Milpa, a Long-Standing Polyculture for Sustainable Agriculture

Abstract

Polyculture, or intercropping, is the practice of growing two or more crops simultaneously in time and space. The milpa is a systematic polyculture involving the simultaneous cultivation of maize (Zea mays), beans (Phaseolus spp.), squash (Cucurbita spp.), and other crops. Milpa polyculture initially emerged in the Mesoamerican region (Mexico and Central America) through the concurrent processes of managing, utilizing, and domesticating its constituent crops. It subsequently spread throughout the Americas via the diffusion of maize and the convergence of its domestication with that of its companion crops and other domesticated plants in the continent. Mesoamerican farmers made an outstanding contribution by domesticating and bringing together crops with contrasting morphological and physiological traits that are ecologically, agronomically, and nutritionally complementary. Despite its importance, few quantitative evaluations of this polyculture exist. However, these evaluations indicate that its productivity and land efficiency use (Land equivalent ratio = 1.34) are comparable to those of other intercrops studied on a global scale. We emphasize the importance of transdisciplinary efforts to study this polyculture and highlight its potential applications related to ecological interactions, plant microbiomes and breeding in order to reach sustainable production goals.

1. Introduction

The primary objective of the sustainable production of food and other organic materials is to ensure the continued productivity and quality of agro-ecosystems and ecosystems over time to meet the needs of a growing human population [1,2,3]. However, socioeconomic inequality, unequal access to land, population growth, the depletion of renewable natural resources, the industrial model of agriculture, and climate change, pose complex challenges to achieving sustainability [3,4,5]. Over the last one hundred years, agricultural production yields, especially those of agro-industrial production, have increased based on monocultures with limited genetic diversity that require significant inputs [6]. However, these monocultures have also negatively impacted ecosystems, agro-ecosystems, and human health [4,5], contributing to global change [7]. Agro-ecological strategies based on spatial and temporal crop diversification, such as intercropping, agroforestry, and crop rotation, can maintain and strengthen the productivity, stability, and sustainability of our agricultural systems [8,9,10]. This review focuses on intercropping, particularly on a long-standing polyculture practiced in the Americas: milpa or the three sisters.

Polycultures, or intercrops, are ancient and current agricultural practices involving the planned, simultaneous cultivation of two or more crops in time and space [11,12]. Polycultures configure agro-ecosystems, which are environments modified by management and containing multiple domesticated plants (crops) associated with a high diversity of useful wild and weedy plant species [13,14]. These agro-ecosystems represent farmers’ strategies for the integral use of environmental resources and date back centuries or millennia [15,16]. Polycultures function as productive, ecologically efficient interfaces between natural and simplified ecological systems [17,18]. These can include forest interventions that favor beneficial species [15,19]; diversified intercropping systems under or around the canopy of managed forests [20,21]; and agroforestry systems with native or exotic species that have multiple uses, such as for food, medicine, timber, and fuelwood [16,22]. Examples include ancient polycultures, such as the maize–bean–squash triad or milpa [23], hanfets, a practice in Ethiopia and Eritrea involving the cultivation of a barley–wheat mixture [24], and the grapevine coltora promiscua, which integrates agroforestry and intercropping [25] practice in the Mediterranean region [25,26]. In addition, various combinations of commercial crops, each grown in rows or strips within the same field, can be mentioned [12,27,28].

Due to their productivity, stability, and contributions to food security and environmental benefits, there has been a recent surge in research interest in polycultures [29,30]. Global estimates indicate that these require 20–30% less land and 19–36% less fertilizer than monocultures [31] and can increase farmers’ gross profits by an average of 33% [32]. These benefits stem from the diverse crop aerial architecture, photosynthetic mechanisms, and root systems of polycultures, as well as their favorable ecological interactions, such as niche differentiation, cooperation, and facilitation, with agro-ecosystem diversity [18,30,33]. These interactions allow for a more efficient use of solar radiation, water, and nutrients [18,30,33]. Crop diversity helps to regulate weeds and pathogens through biochemical, allelopathic, or physical effects, such as shading or forming barriers [34,35]. This increases the presence of pollinators and natural enemies of pests [36,37]. The diversity of root systems in polycultures optimizes the use of nutrients, such as nitrogen and phosphorus [38], thereby facilitating the symbiotic processes between crops, soil bacteria, and mycorrhizal fungi [17,39]. Consequently, polycultures promote higher crop yields and agricultural stability [31,40]. These characteristics make polycultures a viable alternative for meeting short-term production goals, while reducing the agriculture’s environmental footprint [29,32].

Polycultures are essentially a method of using multiple resources and a risk management strategy [41]. They enable households to produce goods for their own consumption and trade [42]. In the event of risks due to variations in climate or market conditions, polycultures increase the probability of obtaining resources from the diversified system [43]. This improves the allocation and use of labor throughout the production cycle [44]. Polycultures contribute to better nutrition and food security for rural families by conserving and promoting agrobiodiversity [42,45].

Despite these benefits, there are critical constraints to the wider adoption of intercrops, including higher labor requirements, low mechanization, and a lack of basic and applied knowledge [16,33,46,47]. However, interest in research aimed at overcoming these disadvantages is growing [30,33,47,48,49,50,51].

Cereal–legume associations are among the most widely used polycultures due to their ecological and nutritional complementarity [27,46,52]. The maize (Zea mays subsp. mays) and bean (Phaseolus spp.) association is particularly widespread [11,16,27]. Of American (specifically Mesoamerican, including Mexico and Central America) origin, the maize–bean association often includes squashes or pumpkins (Cucurbita spp.) as a third crop. Depending on regional, environmental, and production contexts, it may also include other crops and an extensive accompanying diversity [53,54]. These polycultures are generally known as milpa in Mesoamerica (Mexico and Central America) and as the three sisters among North American indigenous peoples with agricultural traditions [55,56,57].

This paper provides a comprehensive review of the milpa system, ranging from its origin and diffusion to its agrobiodiversity, productivity, and importance, as well as perspectives related to the potential of its microbiome, breeding, biotic interactions and other functions as an assemblage that may substantially contribute to sustainability goals. We emphasize the milpa in Mesoamerica, where this polyculture has a long and rich tradition. We also briefly touch on its expansion in North and South America, regions where similar crop associations have existed since ancient times. The milpa polyculture is a remarkable achievement of Mesoamerican agriculture. However, research on this system is limited, especially in topics that are needed in order to face socioeconomic and technological issues, including labor, mechanization, and the scientific and technical basis for its improvement as assemblage. Knowledge of the particularities of the milpa polyculture, such as its structure, properties and capabilities, can contribute to a better understanding and help to seek alternatives to strengthen its multiple benefits for the well-being of the people who preserve and drive the evolution of this system for agricultural sustainability.

