Tuesday, 16 January 2018

In Memoriam Alison Weisskopf (1960-2018)

Alison and Oryza nivara in
Orissa, Sept. 2010
Alison Weisskopf (1960-2018), passed away peacefully in hospice in the presence of her immediate family on 11 January 2018. She was a beloved colleagues at the Institute of Archaeology, a fixture in the archaeobotany laboratory for many years and a leading figure in archaeological phytolith research, respected globally. Her research legacy is substantial as her work takes a distinctively ecological assemblage approach to reconstructing rice cultivation ecology as well as crop processing. This has proved innovative and has proved fruitful, and can be expected to continue to inspire further research and agricultural ecology approaches to phytoliths around the world. Despite first being diagnosed with late stage cancer in 2010, she soldiered on was at her most productive as a researcher over the past half dozen years, which is readily evident from her publications list. 

Bangladesh, Nov. 2013: ethnobotany

She has made lasting empirical contributions on archaeological research in China, Southeast Asia (Vietnam, Thailand, Cambodia), and South Asia (Bangladesh, Sri Lanka, India). Through ethnobotanical fieldwork (in India, Thailand, Laos) and archaeological projects (in China, Bangladesh, Fiji), many further collaborations she was a key colleague in many international networks and she leaves behind many friends around the world.

Alison joined UCL as a BSc Archaeology student in 2000/01, essentially a career reboot as a mid-life adult. She demonstrated a strong affinity for environmental archaeology and archaeobotany from the beginnings of her studies. She took my “Plants and Archaeology” in 2001/02, and a new course on “Origins of Agriculture” the following year. Her BSc dissertation on phytoliths (“A study of the phytoliths from the late Bronze Age site of Krasnoe Smarskoe, Samara Valley, Russia, and the information they provide on agro pastoral economies and environments”) supervised by Dr. Arlene Rosen was passed with distinction in 2003. In receipt of a AHRC scholarship, she continued her studies in the MSc Palaeoecology of Human societies, with a dissertation on “An investigation of the Neolithic ash mound and settlement at Sanganakallu in the south Deccan, India, using phytoliths and macro-archaeobotanical material”, combined analyses of plant macro-remains and phytoliths and received a distinction in 2005.

Liu River, near Huizui, Henan, China, 2006
She began her PhD in 2005, again funded through an AHRC studentship. She submitted her PhD thesis, Vegetation, agriculture and social change in Neolithic north central China, a phytolith study, in 2009 and was awarded her doctorate in 2010. Her doctoral research took her on field to China several times, such as to the sites of Huizui and Xipo, where she worked alongside colleagues including Arlene Rosen (now University of Texas at Austin), Gyoung-Ah Lee (University of Oregon) and Liu Li (Stanford University). Her PhD represents years of dedicated laboratory work. She later published a revised version of her PhD as a monograph in 2014.

Sept 2010: Sampling Oryza rufipogin in Orissa, with
Rabi Mohanty and Mukund Kajale

In 2009 she took up a post-doctoral research associate position funded as part of a NERC project  'The Identification of Rice in Prehistory' (2009-2012), which came to be dubbed the Early Rice Project, and spawned follow on research projects, including 'The Impact of Evolving of Rice Systems from China to Southeast Asia' (2013-2016), and 'The impact of intensification and de-intensification of Asian rice production: transitions between wet and dry ecologies' (2016-2019). During a intermission between the first and second NERC projects she secured funding through a British Academy small grant to explore comparisons between phytoliths and diatoms in rice paddy soils, and she received a travel grant from the Thai Ambassador to the UK for ethnobotanical fieldwork on non-rice plant use in Thailand. Her research, and her development of phytolith approaches to rice cultivation ecology was central to these projects and their success. This sent Alison into the field to study modern rice ecologies, both cultivated and wild, in far flung parts of Asia, from central China to Laos and the highlands of northern Thailand, through Bangladesh and Assam, remote parts of Odisha state in India, and the Western Ghats mountains along western coast of India. Her unique experience and expertise has meant that she attracted archaeological collaborations and samples for analysis from an even wider range of countries. She authored 29 academic papers or book chapters, in addition to 1 monograph, with many more still in the pipeline. For a list her published academic papers and chapters: see here.

