Phytolith Research Research Articles

Open Practices in Phytolith Research: A Community Survey

Open Practices in Phytolith Research: A Community Survey

Production of phytoliths in woody plants of the Atlantic Forest in islands of the Paraná River, Brazil

The analysis of phytoliths is a recent addition to the geosciences and has found applications in various fields over the last few decades, including palaeoenvironmental studies in fluvial environments. As a developing field, it is essential to carry out studies aimed at creating a modern reference collection that fills an information gap on the production of phytoliths by plants in this environment. These studies are essential to increase the reliability and accuracy of phytolith research in reconstructing past vegetation patterns and compositions. This study is the first with the aim of creating a pioneer collection of phytoliths in fluvial environments of the Upper Paraná River, addressing woody eudicotyledon species of greater representation on the Três Ilhas (Three Islands) Archipelago. The phytoliths were extracted from the leaves of 51 species from the botanical collection of the Nupélia herbarium (HNUP) using the dry ashing extraction method. The analysis found that 21 plant families established on the site have some kind of silica accumulation and 34 species are producers of phytoliths with an identifiable shape and size (<5um). It was confirmed the Moraceae family produces Acute bulbosus (with ramifications), both considered diagnostic at family level. Confirming the current literature on the subject, redundancy of the spheroid ornate and spheroid psilate morphotypes was observed in woody plants. Although no new morphotypes were found, the information will contribute to studies on the evolution of fluvial geoforms.

A dataset for assessing phytolith data for implementation of the FAIR data principles

Phytolith research contributes to our understanding of plant-related studies such as plant use in archaeological contexts and past landscapes in palaeoecology. This multi-disciplinarity combined with the specificities of phytoliths themselves (multiplicity, redundancy, naming issues) produces a wide variety of methodologies. Combined with a lack of data sharing and transparency in published studies, it means data are hard to find and understand, and therefore difficult to reuse. This situation is challenging for phytolith researchers to collaborate from the same and different disciplines for improving methodologies and conducting meta-analyses. Implementing The FAIR Data principles (Findable, Accessible, Interoperable and Reusable) would improve transparency and accessibility for greater research data sustainability and reuse. This paper sets out the method used to conduct a FAIR assessment of existing phytolith data. We sampled and assessed 100 articles of phytolith research (2016–2020) in terms of the FAIR principles. The end goal of this project is to use the findings from this dataset to propose FAIR guidance for more sustainable publishing of data and research in phytolith studies.

Looking at Phytoliths in Archaeological Soil and Sediment Thin Sections

ABSTRACT Traditionally, phytolith research focusses on the study of bulk samples collected during archaeological field campaigns. However, phytoliths are frequently reported by soil micromorphologists studying their archaeological soil and sediment thin sections. Within these thin sections all components, including the phytoliths, are captured in the position they had in the original soil and sediment profiles. This opens perspectives towards a better understanding of phytolith depositional and post-depositional histories, but also towards the identification of invisible archaeological remains, such as previous vegetal floor covers. Furthermore, the study of phytoliths in thin sections opens up prospects for morphometrical analysis. Despite a series of limitations – the phytolith record is not concentrated, issues of visibility, the fact that phytoliths cannot be rotated and are cut at random angles – the study of phytoliths in thin sections is a rewarding effort. Beyond being a feasible task, it is also a promising asset, given a full integrative approach involving both phytolith specialists and micromorphologists.

Phytoliths from Woody Plants: A Review

Phytoliths are efficient proxies in archaeology, plant taxonomy, palaeoenvironment, and palaeoecology reconstruction, the research of which has been developing rapidly in recent years. Phytolith morphology is the basis of phytolith research. The morphological identification and classification of grass phytoliths are clear and detailed enough for application. However, the morphology of phytoliths from woody plants is ambiguous and unsystematic because of the relatively rare research on modern phytoliths and consequently seldom used in archaeology and palaeoenvironment reconstruction. This paper summarizes and concludes the research of woody phytolith morphology in the past decades. Previous studies show that palms and conifers produce some diagnostic phytoliths for identification and classification. There is progress in micromorphology, morphometry, and taxonomic identification of palms and conifers phytoliths. The phytolith morphology of broad-leaved trees is summarized according to produced parts of phytoliths in plants. The potential of further classification for broad-leaved phytoliths was discussed.

