Amber M. VanDerwarker’s research while affiliated with University of California, Santa Barbara and other places

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Publications (41)


Fig. 1. (A)-Map of Central and northern South America, showing the presumed native ranges of major avocado horticultural groups (Mexican [drymifolia], Guatemalan [guatemalensis], Lowland and Colombian [americana]; (2, 4, 7, 17), the distribution of genetic samples (3, 4, 12); and notable sites with archaeologically preserved avocado specimens and environmental DNA (18). (B)-Representative photographs of three major avocado groups (Photos by Alejandro F. BarrientosPriego).
Early evidence of avocado domestication from El Gigante Rockshelter, Honduras
  • Article
  • Full-text available

March 2025

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340 Reads

Proceedings of the National Academy of Sciences

Amber M VanDerwarker

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Heather B Thakar

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Kenneth Hirth

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Molecular research suggests that avocados (Persea americana Mill.) were domesticated multiple times in the Americas. Seed exchange, hybridization, and cloning have played an essential role across their wild distribution from Mexico to South America to create the modern varieties of today. Archaeological sites with well-preserved and directly radiocarbon-dated botanical assemblages are rare, however, so we know very little about the complexities of the domestication process. Here, we define an early locus of avocado domestication using well-dated desiccated and carbonized avocado remains from El Gigante rockshelter in western Honduras spanning the last 11,000 y. Measurements of avocado seeds and rinds show evidence for long-term management resulting in selection for larger, more robust fruits through time that culminated by 2,250 to 2,080 calendar B.P. (cal. B.P.). However, human-directed selection for larger fruits with thicker rinds is evident as early as 7,565 to 7,265 cal. B.P. Seed morphology is similar to P. americana var. guatemalensis and is congruent with genetic data for the development of this variety in both the highlands of Guatemala and Honduras. Increases in seed size and rind thickness through time are consistent with genetic evidence for the enrichment of putative candidate genes for fruit development and ripening in this variety.

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Archaeobotanical evidence supports indigenous cucurbit long-term use in the Mesoamerican Neotropics

May 2024

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138 Reads

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1 Citation

The squash family (Cucurbitaceae) contains some of the most important crops cultivated worldwide and has played an important ecological, economic, and cultural role for millennia. In the American tropics, squashes were among the first cultivated crop species, but little is known about how their domestication unfolded. Here, we employ direct radiocarbon dating and morphological analyses of desiccated cucurbit seeds, rinds, and stems from El Gigante Rockshelter in Honduras to reconstruct human practices of selection and cultivation of Lagenaria siceraria, Cucurbita pepo, and Cucurbita moschata. Direct radiocarbon dating indicates that humans started using Lagenaria and wild Cucurbita starting ~ 10,950 calendar years before present (cal B.P.), primarily as watertight vessels and possibly as cooking and drinking containers. A rind directly dated to 11,150–10,765 cal B.P. represents the oldest known bottle gourd in the Americas. Domesticated C. moschata subsequently appeared ~ 4035 cal B.P., followed by domesticated C. pepo ~ 2190 cal B.P. associated with increasing evidence for their use as food crops. Multivariate statistical analysis of seed size and shape show that the archaeological C. pepo assemblage exhibits significant variability, representing at least three varieties: one similar to present-day zucchini, another like present-day vegetable marrow, and a native cultivar without modern analogs. Our archaeobotanical data supports the hypothesis that Indigenous cucurbit use started in the Early Holocene, and that agricultural complexity during the Late Holocene involved selective breeding that encouraged crop diversification.



