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MAIZE DOMESTICATION tables S2 and S3) and analyzed them alongside


published modern (n = 68) and ancient (n = 2)
maize and teosinte genomes (15).
Multiproxy evidence highlights Model-based clustering highlights extensive
admixture and population overlap between maize

a complex evolutionary legacy populations, but we observe several robust lin-


eages (15) (Fig. 1): (i) the Andes and the Pacific
coast of South America; (ii) lowland South
of maize in South America America, including the Amazon and Brazilian
Savanna; (iii) North America north of the do-
Logan Kistler1,2*, S. Yoshi Maezumi3,4, Jonas Gregorio de Souza3,
mestication center; and (iv) highland Mexico and
Central America, previously observed to contain
Natalia A. S. Przelomska1,5, Flaviane Malaquias Costa6, Oliver Smith7,
introgression from wild Z. mays ssp. mexicana
Hope Loiselle1,8, Jazmín Ramos-Madrigal7, Nathan Wales9, Eduardo Rivail Ribeiro1,
(14, 16). We also observe a widespread “Pan-
Ryan R. Morrison2, Claudia Grimaldo10, Andre P. Prous11, Bernardo Arriaza12,
American” lineage spanning from northern Mexico
M. Thomas P. Gilbert7,13, Fabio de Oliveira Freitas14*, Robin G. Allaby 2* into lowland South America. In a previous analysis
based on multiple nuclear microsatellites, maize
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning
formed a monophyletic subset of teosinte, with
around 9000 years before the present (yr B.P.), traversed Central America by ~7500 yr B.P.,
South American lineages as the most derived
and spread into South America by ~6500 yr B.P. Landrace and archaeological maize genomes elements in a phylogenetic tree (13). This pattern
from South America suggest that the ancestral population to South American maize was has been interpreted as evidence for a single

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brought out of the domestication center in Mexico and became isolated from the wild teosinte
episode of domestication followed by dispersal
gene pool before traits of domesticated maize were fixed. Deeply structured lineages then culminating in the Andes after maize became
evolved within South America out of this partially domesticated progenitor population. established throughout the rest of the range
Genomic, linguistic, archaeological, and paleoecological data suggest that the southwestern of cultivation (13). However, archaeological
Amazon was a secondary improvement center for partially domesticated maize. Multiple waves
evidence for persistent maize cultivation in-
of human-mediated dispersal are responsible for the diversity and biogeography of modern dicates it was established in numerous loca-
South American maize. tions throughout South America by ~6500 to