Assessing Open Science Practices in Phytolith Research

Open science is an integral part of all scientific research, but the extent of open science practices in phytolith research is unknown. Phytolith analysis examines silica bodies that are initially formed within and between plant cells during the life of the plant but become deposited in sediments once the plant dies. The use of phytoliths in archaeobotanical and palaeoecological studies has been increasing in recent years resulting in an upsurge in publications. The aims of this article are to assess open science practices in phytolith research by reviewing data and metadata sharing, and open access, in a sample of journal articles containing primary phytolith data from 16 prominent archaeological and palaeoecological journals (341 articles). This study builds on similar studies conducted for zooarchaeology (Kansa <em>et al</em>. 2020) and macro-botanical remains (Lodwick 2019). This study shows that 53% of papers shared data in any format but only 4% of papers contained reusable data, 74% included some pictures of phytolith morphotypes for identification purposes, 69% had a fully described method, 47% used the International code for phytolith nomenclature (ICPN 1.0) and only 13% of articles were open access. Steps forward are then proposed, including planning for open projects, making more articles openly accessible and implementing the FAIR data principles, to use as a starting point for discussions in the wider phytolith and archaeological communities to develop guidelines for greater integration of open science practices.

Responses of phytoliths in topsoil samples to temperature variation in temperate region.

Modern phytolith research is the premise to accurately reconstruct the regional paleovegetation and paleoclimate. It is thus particularly important to study the spatial distribution characteristics of the phytolith assemblages and the response of the phytolith to environmental factors. In this study, we collected 54 topsoil samples along the isohyet of 600 mm in Northeast China to examine the distribution patterns of phytolith along the gradient of single environmental factor. With this special sampling method, we targeted to reveal the responses of phytolith assemblages in the topsoil to the variation of temperature. The results showed that there were a large number of phytoliths with various morphotypes in the 54 topsoil samples in Northeast China. The phytolith morphotypes were the same, including elongate, lanceolate, blocky, cuneiform, tabular, saddle, rondel, bilobate, trapeziform polylobate, prism, silicified stomata, conduit, papillae, sclereid and carinate. In gene-ral, the contributions of elongate and lanceolate were high; the contributions of short cell phytoliths, blocky, tabular and cuneiform were small relatively; the contributions of the other types of phytoliths were less than 1.0% and appeared sporadically in the topsoil samples. Besides, the phytolith assemblages of the topsoil samples were different among Xiaoxing'an Mountains, Songliao Plain and Liaoxi hills. Combined with the discriminant analysis, the samples from the three regions could be effectively separated based on the phytoliths assemblages, with a total accuracy of 94.4%. Specifi-cally, the average percentage of elongate, lanceolate, prism was the largest in Xiaoxing'an Mountains, and was the smallest in Liaoxi hills; the percentage of saddle, bilobate, papillae was the largest in Liaoxi hills and the smallest in Xiaoxing'an Mountains; the percentage of blocky, tabular, cuneiform was the largest in Songliao Plain. Meanwhile, the percentages of the elongate, lanceolate, prism, saddle, bilobate, papillae, blocky, tabular, cuneiform were significant diffe-rences among the three regions. There were significant negative correlations between the percentages of elongate, lanceolate, prism and the annual average temperature, and positive relationships between the percentages of the blocky, tabular, cuneiform, bilobate, papillae and the annual average temperature. However, the percentage of saddle, rondel and trapeziform polylobate did not change with increasing annual average temperature.

Data from “Assessing Open Science Practices in Phytolith Research”

This is a dataset gathered to assess the state of open science practices in phytolith research. All articles presenting primary phytolith data were extracted from 16 prominent archaeological and palaeoecological journals between 2009 and 2018. In total, the dataset contains information on 341 articles. This included archaeological (n = 214), palaeoenvironmental (n = 53) and methodological (n = 74) studies. Information was recorded regarding the data location and what type of data was included in the text and as supplementary files. There was also data recorded in relation to open access, picture inclusion, use of the International code for Phytolith Nomenclature (ICPN) and the inclusion of a full method.

