tive, is how best to elucidate microbialfunction—that is, how they make their liv-ing. No one technique is yet sufficientlywell developed to do this; however, func-tional gene microarray systems, which lookfor expression of genes coding for enzymesinvolved in specific functions, are currentlyunder development (13).

An associated challenge is to determinethe role of community microbial activity inshaping geochemical consequences.Geochemical interest in microbial activityis often restricted to a single metabolicfunction with a relevant geochemical con-sequence, such as metal sequestration (5,7). However, the microbe responsible forthat geochemical impact likely exists with-in a microbial community or consortium(12). The by-products from one organism’smetabolic pathway are the nutrients of thenext strain. Both the series of metabolic re-actants and products associated with a mi-crobial community, and the reaction ener-getics involved, are therefore likely to dif-fer from one location to the next.

Thus, even though commonality ofmetabolic pathways ensures widespreadoccurrence of certain microbially drivengeochemical processes in different envi-ronments, variability in microbial consor-

tia and microgeochemical conditions willselectively refine that geochemical impact.In doing so, they may create community-specific microbial fingerprints on geo-chemical processes.

Microbial growth and activity can onlyproceed through inputs of energy, and arethus constrained geochemically to reac-tions that are thermodynamically feasible.High-resolution analytical tools for geo-chemistry and culture-independent molec-ular microbial techniques have yielded ex-citing insights. Today, microbial activity isviewed to play an important—and quantifi-able—role in aqueous geochemistry. Newmolecular techniques for evaluating micro-bial functional activity will provide key in-formation on how microbes engineer geo-chemical processes, and how they, in turn,are constrained by the geochemical worldin which they find themselves.

Systematic examinations of the linksbetween genome and geochemistry will ex-plore gene expression (that is, function)and determine reaction kinetics of micro-bial communities growing under differinggeochemical and physical conditions (14).Such studies will provide microbial finger-prints for important geochemical processesunder microbial control. Moreover, such

studies should help to quantify the micro-bial influence on important aqueous geo-chemical processes, determine the linkedcontrols for these key processes, and showhow feedback between microbial ecologyand geochemical conditions influences thegeochemical outcomes.

References1. K. Takai, T. Komatsu, F. Inagaki, K. Horikoshi, Appl.

Environ. Microbiol. 67, 3618 (2001).2. P. L. Bond, S. P. Smriga, J. F. Banfield, Appl. Environ.

Microbiol. 66, 3842 (2000).3. F. H. Chapelle et al., Nature 415, 312 (2002).4. Aqueous Microbial Geochemistry in Extreme and

Contaminated Environments, Fall AGU Meeting,San Francisco, CA, 6 to 10 December 2002. Seewww.agu.org/meetings/fm02/program.shtml.

5. G. Morin et al., Fall AGU Meeting, San Francisco, CA,6 to 10 December 2002, abstract B22E-05.

6. C. M. Hansel et al., Fall AGU Meeting, San Francisco,CA, 6 to 10 December 2002, abstract B22E-10.

7. E. A. Haack, L. A. Warren, Fall AGU Meeting, SanFrancisco, CA, 6 to 10 December 2002, abstract B22E-06.

8. P. A. O’Day, Rev. Geophys. 37, 249 (1999).9. N. R. Pace, Science 276, 734 (1997).

10. B. J. Finlay, Science 296, 1061 (2002).11. K. H. Nealson, D. A. Stahl, in Geomicrobiology:

Interactions Between Microbes and Minerals, J. F.Banfield, K. H. Nealson, Eds. (Mineralogical Society ofAmerica, Washington, DC, 1997), vol. 35, pp. 5–34.

12. D. K. Newman, J. F. Banfield, Science 296, 1071(2002).

13. A. S. Beliaev et al., J. Bacteriol. 184, 4612 (2002).14. A.-L. Reysenbach, E. Shock, Science 296, 1077 (2002).15. K. J. Edwards, P. L. Bond, T. M. Gihring, J. F. Banfield,

Science 287, 1796 (2000).

Decades ago, excavations in theTehuacan Valley of Mexico (1) con-vinced many archaeologists that

they now had physical proof of how, when,and where plantswere first domesti-cated in the NewWorld. The proofcame in the form of

preserved seeds and fruits, maize kernelsand cobs, fibers, and the rinds of cultigensfound in cave soils and in preserved humanfeces originally dated as early as 7500 to9000 years old. Little did these archaeolo-gists realize that the puzzle of New Worldplant domestication was far from solved.Decades later, they would learn that themost critical clues come not from the largeand visual remains of plants, but from tiny

microscopic particles that most archaeolo-gists unknowingly discarded.