While many have approached phytoliths typologically and metrically to attempt to look at morphological differentiation between domesticated and wild rice (e.g. bulliforms or double-peaks), Alison’s innovation was to focus on the plant communities that occurred with rice and were sampled in harvests, sub-sampled in crop-processing and ended up to systematically recorded, quantified and discriminated in the micro samples from archaeological sediments. In her fieldwork and analyses, her focus on plant communities and how human communities intersected these is evident. It offers a legacy for phytolith archaeology.
Ethnobotanical fieldwork in Thailand,
Nov. 2012: with Katie Manning.
Alison, herself was a key node in our community. Having worked in the archaeobotany lab as a post-graduate student and post-doctoral staff member for some 15 years, she was often the focus of discussions, both of science and of social life. She has also trained and supported numerous students, offered countless cups of tea, words of encouragement, and a warm sense of humour. She is warmly remembered.

I invite comments to be posted to this blog by those who knew and miss here. And I append below various photos of Alison in action.

Gyoung-Ah Lee and Alison on the Liu river, Henan, China (2006)

Alison collecting rice weeds in Bangladesh, Nov. 2013.

Nov 2011: Northern Thailand: Cristina Castillo (Left) and ALISON (right) with Karen rice farmers in Northern Thailand

Ellie Kingwell-Banham and ALISON WEISSKOPF in Maharashtra, India (Sept. 2010)

14 July 2004, IoA foyer on lab botanical shirt day: Phil Austin, Emma Harvey, Meriel McClatchie, Jon Digby, ALISON WEISSKOPF, Emma Jenkins. Alison was an MSc student at the time, and was apparnelty the original source of the idea for this day.  Below a full photos of the whole lab group.

Dorian, ALISON, and Deepika Tripathi at the IWGP in Thessaloniki (2014)

Indo-Pacific Prehistory Association conference, Siem Reap, Jan. 2014. Participants in session on "Foraging and Farming". Alison fifth from Left.

Early Rice and Its Weed Flora, Symposium at Peking University May 2011

Rice bulliform phytoiths and morphological change

In preparing for a recent Bangkok workshop on the archaeology of rice, I have collected some thoughts of the proposed methodology for tracking rice domestication using rice bulliform phytoliths.

Fan shaped bulliform phytoliths form along the veins of rice leaves. Rice (genus Oryza) has a distinctive shape although some fanlike bulliforms do occur in other grasses, but with different shapes. These are also sometimes referred to “motor cells” as these cells function, when alive, to fold and unfold the leaf and thus to control sunlight exposure, which in turn relates to amounts of photosynthesis and water evaporation from the leave. Once they are silicified and have become phytoliths they stop functioning so this tend to mean that the phytoliths come from older rather than younger leaves.

These are relatively large for single celled phytoliths (28-40 µm) and therefore fairly easy to recover and to spot in phytolith slides. Bulliforms have suggested to be useful for tracking domestication, separating subspecies japonica and indica, and for studying crop processing. Identification approaches relies on measurements and/or counting variation in the number of chips along the scalloped edge of the fan. In terms of crop-processing they are an indicators of leaf presence (i.e. straw), i.e from harvested rice and/or threshing by-production as opposed to husk phytoliths that represent dehuksing waste.

A study of bulliforms from Lower Yangtze archaeological sites suggest that they became large and more pronounced in their japonica morphological metrics over time, 5000 and 2000 BC, over the period when domestication was completed and grain size increased (Zheng et al 2003a). Measurements on controlled experimental crosses indicate the bulliform shape is influenced by numerous genes, with 16 genes (QTLs) suggested, but these QTLs only explain somewhere between 37% and 54% of the variation, suggesting the environment (growing conditions) play a major role (Zheng et al 2003b). No QTLs were correlated with the b/a ratio suggesting this may be largely environmental.

Bottom line on metrics: May be useful for separating indica from japonica when it can be assumed that rice was fully domesticated; and trends may be found alongside domestication. Further work is needed, especially on aus and more variation found in South Asia and more tropical varieties in Southeast Asia.

Bulliform scalloped margins: scale counts and domestication. Another approach to documenting bulliforms is to count the “scale-like” facets along the rounded edge of the “fan”. The fans in domesticated rices tend to have more facets. Initially Lu et al (2002) proposed that phytoliths with 9 or more facets are likely domesticated, while less than 9 are wild. This has been backed up by field comparisons of wild and cultivated rices in South China (Huan et al 2015) These studies indicate that example with less than 9 facets occur in cultivated rice and more than 8 occur in wild rice but the frequency differences are substantial (see below). 