Complex environmental research: Do we need exact knowledge of plant anatomy? A critical discussion of

Phytoliths (silica bodies in plants) are used as proxies in paleoecological and archaeological studies because of their taxonomical relevance and persistence in soils and sediments after the degradation of the plant. In the recent review of Rashid et al. (2019), which summarized the literature of phytolith research, Figure 2 presented an inaccurate description of the anatomical structure of a rice plant in connection with creating phytoliths in the plants. It is essential to correct the errors of this imprecise illustration.Complex environmental research needs to rely on different scientific fields, including plant anatomy. We have to take into account that the inaccurate descriptions as well as knowledge of the anatomical structure of the plants may result in incorrect conclusions with respect to physiological processes of creating phytoliths and evaluating the effects of environmental factors on them.

Plant Silicon and Phytolith Research and the Earth-Life Superdiscipline.

No abstract available Keywords: earth system; phytolith; plants; silicon; superdiscipline.

Phytolith research in the South of Western Siberia

&lt;p&gt;The research of modern and fossil soils was conducted at three archaeological sites: Nizhniy Kayancha, Novoilinka-3, and Tytkesken-2. Nizhniy Kayancha is a burial ground (dated 5th century BC) situated on the left bank of the Katun River (400-700 m above sea level). An archaeological site is a burial mound with seven mounds which can be visually separated within the site, and which are placed by small chains with 2–3 objects. The south mound of the first group was examined for a phytolith analysis. Еhe Novoilinka-3 settlement (dated 3rd millennium BC) is situated in the north of Kulunda, in the southern part of a hill formed by the false River Burla. The Tytkesken-2 settlement is situated on the verge of the stream Tytkesken, the left tributary of the Katun River, on its second terrace above the flood plain.&lt;/p&gt;&lt;p&gt;Geobotanical research was conducted in the territory of the archaeological sites under study. Grass phytoliths of modern flora were examined. Soil samples from different layers of the walls of excavation sites were collected. Phytolith extraction was based on the methods described by A.A. Golyeva. 20 g of soil, and 100 g of plant material of each species were processed during the initial period. The examination of the phytoliths of leaves, stalks and flower heads from the samples obtained from the plant material was carried out with the help of an optical microscope (Olympus BX-51). The phytoliths were counted to 250 (in ashed plants) and to 300 (in soils) particles.&lt;/p&gt;&lt;p&gt;More mesophytic plant communities of the ancient epochs have been reconstructed for all three examined archaeological sites. The territory of the Nizhniy Kayancha burial ground was covered by birch forest at the time prior to formation of the archaeological site. The territory of Novoilinka-3 settlement was covered by pine and birch steppificated forest in the Eneolithic period, but the territory was deforested as the settlement developed. Several stages of vegetation change have been reconstructed for the Tytkesken-2 archaeological site. This includes deforestation of pine forest and further steppe formation in the late Neolithic Age, prairiefication in the Eneolithic Age and new steppe formation in the Bronze Age up to the present time.&lt;/p&gt;

Issues and directions in phytolith analysis

This special issue examines new trends in phytolith scholarship and assesses the future direction of this field of research. The papers presented represent a broader shift in phytolith research into a new phase called the “Period of Expanding Applications”. It is characterized by 1) a rapid increase in the number of phytolith publications; 2) a diversification of research topics; 3) a reassessment of the use of radiocarbon and other isotopes in phytoliths; 4) the development of digital technologies for refining and sharing phytolith identifications; 5) renewed efforts for standardization of phytolith nomenclature and laboratory protocol; and 6) the development of the field of applied phytolith research. This paper argues that interdisciplinary collaborations and a continued effort to understand the basics of phytolith production patterns are essential for the growth of the discipline and its application in archaeological studies.

