Ancient DNA and Plant Domestication Environmental DNA (eDNA)
Many Applications in Biology and Conservation: • Modern eDNA allows for large-scale biodiversity monitoring with limited fieldwork. • Ancient eDNA provides a way to study long-term changes in biodiversity and ancient environmental conditions. Lake cores Applications in Archaeology? • eDNA can be used to identify the presence of humans (or extinct hominins!), animals, or plants in the archaeological record even when bones, seeds, or other physical remains do not preserve.
Researchers plan the sampling of sediments in Siberia's Denisova cave. Outline of Today’s Class: Ancient DNA and Plant Domestication
2) Archaeological Perspectives on Domestication
3) Paleoethnobotanical and Genetic Methods for Documenting Plant Domestication
4) Important Plant Domesticates Worldwide Paleoethnobotany = the analysis of plant remains from archaeological sites in order to study human-plant- environmental interactions Paleoethnobotany
Macrobotanical Remains:
• Wood and other plant remains collected from sites in dry climates or from waterlogged sites.
• Carbonized seeds and charcoal collected through flotation.
Flotation bucket and screen
Wooden beams preserved at Chaco Canyon, New Mexico Carbonized rice grains Paleoethnobotany
Microbotanical Remains:
• Pollen, phytoliths, and starch grains found in soils or in residues on artifact surfaces.
Comparisons of starch grain morphology Plant Exploitation Strategies
Cultivation Agriculture Planting and harvesting wild species. Systematic tillage of at least some fully domesticated plants.
Zeder, Melinda. A. (2012). Pathways to Animal Domestication. In Paul Gepts, Thomas R. Famula, Robert L. Bettinger, Stephen B. Brush, Ardeshir B. Damanica, Patrick E. McGuire, Calvin O. Qualset (eds.), Biodiversity in Agriculture: Domestication, Evolution, and Sustainability (pp.227-259). Cambridge: Cambridge University Press. Domestication = a mutualistic relationship between humans and the domesticated plant or animal species that causes morphological and genetic changes to that species. Domestication occurs along a continuum.
Cultivation Agriculture
Zeder, Melinda. A. (2012). Pathways to Animal Domestication. In Paul Gepts, Thomas R. Famula, Robert L. Bettinger, Stephen B. Brush, Ardeshir B. Damanica, Patrick E. McGuire, Calvin O. Qualset (eds.), Biodiversity in Agriculture: Domestication, Evolution, and Sustainability (pp.227-259). Cambridge: Cambridge University Press. The Neolithic 1) Agriculture. 2) Sedentism (life in permanent villages) and storage. 3) Ground stone tools and pottery. 4) Greater social complexity.
The Neolithic transition is a series of gradual changes. Points 1-4 do not always have to emerge at the same time, nor are they exclusive to Neolithic societies.
Yellow areas on the map are independent centers for the origins of agriculture.
Diamond, J., & Bellwood, P. (2003). Farmers and their languages: the first expansions. Science, 300(5619), 597-603. Why Domestication? Anthropologists have proposed many models to explain the origins of agriculture and domestication. They can be categorized as push models, pull models, and social models:
PUSH PULL SOCIAL
1. V.G. Childe’s “Oasis Hypothesis” 1. Robert Braidwood’s “Natural 1. Brian Hayden’s “Competitive (early 20th Century) Habitat Hypothesis” (1950s) Feasting Hypothesis” (1970s and 80s) 2. Lewis Binford’s “Marginal Zones 2. David Rindos’ “Co-Evolution” Hypothesis” (1960s) models (1980s)
3. Dolores Piperno et al.’s “Optimal 3. Melinda Zeder, Nicole Boivin, et Foraging Theory” models (early al.’s “Niche Construction Theory” 2000s) models (2010s) Documenting Plant Domestication
1. Phenotypic changes and size increase 2. Changes in frequency 3. Archaeological and biogeographic context 4. Stable isotopes and dietary changes 5. Genetic changes 1. Phenotypic Changes and Size Increase Wild Plants: defense (toxins); variable maturation rates; easy seed dispersal (e.g., brittle rachis). Domesticated Plants: toxins and defenses removed; self-dispersal mechanisms removed (e.g., tough rachis); self pollination/rapid germination; uniform ripening times; larger seed size; improved starch and protein quality. Case Study: Maize Domestication
Maize was domesticated from wild teosinte by 8,700 cal. BP in Southern Mexico. The earliest evidence comes from starch grains and phytoliths (Piperno et al. 2009). Later evidence comes from charred macrobotanical remains.
