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Concept: Palynology

37

There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.

Concepts: Scientific method, Biology, Fungus, Pollen, A priori, A priori and a posteriori, Archaeology, Palynology

27

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.

Concepts: Fungus, Ecology, Lake, Sediment, Natural environment, Pollination, Fossil, Palynology

4

Species flower production and flowering phenology vary from year to year due to extrinsic factors. Inter-annual variability in flowering patterns may have important consequences for attractiveness to pollinators, and ultimately, plant reproductive output. To understand the consequences of flowering pattern variability, a community approach is necessary because pollinator flower choice is highly dependent on flower context. Our objectives were: 1) To quantify yearly variability in flower density and phenology; 2) To evaluate whether changes in flowering patterns result in significant changes in pollen/nectar composition. We monitored weekly flowering patterns in a Mediterranean scrubland community (23 species) over 8 years. Floral resource availability was estimated based on field measures of pollen and nectar production per flower. We analysed inter-annual variation in flowering phenology (duration and date of peak bloom) and flower production, and inter-annual and monthly variability in flower, pollen and nectar species composition. We also investigated potential phylogenetic effects on inter-annual variability of flowering patterns. We found dramatic variation in yearly flower production both at the species and community levels. There was also substantial variation in flowering phenology. Importantly, yearly fluctuations were far from synchronous across species, and resulted in significant changes in floral resources availability and composition at the community level. Changes were especially pronounced late in the season, at a time when flowers are scarce and pollinator visitation rates are particularly high. We discuss the consequences of our findings for pollinator visitation and plant reproductive success in the current scenario of climate change.

Concepts: Pattern, Pollination, Flower, Pollinator decline, Pollination syndrome, Pollen, Flowers, Palynology

4

Seasonal allergic rhinitis (SAR) caused by Japanese cedar pollen (JCP; ie, sugi-pollinosis) is the most common disease in Japan and has been considered a national affliction. More than one third of all Japanese persons have sugi-pollinosis, and this number has significantly increased in the last 2 decades. In our opinion the reason why sugi-pollinosis became a common disease in the last half century is the increased number of cedar pollens, with global climate change and forest growth caused by the tree-planting program of the Japanese government after World War II playing substantial roles; dust storms containing small particulate matter from China might also contribute to the increased incidence of sugi-pollinosis. To help minimize their symptoms, many Japanese wear facemasks and eyeglasses at all times between February and April to prevent exposure to JCP and aerosol pollutants. Forecasts for JCP levels typically follow the weather forecast in mass media broadcasts, and real-time information regarding JCP levels is also available on the Internet. Because a large amount of JCP is produced over several months, it can induce severe symptoms. Japanese guidelines for allergic rhinitis recommend prophylactic treatment with antihistamines or antileukotrienes before the start of JCP dispersion. Additionally, sublingual immunotherapy will be supported by health insurance in the summer of 2014. However, many patients with sugi-pollinosis do not find satisfactory symptom relief with currently available therapies. Collaboration between scientists and pharmaceutical companies to produce new therapeutics for the control of sugi-pollinosis symptoms is necessary.

Concepts: Disease, Climate, Weather, Allergy, Symptom, Climate change, Government of Japan, Palynology

3

Knowledge of the direct role humans have had in changing the landscape requires the perspective of historical and archaeological sources, as well as climatic and ecologic processes, when interpreting paleoecological records. People directly impact land at the local scale and land use decisions are strongly influenced by local sociopolitical priorities that change through time. A complete picture of the potential drivers of past environmental change must include a detailed and integrated analysis of evolving sociopolitical priorities, climatic change and ecological processes. However, there are surprisingly few localities that possess high-quality historical, archeological and high-resolution paleoecologic datasets. We present a high resolution 2700-year pollen record from central Italy and interpret it in relation to archival documents and archaeological data to reconstruct the relationship between changing sociopolitical conditions, and their effect on the landscape. We found that: (1) abrupt environmental change was more closely linked to sociopolitical and demographic transformation than climate change; (2) landscape changes reflected the new sociopolitical priorities and persisted until the sociopolitical conditions shifted; (3) reorganization of new plant communities was very rapid, on the order of decades not centuries; and (4) legacies of forest management adopted by earlier societies continue to influence ecosystem services today.

Concepts: Ecology, Climate, Ecosystem, Culture, Climate change, Anthropology, Archaeology, Palynology

2

Botanical gardens represent artificial, but stable environments. With this premise, we analyzed the Munich Botanical Garden’s bee fauna in 1997/1999 and again in 2015/2017. The garden covers 20 ha, uses no bee-relevant insecticides, has a protected layout, and on three sides abuts protected areas. Outdoors, it cultivates some 10,871 species/subspecies, many suitable as pollen and nectar sources for bees. The first survey found 79 species, the second 106, or 55% of the 192 species recorded for Munich since 1990. A Jackknife estimate for the second survey suggests 115 expected species. Classifying bees according to their thermal preferences (warm habitats, cool habitats, broad preferences, or unknown) revealed that 15 warm-loving species were gained (newly found), two lost (no longer found), and 12 retained, but only one cool-loving species was gained, three lost, and none retained, which multinomial models show to be significant differences. Of the 62 retained species, 27 changed in abundance, with 18 less frequent and nine more frequent by 2017 than they had been in 1997/1999. Retention, gain, or loss were unconnected to pollen specialization and Red List status of bee species. Between 1997 and 2017, average temperatures in Munich have increased by 0.5 °C, and climate warming over the past century is the most plausible explanation for the directional increase in warm-loving and the decrease in cool-adapted species. These results highlight the potential of botanic gardens with their artificially diverse and near-pesticide-free floras as systems in which to investigate climate change per se as a possible factor in shifting insect diversity.