M
4000 yr B.P. regionally. On the basis of this
aize (Zea mays ssp. mays) evolved remains establish that maize was brought to the information, we propose that South American
from wild Balsas teosinte (Z. mays southwestern United States and the Colorado maize was carried away from the Mesoamerican
ssp. parviglumis, hereafter parviglumis) Plateau by ~4000 years before the present (yr B.P.) domestication center soon after initial stages
in modern-day lowland Mexico beginning (7), traversing Panama by ~7500 yr B.P. (8) and of domestication and may have been one of
around 9000 years ago (1) and spread arriving in Coastal Peru (9), the Andes (10), and several partially domesticated maize lineages
to dominate food production systems through- lowland Bolivian Amazon (11) between ~6500 that independently fissioned from the primary
out much of the Americas by the beginning of and 6300 yr B.P. (Fig. 1 and table S1). Today, gene pool after the onset of domestication in
European colonization in the 15th century. maize is a staple food species, yielding over 6% Mexico (Fig. 2).
Archaeological and genetic data from ancient of all food calories for humans, plus more in Using f4 statistics (17), we observe asymmetry
DNA studies have highlighted aspects of maize livestock feed and processed foods (12). in parviglumis ancestry among modern maize
natural history, including the evolution and fixa- Maize domestication is thought to have oc- populations (Fig. 2). This reveals that maize-
tion of agricultural traits and adaptation of maize curred once, with little subsequent gene flow parviglumis gene flow was ongoing in some
to diverse new environments (2–6). Archaeological from parviglumis (13, 14). However, archaeoge- lineages after others became reproductively
nomic evidence reveals maize was only partially isolated. Whereas later gene flow from Z. mays
1
domesticated in Mexico by ~5300 yr B.P. (2, 3), ssp. mexicana, a highland subspecies of teosinte,
Department of Anthropology, National Museum of Natural
History, Smithsonian Institution, Washington, DC 20560,
carrying a mixture of wild-type and maize-like is well documented in some maize (6, 14, 16), this
USA. 2Department of Life Science, University of Warwick, alleles at loci involved in the domestication syn- finding contradicts the assumption that dis-
Coventry CV4 7AL, UK. 3Department of Archaeology, College drome. For example, the domestic-type TGA1 persal and diversification throughout the Americas
of Humanities, University of Exeter, Laver Building, North gene variant responsible for eliminating the tough happened only after the severance of gene flow
Park Road, Exeter EX4 4QE, UK. 4Department of Geography
and Geology, The University of the West Indies, Mona
teosinte fruitcase was already present by this time from parviglumis (13, 14). Thus, while South
Campus, Kingston, Jamaica. 5Center for Conservation period (2), whereas other loci associated with American maize became reproductively isolated
Genomics, Smithsonian Conservation Biology Institute, changes to seed dispersal and starch production from the wild progenitor when it was carried
National Zoo, Washington, DC 20008, USA. 6University of during domestication still carried wild-type var- away from the domestication center, maize lin-
São Paulo, Escola Superior de Agricultura Luis de Queiroz,
Piracicaba, SP 13418-900, Brazil. 7Centre for GeoGenetics,
iants (2, 3). The state of partial domestication eages remaining in Mexico underwent continued
Natural History Museum of Denmark, University of sets these archaeogenomes apart from modern crop-wild gene flow before diversifying into extant
Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, fully domesticated maize, which carries a com- landraces over subsequent millennia. The Pan-
Denmark. 8Department of Anthropology, University of plete, stable set of domestication alleles con- American lineage shows excess shared ancestry
Washington, Denny Hall 314, Seattle, WA 98195, USA.
9
Department of Archaeology, University of York, King's
ferring the domesticated phenotype. This partially with parviglumis relative to all other major groups
Manor, York YO1 7EP, UK. 10Department of Oncology, domesticated maize was grown in Mexico well (Fig. 2B), suggesting that this group emerged from
University of Oxford, Old Road Campus Research Building, after maize had become established in South the domestication center and dispersed after other
Roosevelt Drive, Oxford, OX3 7DQ, UK. 11Museu de Historia America, which raises the question of how South maize lineages became regionally established.
Natural e Jardim Botânico da Universidade Federal de Minas
Gerais, Belo Horizonte, MG 31270-901, Brazil. 12Instituto de
American maize came to possess the full com- Because the Pan-American lineage carries excess
Alta Investigación, Universidad de Tarapacá, Arica, Chile. plement of fixed domestication traits. To reconcile parviglumis ancestry relative to the strictly South
13
Norwegian University of Science and Technology, archaeobotanical and genomic data concerning American lineages, it appears to represent a
University Museum, 7491 Trondheim, Norway. 14Embrapa the domestication and dispersal history of maize second episode of maize dispersal from Meso-
Recursos Genéticos e Biotecnologia, Brasília, DF, CEP
70770-901, Brazil.
in South America, we sequenced maize genomes america, reinforcing two major waves of maize
*Corresponding author. Email: kistlerl@si.edu (L.K.); fabio.freitas@ from 40 indigenous landraces and 9 archaeo- movement into South America as previously
embrapa.br (F.O.F.); r.g.allaby@warwick.ac.uk (R.G.A.) logical samples from South America (Fig. 1 and suggested (5).

Kistler et al., Science 362, 1309–1313 (2018) 14 December 2018 1 of 4


R ES E A RC H | R E PO R T

The genomes of two ancient maize cobs from


the Tehuacan Valley of Mexico at ~5300 yr B.P.
recently revealed a state of partial domestication,
a mixture of maize- and parviglumis-like alleles 4383 B.P.
at loci involved in domestication (2, 3). This is
North American
puzzling, given the sustained use of domesti- Pan-American
k= 5
cated maize from ~6500 yr B.P. onward in South 4030 B.P. ancestry groups Mex. and C. America Highlands
America (Fig. 1 and table S1) (11, 18). However, Lowland South America
Andean-Pacific
principal components analysis and f3 statis- Zea mays ssp. parviglumis
4363 B.P.
tics reveal considerable genomic distance be- Archaeological Genome
tween these two Mesoamerican archaeogenomes parviglumis range
Tehuacan
(Fig. 1 and fig. S2), and f3 statistics confirm that San Marcos
6655 B.P.
the SM10 genome (3) is more maize-like, whereas 8750 B.P.
the Tehuacan162 genome (2) is more parviglumis- 6589 B.P.
like (fig. S2). In total, the two genomes are from
the same region and time period, and both are
partially domesticated, but otherwise, they appear 7746 B.P.
4030 B.P.
to represent independent samples out of a diverse
semidomesticated population containing an array
of domestic and wild-type alleles. 6000 B.P.

