Introgression and the origin of maize in Mexico and the Southwest US

Introgression and the origin of maize in Mexico and the Southwest US

Jeffrey Ross-Ibarra @jrossibarra • www.rilab.org

Dept. Plant Sciences • Center for Population Biology • Genome Center University of California Davis

acknowledgements

Matt Hufford (Iowa State)

Rute Fonseca (Copenhagen)

Joost van Heerwaarden (Wageningen)

Tom Gilbert (Copenhagen) John Doebley (Wisconsin)

maize origins

maize origins

maize origins

Meyerowitz 1994 Current Biology Duvick et al. 1999 US 6639132 B1

maize origins

Tripsacum extinct maize


maize origins

Tripsacum extinct maizeF1


maize origins

Tripsacum extinct maizeF1


maize origins

Tripsacum extinct maizeF1F1

Matsuoka et al. 2002 PNAS Piperno et al. 2009 PNAS

mex

parv

mays

single origin from teosinte

Matsuoka et al. 2002 PNAS Piperno et al. 2009 PNAS

mex

parv

mays

paradox of maize ancestry

1,400 mm annually with over 90% falling during the June-to-October rainy season. The potential vegetation of the region istropical deciduous forest, seen today in remnants scatteredthroughout the region. Vegetational reconstructions indicatethat a species-diverse seasonal tropical forest f lourished thereafter the Pleistocene ended and until systematic human distur-bance began (27). The native vegetation contains legumes andmany other plants that would have been important subsistenceresources, such as Pithecolobium dulce, Prosopis spp, Leucaenaspp., Spondias spp., palms, Dioscorea spp., and others (27).Bedrock in the study area is predominantly limestone, althoughextrusive igneous formations are found in the eastern portion ofthe area. Both limestone and igneous formations provide cavesand overhangs that early occupants of the region used as shelters.The karstic landscape also resulted in the formation of anumber of permanent lakes near the shelters that offered astable and abundant supply of animal protein as well as diverseplant foods (27).

Our survey focused on caves and rock shelters because theywere commonly used by ancient peoples and because theyprovide better protection for perishable materials, such as plantremains, than open-air sites. We located 15 caves and rockshelters that had been occupied sometime in prehistory, basedon the stone and ceramic artifacts recovered from the sitesurfaces, and carried out excavations in 4 of these sites (Fig. 1).Two of the sites, Cueva del Agua and El Abra 2, contained onlyceramic-aged deposits. A third site, El Abra, was occupied atleast as early as 8330–8160 cal B.P. (14C AMS date of 7400 ! 40

B.P.), but the reworking of the rock shelter deposits in the early20th century has left them thoroughly mixed over most of thesite. At a fourth site, the Temaxcalapa Shelter, we recovered alarge number of chipped stone artifacts from the eroded slope infront of the shelter, including preceramic-aged spear points. Wewere unable to excavate this site (see SI Text, Site Descriptions foradditional information on these 4 sites). In a fifth site, theXihuatoxtla Shelter, our excavations encountered undisturbedpreceramic and ceramic deposits containing both chipped andground stone tools, plant remains, and ceramics (see Table S1 for14C dates from these sites).

ResultsThe Xihuatoxtla Shelter (964 m asl) is formed by the overhangof an enormous boulder (17 " 16 " 14 m) and contains #75 m2

of protected floor space inside the dripline (Fig. 2 and Fig. S1).It is located 260 m from Barranca Xihuatoxtla near the pointwhere the now-seasonal stream opens out onto a flat basin. Thenearly 1-m-deep stratigraphic sequence (Fig. 3) is anchored by4 radiocarbon dates on charcoal: (1) 1200 ! 40 B.P. (1240–1000cal B.P.) from layer B, 20–30 cm below surface, (2) 2790 ! 40B.P. (2970–2780 cal B.P.) from layer B, 30–40 cm below surface,(3) 4730 ! 40 B.P. (5590–5320 cal B.P.) from layer C, 49 cmbelow surface, and (4) 7920 ! 40 B.P. (8990–8610 cal B.P.) fromlayer D, 65 cm below surface. The cultural deposits extendedanother 35 cm below the 8990–8610 cal B.P. level, but we wereunable to date any of the samples recovered from these earlierdeposits. Though starch grains and phytoliths were well pre-

Fig. 2. A view of the enormous boulder that formed the Xihuatoxtla Shelter.

