Genome analysis of yams reveals new cradle of crop domestication in West Africa

Genome analysis of yams reveals new cradle of crop domestication in West Africa

Yam genomics supports West Africa as a major cradle of crop domestication

yams
Wild yams, photo credits: Marco Schmidt [1], CC BY-SA 2.5
Yams as seen today in West Africa descended from a forest species, a new study finds. The results challenge the hypothesis that domestication of sub-Saharan African plants mostly arose in tropical savannahs. Critically, they also advance researchers' understanding of West African crops' domestication history, helping to identify a major cradle of domestication around the Niger River. One of the best-known domestication cradles in the world is the Fertile Crescent in the Middle East, where wheat, barley, oat, lentil and chickpea, among other crops, first appeared in the archaeological records.

The history of crop domestication is much less documented in sub-Saharan Africa, in part because archaeological studies are largely fragmentary. Previous studies of domestication in Africa suggest an origin encompassing a large area from Senegal to Somalia, while more recent studies have challenged this hypothesis - proposing a more restricted domestication origin near the Niger River Basin. To assess whether areas near the Niger Basin could be considered major hotspots of domestication, Nora Scarcelli and colleagues investigated the domestication of yam, a major staple crop originating from Africa. They used genome re-sequencing to analyze 167 "wild" and domesticated yam species from the country.

Their analysis, which included sophisticated statistical modeling, suggests that that cultivated yam was domesticated from a forest species, D. praehensilis, starting in the Niger River basin. Its domestication process involved adaptations to the open field environment and human selection that increased tuber size and starch content in the cultivated yam. The study further suggests that the Niger River region played a major role in African agriculture, comparable to the Fertile Crescent in the Near East.

 

Press release from the American Association for the Advancement of Science


New study shows people used natural dyes to color their clothing thousands of years ago

New study shows people used natural dyes to color their clothing thousands of years ago

Samples like these were examined by the chemists from MLU. Credit: Annemarie Kramell

Even thousands of years ago people wore clothing with colourful patterns made from plant and animal-based dyes. Chemists from Martin Luther University Halle-Wittenberg (MLU) have created new analytical methods to examine textiles from China and Peru that are several thousand years old. In the scientific journal Scientific Reports they describe their new method that is able to reconstruct the spatial distribution of dyes, and hence the patterns, in textile samples.

Chemists Dr Annemarie Kramell and Professor René Csuk from MLU examined two ancient textile samples. One comes from the ancient Chinese city of Niya and was probably once part of a shirt. It is over 2,000 years old. The other sample comes from Peru and dates back to 1100 to 1400 AD. It was produced by the Ichma people who lived in Peru at that time. Today, there is often little evidence of the colourfulness of such ancient clothing. "Time has not treated them well. What was once colourful is now mostly dirty, grey and brown," says René Csuk. Over time, the natural dyes have decomposed as a result of the effects of light, air and water, explains the chemist. In the past, only natural dyes were used. "The roots of a genus of plants called Rubia, for example, were used to create the red colours, and ground walnut shells produced the brown tones," says Annemarie Kramell. Even back then, people mixed individual materials to create different shades.

natural dyes imaging mass spectrometry
With the help their new method the researchers were able to reconstruct the distribution of the dyes. Credit: Annemarie Kramell

The researchers have developed a new analytical method that allows them to detect which materials were used for which colours. With the aid of modern imaging mass spectrometry, they have succeeded in depicting the dye compositions of historical textile samples as isotopic distributions. Previously, the dyes had to be removed from the textiles. However, that previous method also destroyed the pattern. This new approach enables the chemists from MLU to analyse the dyes directly from the surface of the textile samples. To do this, the piece of material under investigation is first embedded in another material. "The piece is placed in a matrix made up of a material called Technovit7100. Slices are produced from this material that are only a few micrometres thick. These are then transferred to special slides," explains Csuk. Similar methods are used, for example, in medical research to examine human tissue. The advantage is that this method can be used to study very complex samples on a micrometre scale. "This enables us to distinguish between two interwoven threads that held originally different colours," says Csuk.

This is chemist René Csuk inspecting a textile sample. Credit: MLU / Michael Deutsch

As part of the new study, researchers were able to detect indigo dyes in the samples. However, the method can also be applied to many other dye classes and provides insights into the process of textile production in past cultures, the two scientists conclude.