Given the state of partial domestication ob-

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served in the Tehuacan and San Marcos ge- 6700 B.P.
Z61
nomes (2, 3), early South American maize emerging
0.1

Z64
from their common ancestral population would 6500 B.P.
Z6
likely also have been a partially domesticated Z65
Z2
San Marcos
form of maize containing an assortment of wild
Z66
0.0

Arica4
and domestic alleles. This ancestral population Z61
Z6 Arica5
Z2 3770 B.P.
likely harbored the building blocks for fully Z64 Arica5
PC2

Z67
domesticated maize but lacked the allelic fixa- Z65
Tehuacan Arica4
tion and linkage of the modern domesticated Z67 Z66
−0.1

crop. We expect that in this ancestral semi-


domesticated population, domestication loci under
3730 B.P.
ongoing selection would have been continually
−0.2

decoupled from their chromosomal neighborhood


through recombination (19, 20), resulting in an
enrichment of the original parviglumis genomic
PC1
background near domestication genes relative −0.20 −0.15 −0.10 −0.05 0.00 0.05 0.10
to its genome-wide retention. If the domestica-
tion syndrome was fully established in the com- Fig. 1. Distribution and ancestry proportions of maize genomes and principal components analysis
mon ancestor of all extant maize, no modern (PCA) of maize and parviglumis genomes. Pie colors reflect ancestral proportions estimated by
parviglumis genome should carry this enriched means of model-based clustering (k = 5) of modern maize genomes (15). Archaeological
affinity to domestication loci to differing degrees genomes were projected onto the PCA to mitigate degradation biases (15). Dates reflect early
in different maize lineages, because the same regional maize archaeobotanical remains (table S1 and fig. S1). C., Central; Mex., Mexico; PC1,
background would have become fixed in their First principal component; PC2, second principal component.
common ancestor. However, if South American
maize became isolated while fundamental do-
mestication was still ongoing, as we hypothesize, we observe that parviglumis ancestry is enriched ing sufficient diversity and ecological context to
then components of the parviglumis genomic near domestication genes in a pattern demon- continue the domestication process. Others, like
background are expected to differ between early strating that domestication-associated selec- ancestral South American maize, evolved into
stratified maize lineages. Therefore in this case, tion was still ongoing after the stratification fully domesticated lineages under continuing
modern parviglumis genomes would carry a of the major extant lineages from their semi- anthropogenic pressures.
specifically South American or non–South domesticated ancestral population. This pat- The earliest evidence places maize in the
American affinity for the enriched wild-type tern validates a model in which the ancestral southwestern Amazon by ~6500 yr B.P. (11), a
background near domestication loci. population in South America was itself only region serving as a geographic interface of the
We compared D-statistics (21) across the whole partially domesticated during its dispersal lowland and Andean-Pacific genetic lineages
genome (DWG) and within 10 kb of 186 known away from the domestication center. (Fig. 1). We hypothesize that the southwestern
domestication loci (Ddom) to test for these asym- In total, we find support for a model of strat- Amazon may have been a secondary improve-
metrical parviglumis contributions between pairs ified domestication in maize (Fig. 2). The initial ment center for the partially domesticated crop
of extant South American and non–South American stages of maize domestication likely occurred before the divergence of the two South American
maize around domestication genes (15). We only once within a diverse wild Balsas River basin groups. When maize arrived, southwestern
found that parviglumis enrichment associated gene pool, as previously suggested (13). However, Amazonia was a plant domestication hotspot
with domestication is highly patterned among before the domestication syndrome was fixed and (22). Additionally, microfossil assemblages (11, 22)
major ancestry groups, with several parviglumis stable, multiple lineages separated, and selection reveal the presence of polyculture (mixed crop-
genomes associated exclusively with either South pressures on domestication loci continued inde- ping) from ~6500 yr B.P. onward, such that a
American or non–South American Ddom enrich- pendently outside of the primary domestication new crop species could be integrated into ex-
ment and a significant association with ancestry center. Some of these divergent semidomesticated isting food production systems supporting do-
overall (Fig. 2C; c2 test P = 2.74 × 10−6). That is, populations likely led to terminal lineages lack- mestication activities.