Fortunately, a few researchers (2, 3)were not convinced by the traditional sto-ry of New World cultigen origins. Pipernoand a few others devoted more than threedecades to searching the archaeologicalsoils of Central and South America for

microscopic phytoliths (plant crystals),tiny starch grains from domesticatedplants, and fossil pollen (see the figure).As noted by Piperno and Stothert onpage 1054 of this issue (4) and byPiperno and Pearsall in a recent book (5),these microscopic traces of plants reli-ably record the earliest use of domesti-cated plants.

Early speculation about the origins ofNew World plant domestication focusedon the upland regions of Mexico andSouth America. These regions were fa-vored because they were easy to reach, of-ten contained caves or rock shelters filledwith preserved plant remains, and hadyielded previous successes that ensured

A R C H A E O L O G Y

Invisible Clues to New World

Plant DomesticationVaughn M. Bryant

The author is in the Center for Ecological Arch-aeology, Department of Anthropology, Texas A&MUniversity, College Station, TX 77843, USA. E-mail:vbryant@neo.tamu.edu

Enhanced online at

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content/full/299/5609/1029

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Archaeology under the microscope. (A) Radiocarbon-dated 10,000-year-old phytolith (diameter

100 µm) of domesticated Cucurbita, collected from soil at the Vegas Site 80 in Ecuador. (B) Reserve

starch grains from the root of a modern manioc plant. (C) Maize pollen grain (diameter 75 µm) from

cultural levels of the Kob Site, Belize, radiocarbon dated to ~5000 years ago.

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continued funding. Few archaeologistswere willing to search for the origin ofplant cultigens in lowland and jungle re-gions, where seeds, wood, rinds, and cobsdid not preserve well. Many also won-dered how tropical lowlands could havesupported foragers making the switch toearly sedentary farming. And most be-lieved incorrectly that all lowland andjungle soils were infertile, similar to onesknown from the non–flood plain regionsof the Amazon. But Piperno and a fewothers remained convinced that the longsearch for cultigen origins had focused onthe wrong areas and the wrong kind ofclues.

It is true that, except for charcoal, thevisual evidence of plant remains quicklydisappears in most tropical soils. Butsome clues remain, if you know where tolook. By the early 1990s, Piperno (2, 6)had shown that plant phytoliths were plen-tiful in the lowland soils of many regionsof Central and South America. She notedthat the size and shape of phytoliths wereoften unique to a family, genus, or speciesof plant (see panel A of the figure).Piperno and Pearsall then led the way indeveloping phytolith keys to a wide vari-ety of New World cultigens and tropicalplants (5). Armed with this knowledge,scientists began to search for microscopicclues in the soils of early, well-dated ar-chaeological sites throughout Central andSouth America.

New studies based on phytolith data (3,6) soon began to contradict the long-heldtheory that plant domestication began inupland regions, where many envisionedcave-living foragers switching to raisingcultigens (1). Archaeologists challengingthe new discoveries pointed to potential er-rors in dating, saying that the phytolith ev-idence could not possibly be as old as thedates indicated. To quell the critics, phy-tolith researchers developed new ways ofdating tiny bits of carbon trapped insidephytoliths as they were formed.

The new techniques, which use acceler-ator mass spectrometry (AMS) dating, re-quire the careful collection and separationof many phytoliths (4). Precise phytolithidentification is also critical. Piperno andStothert (4) collected and measured phy-toliths from more than 150 mature fruitsfrom wild and domesticated species ofCucurbita (squash and gourds) grown in100 different locations. The phytolithsfrom domestic species were substantiallylarger than those from wild species. Theauthors then used phytolith size to confirmthat domesticated Cucurbita were grownand used during the early Holocene incoastal Ecuador, between 9000 and 10,000years ago.

Piperno (7) has also been at the fore-front of searching for archaeological evi-dence of cultigen starch grains. In tropicalregions of Central and South America, rootcrops—including yams, sweet potatoes,and manioc—are the mainstay of many in-digenous cultures. These high-calorie tubercrops grow well in the wet soils and areascreated by recently cleared tropical forests.But it has been difficult to prove whenand where these plants were first domesti-cated. Tuber-producing crops do not car-bonize well; furthermore, most producesmall amounts of pollen and do not pro-duce diagnostic phytoliths. However, theydo produce copious numbers of water-insoluble granules called “reserve starchgrains” (panel B), which preserve well onthe surfaces of food preparation imple-ments and in many types of tropical soils.Starch grains from tuber cultigens have re-cently been identified on early Holocenegrinding stones used in Colombia and cen-tral Panama (8).