2. Methodology

“Milpa” is often associated with the literature on intercropping [56], but there is confusion about this term [58]. To put the term in context, an initial search was carried out to clarify its main meanings. A Web of Science database search using the term ‘intercropping’ yielded 10,329 records, only 18 of which included the combination ‘intercropping AND milpa’ (2 August 2023). A Web of Science database search (Science Citation, range 1900 to present, Core Collection, field ‘topic’) using the terms ‘milpa NOT alta’ yielded 236 records, eliminating possible unrelated results due to the location of Milpa Alta in Mexico. After excluding publications not directly related to the topic of interest, the scope of the analysis was limited to 63 records. We first examined the term “milpa” in these records, specifically the 52 that reported definitions of “milpa” and geographic information, used to map this polyculture. In this initial review, three main recurrent meanings related to milpa were found: as a site or agro-ecosystem of cultivation (17 mentions), as a cultivation system, largely related to shifting or fallow systems (34 mentions), and as a polyculture (45 mentions) (see Supplementary Information-Table S1; [37,42,45,54,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105]). We consulted, mapped, and analyzed archaeobotanical records related to the origin and spread of the main crops (maize, beans and squash) of this polyculture. Additional information from books, book chapters, dissertations, and journal articles from the Google Scholar database, as well as from scientific journal web pages, was included in the results of this review. The following terms were used: ‘milpa,’ ‘three sisters,’ and ‘maize, beans, squash polyculture’ (in Spanish and English). Available statistical information from agricultural censuses on the maize polyculture in Mexico was also reviewed.

On 1 March 2024, a specific search was performed in the Web of Science database to compare the productivity of the milpa polyculture (maize, beans, and squash) with its corresponding combinations (maize and beans, maize and squash). This comparison was based on the LER (Land Equivalent Ratio), an index commonly used to analyze intercropping. Three specific searches were performed: Maize AND Phaseolus AND Intercropping AND LER; Maize AND Cucurbita AND Intercropping; and Maize AND Squash AND Beans AND Intercropping. These searches yielded 39, 15, and 7 results, respectively. Only three papers [96,106,107] reported LER values specifically on the traditional maize–bean–squash triad. Three additional works [57,108,109] that resulted from the initial search, and that presented LER values on milpa polyculture, were included. Average LER values were taken or calculated from these papers. The data for maize–bean intercrops were separated into data corresponding to maize–bush bean intercrops and data corresponding to maize–pole bean intercrops. In total, to assess productivity, we obtained, reviewed and analyzed 18 reports of maize–bush bean, four reports on maize–pole bean, four reports on maize–squash and five reports on milpa polyculture. We used five papers on maize–bean intercrops that presented data with a coefficient of variation for their respective monocrops and intercrops as an indicator of stability.

The information was organized by first presenting the main meanings of milpa. Subsequent information focuses mainly on milpas as polyculture and is presented from a historical perspective, starting with the origin and diffusion of the polyculture and ending with its current state and current perspectives. Its main facets and multifunctionalities are described. Its particularities, in relation to other intercropping patterns, and its main ecological and productive traits are highlighted. Finally, the need for further research and the exploration of new directions is discussed.

3. What Is Milpa

The term “milpa” is practically restricted to the Mesoamerican region [42,53,59,85,110], where it has multiple meanings. It is most commonly understood as a cultivation site, or an agro-ecosystem, or the typical polyculture of maize–bean–squash. It is also associated with swidden cultivation (Figure 1).

3.1. Milpa, Defined as a Crop Site and Agro-Ecosystem

Etymologically, milpa is the Spanish modification of the Nahuatl term millpan. Olmos reported in 1547 [111] that the Spanish spelling was milhpa. The term is formed by the roots milli (meaning land, real estate, or cultivated land) and pan (in, on, during, by), meaning within or on cultivated land [112]. Molina, in 1571 [113], translated millpan as “in the maize field, or in the cultivated land”.

Several agricultural management systems, incorporating or excluding maize, are associated with the Nahuatl term millpan or its etymological root milli (Table 1). This underscores the importance of this agro-ecosystem and the profound historical influence of the Nahuatl language in the Mesoamerican region [114,115].

Rojas-Rabiela [114] observed that for Mesoamerican peoples, the term milpa denotes the sense of appropriation and identity of the humanized space, the agro-ecosystem, shaped to provide and sustain a livelihood based on the primary crop, maize. Other Mesoamerican peoples have comparable lexical resources for the term “milpa” (see Supplementary Information, Table S2 [111,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138]). In the Andean region of South America, a similar term in Kechua is chakra, chagra, or chacara, which is used to refer to the agricultural space where potatoes, maize, quinoa, pumpkins, cassava, and other local crops are grown [139,140,141].

In the context of agricultural space, the milpa constitutes an agro-ecosystem, i.e., a space that has undergone ecological modification by humans and exhibits interrelated biotic and abiotic components, with structural and dynamic complexity, and with energy and material inputs and outputs that are oriented toward satisfying human needs [23,142].

Table 1. Nahuatl root milli applied to milpa agro-ecosystem or cultivation systems in Mesoamerica.

Term a	Meaning a	Area	Reference
Milpa	Mil-pa (milli, sowing field; pa, in). “In the sowing field, inheritance”; or “in the maize field”	Mexico; Belize; Guatemala; El Salvador	[42,53,59,85]
Coamil	Coatl-mil (coatl, planting sitck; milli, sowing field). Maize field sowing with planting stick	Colima, Jalisco (Mexico)	[101]
Huamil	Huac-mil (huacqui, dry; milli, sowing field). Sowing field in drylands	Guanajuato (Mexico)	[143]
Calmil	Cal-mil (calli, house; milli, sowing field). Sowing field near to the house	State of México (Mexico)	[144]
Tonamil	Tona-mil (tonalli, warmth of the sun; milli, sowing field). Maize field sowing in winter season.	Tabasco, Oaxaca, Veracruz, Puebla (Mexico)	[114]
Xopamil	Xopa-mil (xopan, spring, raining; milli, sowing field). Maize field sowing in spring–summer or rainy season.	Veracruz, Puebla (Mexico)	[114]
Amilpa	A-mil-pa (atl, water; milli, milli, sowing field; pa, in). Maize sowing fields with irrigation	Valley of Mexico, Puebla, Tlaxcala, Guerrero, Michoacán, Jalisco (Mexico)	[114,145]
Cacaomile	Cacao-mile (cacahatl, cocoa; milli, sowing field). Field planted with cocoa trees	Tabasco, Chiapas, Oaxaca, Veracruz, Guerreo (Mexico)	[114,145]
Ahuacamile	Ahuaca-mile (ahuacatl, avocado; milli, sowing field). Field planted with avocado trees	State of México, Morelos, Puebla (Mexico)	[114,145]

^a Terms in Náhuatl language and their meanings according to [111,112,113].

Table 1. Nahuatl root milli applied to milpa agro-ecosystem or cultivation systems in Mesoamerica.