Directions in current and future phytolith research

The analysis of phytoliths has progressed immensely in recent years. Increases in the number of phytolith works within several disciplines has substantially extended our knowledge about these microfossils, while at the same time diversifying the approaches by which they can be used as archaeological and palaeoenvironmental proxies. The insufficient standardisation of these works, however, greatly increases the difficulty of utilising this body of research within a broader framework of powerfully integrated methodologies and models in archaeobotany and palaeoenvironmental studies. Further standardisation will facilitate the broadening of phytolith research beyond technique-oriented work, permitting greater opportunity for its application to inform on past cultures and their strategies of plant resources exploitation as well as the dynamics related to climate change and anthropic-driven environmental modifications. The aim of this paper is to drive our discipline towards a set of “best practices” that arise from current phytolith research but that are often applied in an unsystematic manner.

Bulliform Phytolith Research in Wild and Domesticated Rice Paddy Soil in South China.

Bulliform phytoliths play an important role in researching rice origins as they can be used to distinguish between wild and domesticated rice. Rice bulliform phytoliths are characterized by numerous small shallow fish-scale decorations on the lateral side. Previous studies have shown that domesticated rice has a larger number of these decorations than wild rice and that the number of decorations ≥9 is a useful feature for identifying domesticated rice. However, this standard was established based on limited samples of modern rice plants. In this study, we analyzed soil samples from both wild and domesticated rice paddies. Results showed that, in wild rice soil samples, the proportion of bulliform phytoliths with ≥9 decorations was 17.46% ± 8.29%, while in domesticated rice soil samples, the corresponding proportion was 63.70% ± 9.22%. This suggests that the proportion of phytoliths with ≥9 decorations can be adopted as a criterion for discriminating between wild and domesticated rice in prehistoric soil. This indicator will be of significance in improving the application of fish-scale decorations to research into rice origins and the rice domestication process.

A conceptual framework for a computer-assisted, morphometric-based phytolith analysis and classification system

Although automated approaches to shape analysis and object classification have been widely applied in the biological sciences, technical and time considerations have limited their use in phytolith research. As advanced microscopy systems become more affordable and accessible and digital imaging software provides a wider range of sophisticated analytical tools, there is increased potential for effective use of machine-vision and automation in phytolith research. In this paper, we describe technical limitations of phytolith imaging and identify several techniques that might improve results. Drawing on examples of software developed for related disciplines, we then describe a conceptual framework for development and integration of automated phytolith analysis software for: separating phytoliths from non-phytolith material in digital images; segmentation of phytolith boundaries; quantitative phytolith feature extraction, including a discussion of potentially more powerful, non-traditional parameters of phytolith shape and texture; phytolith classification and identification; and phytolith database image retrieval. While recognizing the difficulty of implementing this framework and the need for extensive empirical testing of suggested approaches on phytoliths, we examine the possibility of aggregating quantitative phytolith data collected in studies worldwide to construct a cloud-based database of phytolith images with associated morphotype data.

An enigma revisited: identification of palm phytoliths extracted from the 1983 Rapa Nui, Rano Kao2 core

Collection of climatic, environmental and archaeological data from the remote southern oceanic island of Rapa Nui is a continuous process. There are many enigmas, such as the unique Moai statuary and sparsity of vegetation. Pollen studies concluded that the pre-human island Rapa Nui was dominated by a now extinct palm, Paschalococos disperta. The phytolith research reported here has identified the presence through time of other palm species. Plant biogenic silica phytolith microfossils were extracted from Rano Kau core sediments, a nearby ahu and pan-Pacific palm material for reference purposes. A palm phytolith classification was constructed from the many micrographs produced and all extracted sediment and palm phytoliths were classified and compared visually with each other. Six palm species were identified. Robust identification of these, now extinct on Rapa Nui, palms by phytolith analysis has shown them to belong to extant palm species occurring on Pacific islands in a north-west arc from Rapa Nui and on mainland South America. Data on the current habitats of these palms, when applied to Rapa Nui, has the potential to add to the vegetation and environmental history data base of the island.