Map indicting the location of El Gigante rockshelter in western Honduras and planview map of the rockshelter showing the locations of test excavations and looters’ pits
All elements of the map come from Natural Earth (http://www.naturalearthdata.com/) and are compatible with the CC-BY 4.0 license.
An example stratigraphic profile and associated distribution of radiocarbon dates
A. Intact stratigraphy at El Gigante, Units 1, 3 and 7 (south profiles; 2001 excavations). B. Stratigraphic distribution of ¹⁴C-dated materials, with excavated mean stratum thickness and superpositioning of main cultural components (data in S4 Table in S1 File).
The distribution of all 369 ¹⁴C dates from El Gigante rockshelter
A. Calibrated dates are grouped according to their inclusion or exclusion in the chronological model and categorized by model phase. The relative depositional intensity of these habitational episodes is generated using kernel density estimation (KDE; light gray) of calibrated ¹⁴C dates with a 50-year bandwidth. This record compares favorably with additional proxy records: the depositional rate of paleobotanical specimens (green with light green shading showing 4x exaggeration so earlier trends are visible) and the rate of sedimentation across all units (light orange). B. Sequenced radiocarbon chronology displaying modeled occupational phases shown relative to the regional cultural chronology. Probability distributions for all ¹⁴C dates and the modeled phase boundaries are provided in S1 Fig OxCal model, graphical output. Given the extensive nature of the sampled materials, gaps present in the ¹⁴C record are likely indicative of gaps in the site’s occupational sequence. The raw data, model output and model code can be found in S1–S3 Tables in S1 File.
Summed probability distributions of dated paleobotanicals from El Gigante rockshelter
Genera representative of tree crops, field crops, and other agricultural domesticates are compared against the regional archaeological chronology and the summed probability distribution of all the available radiocarbon dates for the rockshelter. Regional cultural periods defined in Fig 3 are shaded to provide chronological context for the appearance of economically important plant species.
Percentages of select tree crops (green) and field crops (yellow) from the El Gigante rockshelter and an index of tree crop to field crop (TC/FC) use
Taxa with comparatively low counts are additionally plotted with a 4x exaggeration (gray) to show trends. Changing percentages of tree and field crops are shown relative to the regional archaeological chronology. This general index shows the use of field crops peaked during the Late Formative and Classic periods at El Gigante, while tree crops were predominant during all other periods.
Trans–Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras

June 2023

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253 Reads

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5 Citations

El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human–environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100–2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.


Reconstructing Middle Horizon Camelid Diets and Foddering Practices: Microbotanical and Isotope Analyses of Dental Remains from Quilcapampa, Peru

January 2023

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264 Reads

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9 Citations

Latin American Antiquity

This study uses isotope and microbotanical data from the analysis of teeth and dental calculus to investigate camelid diet and foddering practices at Quilcapampa (AD 835–900). By providing taxonomically specific evidence of foods consumed, botanical data from dental calculus complement the more general impressions of photosynthetic pathways obtained through isotopic analysis. Results suggest that the camelid diet incorporated maize ( Zea mays ), algarrobo ( Prosopis sp.), potato chuño ( Solanum sp.), and other resources. The life-history profile of one camelid (Individual 3) reveals dietary change from mainly C 3 plants to more C 4 plant contributions as the animal aged. This pattern is supported by carbonate isotope results indicating that this individual spent its youth in the mid-valley ecozone before becoming more mobile later in life. As this life-history example shows, isotopic and microbotanical analyses are complementary approaches, clarifying a pattern of seasonal transhumance that linked the lives of humans and animals along the Middle Horizon (AD 600–1000) caravan networks that crisscrossed the central Andes.


Between land and water: Hydraulic engineering in the Tlalixcoyan basin, Veracruz, Mexico

March 2021

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107 Reads

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13 Citations

Journal of Anthropological Archaeology

Recent remote sensing research in the Tlalixcoyan basin, Veracruz, has identified patterns of raised fields and public civic-ceremonial plaza groups that suggest a local and decentralized strategy of cooperation to develop hydraulic and agricultural resources. This perspective provides support for Scarborough and Lucero’s (2010) cross-cultural conceptualization of hydraulic strategies in the semi-tropics, but we note some exceptions to their model as well. We conclude based on the remotely sensed data that (1) most of the interconnected field systems are too large or complex for a single family or lineage to have built and maintained alone; (2) the Tlalixcoyan settlement system is divided into clusters that likely represent social groupings akin to administrative districts; (3) each residential cluster possessed its own public civic-ceremonial plaza group; (4) each plaza group could have provided the seat of cooperation in the creation and maintenance of common-pool resources like raised fields; and (5) despite the implication of local hydraulic management within districts, the region as a whole presents a hierarchical settlement distribution with the Tlalixcoyan Monumental Complex at the top. The last two points represent central hypotheses generated from the remote sensing data that will be tested in future field research.


