantly with climate fluctuations (revealed by synthesized temperature of China and stable oxygen isotope record from Dongge Cave) before AD 800, indicating a climate dominant condition. Then, the correlation between vegetation diversity and climate declined after AD 800, representing a progressive transition to human-dominant condition. In addition, the compositional turnover based on DCCA of the fossil pollen assemblage revealed a stepwise decrease, indicating reduced vegetation turnovers under anthropogenic influences.

The modern pollen–vegetation relationship in Jammu, India: a comparative appraisal

An understanding of the relationship between modern pollen and vegetation is a prerequisite for reconstruction of vegetation and climate change from fossil pollen records. We conducted palynological studies of thirty-five surface soil samples from the Jammu region of India, which revealed that Pinus, among the conifers (regional needle-leaved taxa), is over-represented in the pollen assemblage due to its high production and effective dispersal of pollen. Other coniferous and broadleaved (regional and/or extra-regional) taxa have comparatively lower values in the pollen assemblages, similar to the representation of subtropical deciduous forest elements (regional), as well as shrubby (regional and/or extra-regional) taxa. This inconsistency in the pollen assemblage could be due to long-distance transport of the former by wind and/or water from the higher reaches of the Himalayas, and also because the latter have an entomogamous pollination syndrome and are not high pollen producers. The recovered pollen assemblage presents a distorted picture of the extant vegetation; hence, caution should be exercised in interpreting fossil pollen records from the study area. Principal component analysis (PCA) shows variability in the distribution of pollen from different sites in the Jammu region, perhaps the result of transport (by wind and/ or water), altitude and/or edaphic factors of the Himalayan terrain. The study should improve our understanding of the modern pollen-vegetation relationship and aid further calibration and interpretation of fossil pollen records.

Vegetation Changes around Haven Lake, Adak Island, Central Aleutians, Alaska, Determined from Pollen Analysis

ABSTRACTWe collected peat sediments (sediment core ADK13083002) from Haven Lake on the north side of Adak Island (central Aleutian Islands, Alaska) to determine whether the vegetation has changed. We confirmed the presence of six tephra layers, including Forty Years (0.3 cal ka BP), T2, YBO (3.3 cal ka BP), Intermediate (6.4 cal ka BP), Main (9.5 cal ka BP), and T6. We identified four major pollen assemblage zones (HL-1 to HL-4, in descending order) in the cored sediment. HL-1 was dominated by Ranunculaceae and Empetrum pollen; H-2 was dominated by Poaceae, Ranunculaceae, and Empetrum pollen; HL-3 was dominated by Poaceae and Empetrum pollen; and HL-4 was dominated by Poaceae, Cyperaceae, Lycopodiaceae, and Empetrum pollen. Small charcoal particles, likely transported from a distance, were found at low frequencies until 6.4 cal ka BP. The total cross-sectional area of charcoal particles increased to 1500 μm2 or more by 6.4 cal ka BP, implying that the large charcoal particles originated from nearby Aleut settlements, which were established around the same time.