This means in in time series data assemblages can be used to track changes over time (below). This is nicely demonstrated in a time series through the Early and Middle Holocene for the Lower Yangtze by Ma et al (2016). It should be noted also that current approach of Ma et al (2016) exclude from counts any assymetric phytoliths.

Time series of rice bulliform facet counts (% of ≥9) from Lower Yangtze sites (Ma et al 2016).
These data show a direction of travel over time that is similar to non-shattering, grain size increase and other indicators. However, much variation is hidden by the fact that difference between 8 facets (very common in wild rices) and 9 facets (probably the most common value in domesticated rices).
In addition, an explanatory mechanism is not yet firmly established, unlike established domestication traits such as non-shattering and seed size. While ~16 genes may affect bulliform shape, environmental factors are also essential, and domestication is ultimately about genetic changes that differentiate domesticates from their wild ancestors. Therefore it is essential to understand how much of this shift phenotypic response to environmental conditions as opposed to evolution. Huan et al (2015) suggest that the increase faceting in domesticated rice is due to increased use of leaf folding to control evaporation from leaves. They hypothesis that the erect growth habit of rice and drier growing conditions than wild rice would lead to increased faceting. If this is merely a phenotypic response then it becomes a less useful domestication indicator. But this can also be questioned, as ecological indices (see below) suggest that early rice in China was grown under wet, wild-like conditions (at least at Tianluoshan) and that erect growth habit and drier conditions occurred only from the later Majiabang period, and then returned to very wet conditions (Weisskopf et al 2015). So further work is needed to understand genetic and phylogenetic signal in bulliform facet variation as opposed to difference to due with habitat.

The bottom line: on the whole this looks like a promising and worthwhile complementary dataset, but it remains no substitute for morphological domestication data from macro-remains, as other environmental factors seem to be at play. In addition it is worth noting some studies that question the reliability of this approach.

Applications in India that raise questions over the universal applicability of this approach.   Harvey (2006 PhD, UCL) counted this chips on bulliforms from Chalcolithic sites in Orissa (Golbai Sassan and Gopalpur, dating 1500-1000 BC), both of which have domesticated rice (based on spikelet base data), and wet field ecology (further work by Kingwell-Banham 2015, PhD UCL). In this material the average number of chips is 8.6 and thus “wild “ according chip count standards used by Chinese researchers.This is out of agreement with the non-shattering spikelet base data, weed flora and the large village context all of which indicate fully domesticated, wet-rice based agricultural economies.

Saxena et al (2006) applied this to phytoliths from the lake sedimentary sequence at Lahuradewa, next to a Neolithic site in the Ganges plain of the same name. They reported both wild and domesticated bulliforms through the core is roughly equal proportions between 8600 and 3500 BP after which wild forms declined. While Lahuradewa is often discussed an an early site of rice cultivation in India, critical review suggest this was primarily wild rice gathering prior to ca. 2000 BC or so after domesticated rice became available through hybridization with japonica (the proto-indica hypothesis) (Fuller and Qin 2009; Choi et al. 2017; Murphy and Fuller 2017). Thus the phytolith data here appear out of agreement with macro-remains and rice genetics.

Applications in Southeast Asia and China that raise questions over the universal applicability of this approach. The initial introduction of this approach (Lu etal 2002) included a dataset on a see floor core between China and Taiwan, an area that would have been flooded after the Last Glacial. This palaeoenvironmental sequence produced rice phtyoliths- and rice would be expected in fresh water wetlands in such areas when they were above sea level. However, this included substantial numbers of the “domesticated” type. Is it realistic to believe that domesticated rice was already cultivated in flooded regions of Southeast China during the Last Glacial (LGM)? If so, then it must have been a dead-end experiment, as the evolution of domesticates rice is documented over the course the Early and Middle Holocene, starting anew apparently. However, if the bulliform faceting is responding to environmental conditions this LGM population may have nothing to do with human selection and domestication

The Loagan Bonut pollen core on Borneo near Niah Cave produced substantial quantities of rice bulliforms with high facet counts (i.e. “domesticated”) around 8000-7500 BP, but not later (Hunt and Premathilake2012). Is this also to be interpreted as a lost domestication of rice? Or could this be a particular situation in terms of environmental conditions that encouraged wild rice and more leaf folding and bulliform faceting?

Most of the above cases have all been presented as evidence of early farming, which would represent “stealth domestication” without other clear indicators for cultivation over the millennia leading to these nor continuing into subsequent period. In all cases phenotypic plasticity in response to environmental change needs to be considered, and realistically dismissed before domestication can be adequately diagnosed.