Comparison of dry ashing and wet oxidation methods for recovering articulated husk phytoliths of foxtail millet and common millet from archaeological soil

Phytolith research on foxtail and common millets represent one of the keys to explore early agricultural activities in the Yellow River basin in China. However, the phytoliths of these two millets easily disintegrate during burial and the extraction process. In this paper, both dry ashing and wet oxidation methods were applied to determine the effects on phytolith extraction from archaeological soil samples. The results indicated that the dry ashing method had two significant advantages over wet oxidation: (1) the morphology of husk phytoliths was retained to a greater extent; and (2) nearly all the charcoalified tissues were removed successfully. The dry ashing method proved to be a better method for phytolith extraction of both foxtail millet as well as common millet from archaeological samples.

The Study of Indigenous Management Practices in California: An Introduction

The purpose of this special issue is to present the findings of a collaborative, interdisciplinary eco-archaeological project that is examining evidence for indigenous landscape management practices in central coastal California in Late Holocene and historic times. In this introductory paper, we provide some background about traditional resource and environment management (TREM) practices in California, discuss the goals of the eco-archaeological project, outline testable expectations for anthropogenic burning, and introduce the papers in the volume. The papers represent a coordinated suite of investigations that empirically evaluate the degree to which native people may have ignited fires in and around the Quiroste Valley Cultural Preserve near Point Año Nuevo. Employing diverse lines of evidence derived from archaeology, silica phytolith research, palynology, plant population genetics, and dendroecology, the authors reconstruct past fire histories, faunal and floral resources, vegetation conversions, and indigenous cultural practices in the study area. The findings of these investigations indicate that people implemented sustained landscape burning practices that maintained productive grassland habitats from about AD 1000 to the time of Spanish colonization.

Poaceae phytoliths from the Niassa Rift, Mozambique

The most common grass phytoliths from “Zambezian” miombos are described here for the first time. Their potential for long term preservation in sediments makes them a useful tool in the reconstruction of ancient plant communities and plant/human interactions. We processed 60 plant samples (26 identified genera and species), with an average of 300 phytoliths counted per sample to a total of 18,586. Forty-seven morphotypes were described as per the International Code for Phytolith Nomenclature, with exceptions, including forty-five discreet shapes and two articulated forms, which can be used as comparative reference materials. We conducted three forms of statistical analyses: Discriminant Analysis, Cluster Analysis, and Principal Component Analysis. The highest biomineral content was recorded among the Bambuseae and Paniceae, while the lowest silica production is detected in the Cynodonteae tribe. Typologically, the subfamily Panicoideae yielded 50% of the types reported here, 32% are from the Chloridoideae, 12% from the Bambusoideae, and 8% from the Arundinoideae sensu lato. Overall, the idealized Zambezian Poaceae phytolith spectrum is dominated by a small subset of Poaceae short cells, which include five morphotypes conventionally associated with Panicoid grasses (Bilobate concave outer margin long shaft, Bilobate concave outer margin short shaft, Bilobate convex outer margin long shaft, Bilobate convex outer margin short shaft, Cross), one morphotype commonly seen in Chloridoid taxa (saddle), and two types that appear across subfamily boundaries (tower, tower horned). The next logical step to take in regional phytolith research is the account of phytoliths deposited in soils underneath living plants, for they represent the interface between existing vegetation communities and the inevitably distorted fossil assemblages that the paleobotanist uses for environmental reconstruction.

Extended depth of focus image for phytolith analysis

This paper proposes a new phytolith analysis method by extended depth of focus technology. The extended depth of focus image is sharp throughout by the image processing of a series of photos, while each acquisition of the original photo will be compromised and show certain parts of the specimen in and out of focus. Consequently, the extended depth of focus image is suitable for computer-assisted morphometrics analysis. Meanwhile, the extended depth of focus image can be used for three-dimensional reconstruction images. Experiments on rice husk multi-cell panel show that the three-dimensional reconstruction image method can reconstruct multiple double-peaked phytoliths at one time. We also measure the parameters of multiple double-peaked phytoliths from the reconstructed three-dimension image. Comparative experiments show that the reconstructed three-dimensional image is precise enough for rice identification. Based on the above experiments, we recommend the extended depth of focus method as a promising tool in phytolith research.