Phenotypic Changes: • Larger seeds/kernels • More rows of seeds • Removal of hard seed coatings • More protein and starch
Piperno, D. R., Ranere, A. J., Holst, I., Iriarte, J. & Dickau, R. (2009). Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico. Proc. Natl Acad. Sci. USA 106, 5019–5024. Staller, J. Tykot, R., and Benz, B. (eds.) (2006). Histories of Maize: Multidisciplinary Approaches to the Prehistory, Linguistics, Biogeography, Domestication, and Evolution of Maize. Burlington, MA: Academic Press. 2. Changes in Frequency
An increase in the number of plant remains identified at an archaeological site is often a signal of domestication. 3. Archaeological and Biogeographic Context
• Grinding stones, sickles, agricultural tools, etc.
• Arrival of new taxa into regions without wild progenitors Case Study: Maize Domestication
Maize domestication began in Mesoamerica. Domesticated maize then spread north into the Southwest US and south into the Andes.
Blake, M..(2006). Dating the Initial Spread of Zea Mays. In Staller, J. Tykot, R., and Benz, B. (eds.) Histories of Maize: Multidisciplinary Approaches to the Prehistory, Linguistics, Biogeography, Domestication, and Evolution of Maize (pp. 55-72). Burlington, MA: Academic Press. 4. Stable Isotopes and Dietary Changes
• Bone stable isotope ratios reflect ancient diets.
• Carbon Isotopes: • C3 plants (trees, rice, beans, wheat, etc.), and C4 plants
(grasses, millet, maize/corn, Domestication etc.) have different photosynthetic pathways. • Some C4 plants such as millet and maize/corn were important agricultural products in ancient societies. • δ13C values in bone samples increase as the amount of C4 plants in a human or animal’s diet increases. Case Study: Maize Domestication
North American populations in the Ohio Valley ate more maize after ca. 900 A.D. (the start of the Mississippian period).
Greenlee, D. (2006). Dietary variation and prehistoric maize farming in the middle Ohio Valley. In Staller, J. Tykot, R., and Benz, B. (eds.) Histories of Maize: Multidisciplinary Approaches to the Prehistory, Linguistics, Biogeography, Domestication, and Evolution of Maize (pp. 215-230). Burlington, MA: Academic Press. 5. Genetic Changes
Modern and ancient DNA contribute to domestication studies in two main ways:
1) Reconstruction of phylogenetic relationships to reveal the wild progenitors of domesticated plants and potential centers of origin.
2) Identification of domestication genes that were subject to selection in order to reveal the genotypic (and phenotypic) changes that occurred during the domestication process.
Hypotheses based on modern DNA must be tested with ancient DNA. Case Study: Ancient DNA and Maize Domestication
Genome of a 5310 cal BP maize cob from the Tehuacan Valley, Mexico (Ramos-Madrigal et al. 2016):
• Basal lineage equally related to all modern varieties of maize.
• Selection for genes associated with removal of hard seed coatings and changes in flowering time.
• Genes associated with sugar content and dispersal of kernels were not yet subject to selection, showing that the domestication process was gradual and that different traits associated with domestication emerged at different times.
A) Distributions of the wild progenitor of maize, teosinte (Zea mays parviglumis) and a highland variety of maize (Zea mays mexicana); B) Archaeological maize cob from the Tehuacan Valley.
Ramos-Madrigal, J. et al. (2016). Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication. Current Biology 26: 3195-3201. Vallebueno-Estrada, M. et al. (2016). The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding. PNAS 113 (49): 14151-14156. Plant and Animal Domesticates Worldwide
PLANTS ANIMALS OLD WORLD West and South Asia Wheat, Barley, Oats, Flax, Peas Sheep, Goat, Cattle, Pig, Water Buffalo, Horse, Dog Africa Sorghum, Yams, Gourds Donkey East Asia Rice, Millet, Soybean Pig, Chicken, Silk Worm, Dog? New Guinea Taro, Bananas Polynesian Rat, Chicken
NEW WORLD North America Goosefoot, Mayflower, Sunflower Turkey, Dog Mesoamerica Maize, Beans, Chili Peppers, Cacao, Turkey, Dog Tomato South America Potato, Quinoa, Peanut Llama, Alpaca, Guinea Pig, Dog
Modern crop distributions are products of the last 500 years of contact and exchange.
Most “traditional” cuisines are recent developments (e.g., tomato sauce in Italy, chocolate in Switzerland, peanut dishes in West Africa, etc.). Next time…animal domestication!