Term a	Meaning a	Area	Reference
Milpa	Mil-pa (milli, sowing field; pa, in). “In the sowing field, inheritance”; or “in the maize field”	Mexico; Belize; Guatemala; El Salvador	[42,53,59,85]
Coamil	Coatl-mil (coatl, planting sitck; milli, sowing field). Maize field sowing with planting stick	Colima, Jalisco (Mexico)	[101]
Huamil	Huac-mil (huacqui, dry; milli, sowing field). Sowing field in drylands	Guanajuato (Mexico)	[143]
Calmil	Cal-mil (calli, house; milli, sowing field). Sowing field near to the house	State of México (Mexico)	[144]
Tonamil	Tona-mil (tonalli, warmth of the sun; milli, sowing field). Maize field sowing in winter season.	Tabasco, Oaxaca, Veracruz, Puebla (Mexico)	[114]
Xopamil	Xopa-mil (xopan, spring, raining; milli, sowing field). Maize field sowing in spring–summer or rainy season.	Veracruz, Puebla (Mexico)	[114]
Amilpa	A-mil-pa (atl, water; milli, milli, sowing field; pa, in). Maize sowing fields with irrigation	Valley of Mexico, Puebla, Tlaxcala, Guerrero, Michoacán, Jalisco (Mexico)	[114,145]
Cacaomile	Cacao-mile (cacahatl, cocoa; milli, sowing field). Field planted with cocoa trees	Tabasco, Chiapas, Oaxaca, Veracruz, Guerreo (Mexico)	[114,145]
Ahuacamile	Ahuaca-mile (ahuacatl, avocado; milli, sowing field). Field planted with avocado trees	State of México, Morelos, Puebla (Mexico)	[114,145]

^a Terms in Náhuatl language and their meanings according to [111,112,113].

3.2. The Term Milpa Used to Describe a Type of Polyculture

The maize–bean–squash association is distinctive to Mesoamerican cropland, where this polyculture occurs, adapts, and evolves to become the foundation of the region’s agriculture, food production, and culture [53,110,141]. Within the environmental and agro-ecological diversity in which the polyculture is established, maize emerges as the predominant crop, accompanied by five species each of beans and squash [55,146,147]. Depending on the region and the environmental or technological context, the polyculture may include other native and introduced crops, as well as a diverse array of herbaceous, shrubby, and arboreal species that are managed at various stages of vegetation succession for food, medicine, ornamentation, and fodder [21,22,53,54,148]. Socioeconomic or technological shifts may constrain the polyculture to specific combinations, such as maize–bean, maize–squash, or maize and its associations with other crops [55,56]. Given the significance of maize in Mexico, the plant itself is also referred to as milpa, after the name of the polyculture system [55,149].

3.3. Milpa as Cultivations System

At the landscape level, milpa intercropping agro-ecosystems are components of spatially interconnected agricultural systems, situated within a continuum between agro-ecosystems and vegetation succession management systems [21,22,116]. The establishment of the milpa management system for maize cultivation or intercropping is associated with different farming systems, primarily the shifting or swidden cultivation system, which is practiced in various regions of Mesoamerica.

In the Maya region, which includes the Yucatán Peninsula and the state of Chiapas in Mexico, as well as Belize, Guatemala, and northern Honduras, the typical swidden or shifting cultivation system is known as “milpa”, the milpa cultivation system [22,59,61,150]. In this region, milpa cultivation involves the strategic management of vegetation succession by modifying it for the cultivation of multiple crops and utilizing a diverse array of resources and ecosystem services [21,22,60]. Milpa cultivation involves selecting plots, clearing, slashing, and burning them, and establishing maize, either alone or in association with crops such as beans, squash, chili peppers, tubers, and others, within the same agro-ecosystem [22,60,150]. The initial annual cropping cycle is called milpa roza (slash and burning milpa) or milpa de año (annual milpa), and subsequent cycles are called milpa caña (cane milpa) [68,125]. After the third cycle, the vegetation is usually left fallow, resulting in the formation of acahual (vegetation in various stages of succession) or mature forest [22,150]. After a period of 20 to 30 years (or another designated timeframe) the forest undergoes another transformation to establish new cropping areas [22,150].

In regions outside of the Maya area, such as the southern Pacific slope of Mexico, the itinerant short fallow cycles are referred to as tlacolol or coamil [101,114], émlom (in the Teenek language) among the Huastec who settled on the tropical Atlantic slope [116], or mawechi among the Tarahumara of Chihuahua, northern Mexico [131]. In a comparable itinerant system in South America called the conuco, maize is associated with cassava, yam, bean, winter squash, and arboreal species [151].

4. Origin and Configuration of the Milpa Polyculture

The processes of plant domestication and agro-ecosystem configuration are concomitant long-term phenomena resulting from mutualistic and coevolutionary interactions between human groups and their surrounding environment, especially with regard to plant diversity [152,153]. According to Hernández-Xolocotzi [154] and Casas et al. [13,155], traditional milpas are the result of the applying of knowledge, use and selection of plant diversity, in conjunction with the management of plant populations and the modification of the environment through various practices and processes. These practices and processes include protection, gathering, forest management, cultivation, domestication, diffusion, isolation, hybridization, and gene flow that occurs between populations of crops and their wild relatives, which often inhabit areas near cultivated land [13,153,156,157]. This is particularly accentuated in the regional centers of origin and crop domestication, as evidenced by studies in Mesoamerica, the Andes, and the Amazon region [141,155,156,157,158,159,160,161].

The prolonged contact with, and the knowledge, use, and management of biodiversity in the Americas began shortly after human populations arrived, which, according to the recent findings by Ardelean et al. [162], occurred nearly 33,000 years ago. The domestication of the primary crops of the milpa polyculture—maize, five species of squash (Cucurbita spp.), and five species of beans (Phaseolus spp.)—occurred in Mesoamerica and other regions of the Americas between 10,000 to 1100 years before present (BP) (see Supplementary Information, Table S3 [147,160,163,164,165,166,167,168,169,170,171,172,173,174,175]).

The following factors may have influenced the origin of the milpa polyculture: (1) The presence of sympatric populations of wild relatives of milpa crops in Mesoamerica [146,176,177], (2) the Mesoamerican domestication of maize [163,164] and its diffusion and consolidation as a crop in different regions of the Americas [160,178,179,180], (3) the independent and parallel domestication of different bean and squash crop species across the Americas [147,181], (4) the horticultural management of crop diversity across the Americas [141,154,159,182], and (5) the ecological and nutritional complementarity achieved by these crops [141,146].

As Miranda-Colín [176], and later Flannery [177] have noted, the model for assembling the milpa polyculture likely originates from the natural association of the wild relatives of its crops that evolved in the Mesoamerican territories. These natural associations have been documented in various regions of Mexico and Guatemala, where population of teosinte (Zea spp.), the ancestor of maize, and wild beans coexist (Figure 2; Supplementary Information, Table S4 [176,177,183,184,185]). Furthermore, the distribution of wild relatives of squash also coincides in these regions [103,167,186].