The research was funded by the Federal Ministry of Education and Research as part of the project "Silk road fashion: Clothing as a means of communication in the 1st millennium BC, Eastern Central Asia". The Hans Knöll Institute in Jena and Dr Gerd Hause from MLU's Biocentre were also involved in the project.

 

About the study: Kramell A. E. et al. Mapping Natural Dyes in Archeological Textiles by Imaging Mass Spectrometry. Scientific Reports (2019). doi: 10.1038/s41598-019-38706-4

 

Press release from the Martin Luther University Halle-Wittenberg / Martin-Luther-Universität Halle-Wittenberg


Sorghum bicolor introgression North-East Africa

Beer and fodder crop has been deteriorating for 6,000 years

Beer and fodder crop has been deteriorating for 6,000 years

Sorghum bicolor introgression North-East Africa
The inflorescence of Sorghum bicolor. Photo by Matt Lavin from Bozeman, Montana, USA, CC BY-SA 2.0

The diversity of the crop Sorghum, a cereal used to make alcoholic drinks, has been decreasing over time due to agricultural practice. To maintain the diversity of the crop and keep it growing farmers will need to revise how they manage it.

Sorghum bicolor is a crop widely used for animal feed, and making beer.

The history of sorghum from its original domesticated state to todays domesticated cereal has been found to be heavily influenced by human action, continuing to treat the plant as we currently do could mean the continued degradation of the crop.

One current type of sorghum harvested is called Sorghum bicolor, but there are several different sorghum types, and in the past they have been saving each other by sharing undamaged genes, in a process called introgression.

The wild ancestors of sorghum represent genomes that have not been damaged through cultivation. Although we don't harvest the wild ancestors of sorghum it's necessary to keep them alive as the ability to adapt to their surroundings by introgression could be crucial in the future of Sorghum bicolor to threats of climate change, meaning crops have to adapt to new environments.

In Sorghum bicolor, damage to their genes is happening by the way it's farmed, meaning their core genome functions are accumulating damage over time, therefore we need to repair the crops genomic damage or productivity could decline.

Professor Robin Allaby, from the School of Life Sciences at the University of Warwick comments:

"Sorghum bicolor is the world's fifth most important cereal crop and the most important crop in arid zones. It's used for animal feed and beer and is grown particularly in North-Eastern Africa generating an economy there.

"If we can't save sorghum's ancestors and use those genes to help Sorghum bicolor repair its genomic damage we could risk damaging the crop further. This could mean less animal feed, food and beer, as well as potentially damaging trade in North-East Africa."

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Medicinal plants may be a key to understanding other cultures

Medicinal plants may be a key to understanding other cultures

medicinal plants herbal medicine ethnobotany Amazigh Morocco High Atlas
Irene Teixidor-Toneu together with one of the Amazigh women who contributed to her thorough research on plant use in the High Atlas. Credit: Dag Inge Danielsen/UiO

A new methodology for comparing herbal medicine across societies can also be used to understand the transfer of cultural traditions.

“I did a thorough documentation of the natural remedies, mostly plants, used by the Amazigh people in the High Atlas. Then, I studied how modernization in its various forms influences the use of plants,” explains Irene Teixidor-Toneu, a postdoctoral fellow at the University of Oslo, Norway.

“To summarize, there is a change in the use of substances, since people are open to medication prescribed by the doctor. At the same time, traditional knowledge and beliefs concerning plant use are kept alive, although traditions also change over time.”

Having spent almost a year in the Moroccan High Atlas mountains, ethnobotanist Irene Teixidor-Toneu finished her PhD on the use of medicinal plants in Amazigh (Berber) villages.

Her scientific article, describing the methodology, was published in the October issue of the journal Nature Plants. She is currently working at the Natural History Museum in Oslo, where her methods will be applied to map the use of medicinal plants in Scandinavia from Viking times until today, in a project that was launched in November 2018.

"The traditional way of life is under threat a lot of places, it's not simply about biodiversity, says Irene Teixidor Toneu. Credit: Dag Inge Danielsen/UiO

Modern or traditional medicine?Her PhD dissertation was devoted to the transmission of knowledge about medicinal plants used by a defined group of people.These were some of the basic questions Teixidor-Toneu studied:

  • Why are certain plants selected for medical use?
  • How are they used?
  • How does usage change over time?

If you were to ask a pharmacist, one obvious explanation to why certain plants are used,is that they contain phytochemicals. Phytochemicals are compounds developed in order help plants thrive or fight competitors, predators, or pathogens. Many phytochemicals have therapeutic effects.