Fig. 3. Stratigraphy of units 1 and 2 in the Xihuatoxtla Shelter.

Ranere et al. PNAS ! March 13, 2009 ! vol. 106 ! no. 13 ! 5015

AN

THRO

POLO

GY

SEE

COM

MEN

TARY

van Heerwaarden et al. 2011 PNAS

landrace and teosinte sampling

SNPs show highland similarity to teosinte


admixture explains patterns of diversity


mexicana parviglumis South/Caribbean West Highland

05001000150020002500

m

admixture explains patterns of diversity


0.0 0.2 0.4 0.6 0.8 1.0

0.2

00

.25

0.3

00

.35

0.4

00

.45

admixture proportion

F

0.0 0.2 0.4 0.6 0.8 1.0

0.2

50

.26

0.2

70

.28

0.2

9

admixture proportion

H

Genetic distance to parviglumis Heterozygosity

observed

observed

Pesach Lubinsky

Norm

Ellstrand

hybrids commonly observed

Pesach Lubinsky

admixture along the genome

maize

mexicana

Mb

% p

opul

atio

n ad

mix

ed

Chromosome 4

Hufford et al. 2013 PLoS Genetics

El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric

admixture localized, asymmetric

El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric

Hufford et al. 2013 PLoS Genetics Pyhäjärvi et al. 2013 GBE

El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric


El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric

Inv4n


El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric


El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric

Inv4n


El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric


El Porvenir

Opopeo

Xochimilco

Puruandiro

Tenango del Aire

Ixtlan

Nabogame

Santa Clara

San Pedro

Allopatric

*

**

* *Inv4n


Lauter et al. 2004 Genetics Moose et al. 2004 Genetics

introgressions overlap with mexicana QTL

b1 in maize

Inv4n


introgressions show mexicana phenotypesN

o In

trogr

essio

nIn

trogr

essio

n


macrohairs

pigmentaton

introgressions grow faster at low temp

Introgressed

Not Introgressed


admixture confounds ancestral inference

compare to wild ancestor

origininferred origin

admixture confounds ancestral inference


origininferred origin

gene flow

origin

inferred origin


Gen

e fre

quen

cya solution: ancestral reconstruction

Nicholson et al 2002 J Roy Stat Soc. B

wild ancestor

0

1

origin

Gen

e fre

quen



wild ancestor

0

1

0

1

origin

Gen

e fre

quen



wild ancestor derivative 1 derivative 2

drift

drift

0

1

0

1

0

1

0

1

ancestral reconstruction resolves origins

gene flow

origin

inferred origin

wild ancestor

ancestral reconstruction resolves origins

ancestral reconstruction

origin

inferred origin

gene flowgene flow

origin

inferred origin

wild ancestor

maize origins in lowland west Mexico


Genetic distance from ancestor

dens

ity

Compared to wild teosinte Compared to ancestral maize

similarity of some of our maize groups violates the assumption ofindependent drift, we infer ancestral frequencies by averagingover estimates obtained for pairs of diverged maize groups andcalculate drift of individual populations with respect to thesefrequencies. In contrast to previous results, this comparisonidentifies the West Mexico group as being most similar to thecommon domesticated ancestor, followed by the MexicanHighland and Meso-American Lowland groups (Fig. 3C).Moreover, splitting the West Mexico group into highland(>2,000 m) and lowland (<1,500 m) components reveals that thelowland West Mexico group is most similar to the inferred an-cestral maize. Direct comparison of genetic drift among thelowland West Mexico, Mexican Highland, and each of theremaining eight clusters shows further that the lowland WestMexico group is significantly closer than the Mexican Highlandgroup to the inferred ancestor of each triplet (Fig. S4). Theseresults strongly suggest that maize from the western lowlands ofMexico is genetically most similar to the common ancestor ofmaize and is more closely related to other extant populationsthan is maize from the highlands of central Mexico.The ancestral position of the lowland West Mexico group is