Concepts: Insect, Climate change, Botany, Flower, Bee, Herbal, Palynology, Botanical garden

2

Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. However, its use has previously been limited by the need for a high level of specialization by expert palynologists, slow speeds of identification, and relatively poor taxonomic resolution (typically to the plant family or genus level). By contrast, identification of pollen through DNA barcoding has the potential to overcome all three of these limitations, and it may seem surprising that the method has not been widely implemented. Despite what might seem a straightforward application of DNA barcoding to pollen, there are technical issues that have delayed progress. However, recent developments of standard methods for DNA barcoding of pollen, along with improvements in high-throughput sequencing technology, have overcome most of these technical issues. Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations.

Concepts: Bioinformatics, Molecular biology, Species, Taxonomy, DNA sequencing, DNA barcoding, Identification, Palynology

2

Interaction of orbital insolation cycles defines a predictive model of alternating phases of high- and low-climate variability for tropical East Africa over the past 5 million years. This model, which is described in terms of climate variability stages, implies repeated increases in landscape/resource instability and intervening periods of stability in East Africa. It predicts eight prolonged (>192 kyr) eras of intensified habitat instability (high variability stages) in which hominin evolutionary innovations are likely to have occurred, potentially by variability selection. The prediction that repeated shifts toward high climate variability affected paleoenvironments and evolution is tested in three ways. In the first test, deep-sea records of northeast African terrigenous dust flux (Sites 721/722) and eastern Mediterranean sapropels (Site 967A) show increased and decreased variability in concert with predicted shifts in climate variability. These regional measurements of climate dynamics are complemented by stratigraphic observations in five basins with lengthy stratigraphic and paleoenvironmental records: the mid-Pleistocene Olorgesailie Basin, the Plio-Pleistocene Turkana and Olduvai Basins, and the Pliocene Tugen Hills sequence and Hadar Basin-all of which show that highly variable landscapes inhabited by hominin populations were indeed concentrated in predicted stages of prolonged high climate variability. Second, stringent null-model tests demonstrate a significant association of currently known first and last appearance datums (FADs and LADs) of the major hominin lineages, suites of technological behaviors, and dispersal events with the predicted intervals of prolonged high climate variability. Palynological study in the Nihewan Basin, China, provides a third test, which shows the occupation of highly diverse habitats in eastern Asia, consistent with the predicted increase in adaptability in dispersing Oldowan hominins. Integration of fossil, archeological, sedimentary, and paleolandscape evidence illustrates the potential influence of prolonged high variability on the origin and spread of critical adaptations and lineages in the evolution of Homo. The growing body of data concerning environmental dynamics supports the idea that the evolution of adaptability in response to climate and overall ecological instability represents a unifying theme in hominin evolutionary history.

Concepts: Natural selection, Evolution, Prediction, Futurology, Evolutionary biology, Paleontology, Human evolution, Palynology

2

Pollen of common ragweed (Ambrosia artemisiifolia) is a main cause of allergic diseases in Northern America. The weed has recently become spreading as a neophyte in Europe, while climate change may also affect the growth of the plant and additionally may also influence pollen allergenicity. To gain better insight in the molecular mechanisms in the development of ragweed pollen and its allergenic proteins under global change scenarios, we generated SuperSAGE libraries to identify differentially expressed transcripts.

Concepts: Allergy, Allergen, Pollen, Ragweed, Ambrosia artemisiifolia, Goldenrod, Palynology, Ambrosia

1

The evolution of cetaceans is one of the best examples of macroevolution documented from the fossil record. While ecological transitions dominate each phase of cetacean history, this context is rarely stated explicitly. The first major ecological phase involves a transition from riverine and deltaic environments to marine ones, concomitant with dramatic evolutionary transformations documented in their early fossil record. The second major phase involves ecological shifts associated with evolutionary innovations: echolocation (facilitating hunting prey at depth) and filter-feeding (enhancing foraging efficiency on small prey). This latter phase involves body size shifts, attributable to changes in foraging depth and environmental forcing, as well as re-invasions of freshwater systems on continental basins by multiple lineages. Modern phenomena driving cetacean ecology, such as trophic dynamics and arms races, have an evolutionary basis that remains mostly unexamined. The fossil record of cetaceans provides an historical basis for understanding current ecological mechanisms and consequences, especially as global climate change rapidly alters ocean and river ecosystems at rates and scales comparable to those over geologic time.

Concepts: Evolution, Ecology, Climate, Fossil, Paleontology, Charles Darwin, Whale, Palynology