The potential role of genetic assimilation during maize domestication.

Domestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. In recent research, the exposure of teosinte (i.e., wild maize) to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial changes in co-expressionnal networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

Preceramic maize from Paredones and Huaca Prieta, Peru.

Maize (Zea mays ssp. mays) is among the world's most important and ancient domesticated crops. Although the chronology of its domestication and initial dispersals out of Mexico into Central and South America has become more clear due to molecular and multiproxy archaeobotanical research, important problems remain. Among them is the paucity of information on maize's early morphological evolution and racial diversification brought about in part by the poor preservation of macrofossils dating to the pre-5000 calibrated years before the present period from obligate dispersal routes located in the tropical forest. We report newly discovered macrobotanical and microbotanical remains of maize that shed significant light on the chronology, land race evolution, and cultural contexts associated with the crop's early movements into South America and adaptation to new environments. The evidence comes from the coastal Peruvian sites of Paredones and Huaca Prieta, Peru; dates from the middle and late preceramic and early ceramic periods (between ca. 6700 and 3000 calibrated years before the present); and constitutes some of the earliest known cobs, husks, stalks, and tassels. The macrobotanical record indicates that a diversity of racial complexes characteristic of the Andean region emerged during the preceramic era. In addition, accelerator mass spectrometry radiocarbon determinations carried out directly on different structures of preserved maize plants strongly suggest that assays on burned cobs are more reliable than those on unburned cobs. Our findings contribute to knowledge of the early diffusion of maize and agriculture and have broader implications for understanding the development of early preindustrial human societies.

Pre-Columbian agricultural landscapes, ecosystem engineers, and self-organized patchiness in Amazonia.

The scale and nature of pre-Columbian human impacts in Amazonia are currently hotly debated. Whereas pre-Columbian people dramatically changed the distribution and abundance of species and habitats in some parts of Amazonia, their impact in other parts is less clear. Pioneer research asked whether their effects reached even further, changing how ecosystems function, but few in-depth studies have examined mechanisms underpinning the resilience of these modifications. Combining archeology, archeobotany, paleoecology, soil science, ecology, and aerial imagery, we show that pre-Columbian farmers of the Guianas coast constructed large raised-field complexes, growing on them crops including maize, manioc, and squash. Farmers created physical and biogeochemical heterogeneity in flat, marshy environments by constructing raised fields. When these fields were later abandoned, the mosaic of well-drained islands in the flooded matrix set in motion self-organizing processes driven by ecosystem engineers (ants, termites, earthworms, and woody plants) that occur preferentially on abandoned raised fields. Today, feedbacks generated by these ecosystem engineers maintain the human-initiated concentration of resources in these structures. Engineer organisms transport materials to abandoned raised fields and modify the structure and composition of their soils, reducing erodibility. The profound alteration of ecosystem functioning in these landscapes coconstructed by humans and nature has important implications for understanding Amazonian history and biodiversity. Furthermore, these landscapes show how sustainability of food-production systems can be enhanced by engineering into them follows that maintain ecosystem services and biodiversity. Like anthropogenic dark earths in forested Amazonia, these self-organizing ecosystems illustrate the ecological complexity of the legacy of pre-Columbian land use.

Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico.

Questions that still surround the origin and early dispersals of maize (Zea mays L.) result in large part from the absence of information on its early history from the Balsas River Valley of tropical southwestern Mexico, where its wild ancestor is native. We report starch grain and phytolith data from the Xihuatoxtla shelter, located in the Central Balsas Valley, that indicate that maize was present by 8,700 calendrical years ago (cal. B.P.). Phytolith data also indicate an early preceramic presence of a domesticated species of squash, possibly Cucurbita argyrosperma. The starch and phytolith data also allow an evaluation of current hypotheses about how early maize was used, and provide evidence as to the tempo and timing of human selection pressure on 2 major domestication genes in Zea and Cucurbita. Our data confirm an early Holocene chronology for maize domestication that has been previously indicated by archaeological and paleoecological phytolith, starch grain, and pollen data from south of Mexico, and reshift the focus back to an origin in the seasonal tropical forest rather than in the semiarid highlands.

The cultural and chronological context of early Holocene maize and squash domestication in the Central Balsas River Valley, Mexico.

Molecular evidence indicates that the wild ancestor of maize is presently native to the seasonally dry tropical forest of the Central Balsas watershed in southwestern Mexico. We report here on archaeological investigations in a region of the Central Balsas located near the Iguala Valley in Guerrero state that show for the first time a long sequence of human occupation and plant exploitation reaching back to the early Holocene. One of the sites excavated, the Xihuatoxtla Shelter, contains well-stratified deposits and a stone tool assemblage of bifacially flaked points, simple flake tools, and numerous handstones and milling stone bases radiocarbon dated to at least 8700 calendrical years B.P. As reported in a companion paper (Piperno DR, et al., in this issue of PNAS), starch grain and phytolith residues from the ground and chipped stone tools, plus phytoliths from directly associated sediments, provide evidence for maize (Zea mays L.) and domesticated squash (Cucurbita spp.) in contexts contemporaneous with and stratigraphically below the 8700 calendrical years B.P. date. The radiocarbon determinations, stratigraphic integrity of Xihuatoxtla's deposits, and characteristics of the stone tool assemblages associated with the maize and squash remains all indicate that these plants were early Holocene domesticates. Early agriculture in this region of Mexico appears to have involved small groups of cultivators who were shifting their settlements seasonally and engaging in a variety of subsistence pursuits.