confirmed in a spatially explicit analysis of current allele fre-quencies in modern landraces, in which we mapped the momentestimator of F with respect to inferred ancestral allele frequen-cies. Mapping against allele frequencies observed in parviglumis

(Fig. 4A) recapitulates earlier genetic results identifying highlandmaize as most similar to its wild ancestor (5). Points in the lower0.05 quantile of F cluster in the highlands, with a mean altitudeof 1,745 m. In contrast, mapping F with respect to inferred an-cestral allele frequencies (Fig. 4B) identifies the lowest 0.05quantile of F values in the lowlands of western Mexico, includingthe Balsas region and the region south of the Mexican highlands,resulting in an average altitude of 1,268 m; this analysis alsoclearly estimates higher values of F for maize in the Mexicanhighlands, particularly in areas of high inferred introgressionfrom mexicana (Fig S5).

DiscussionResolving the origins and spread of domesticated crops is a fas-cinating and challenging endeavor that requires the integrationof botanical, archeological, and genetic evidence (26, 27, 28).Maize provides an exceptional opportunity for studying theprocesses of domestication and subsequent diffusion because ofthe wealth of existing archaeobotanical data, germplasm acces-sions, and molecular markers. The contradiction between evi-dence supporting the earliest cultivation in the lowlands and thegenetically ancestral position of Mexican Highland maize istherefore of particular interest. The disagreement is important,because the adaptive differences between highland and lowlandmaize are profound (14, 29). In other crops, uncertainty about

mexicana parviglumis Meso-American Lowland West Mexico Mex. Highland

05001000150020002500

m

Fig. 2. (Lower) Bar plot of assignment values for the sample of Mexican accessions: Mexicana (red), parviglumis (green), and mays (blue). (Upper) The solidblack line indicates the altitude for each sample. The dotted line marks the minimum altitude at which mexicana occurs.

0.1 0.2 0.3 0.4

F F

0.1 0.2 0.3 0.40.1 0.2 0.3 0.4

F

South-West USCentral USS American Lowland Bolivian LowlandMeso-American Lowland West MexicoCoastal BrazilMexican Highland North USAndean Highland

A B C

Fig. 3. Posterior densities of the genetic drift parameter F for 10 genetic groups with respect to (A)mexicana and (B) parviglumis. Only lowland accessions ofthe West Mexico group (light blue) were included. (C) Drift of all 10 genetic groups with respect to inferred ancestral frequencies. Light blue represents WestMexico; dotted line indicates the division between lowlands (<1,500 m, solid line) and highlands (>2,000 m).

van Heerwaarden et al. PNAS Early Edition | 3 of 5

EVOLU

TION

similarity of some of our maize groups violates the assumption ofindependent drift, we infer ancestral frequencies by averagingover estimates obtained for pairs of diverged maize groups andcalculate drift of individual populations with respect to thesefrequencies. In contrast to previous results, this comparisonidentifies the West Mexico group as being most similar to thecommon domesticated ancestor, followed by the MexicanHighland and Meso-American Lowland groups (Fig. 3C).Moreover, splitting the West Mexico group into highland(>2,000 m) and lowland (<1,500 m) components reveals that thelowland West Mexico group is most similar to the inferred an-cestral maize. Direct comparison of genetic drift among thelowland West Mexico, Mexican Highland, and each of theremaining eight clusters shows further that the lowland WestMexico group is significantly closer than the Mexican Highlandgroup to the inferred ancestor of each triplet (Fig. S4). Theseresults strongly suggest that maize from the western lowlands ofMexico is genetically most similar to the common ancestor ofmaize and is more closely related to other extant populationsthan is maize from the highlands of central Mexico.The ancestral position of the lowland West Mexico group is

confirmed in a spatially explicit analysis of current allele fre-quencies in modern landraces, in which we mapped the momentestimator of F with respect to inferred ancestral allele frequen-cies. Mapping against allele frequencies observed in parviglumis