In 1957, the British pollen analystDimbleby (9) stated that soils with a pHabove 6 are virtually useless for fossilpollen studies. Because the pH values ofalmost all tropical soils exceed 6, pollenanalysts have for decades rarely searchedthe tropical soils of Central or SouthAmerica. I was one of those pollen ana-lysts who spent more than 30 years work-ing at sites in Mexico and South America.I never found well-preserved pollen in anyof those sites.

To the astonishment of many, Jones andcolleagues recently recovered pollen fromkey archaeological sites in Central America(10). His pollen data confirm the use ofearly cultigens, including maize and man-ioc, from the San Andres site in theMexican tropical lowlands near La Venta,Tabasco. Radiocarbon dating shows thatthe archaeological deposits containingcultigen pollen are 5800 to 6200 years old.

Perhaps DNA studies of soils in archae-ological sites may soon replace our currenttechniques. Until then, our best New Worldrecords for cultigen origins are comingfrom the invisible clues: phytoliths, starchgrains, and fossil pollen.

References1. R. S. MacNeish, in The Prehistory of the Tehuacan

Valley: Environment and Subsistence, D. S. Byers, Ed.(Univ. of Texas Press, Austin, TX, 1967), vol. 1, pp.290–309.

2. D. R. Piperno, Phytolith Analysis: An Archaeological and

Geological Perspective (Academic Press, San Diego,

CA, 1988).

3. D. M. Pearsall, in Current Research in Phytolith Analysis:

Applications in Archaeology and Paleoecology, D. M.

Pearsall, D. R. Piperno, Eds. (University Museum of

Archaeology and Anthropology, Philadelphia, 1993),

pp. 109–122.

4. D. R. Piperno, K. E. Stothert, Science 299, 1054

(2003).

5. D. R. Piperno, D. M. Pearsall, The Origins of Agriculture

in the Lowland Neotropics (Academic Press, San Diego,

CA, 1998).

6. D. R. Piperno, J. World Prehist. 5, 155 (1991).

7. ———, I. Holst, J. Archaeol. Sci. 25, 765 (1998).

8. ———, A. J. Ranere, P. Hansell, Phytolitharien 13, 1

(2001).

9. G. W. Dimbleby, New Phytol. 56, 12 (1957).

10. K. O. Pope et al., Science 292, 1370 (2001).

Recently, there has been an explosionof interest among immunologists ina subset of T lymphocytes that pre-

vent harmful immune pathology. Theseregulatory T cells (TR), most of which ex-press the activation marker CD25, consti-tute a small number (5 to 10%) of the to-tal population of CD4+ T lymphocytespresent in healthy individuals. CD4+ TRcells prevent a number of immune-medi-ated diseases, including autoimmune dis-orders, transplant rejection, and inflam-matory bowel disease (1). Recent studiesincluding two papers in this issue, by Horiet al. (2) on page 1057 and Pasare andMedzhitov (3) on page 1033, are begin-

ning to elucidate TR cell biology in moredetail, particularly aspects of their differ-entiation and functional capabilities.These studies emphasize that TR lympho-cytes do not act in isolation, but are them-selves influenced by cells of the innateimmune system. An equilibrium is there-by established that allows effective re-sponses against dangerous microbes whileminimizing immune pathology.

The identification of transcription fac-tors that direct the differentiation of naïveCD4+ T cells into functionally distinct Thelper 1 (TH1) and TH2 cells has trans-formed our understanding of the molecu-lar basis of CD4+ effector T cell responses(4). The study by Hori et al. (2) identifiesthe forkhead/winged helix transcriptionfactor Foxp3 as a master regulator thatpromotes TR cell differentiation. These in-vestigators noted that both humans and

I M M U N O L O G Y

Regulating the RegulatorsFiona Powrie and Kevin J. Maloy

The authors are at the Sir William Dunn School ofPathology, University of Oxford, South Parks Road,Oxford OX1 3RE, UK. E-mail: fiona.powrie@path.ox.ac.uk

1030 14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org

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