Identification of teosinte, maize, and Tripsacum in Mesoamerica by using pollen, starch grains, and phytoliths.

We examined pollen grains and starch granules from a large number of modern populations of teosinte (wild Zea spp.), maize (Zea mays L.), and closely related grasses in the genus Tripsacum to assess their strengths and weaknesses in studying the origins and early dispersals of maize in its Mesoamerican cradle of origin. We report new diagnostic criteria and question the accuracy of others used previously by investigators to identify ancient maize where its wild ancestor, teosinte, is native. Pollen grains from teosinte overlap in size with those of maize to a much greater degree than previously reported, making the differentiation of wild and domesticated maize in palynological studies difficult. There is presently no valid method for separating maize and teosinte pollen on a morphological basis. Starch grain analysis, a recently developed tool of archaeobotany, appears to be of significant utility in distinguishing the seeds of teosinte from maize. We propose that the differences in starch grain morphology and size between wild and domesticated maize defined in this study may be associated with domestication genes in Zea that have been documented in the starch biosynthesis pathway. As previously reported, phytoliths effectively discriminate the female reproductive structures of Tripsacum, teosinte, and maize. Multiproxy microfossil studies of archaeological and paleoecological contexts appear to be effective tools for investigating the earliest stages of maize domestication and dispersals.

Starch fossils and the domestication and dispersal of chili peppers (Capsicum spp. L.) in the Americas.

Chili peppers (Capsicum spp.) are widely cultivated food plants that arose in the Americas and are now incorporated into cuisines worldwide. Here, we report a genus-specific starch morphotype that provides a means to identify chili peppers from archaeological contexts and trace both their domestication and dispersal. These starch microfossils have been found at seven sites dating from 6000 years before present to European contact and ranging from the Bahamas to southern Peru. The starch grain assemblages demonstrate that maize and chilies occurred together as an ancient and widespread Neotropical plant food complex that predates pottery in some regions.

Evidence for cultivar adoption and emerging complexity during the mid-Holocene in the La Plata basin.

Multidisciplinary investigations at the Los Ajos archaeological mound complex in the wetlands of southeastern Uruguay challenge the traditional view that the La Plata basin was inhabited by simple groups of hunters and gatherers for much of the pre-Hispanic era. Here we report new archaeological, palaeoecological and botanical data indicating that during an increasingly drier mid-Holocene, at around 4,190 radiocarbon (14C) years before present (bp), Los Ajos became a permanent circular plaza village, and its inhabitants adopted the earliest cultivars known in southern South America. The architectural plan of Los Ajos during the following Ceramic Mound Period (around 3,000-500 14C yr bp) is similar to, but earlier than, settlement patterns demonstrated in Amazonia, revealing a new and independent architectural tradition for South America.

Processing of wild cereal grains in the Upper Palaeolithic revealed by starch grain analysis.

Barley (Hordeum vulgare L.) and wheat (Triticum monococcum L. and Triticum turgidum L.) were among the principal 'founder crops' of southwest Asian agriculture. Two issues that were central to the cultural transition from foraging to food production are poorly understood. They are the dates at which human groups began to routinely exploit wild varieties of wheat and barley, and when foragers first utilized technologies to pound and grind the hard, fibrous seeds of these and other plants to turn them into easily digestible foodstuffs. Here we report the earliest direct evidence for human processing of grass seeds, including barley and possibly wheat, in the form of starch grains recovered from a ground stone artefact from the Upper Palaeolithic site of Ohalo II in Israel. Associated evidence for an oven-like hearth was also found at this site, suggesting that dough made from grain flour was baked. Our data indicate that routine processing of a selected group of wild cereals, combined with effective methods of cooking ground seeds, were practiced at least 12,000 years before their domestication in southwest Asia.

Evidence for the control of phytolith formation in Cucurbita fruits by the hard rind (Hr) genetic locus: Archaeological and ecological implications.

Many angiosperms, both monocotyledons and dicotyledons, heavily impregnate their vegetative and reproductive organs with solid particles of silicon dioxide (SiO(2)) known as opaline phytoliths. The underlying mechanisms accounting for the formation of phytoliths in plants are poorly understood, however. Using wild and domesticated species in the genus Cucurbita along with their F(1) and F(2) progeny, we have demonstrated that the production of large diagnostic phytoliths in fruit rinds exhibits a one-to-one correspondence to the lignification of these structures. We propose that phytolith formation in Cucurbita fruits is primarily determined by a dominant genetic locus, called hard rind (Hr), previously shown to code for lignin deposition. If true, this evidence represents a demonstration of genetic control over phytolith production in a dicotyledon and provides considerable support to hypotheses that silica phytoliths constitute another important system of mechanical defense in plants. Our research also identifies Hr as another single locus controlling more than one important phenotypic difference between wild and domesticated plants, and establishes rind tissue cell structure and hardness under the effects of Hr as an important determinant of phytolith morphology. When recovered from pre-Columbian archaeological sites, Cucurbita phytoliths represent genetically controlled fossil markers of exploitation and domestication in this important economic genus.