Kistler et al., Science 362, 1309–1313 (2018) 14 December 2018 2 of 4


R ES E A RC H | R E PO R T

Fig. 2. A stratified domestication model


A for maize. (A) Schematic comparing
the conventional domestication model
under which maize became fully
domesticated and then dispersed
throughout the Americas, versus a
stratified domestication model in which
Domestication center parviglumis semidomesticated ancestral
domestic maize partially domesticated subpopulations
became reproductively isolated before
the fixation of the domestication syndrome.
H0 – Simple domestication diverse landraces
(B) f 4 statistics demonstrating excess
allele sharing between the Pan-American
lineage and wild parviglumis compared
Secondary improvement center H1 – Stratified domestication with other maize, revealing nonuniform
crop-wild gene flow after initial
domestication. Bars are three standard
errors under a block jackknife (15).
(C) Bar plot of enriched parviglumis
contributions to ancestry near domestication
genes, in which each bar is a parviglumis

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genome contributing to South American
parviglumis semidomesticated maize (blue) or other maize (red)
semidomesticated
diverse landraces D dom enrichment. Geographic segregation
B
subgroups
C
Number of significant D dom enrichment cases

p1 p2 parviglumis p1 p2 parv. p1 p2 parv. in D dom enrichment among parviglumis


Tripsacum Trip. Trip. genomes suggests that the domestication
10 Enriched in South American maize syndrome was not yet fixed in a common
p1 p2 Enriched in other lineages
domesticated ancestor of modern maize.
Pan-American North American 8 2
test: p=2.74 x 10 -6
Pan-American Lowland South American
6
Pan-American Andean/Pacific
North American Lowland S. American 4

North American Andean/Pacific


2
Lowland South American Andean/Pacific

0 TI T T T T T T T T T T
−0.003 0.000 0.003 L1 IL0 IL0 IL0 IL0 IL1 IL0 IL1 IL0 IL0 IL1
2 9 3 6 1 5 7 0 2 4 1
f4(((p1,p2),parviglumis ),Tripsacum)

Fig. 3. Genomic relatedness overlapping


5500 linguistic and archaeological patterns in low-

4300
land South America. Maize genomes with
≥50% Andean-Pacific ancestry and ≥99% South
American ancestry are connected by lines with
the two other genomes with which they share
2300
the highest outgroup-f3 value. Geometric
530
enclosures and mound ring villages of southern
10°S
3630 Amazonia broadly coincide with the expansion
6500 940
700 of Arawak languages, whereas the Uru and Aratu
4310 850 ring villages coincide with the distribution of
700 1070 980 Macro-Jê languages (15) (figs. S3 and S4).
3770 Only the earliest regional dates for each
940
810
archaeological tradition are shown (see table
20°S
S4). Macro-Jê languages borrowing an Arawak
loanword for “maize” are based on (24).
Arawak homeland is shown approximately
in the modern location of Apurinã, in accordance
80°W 70°W 60°W 50°W 40°W with (29).
Maize genomes Archaeological traditions
Geometric enclosures Aratu and Uru
Modern Archaeological
and mound villages ring villages
Earliest dates Earliest dates
outgroup-f3 allele sharing
0.191 - 0.195 0.182 - 0.186 Language contact Paleoecology
Arawak homeland Early maize sites
0.196 - 0.201 0.187 - 0.190
‘maize’ loanword from
0.202 - 0.207 0.191 - 0.195 Arawak into Macro-Jê