However, it is important to note that the first documented evidence of domestication of squash and maize comes from the archaeobotanical record. In central Mexico, the archaeological evidence indicates the presence of domesticated varieties of Cucurbita pepo dating to 10,000 years ago [165]. Maize, the primary crop in the milpa system, is considered to have been domesticated approximately 9000 years ago from teosinte (Zea mays subsp. parviglumis) populations in the Middle Balsas River Basin [163,164]. However, Kato et al. [187] propose a multicentric origin of maize in Mesoamerica. According to the findings of Yang et al. [178], an important genetic component, accounting for 15–25% of the maize genome, has been contributed by the teosinte (Z. mays subsp. mexicana) populations of the central Mexican highlands. This contribution has been critical for understanding the crop’s expansion and its environmental adaptation across the Americas [178,179,180].

The earliest archaeobotanical evidence of domesticated maize was reported by Piperno et al. [164] in the Balsas Basin, Guerrero, México, corresponding to micro-botanical remains (pollen) with an age of 8700 calendar years BP, recovered from the Xihuatoxtla site. Concurrently, phytoliths from the area suggest that squash (probably C. argyrosperma) was also domesticated in that region [164]. Piperno et al. [188] reported that evidence based on palaeoecological micro-remains (pollen, starch, phytoliths), as well as charcoal recovered from the nearby lakes, particularly Laguna Tuxpan, in this region “indicates human use and alteration of the near shore environment through frequent fire and some vegetation clearing” [188] (p. 11880). They also noted that “maize and squash were grown at lake edges starting between 10,000 and 5000 BP, most likely sometime during the first half of that period” [188] (p. 11874). This estimation is considered the earliest known evidence of the intentional association of these crops in the emerging milpa polyculture in Mesoamerica. This polyculture was managed in an agro-ecosystem resulting from the management of natural vegetation through ancient clearing by using fire.

As maize spread throughout the Americas, it was incorporated into the diversity of crops managed and domesticated by pre-Columbian peoples, becoming relevant to diet, management systems, and agricultural landscapes [76,160,189]. Archaeobotanical remains demonstrate that maize, squash, beans, and seafood had been part of the diet of the inhabitants of the northwestern coast of Peru since approximately 6700–4000 BP (Dillehay et al. 2012; Piperno and Dillehay 2008) [166,190].

Maize, squash, and beans were cultivated alongside cassava, yam, and tuberous species of the Marantaceae family (leren and arrowroot) in tropical regions of Central and South America [159,160], with quinoa in the Andean region [191], and with sunflower and Chenopodium berlandieri in North America [192]. According to Maezumi et al. [189], the cultivation of maize was part of an agroforestry polyculture system in the Amazonian lowlands, involving the intercropping of maize with yam (Ipomoea batatas), cassava (Manihot esculenta), squash (Cucurbita sp.), and tropical fruit trees. This system emerged after 4300 cal (calibrated) years BP, when maize was introduced to the region [189]. The maize–bean–squash association, as it is recognized today, has been consistently preserved in the remains of croplands buried by a volcanic eruption that occurred at Joya de Cerén, in El Salvador, ca. 592 to 660 CE (Common Era) [193]. By 1400 CE, the agrarian indigenous peoples in North America had adopted this polyculture at the limits of North American agriculture ([192], Figure 3).

5. Milpa Polyculture at Present

By 1492, variations of the maize–bean–squash triad, along with other native crops, had been extensively cultivated throughout the Americas [139,140,141,145,192,222].

In the following centuries, the European invasion led to the decimation of the human populations in the Americas [223]. This could have also led to the imposition of an agricultural tradition based largely on monocultures, characteristic of the agricultural tradition of the Old World [141,154]. These processes may have impacted the use of polyculture systems [139,141,154]. However, this also introduced crops, animals, techniques and tools that were adopted in agriculture and in the practice of milpa systems [154,224,225]. The introduction of temperate fruit trees, in particular, contributed to the enrichment of traditional agroforestry systems, such as metepantles (traditional terraced camps bordered by agaves) or calmiles (milpas or sowing land near or around houses) [148,226]. These systems are currently the basis of agroforestry systems promoted by technicians and government, called “milpa intercropped with fruit trees” or MIAF (in Spanish) [227].

In certain regions of Latin America, the practice of milpa and other polycultures has persisted under various modalities and combinations with local and introduced crops [16,53,56,228]. By the 1970s, Francis [229] estimated that 60% of the maize and 80% of the beans produced in Latin America came from associated cropping systems. In Mexico, data on maize and bean “intercalados” (intercropped) associated with milpa polyculture only appear in the early agricultural censuses (1930–1970; Figure 4). According to the census reports, by 1930, 21% of the national land sown with maize, and 15% of the maize produced nationally, were intercropped [230]. However, by 1970 these figures had decreased to 11% and 10%, respectively [231]. The extant census data reveal that, by 1930, 43% of national bean production was intercropped [230]. However, this figure declined, reaching 33% in the 1970s [231]. Although national-level censuses after 1970 no longer collect information on milpa polyculture, numerous reports from 1993 to 2024 (see Supplementary Information, Table S6) document its presence in this country and in the Mesoamerican region. Forty of these reports were revised and mapped (see Figure 3). These reports and related literature detail the characteristics, importance, value and prospects of milpa polyculture, among other aspects, which are discussed below.

6. Structural, Ecological and Agronomic Traits of Milpa Polyculture

6.1. Cultivated and Associated Diversity

The current milpa polyculture system encompasses an extensive diversity of crops, including maize, beans, squash, and many others. Farmers have played a pivotal role in shaping the genetic diversity of maize and the rich variety of domesticated species within the genera Phaseolus and Cucurbita in this system, as well as in other analogous multiple-cropping systems across the Americas [146,147,181,237]. At the intraspecific level, maize’s genetic plasticity, as the primary crop in milpa polyculture, manifests in over 260 races, constituting 90% of global maize diversity [237,238]. Within each race, there is extensive genetic, morphological, and phenological diversity [238,239]. This phenomenon is consistent across different species of beans and squash. Beans exhibit growth habits ranging from determinate to indeterminate, and different seed sizes and colors [146,228] are observed between and within milpa agro-ecosystems [240]. In squashes, pumpkins and some gourds, the range of fruit and seed forms, colours, and sizes is similarly extensive [147,186,241]. This resulting diversity has successfully crossed the agricultural spectrum of the continent, from central Chile and Argentina to southern Canada, and at elevations ranging from 0 to 3800 m above sea level (masl) (Figure 5, [238,242,243,244]).

This extensive geographic range is characterized by the predominance of a broad diversity of maize landraces, comprised of at least four large conspicuous genetic and ecological groups: (1) highland Mexican, (2) tropical lowland, (3) Andean, and (4) northern US [245]. These are associated in turn with the wide interspecific and intraspecific diversity of squash and bean species that were domesticated from different wild relatives’ gene pools that have evolved in distinct regions of the continent since ancient times ([147,246]; see also Supplementary Information, Table S3). This is evident in the common bean (P. vulgaris) and the lima bean (P. lunatus), which were domesticated at different times and in different regions from allopatric wild relatives’ gene pools: the Andean and Mesoamerican gene pools [181]; and the year bean (P. dumosus), which evolved and was domesticated from populations resulting from the natural hybridization of P. vulgaris and P. coccineus. This allowed it to occupy the intermediate environments of its parents [174].