Fig. 1. Maize cobs from El Gigante rock shelter (HN) with genomewide data. (A) Photographs of cobs showing morphological characteristics. (B) Map of Central America indicating location of El Gigante rock shelter. (C) Radiocarbon date distributions for the three maize cobs with genomewide data.
Fig. 3. Population relationships and genome size characteristics. (A) Admixture graph with a good fit to the genomic data, showing El Gigante maize as an early branch of the Pan-American cluster carrying excess parviglumis ancestry. South American members of the Pan-American population carry excess ancestry from earlier-dispersed South American lineages, revealing hybridization in South America. (B) f 4 -statistics showing that all individual Pan-American genomes and the El Gigante maize carry excess parviglumis ancestry compared with South American and North American lineages. Errors bars at 1 and 3 SEs computed using a block jackknife in 5-Mb blocks. (C) Proportion of characteristic South American lineage alleles at AIMs among geographically southern (samples physically originating in South America) and northern (originating in North and Central America) maize genomes, showing that El Gigante maize is the most South American-like of northern maize. (D) 180 bp heterochromatic knob frequency (RPKM) as a proxy for genome size, compared with distance from the domestication center. The two regression lines show 1) the correlation between distance and genome size in all samples-a general trend to genome contraction with distance-and 2) the reverse trend in samples with ≥90% Pan-American ancestry.
Maize cobs with endogenous DNA sufficient for genomewide sequencing
Archaeological Central American maize genomes suggest ancient gene flow from South America

December 2020

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363 Reads

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62 Citations

Proceedings of the National Academy of Sciences

Significance Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently fixed and improved varieties developed away from the influence of wild gene flow. We demonstrate that hybrids of some of these improved varieties were likely reintroduced back to Central America. We hypothesize that this backflow of South American genetic material may have contributed to the development of a more productive staple, which was related to the growth and aggregation of human populations, and the formation of more complex social and political structures regionally.




Citations (32)


... En el caso del NDVI máximo, que es un indicador del nivel de vigorosidad al que puede llegar la vegetación, se encontró una relación moderada entre la densidad poblacional de venados y el NDVI máximo (R² = 0.49; p-value = 0.0026) correspondiente al año anterior (Fig. 7), fenómeno que se NDVI máximo debería a que la imagen satelital muestra indirectamente la disponibilidad de alimentos en el momento en el que fue tomada y que la fauna local consumirá en los siguientes meses, por lo que una escena que muestre una mayor vigorosidad de la vegetación, tendría como efecto una mejora en los inventarios o censos de fauna en el periodo siguiente. Y dado que la dieta de los venados consiste en ramoneo leñoso, hierbas, leguminosas [49] y menor medida gramíneas, tendrán un mayor consumo cuando haya mayor cantidad de brotes tiernos como sucede después de un periodo de intensas lluvias [50]. Asimismo, se obtuvo una relación moderada entre el número de venados cobrados por año y el NDVI máximo (R² = 0.50; p-value = 0.0007) que se debería al mismo efecto que tiene el nivel de vigorosidad de la vegetación sobre las poblaciones de esta especie (Fig. 8), que permitiría una mayor disposición de individuos para su aprovechamiento comercial sin afectar la viabilidad de su población. ...

Reference:

Impact of droughts and El Niño Costero on dry forest and white-tailed deer in Coto de Caza El Angolo - Perú
Deer, drought, and warfare: Managing risk in the central Illinois river valley (CIRV) from the eleventh through fourteenth centuries
  • Citing Article
  • August 2023

Quaternary International

... Avocado pits dating between 11,000 and 9,000 cal. B.P. have been found in Peru [Huaca Prieta ( 24 )], Colombia [San Isidro, ( 25 )], Honduras [El Gigante ( 26 )], and Mexico [Coxcatlán, ( 2 )]. These assemblages provide early evidence for mutualism with relict avocado stands that set the stage for arboriculture and more directed forms of selection for larger, more robust fruits through time. ...

Trans–Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras

... The ritualized consumption of special foodstuffs and drink by camelids has also been confirmed, with the intake of chili peppers and beans, in anticipation of the animals being sacrificed, identified for Late Intermediate Period juvenile camelids in a Chimu context (Cagnato et al. 2021). Foddering of camelids on maize, algarrobo and potato ( probably chuño negro) has been identified at the Middle Horizon site of Quilcapampa in the south coastal Sihuas Valley (Melton et al. 2023). ...