Kistler et al., Science 362, 1309–1313 (2018) 14 December 2018 3 of 4


R ES E A RC H | R E PO R T

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Fig. 4. Genome-wide mutation load across
dryad.70t85k2.
maize with possible Andean origins was trans- ancestry groups (non-admixed samples only
mitted from Amazonian Arawak languages—most in top panel) and load compared with dis- AC KNOWLED GME NTS
likely originating in southwest Amazonia (24)— tance to the domestication center. Mutation We thank Admera Health for assistance with sequence data
into Macro-Jê stock languages in the Brazilian load is calculated as a proportion of the collection and D. Piperno for comments on the manuscript.
savanna and Atlantic coast (24) (fig. S3). Archae- Funding: Work was supported by Natural Environment Research
theoretical maximum load over observed single-
Council Independent Research Fellowship NE/L012030/1 to L.K.,
ological evidence suggests this expansion occurred nucleotide polymorphisms, and ancient load and a sub-award from Science and Technology Facilities Council
~1200 to 1000 yr B.P. with the spread of a cultural scores are rescaled for missingness using a grant ST/K001760/1 (PI Thomas Meagher, co-I Peter Kille) to
horizon of geometric enclosures and mound ring Procrustes transformation (15). Euclidean dis- L.K. and R.G.A. Author contributions: Study conceptualization
villages throughout southern Amazonia and ring and design: L.K., F.O.F, and R.G.A.; Sample acquisition: F.O.F., A.P.P.,
tance in degrees to the Balsas River valley is
C.G., B.A., and M.T.P.G.; Genomic data collection: L.K., F.O.F., O.S.,
villages in the central Brazilian savannas and the shown. And./Pac., Andean-Pacific. N.W., and R.R.M.; Genomic data analysis: L.K. and N.A.S.P.;
Atlantic coast (Fig. 3 and fig. S4) (25–27). This Archaeology and linguistic background and interpretation: J.G.S.,
process is roughly contemporaneous with archae- S.Y.M., F.O.F., F.M.C., and E.R.R.; Interpretation and integration of
ological Andean-admixed genomes in the area. pressures for regional adaptation, and the lat- results: L.K., S.Y.M., J.G.S., F.M.C., J.R.-M., N.W., F.O.F., and R.G.A.;
Visualization: L.K., S.Y.M., J.G.S., H.L., and N.A.S.P.; Manuscript
Thus, Arawak speakers likely brought nonlocal ter stages of domestication after isolation from
drafting: L.K., S.Y.M., and J.G.S., with input from N.A.S.P., F.O.F., and
Andean-Pacific maize lineages into a landscape the founding gene pool. We also find that R.G.A. All authors reviewed and contributed to the final manuscript.
where maize was an established component of Andean and Pacific maize from ~1000 yr B.P. Competing interests: We declare no competing interests. Data and
long-term land management and food produc- to the early colonial period has a low mutation materials availability: Raw sequence data, NCBI Sequence Read
Archive accession SRP152500. In-house scripts for data handling and
tion strategies. load compared with its modern Andean-Pacific
analysis (allele frequency estimation, f and D statistic calculation,
Finally, we quantified the mutation load in counterparts (Wilcoxon P = 0.002477) (15) (Fig. 4); genome alignment conformation for mutation load analysis, and
maize genomes—the accumulation of potentially although still elevated compared with non–South exclusion amplification duplicate removal), genome-wide GERP
deleterious alleles due to drift and selection American lineages. It is possible that Andean scoring details, genomic mappability bed file, SNP calls, and
mapDamage results are available in (30). Germplasm for newly
(16)—using a phylogenetic framework to estimate maize experienced a wave of deleterious allele
sequenced maize landraces is curated at the Embrapa gene bank in
evolutionary constraint (15). We observe that accumulation as human and crop populations Brasilia, Brazil, and Programa Cooperativo de Investigaciones en
South American lineages carry a higher muta- were disrupted by changes caused by the arrival Maíz in Peru, which provided sample material for this study to F.O.F.
tion load than other maize lineages. Mutation of Europeans (28). Alternatively, the increasing and C.G. Archaeological samples from Santa, Chorrillos, Ica, and Jujuy
were originally obtained from the PSUM Archaeological Project,
load increases linearly with distance from the mutation load in modern crops could repre-
Paurarku Archaeological Project and Samaca Archaeological Project,
domestication center and is linked with ancestry, sent the ongoing effects of burdensome allele facilitated by archaeologists V. Pimentel, K. Lane, D. Beresford-Jones,
and the Andean-Pacific group carries the highest accumulation over nine millennia of human and H. Yacobaccio.
burden of potentially deleterious variants (Fig. 4) intervention.
(15). The mutation load in the Andes has been SUPPLEMENTARY MATERIALS
attributed to selection for high-altitude adapta- RE FERENCES AND NOTES www.sciencemag.org/content/362/6420/1309/suppl/DC1
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Kistler et al., Science 362, 1309–1313 (2018) 14 December 2018 4 of 4


Multiproxy evidence highlights a complex evolutionary legacy of maize in South America
Logan Kistler, S. Yoshi Maezumi, Jonas Gregorio de Souza, Natalia A. S. Przelomska, Flaviane Malaquias Costa, Oliver
Smith, Hope Loiselle, Jazmín Ramos-Madrigal, Nathan Wales, Eduardo Rivail Ribeiro, Ryan R. Morrison, Claudia Grimaldo,
Andre P. Prous, Bernardo Arriaza, M. Thomas P. Gilbert, Fabio de Oliveira Freitas and Robin G. Allaby

Science 362 (6420), 1309-1313.


DOI: 10.1126/science.aav0207

The complexity of maize domestication


Maize originated in what is now central Mexico about 9000 years ago and spread throughout the Americas before

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European contact. Kistler et al. applied genomic analysis to ancient and extant South American maize lineages to
investigate the genetic changes that accompanied domestication (see the Perspective by Zeder). The origin of modern
maize cultivars likely involved a ''semidomesticated'' lineage that moved out of Mexico. Later improvements then
occurred among multiple South American populations, including those in southwestern Amazonia.
Science, this issue p. 1309; see also p. 1246

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