Figure 5. Altitudinal adaptation (meters above sea level, masl) of main species of milpa polyculture in the Americas. M, maize (Zea mays ssp. mays); Pa, tepary bean (Phaseolus acutifolius); Pd, year bean (P. dumosus); Pl, lima bean (P. lunatus); Pv, common bean (P. vulgaris); Pc, scarlet runner bean (P. coccineus); Ca, silver-seed gourd or pipiana squash (Cucurbita artgyrosperma); Cms, butternut squash (C. moschata); Cp, squash or pumpkin (C. pepo); Cmx, buttercup or kabosha (C. maxima); Cf, black-seeded squash (C. ficifolia.) (Elaborated based on Supplementary Information, Table S7 [186,228,238,241,243,244,247]).

Figure 5. Altitudinal adaptation (meters above sea level, masl) of main species of milpa polyculture in the Americas. M, maize (Zea mays ssp. mays); Pa, tepary bean (Phaseolus acutifolius); Pd, year bean (P. dumosus); Pl, lima bean (P. lunatus); Pv, common bean (P. vulgaris); Pc, scarlet runner bean (P. coccineus); Ca, silver-seed gourd or pipiana squash (Cucurbita artgyrosperma); Cms, butternut squash (C. moschata); Cp, squash or pumpkin (C. pepo); Cmx, buttercup or kabosha (C. maxima); Cf, black-seeded squash (C. ficifolia.) (Elaborated based on Supplementary Information, Table S7 [186,228,238,241,243,244,247]).

Most domesticated species of Cucurbita (C. pepo, C. argyrosperma, C. moschata, and C. maxima) and Phaseolus (P. vulgaris, P. lunatus, P. dumosus, and P. acutifolius) cannot survive to above 3000 masl, with notable exceptions in the Andean region, where C. ficifolia can survive at 3400 masl and P. coccineus reaches 3600 masl [186,228,241,243,247]. At elevations above 3000 masl, the viability of other native crops, such as potatoes (Solanum tuberosum), tarwi (Lupinus mutabilis), and quinoa (Chenopodium quinoa), as well as introduced crops such as broad beans (Vicia faba) and peas (Pisum sativum), is enhanced [228]. In the tropical lowlands, the crops cultivated in the polyculture include the native Manihot esculenta, Ipomoea batatas, Marantha arundinacea, Dioscorea trifida, and Calathea allouia [151,160], as well as the introduced Vigna unguiculata and Cajanus cajan, which are of Asian and African origin, respectively [228,242].

In Mexico, the basic crop diversity of the milpa (maize–bean–squash) is associated with significant diversity, depending on the environmental context. It ranges, at regional level, from 109 species in temperate regions [248] to 122 species in dryland regions [92], and up to 149 species of useful plants inventoried by Heindorf et al. [54,116] in Téenek milpa agro-ecosystems (Supplementary Information, Table S8 [53,60,92,116,182,248,249,250]). These latter agro-ecosystems are located in a transitional area between the tropical and temperate zones in the Huasteca region. These studies have found that edible plants are the most numerous group (mean = 44 species), followed by species used for fodder, timber, fuel, and medicine. Together, these species form complex polyculture agroforestry systems [22,92,116].

The milpa agro-ecosystem is a dynamic space of domestication and cultivar origin. Chili peppers (Capsicum spp.), husk tomatoes (Physalis spp.), and tomatoes (Solanum lycopersicum) initially occur as weedy plants. Farmers often promote and cultivate these plants in or around milpa areas [251]. These practices involve human selection and management processes [13,251,252]. Milpas are also home to native and introduced plant species that are used as greens for their edible leaves, stems, inflorescences, and infructescences (known as quelites in Mexico [252]). These plants are subject to varying degrees of management—tolerated, protected, favored, or cultivated—and domestication processes [13,252]. In Mexico, Mapes and Basurto [253] registered 250 species of quelites, 127 of which are associated with milpa agro-ecosystems [254]. Depending on their use (e.g., as medicine or fodder), farmers either tolerate or suppress populations of weedy plant species. They harvest these species in their early growth stages at the onset of the rainy season. Then, they eliminate or limit their presence in later growth stages through weeding or hilling practices [126,252]. Farmers allow some individuals to remain as sources of propagules [255], or reserve spaces, within the agro-ecosystem, where herbicides are excluded, to allow the growth of edible greens for consumption [102].

6.2. Intercrop Types

In the context of spatial organization, polycultures and intercropping can be categorized in the following manner: (i) mixed intercropping, where two or more crops are cultivated simultaneously with no or limited distinguishing arrangement; (ii) relay intercropping, where two or more crops are grown concurrently during part of their life cycle; (iii) row intercropping, where two or more crops are cultivated in alternating rows; and (iv) strip intercropping, where two or more crops are cultivated in strips simultaneously, enabling some degree of crop interaction while requiring distinct management practices (Figure 6, [31,33].

Milpa polyculture crops (maize, beans, squash, and other related crops) can be grown in various configurations, including row or strip intercrops. Examples of such configurations include maize–bean, maize-squash, maize and broad bean, maize and potato, and maize and wheat. As demonstrated by the research of Baudoin et al. [228], Thierfelder et al. [257], Woolley et al. [242], and Yu et al. [27], these configurations occur at different latitudes. Additionally, these configurations have been observed in relay intercrops, such as maize and beans, which are commonly managed in tropical America [228,229,242]. These associations are facilitated by the crops’ morphological and biological characteristics. In the case of the maize–bean–squash polyculture, the association is primarily due to the distinct growth patterns of the beans. Common maize–bean intercrops principally consist of combinations of maize with bush (or determinate growth habit) beans. Milpa polyculture comprises pole or climbing beans of indeterminate or semi-indeterminate growth, which are present in all domesticated Phaseolus species [146,181]. This seemingly straightforward condition endows the milpa polyculture with distinctive structural and agro-ecological characteristics. In the milpa polyculture, maize and bean seeds are planted concurrently at the same point in the row hill, enabling effective, simultaneous, and integrated growth in space and time. Each set of maize and beans is appropriately spaced, generating spaces in the agro-ecosystem that are used by a third crop, such as squash, pumpkins or gourds, or that allow for the development of voluntary vegetation suitable for use. This management technique generates an ordered, systematic arrangement of maize, beans, and squashes, that forms a mosaic pattern in the agro-ecosystem. Zhang et al. [106] have noted this pattern in the agricultural context of some Latin American countries. Mota-Cruz [256] has documented this cultivation pattern in the milpa polyculture practiced in southern Puebla, Mexico (Figure 6, see also Figure 1B).

6.3. Complementarity

Biodiversity is widely recognized as a critical factor influencing the productivity and stability of ecosystems and agro-ecosystems [40,258,259]. This positive relationship can be explained, at least in part, by the effects of ecological or productive complementarity between species, functional groups, and genotypes [258,259]. Selection effects favoring the development of the more productive components also play a role [258]. However, complementarity promotes the synergy of the functioning, productivity, and stability in agro-ecosystems and ecosystems in general [40,260,261].

