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Thomas Harper

Thomas Harper

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Pennsylvania State University · Pathology

Active 2013–2024

h-index21
Citations2.7k
Papers4527 last 5y
Funding
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Research topics

  • Geography
  • Biology
  • Sociology
  • Archaeology
  • Demography
  • Genetics
  • Ecology
  • Evolutionary biology
  • Agroforestry
  • Forestry
  • Botany
  • Cartography
  • History
  • Ancient history
  • Agronomy

Selected publications

  • Two teosintes made modern maize

    Science · 2023 · 146 citations

    • Sociology
    • Biology
    • Geography

    in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.

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

    PLoS ONE · 2023 · 7 citations

    • Archaeology
    • Geography
    • Biology

    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.

  • Scarlet Macaws, Ritual, and Sociopolitical Organization in Chaco Canyon, New Mexico

    University of Arizona Press eBooks · 2022 · 7 citations

    Senior authorCorresponding
    • Geography
    • Archaeology
    • Ancient history
  • South-to-north migration preceded the advent of intensive farming in the Maya region

    Nature Communications · 2022 · 116 citations

    • Geography
    • Agroforestry
    • Biology

    The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.

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

    Proceedings of the National Academy of Sciences · 2020 · 82 citations

    • Sociology
    • Biology
    • Geography

    ) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300-1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.

  • A Paleogenomic Reconstruction of the Deep Population History of the Andes

    Cell · 2020 · 191 citations

    • Biology
    • Evolutionary biology
    • Demography

    There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Frequent coauthors

  • Douglas J. Kennett

    35 shared
  • David Reich

    Broad Institute

    31 shared
  • Swapan Mallick

    Broad Institute

    27 shared
  • Kristin Stewardson

    Howard Hughes Medical Institute

    19 shared
  • Jonas Oppenheimer

    Howard Hughes Medical Institute

    18 shared
  • Brendan J. Culleton

    Pennsylvania State University

    18 shared
  • Nadin Rohland

    16 shared
  • Megan Michel

    Max Planck Institute for Evolutionary Anthropology

    16 shared
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