(Fig. 4A) recapitulates earlier genetic results identifying highlandmaize as most similar to its wild ancestor (5). Points in the lower0.05 quantile of F cluster in the highlands, with a mean altitudeof 1,745 m. In contrast, mapping F with respect to inferred an-cestral allele frequencies (Fig. 4B) identifies the lowest 0.05quantile of F values in the lowlands of western Mexico, includingthe Balsas region and the region south of the Mexican highlands,resulting in an average altitude of 1,268 m; this analysis alsoclearly estimates higher values of F for maize in the Mexicanhighlands, particularly in areas of high inferred introgressionfrom mexicana (Fig S5).

DiscussionResolving the origins and spread of domesticated crops is a fas-cinating and challenging endeavor that requires the integrationof botanical, archeological, and genetic evidence (26, 27, 28).Maize provides an exceptional opportunity for studying theprocesses of domestication and subsequent diffusion because ofthe wealth of existing archaeobotanical data, germplasm acces-sions, and molecular markers. The contradiction between evi-dence supporting the earliest cultivation in the lowlands and thegenetically ancestral position of Mexican Highland maize istherefore of particular interest. The disagreement is important,because the adaptive differences between highland and lowlandmaize are profound (14, 29). In other crops, uncertainty about

mexicana parviglumis Meso-American Lowland West Mexico Mex. Highland

05001000150020002500

m

Fig. 2. (Lower) Bar plot of assignment values for the sample of Mexican accessions: Mexicana (red), parviglumis (green), and mays (blue). (Upper) The solidblack line indicates the altitude for each sample. The dotted line marks the minimum altitude at which mexicana occurs.

0.1 0.2 0.3 0.4

F F

0.1 0.2 0.3 0.40.1 0.2 0.3 0.4

F

South-West USCentral USS American Lowland Bolivian LowlandMeso-American Lowland West MexicoCoastal BrazilMexican Highland North USAndean Highland

A B C

Fig. 3. Posterior densities of the genetic drift parameter F for 10 genetic groups with respect to (A)mexicana and (B) parviglumis. Only lowland accessions ofthe West Mexico group (light blue) were included. (C) Drift of all 10 genetic groups with respect to inferred ancestral frequencies. Light blue represents WestMexico; dotted line indicates the division between lowlands (<1,500 m, solid line) and highlands (>2,000 m).

van Heerwaarden et al. PNAS Early Edition | 3 of 5

EVOLU

TION

maize origins in lowland west Mexico


1750m 1250m

J. ROSS-IBARRA / UC DAVIS

2. Coastal route

1. Highland route

SW

Mexico

how did maize arrive and adapt to SW US?

Fonseca et al. 2015 Nature Plants

Ronald Humeyestewa

Fonseca et al. 2015 Nature Plants Hufford et al. 2012 Nature Genetics

ancient cobs to investigate chronology


DNA capture to enrich for subset of genome



ancient DNA data analysis: ANGSD


erro

r ra

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SW shares ancestry with highland Mexico