According to Barry et al. [260], complementarity can be explained by three main mechanisms; (1) niche partitioning, which is defined as the product of the species’ traits and differentiated abilities in using space and resources within a system; (2) abiotic facilitation, which is defined as the ability of species to modify the abiotic environment for the benefit of other species; and (3) biotic feedback, which is defined as the product of species’ biotic interactions with other trophic levels [260]. Polycultures manifest these three mechanisms, especially in the milpa polyculture.

6.3.1. Niche Partitioning

Mesoamerican farmers achieved the integration of crops with contrasting morphologies and physiologies. Maize utilizes the C₄ carbon fixation pathway and exhibits greater photosynthetic efficiency than beans and squash, both of which employ the C₃ pathway [262]. These physiological characteristics, along the diversified aerial architectures, enable the simultaneous sowing of maize and beans in the same location. The climbing habit of the bean allows it to grow on the maize stalk to find sunlight. The large leaf lamina of the sparsely sown squash captures the solar radiation that passes through the maize and beans [23,263,264]. The milpa triad’s root systems exhibit various shapes and lengths, enabling the polyculture to access different soil spaces and resources [38,106]. Consequently, the milpa polyculture produces greater amounts of aerial and radical biomass than monocultures, even at low nitrogen concentrations, due to the nitrogen-fixing ability of the beans [106]. Conversely, under phosphorus limitation, maize has a selective advantage due to its higher competitiveness in acquiring this nutrient [106].

6.3.2. Abiotic Facilitation

In the milpa system, the maize serves as a support structure for the pole beans, and the squash’s leaf lamina limits evaporation from the soil [23,263]. Consequently, soil temperature decreases by up to 4.4 °C, and moisture retention increases by up to 45% compared to the same in a monoculture [263]. The substantial growth of squash provides cover that contributes to soil fertility, producing eight to ten tons of dry matter per hectare per cycle [265].

6.3.3. Biotic Feedback

When integrating legume crops into polycultures, farmers leverage these plants’ ability to form symbiotic relationships with nitrogen-fixing bacteria (Rhizobium spp.). This allows for the capture, use, and transfer of nutrients to companion crops, thereby contributing to the integrated functioning of the agro-ecosystem [266]. The close proximity of maize and bean roots in the milpa system stimulates the survival and growth of Rhizobium, which in turn induces genes that promote nodulation and nitrogen fixation in beans [64]. The shade provided by the squash leaves has been observed to limit weed growth [35,265], a phenomenon that may also be favored by an allelopathic effect through root contact [35]. Liao et al. [267] observed that the maize–bean–squash association enhances the maize’s chemical defense against herbivores by increasing the content of primary and secondary metabolites and phytohormones in its leaves. This reduces the survival rate and growth of larvae of the Asian maize borer (Ostrinia furnicaulis) and the fall armyworm (Spodoptera frugiperda) larvae. The crop diversity of the milpa and its associated flora serves as a source of pollen and nectar for pollinator species and provides sustenance for wildlife [37,116,268].

6.4. Productivity and Stability

The functionality and sustainability of ecosystems or agro-ecosystems can be assessed based on their characteristics, such as productivity, stability, resilience, vulnerability, or equity [142,259]. However, due to their ease of measurement and immediate relevance, most assessments focus on productivity and stability. Productivity is quantified by the total biomass or yield produced, and stability is mainly estimated using the coefficient of variation [269].

Polycultures have garnered interest in agriculture because of their demonstrated productivity and temporal stability (Li et al. 2021) [40]. However, comparing polycultures requires contrasting different species, compositions, and densities relative to their individual components. Therefore, establishing a common index is imperative. The Land Equivalent Ratio (LER) is the most widely used index in this regard [12,270].

The LER is a relative measure of polyculture productivity, calculated by summing the relative yields of the intercropped species in polycultures and comparing them to the corresponding monoculture yields [31,270]. The index quantifies the relative land area required by each component crop of the polyculture in monoculture to produce an equivalent yield to that of intercropping [12,270,271]. For example, an LER value of 1.25 indicates that, to achieve an equivalent yield in one hectare of polyculture, the total area of each component crop would need to be 1.25 ha [270]. The LER has been shown to express the savings in cultivated area, inputs, and financial resources [12,32,271]. Yu et al. [27] reported a global estimated LER value of 1.2, and Martin-Guay et al. [32] reported a value of 1.3. According to Li et al. [31] and Willey [12], these values indicate that polycultures result in 20–30% savings in cultivated land area or, indirectly, a 20–30% higher yield compared to the corresponding monocultures.

Among milpa crops, associations between maize and beans have been documented in multiple regions, with a higher prevalence of bush beans than pole beans. Associations between maize and squash are less prevalent, and those between bean and quash are established only with bush beans and are relatively rare. Maize–bean–squash polycultures are predominantly confined to the Americas (Figure 7), particularly to the Mesoamerican region (see Figure 3).

Experimental evaluations of these intercrops report an average LER value of 1.27 (Figure 8), which is similar to the above-mentioned global value reported for intercropping [27,31,32]. In these evaluations, the milpa polyculture (maize–bean–squash) exhibited the highest LER value (1.34), compared to its crop component intercrops (1.32 for maize-bush bean, 1.28 for maize-squash and 1.16 for maize and pole bean combinations; Figure 8). This finding indicates that the milpa polyculture is relatively more productive and efficient than its monocrop and binary combinations, with the potential to save up to 25% of land, a calculation based on van der Werf [270], compared to its monocrops.

However, it is important to note the lack of research on milpa polyculture, especially regarding the different methodologies, arrangements, densities, and LER values reported in these studies. Amador and Gliessman [108] evaluated the maize-cowpea (Vigna ungiculata, an African legume, equivalent to the pole bean, that has been integrated into milpa polyculture in tropical America)-squash polyculture at two densities and reported LER values ranging from 0.56 to 2.03 (with an overall average of 1.30), with the higher value corresponding to the lower density tested. Molina-Anzures et al. [96] found LER values greater than 3.0 for different associations of maize, beans, squash, and fruit trees. However, they did not separate the effect of polyculture yield from the yield of fruit tree species. Ebel et al. [109] reported an LER value of 1.6 for the association of maize, squash, and bush bean. Notably, the latter crop is more frequently cultivated in monoculture (or in strip, row or relay intercrop) than in milpa polyculture [242]. Zhang et al. [106] evaluated the productivity of milpa polyculture, similar to the focus of this review, and found that the polyculture had higher biomass productivity, with an LER value of 1.17 when compared to the corresponding paired crop and monoculture.

In terms of stability, Li et al. [39,40] found that not only was the annual productivity of polycultures maintained, but it also increased over time. They interpreted this increase as the result of improved soil quality and functionality due to the incorporation of large amounts of organic matter, as well as favorable interactions between crop diversity and the belowground microbiome that triggered beneficial cascading effects. As illustrated in

Table 2. Coefficients of variation (CV) calculated in experimental evaluations of maize-common bean intercrops and monocrops in partial and total Land equivalent ratios (pLER and tLER, respectively); a lower CV indicates greater stability.