Reconstructing Middle Horizon Camelid Diets and Foddering Practices: Microbotanical and Isotope Analyses of Dental Remains from Quilcapampa, Peru

Latin American Antiquity

... The numerous artificial plateaus recently discovered in Aguada Fenix, Tabasco, indicate that the cities were interconnected throughout an extensive territory. Although the authors consider that these plateaus were used as ceremonial centers (Inomata et al., 2020), an alternative hypothesis is that they were part of the infrastructure built to protect against flooding, as has been suggested in other studies from the northern Yucatan Peninsula (Fisher, 2023) and Veracruz (Stoner et al., 2021). Additionally, empirical evidence from people living in the floodplain today shows that they shelter their cattle in the "high zones"-probably remnants of these same artificial plateaus now covered by vegetation-when flooding of the Usumacinta River poses a threat. ...

Between land and water: Hydraulic engineering in the Tlalixcoyan basin, Veracruz, Mexico
  • Citing Article
  • March 2021

Journal of Anthropological Archaeology

... In each of these regions, maize took the root, and humans selected and diversified its traits. With the constant human migrations, the resulting maize landraces were exchanged between regions, enriching the diversity of each place where this crop was adopted and grown [4,5]. ...

Archaeological Central American maize genomes suggest ancient gene flow from South America

Proceedings of the National Academy of Sciences

... Given the incongruity between the results of this research and recent research highlighting issues with field schools (Colaninno et al. 2020Douglass et al. 2024; Heath-Stout and Hannigan 2020), we speculate that interviewed students looked favorably on the field school's basis in experiential learning-a high-impact educational practice. However, these students were not confronted with the realities of the financial burden of field school (Douglass et al. 2024;Heath-Stout and Hannigan 2020) or other field-based dangers (Clancy et al. 2014;Colaninno et al. 2020;Meyers et al. 2018;Nelson et al. 2017;VanDerwarker et al. 2018;Voss 2021). Only one student, Pat, suggested that it should not be required if someone can get practical experience through an internship. ...

The UCSB Gender Equity Project: Taking Stock of Mentorship, Equity, and Harassment in California Archaeology Through Qualitative Survey Data
  • Citing Article
  • July 2018

California Archaeology

... As for unsupervised learning, no pre-training labelling of data will occur and unlike in supervised learning, the outputs may not make sense immediately as the user must decide whether the results are comprehensible (Alom et al., 2018). For instance, kmeans clustering and Principal Components Analysis -both commonly used techniques in archaeology -are examples of unsupervised learning algorithms that learn a representation of the original input by reducing it to a lower dimensionality (Goodfellow et al., 2016;Papageorgiou, 2018;VanDerwarker and Marcoux, 2018). Yet, a human must interpret the lower dimensional output from unsupervised learning techniques for the result to be meaningful. ...

Principal Component Analysis
  • Citing Article
  • December 2018

... At various times throughout the development and definition of "Mississippian" as a cultural tradition, maize has been cast as a central feature of Mississippian adaptation. Besides, "other traits include long-distance exchange" (Vanderwarker, Bardolph and Scarry, 2017) and the development of ranked social systems, etc. The culture was centered on maize, beans, squash, and other crops, resulting in "large concentration of population in towns along riverine bottomlands" (Anderson, 2017). ...

Maize and Mississippian Beginnings
  • Citing Chapter
  • August 2017

... This study presents the first chronological modeling work conducted to derive a complete site history for Angel Mounds and expands upon earlier chronological modeling efforts for the Angel polity (Krus, 2016;Monaghan et al., 2013). Additionally, this study contributes to the growing body of Bayesian chronological analyses of Mississippian chronologies in the North American midcontinent (Barrier, 2017;Cobb et al., 2015;Emerson et al., 2019;Kessler et al., 2022;Krus and Cobb, 2018;Krus et al., 2015Krus et al., , 2019Krus et al., , 2022Wilson et al., 2018). ...

Reassessing the chronology of the Mississippian Central Illinois River Valley using Bayesian analysis

Southeastern Archaeology

... The large rockshelter (42 m wide, 17 m deep, 12 m high) was formed through river downcutting of the Miocene/Pliocene bedrock tuff and is currently protected from flooding by its location on an elevated shelf. As one of only a handful of dry caves and rockshelters throughout Mesoamerica, El Gigante has produced an extensive desiccated plant assemblage providing rare insights into the transition from foraging to farming, especially in relation to the development of systems of arboriculture (26,(37)(38)(39)(40). ...

High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras

Proceedings of the National Academy of Sciences