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HUFFORD ET AL. 2012 PLOS GENETICS VAN HEERWAARDEN ET AL 2011 PNAS

allele counts support both hypotheses

J. ROSS-IBARRA / UC DAVISFonseca et al. 2015 Nature Plants

highlandSWUS coast teosinte

K=5

ChapaloteHighlands

Ancient Mexico

SW3KSW2K

SW750

Mex29Mex30Mex31Mex25Mex35

TPa10TPa06

TMx08

USA17

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TMx25

0.00 0.05 0.10 0.15 0.20TeosintesUSAMexicoCentral/South AmericaChile

Z. m. mexicana

Z. m. parviglumis

Coastal

Drift parameter

USA

Mexico

SW3KSW2K

SW750USA17

0.0 0.1 0.2-0.1-0.2

D

Coastal

Highlands

Outgroup

SW Coastal

Highlands

Outgroup

SW

a b c

Figure 1

HUFFORD ET AL. 2012 PLOS GENETICS VAN HEERWAARDEN ET AL 2011 PNAS

allele counts support both hypotheses


highlandSWUS coast teosinte

K=5

ChapaloteHighlands

Ancient Mexico

SW3KSW2K

SW750

Mex29Mex30Mex31Mex25Mex35

TPa10TPa06

TMx08

USA17

Reventador

TMx25

0.00 0.05 0.10 0.15 0.20TeosintesUSAMexicoCentral/South AmericaChile

Z. m. mexicana

Z. m. parviglumis

Coastal

Drift parameter

USA

Mexico

SW3KSW2K

SW750USA17

0.0 0.1 0.2-0.1-0.2

D

Coastal

Highlands

Outgroup

SW Coastal

Highlands

Outgroup

SW

a b c

Figure 1

tree, admixture analyses support results


ancient population genomics


~750 years b.p.

~2000 years b.p.

Changes in shape and size

n=10

n=12


selection affects patterns of diversity


SFSPr

opor

tion

SNPs

0

0.175

0.35

0.525

0.7

Individuals1 2 3 4

Prop

ortio

n SN

Ps

0

0.175

0.35

0.525

0.7

Individuals1 2 3 4

Taj D = 0

Taj D < 0


SFSPr

opor

tion

SNPs

0

0.175

0.35

0.525

0.7

Individuals1 2 3 4

Prop

ortio

n SN

Ps

0

0.175

0.35

0.525

0.7

Individuals1 2 3 4

Taj D = 0

Taj D < 0

PBS

700yr

2000yr

teosinte


methods identify known domestication locimedian PBS values

PBS(parviglumis)

parviglumis

SW2KSW750

dehyd1A

zagl1

su1

parviglumis

SW2KSW750

parviglumis

SW2KSW750

parviglumis

SW2K

SW750

a b

Figure 2Fonseca et al. 2015 Nature Plants

domestication loci

median PBS values

PBS(parviglumis)

parviglumis

SW2KSW750

dehyd1A

zagl1

su1

parviglumis

SW2KSW750

parviglumis

SW2KSW750

parviglumis

SW2K

SW750

a b

Figure 2

J. ROSS-IBARRA / UC DAVISFonseca et al. 2015 Nature Plants Liu et al. 2013 PLOS Genetics

John Doebley

domestication loci

median PBS values

PBS(parviglumis)

parviglumis

SW2KSW750

dehyd1A

zagl1

su1

parviglumis

SW2KSW750

parviglumis

SW2KSW750

parviglumis

SW2K

SW750

a b

Figure 2

J. ROSS-IBARRA / UC DAVISFonseca et al. 2015 Nature Plants Liu et al. 2013 PLOS Genetics

John Doebley


median PBS values

PBS(parviglumis)

parviglumis

SW2KSW750

dehyd1A

zagl1

su1

parviglumis

SW2KSW750

parviglumis

SW2KSW750

parviglumis

SW2K

SW750

a b

Figure 2

Liu et al. 2013 PLOS Genetics

median PBS values

PBS(parviglumis)

parviglumis

SW2KSW750

dehyd1A

zagl1

su1

parviglumis

SW2KSW750

parviglumis

SW2KSW750

parviglumis

SW2K

SW750

a b

Figure 2

adaptation loci

Bill Belknap

John Doebley

chronology of selection on starch pathway


• introgression confounds simple estimates of origin

• ancestral reconstruction provides resolution

• introgression adapted maize to highlands

• Southwest US maize originated in highlands with subsequent gene flow from Pacific Coast

• ancient DNA allows chronology of gene flow, adaptation

concluding thoughts