Traits Evaluated	pLER Common Bean	pLER Maize	tLER (Intercrop)	Reference
Variety, spatial arrangement, inoculation	7.5	0.68	3.09	[278]
Climbing genotypes: maize varieties	18	17.53	14.24	[293]
Agro-ecological zone	9.9	17.4	11.1	[280]
Bean variety	5.6	14.5	5.8	[280]
CV	10.25	12.52	8.55

, the association between maize and common bean has been observed to be more stable, as indicated by a lower coefficient of variation, compared to monocrops.

The stability of milpa polyculture has not been quantitatively determined. However, the long-term stability of this polyculture is suggested by its domestication of components, diffusion, and widespread adoption in the Americas, as well as its continued practice in some regions.

7. Multifunctionality and Limitations of Milpa Polyculture

7.1. Milpa and Food

The cultivation and intercropping of cereals and legumes are important in agricultural and nutritional practices worldwide due to their complementarity in the agro-ecosystem and human diets [11,27,146]. In different regions of the Americas, combinations of maize–bean–squash with tubers, greens (quelites), fruit trees, oilseed crops, and wild or domesticated animal protein sources, can provide a complete and balanced diet for humans [45,57,141,159]. In Mexico, people consume not only the main products of the milpa crops, but also fungi, such as corn smut or ‘huitlacoche’ (Ustilago maydis), insects, such as grasshoppers, and wildlife mammals that feed on the agro-ecosystem [45,251,268,297].

Maize is the main source of energy in the milpa polyculture triad crops and contributes moderate amounts of protein, which is supplemented by beans and squash, which have two to three times the protein content of maize (see Supplementary Information, Table S10 [298,299,300]). Maize lacks amino acids essential for human nutrition, such as lysine and tryptophan, but contains sufficient methionine [57]. Conversely, beans are low in methionine but high in lysine, and squash fruits and seeds provide protein, fat, vitamin A, and dietary fiber [57]. Falkowski et al. [45] found that the 37 species of vegetables, tubers, fruits, and wildlife associated with milpas in the Selva Lacandona region of Chiapas, Mexico, could nearly meet the daily dietary needs of a family of five, except for requirements for saturated fat, cholesterol, sodium, calcium, and iodine. Maize provides nearly half of the calories, total fat, sodium, dietary fiber, protein, iron, zinc, and niacin [45]. The maize–bean–squash triad is also an important dietary source of bioactive compounds, such as phenols, anthocyanins, phytosterols, phytates, resistant starch, and peptides [301]. These compounds may contribute to health through their antioxidant, anti-inflammatory, anti-cancer cell proliferation, anti-hyperglycemic, and anti-diabetic properties [301].

In addition to the aforementioned nutritional diversity provided by the maize–bean–squash association, Sauer [141] and Mota-Cruz [302] noted the variety of edible plant parts, such as leaves, stems, flowers, fruits, and seeds, consumed at different life cycle stages —immature, intermediate, and mature—provided by the milpa. Maize, beans, and squash are the basic ingredients of a long list of dishes that form the core of the diet and gastronomy of the Americas. Echeverría and Arroyo [303] documented more than 600 dishes with maize as the main ingredient in Mexico alone.

7.2. Milpa and the Economy

The various products and by-products (e.g., raw stubber, maize husk) derived from milpa crops and the associated diversity of cash crops cultivated in the agro-ecosystem play a multifaceted role in rural livelihoods and complement other economic activities [42,92,304,305]. These products have been identified as a means of self-supply, income generation, and risk mitigation for peasant economic units [42,131,248,304]. The diversity of native maize, which is traded as a commodity or transformed into traditional dishes, is integrated into local and regional commercialization value chains [304,306]. Sub-products, such as raw maize, stove, and weeds, are an important forage for livestock and backyard animals in temperate [248] and semiarid regions [92]; by-products are also sold locally or regionally [92,248]. In Mexico and South America, the husk (or totomoxtle) and leaves of maize, have historically been used to wrap traditional foods, such as tamales in Mexico or humitas in South America. King [305] documented a notable example of the importance of maize byproducts in family economies in communities of central Veracruz, Mexico. In these communities, families harvest and process maize husks, which they then sell in national markets or export to the United States [305]. Hellin et al. [306] have identified the incorporation of female participation and leadership within these strategies as a critical component of households’ economies.

As Isakson [42] observed in the Guatemalan highlands, milpa polyculture is a ‘multifunctional asset’ in peasant economic units. According to this author, if milpa is considered only for its market value, it could be deemed unprofitable. However, milpa’s multifunctionality makes it primarily a strategy for food security and food sovereignty for farming families [42]. Furthermore, this practice has cultural and recreational value, and it produces and conserves agrobiodiversity [42].

7.3. Milpa and Culture

The cultural significance of maize, beans, and squash among the peoples of the Americas is well-documented. There is a substantial body of research on the cultural manifestations surrounding these crops, including works by Bonfil [307], Poma de Ayala [140], and Sahagún [145]. In Mesoamerica, many ceremonies, celebrations, and fairs are held throughout the year, particularly during the rainy season and the productive cycle of the milpa crops [308,309]. Regarding the profound significance and cultural importance of maize in Mesoamerica and the role of the milpa polyculture as an axis, Bonfil [307] (p. 5) made the following observations: “Maize is a human plant, cultural in the deepest sense of the word, because it does not exist without the intelligent and timely assistance of the human hand”. This crop “marked the sense of time, ordered the [Mesoamerican] space” and “gave rise to multiple aesthetic expressions, becoming a benchmark for understanding different forms of social organization and multiple ways of thinking, knowing and living”. These cultural manifestations, forms of organization, and aesthetic expressions persist and are recreated in both rural and urban contexts in countries such as Mexico [307,310]. The milpa paradigm offers a foundation for formulating strategies and social organizations aimed at safeguarding the genetic resources, cultural heritage, and values associated with native maize [310,311]. This paradigm is based in the symbiotic relationship between diverse crops, a feature that fosters cooperation and complementarity among them. In the context of contemporary challenges posed by transgenic crops and the prevailing capitalist agro-industrial model, milpa serves as a model of resilience, a testament to the adaptability and cultural vitality of traditional agrarian practices [310,311]. Due to their multiple and significant cultural and biological aspects, maize and milpa are regarded as prime examples of biocultural heritage in Mexico [312].

7.4. Labor and Mechanization

Two primary constraints, along with concomitant opportunities, have been identified in the implementation, permanence, and widespread adoption of polycultures: labor and the absence of mechanization [25,43,44,49,257,313].