Rice husk phytoliths and morphological change

In preparing for a recent Bangkok workshop on the archaeology of rice, I have collected some thoughts of the proposed methodology for tracking rice domestication using rice husk phytoliths (the "double peaked" cells from lemma and palea).

The husks of rice are full of silica and often all the cells of silicified. The rows of cells on the rice husk include trapezoidal phytoliths the upper corners of which often form into peaks, as in the image below. These are diagnostic of the genus Oryza, although a few similar forms may occur more rarely in other grasses. These are often the most frequent form of rice phytolith. Because these derive from husk, disposed of after dehusking, they are an indicator of dehusking waste and useful in crop-processing studies. (See Harvey and Fuller 2005)

Size and shape of these varies and has been suggested to be useful in tracking domestication through measurements on populations (Zhao et al (1998)), although these are not definitive because of large degrees of overlap and because cell size is also impacted by environmental conditions. An explanatory mechanism for how these change during domestication has never been satisfactorily elaborated, although some relationship to grain size change seem plausible.

The proposed method for looking at double peak cells and domestication uses 5 measurement on each phytolith as defined below, left (from Zhao et al 1998)- note that H is measured twice on each side of the phytolith. Some of these are then used in squared form. These are combined in discriminant functions that are meant to assign individual phytoliths to like domesticated or wild (i.e. if the domesticated score is greater than the wild score: formula at right).

As originally developed, Zhao et al (1998) reported correct classification in their modern reference set was correct in >70% of test cases. The formulae were developed by taking Bayesian approach to discriminant function analysis. In an attempt to employ and extend this work, we attempted to replicate this in London with modern rice accessions, but found a correct identification in only 44% of cases (Harvey 2006). In addition measurements on phytoliths from Chalcolithic sites in Orissa (Gopalpur and Golbai Sassan) predicted a majority wild rice and on 39% domesticated. However these sites (dating 1500-1000 BC) have spikelets bases that indicate fully domesticated rice (100% non-shattering at Gopalpur and ~70% at Golbai out of a small sample size: unpublished UCL data from Kingwell-Banham 2015). This indicates that this phytolith discrimination method is unlikely to work in India, raising questions about what biogeographic contexts it would be useful in, if at all. One problem is that some of the variation in ancient cultivars may not be well represented in modern landraces. Indeed some of the measurements on archaeological phytoliths from Orissa fell outside the range of modern material, both wild and domesticated.

Also, against this method are two applications in China that have yielded results that are illogical with regards to what is known about rice domestication. As applied by Zhao (1998) to Diaotonghuan cave in Jiangxi and change from predicted wild in pre-ceramic layers and predicted domesticated dominance in early ceramic layers was found. At the time Zhao wrote this it was assumed the that advent of pottery was Neolithic and sometime in the early Holocene, but recent dating work on nearby Xianrendong and another South Chinese cave, Yuchanyuan, indicate the ceramics began to be produced around the Last Glacial Maximum or just after 18,000-16,000 BP. The ceramics at Daiotonghuan are comparable and thus this would re-date the alleged rice domesticated to ~18,000-16,000 BP, nearly 10,000 years earlier than potential sedentary, agricultural villages. An more plausible alternative explanation is that rice husk cells (and grains) changes shape in response to the major and rapid change in climate and atmospheric carbon dioxide levels that took place after the LGM.

As applied by Itzein-Davey et al (2007) in the Lower Yangtze region to a stratigraphic sequence of Qingpu rice bulliforms dating between 2300 BP and 1800 BO (i.e. Warring State through Han Dynasty era), they found the majority of double peaks were predicted as wild, often as much as 80% in some samples. Rice was certainly morphologically domesticated in the Lower Yangtze long before this and we would expect fairly intensive rice agriculture during Han times. These results also call into question this index.

Nevertheless plotting double peak measurements over a time series may provide a line of evidence for rice that is changing and evolving morphologically. This has recently been applied in South America to argue for a lost rice domesticationin the Amazon (Hilbert et al 2017). In the context of Chinese rice domestication the study of Wu et al (2014) demonstrated both that wild and domesticated predictions are very mixed on sites of early cultivation but also that there is trend for more double peak cells to fall towards the apparently domesticated end of the spectrum through time.

The bottom line: Variation in husk phytoliths exists but its significance in terms of domestication, varietal changes, cultivation ecology remains unclear and deserved further study.