However, there is always a combination of reasons why a plant is selected for use, according to Teixidor-Toneu.

From her field work in the High Atlas in Morocco. Credit: Irene Teixidor Toneu

Faith and loreEthnobiology is defined as the interdisciplinary study of how human cultures interact with and use their native plants and animals. Ethnobotany is defined as the plant lore of indigenous cultures, also the systematic study of such lore.

Irene Teixidor-Toneu explains:

“In studies of plant diversity and conservation, there are a lot of ecological models that don’t take people into account at all. If you think of the vegetation in the Mediterranean area, as an example, nothing makes sense if you don’t consider humans and their influence. After all, the region has been shaped and developed by man for millennia.”

From colouring to foodMost of us probably think of food, spice and medicine, when the subject of plant use is brought up. However, there is a multitude of historic and present practices. Like fumigation.

Fumigation is the physical process of burning and making smoke out of a plant. This can be ritual or medical or a combination of both. It can be done to clean out a dirty room, to remove fleas and ticks and other insects. In Morocco, the Amazigh burn plant that are rich in resins in order to clean the stables for their animals.

Other uses vary from producing and dyeing textiles, making furniture and utensils, construction of houses to providing fodder and veterinary medicine.

The interdisciplinary aspect is one reason why Irene Teixidor-Toneu finds ethnobotany so fascinating:

”There has been a patchwork of approaches and methods because people from different backgrounds have come together, with no common theoretical framework. Researchers from the humanities and natural scientists often have different approaches. In recent years, we have seen some articles trying to unite and define ethnobiology as one discipline, but there are still many ways to regard the interaction of people and plants.”

Constructing family treesTeixidor-Toneu has provided a significant contribution through her perspective article recently published in Nature Plants, with co-authors Fiona Jordan (evolutionary anthropologist, University of Bristol) and Julie A. Hawkins (phylogenetist, University of Reading).

Basically, it is a summary of the theoretical analysis for her PhD work. The article proposes a framework to study plant uses. This framework uses phylogenetic comparative methods applied to anthropological data, which involves – to put it simply - the construction of language family trees.

For some time, it has been used by anthropologists to gain understanding of the evolution of political, religious, social and material culture. It has not previously been applied to plant use, as pointed out by the editor of Nature Plants in the editorial:

“Normally we associate the use of (…) phylogenetic analyses to determine the relationships between species and groups of organisms, tracing their evolution back to putative common ancestors. (…) Teixidor-Toneu et al. have applied comparative phylogenetic methods, not to plants themselves but to the medicinal roles to which they have been put. Even within ethnobotany this is not a common approach, but the ability to use multiple types of data can produce robust and detailed information about how cultural information is transmitted”

Medicinal plants are of special interest because of their role in maintaining people’s health. Phylogenetic comparative methods can enable researchers to study the diversity of medicinal plant applications across cultures, and also to infer changes in plant use over time.

These methods can be applied to single medicinal plants as well as the entire set of plants used by a culture for medicine, known as a pharmacopoeia.

One of the Berber villages in Imlil in the Moroccan High Atlas, where Irene Teixidor-Toneu did her field studies. Credit: Dag Inge Danielsen/UiO

Plants and cultural knowledge are both endangered“I think the main significance of our paper is that it opens up new opportunities for studying plant use. At the moment, we are well aware that that biodiversity is threatened. Cultural diversity and traditional lifestyles are also threatened. In other words, many plants as well as the knowledge about how to use them, are endangered. Therefore, there is an urgent need to understand how various threatening factors interact and how use and knowledge change over time,” Irene Teixidor-Toneu explains, and adds:

“We are trying to understand plant use across cultures. The first thing we need to understand is how cultures are related. We use phylogeny models, or pedigrees, to trace relationships between people and cultures, based on language similarities.”

“Having traced evolutionary relationships between cultures, we can identify and try to understand the ways plants are used in different cultures. Within this framework we can also study how uses change, and it can be linked to geographical models. So, we end up with what we could call a biocultural geography.”

Full bibliographic information

Comparative phylogenetic methods and the cultural evolution of medicinal plant use. Irene Teixidor-Toneu, Fiona M. Jordan & Julie A. Hawkins. Nature Plants volume 4, pages 754–761 (2018)

 

Press release from Titan.uio.no/ (NO)