In agricultural settings where labor is scarce, this factor can hinder the adoption of diversification practices such as intercropping. Casagrande et al. [313] have examined this phenomenon in the context of French farming systems. In smallholder farming contexts, as demonstrated by Norman’s [44] analyses in Nigeria and Jodha’s [43] analyses in India, mixed cropping or intercropping allows for the fulfilment of various agricultural objectives and ensures labor distribution and absorption throughout the year, depending on the requirements of different crop combinations. A comprehensive evaluation of polyculture must consider labor, as Thierfelder et al. [257] recently addressed. Their findings acknowledge the increased labor and input costs associated with intercropping but demonstrate that these expenses are counterbalanced by a higher net economic return. Ferrario’s [25] observations align with the assertion that the labor-intensive agricultural system known as ‘coltura promiscua’ (a Mediterranean polyculture) possesses two notable characteristics. First, it demonstrates an ability to produce a greater quantity of crops within a confined area [25]. Secondly, according to Ferrario [25], it exhibits a capacity to absorb labor, a trait that holds particular significance in the context of global change.

Regarding milpa polyculture, Fonteyne et al. [314] reported a range of 27 to 401 workdays per crop cycle and per hectare, based on data from various authors. However, this figure differs from the original source [315], which indicates that the more demanding work treatment does not exceed 118 workdays per hectare. The labor required in milpa polyculture depends on the management system and the level of technological development. On average, 27 labor days per hectare have been reported in annualized systems [93], and up to 100 labor days per cycle per hectare in shifting cultivation systems without firing [315]. For shifting milpa cultivation, however, del Amo and Ramos [88] reported a range of 49 to 69 days of labor, depending on whether maize monoculture or maize–bean–squash polyculture was established. As a shifting cultivation system, milpa demands the greatest labor investment for preparing the agro-ecosystem (including selecting and delimiting plots, clearing, and burning), controlling weeds, and harvesting [88,315].

A comprehensive understanding of the configuration or organization of intercrops is imperative for the implementing adaptation and mechanization initiatives [49,50]. In the context of relay, row, and strip intercrops, mechanization is viable in almost all agricultural activities by adapting existing tools and machinery [31,49,50]. Mota-Cruz [256] studied milpa polycultures in southern Puebla, Mexico, and observed that farmers use machinery for initial agricultural tasks, such as plowing, harrowing, and furrowing. This practice significantly reduces the time and labor required for these tasks. However, for subsequent sowing and hilling activities, farmers opt for animal traction and manual labor due to the absence of adapted tools for sowing the milpa polyculture pattern or because superior management and plant care are attained through manual hilling. The primary technical challenges pertain to the processes of planting and harvesting. The former requires the development or adaptation of suitable seed-drills to be used with a tractor. The latter presents a more substantial challenge due to the crops’ different maturation periods.

8. Future Prospects

In light of the intricate dynamics of the contemporary global climate crisis and the volatility of agricultural inputs, it is necessary to explore various strategies to ensure the production of sufficient, stable, affordable, and culturally appropriate food [1,2,3,4,29]. In this context, intercropping has garnered increasing interest as a sustainable food production alternatives in agriculture [29,30,31,32,33]. Milpa polyculture, a paradigmatic form of intercropping, has undergone a protracted evolutionary process since the initial domestication of its main crops and its configuration in Mesoamerica [164,172,188], achieving multiple expressions and modalities in the Americas [141,159,160,228,242]. In Mexico alone, this system has generated 59 [239] to 65 maize landraces [297], some of which (Tuxpeño, Chalqueño, Bolita, and Cónico) have been sources of breeding to improved crops in the country and other regions [316,317]. In the milpa polyculture, maize provides about half of the energy and protein in the human diet in Mesoamerica [298]. Beans are an important source of protein [57,301] and their ability to fix N is valuable for the cycling and integrating this element into soils [318,319]. Squashes and pumpkins contribute to a balanced diet due to their vitamins, proteins and unsaturated fatty acid content [57,301], as well as adding a valuable amount of biomass to the agro-ecosystem [242]. The production of biomass and the yield of this polyculture is similar to the average production of intercropping on a global scale.

Strengthening above- and below-ground interactions at the agro-ecosystem and landscape levels through the efficient integration of agricultural practices, such as intercropping and crop rotation, is essential for sustainability in crop production [320,321]. Milpa polyculture is successfully managed in Mesoamerica—sometimes with relay cropping and crop rotation with beans or other crops [242]—and is part of a variety of complex landscapes in different successional stages of vegetation [21,116,322]. These landscapes provide ecosystem services, such as pollinator diversity [37] and the presence of pests’ natural enemies, thus avoiding or limiting the use of agrochemicals [36,267]. The milpa agro-ecosystem is also a space and source of food for domestic and wild animals, which in turn are part of the diet of farmers and their families [45,268]. The milpa agro-ecosystem can harbor a high diversity of useful plants (edible, medicinal, fodder, timber, and others) and biodiversity (faunal, fungal, and microbial), which enhances its functionality, productivity, and stability [323]. To better understand the potential and prospects of this polyculture, especially in Mexico, it is important to promote knowledge acquisition, increase research efforts, and effectively incorporate these systems into national agricultural policies. Some of these issues are discussed below.

In Mexico, despite numerous reports documenting milpa polyculture in its different regions (Figure 3), the national agricultural censuses from the past five decades lack data quantifying its geolocation, extent, and persistence. Consequently, there is a lack of information about its current status in the country’s agricultural geography. Given the urgent need to improve the sustainability of agricultural systems through diversified crop production, the recent implementation of national agricultural policies such as “Sembrando Vida” (Sowing Life), which promotes agricultural diversification [324], and the examination of socioeconomic phenomena, such as migration, it is important to determine whether milpa polyculture has been maintained, diminished, abandoned, or is likely to have expanded in response to these factors. The proposed approach, which conceptualizes milpa as a polyculture, agro-ecosystem and agricultural system, could be useful in this endeavor, as it clarifies the concept of milpa. Advancing this objective would require work at the regional level, carried out within a systems framework approach [323], which would include documenting the diversity of milpa polyculture [54,116] and the dynamics of its change [79]. It is also imperative to document and amass the genetic diversity of milpa to ensure the preservation of its genetic resources in national germplasm repositories. To achieve these objectives, it is essential to engage farmers through transdisciplinary working methods in documenting technological, ecological, and cultural knowledge. This documentation will serve as a foundation for the subsequent strengthening and developing polyculture. In parallel, there are two emergent fields with potentialities to be developed in milpa polyculture in which it is important to explore and promote further work and research: microbiome and breeding. In the former, an important and dynamic research community is emerging. In the latter, new directions are yet to be established. In addition, studying the multiple ecological interactions occurring in the milpa as agro-ecosystem requires especial attention.

8.1. Microbiome

The microbiome present in intercropped agro-ecosystems contributes to the processes of nitrogen fixation and phosphorus facilitation, which promote plant growth and stress tolerance through beneficial interactions in the holobiont soil-plant system [17,39,325]. These microbiome processes can help to reduce the environmental impact and make more efficient use of resources, such as synthetic fertilizers, while increasing plant resistance to biotic and abiotic stresses [39,326]. Previous studies have focused on nitrogen fixation and plant growth promotion by rhizobial nodulation in beans and other legumes intercropped with maize [318,319]. However, the diversity and specificity of the microbiomes associated with milpa polyculture in different environments has only recently been explored. For example, Sangabriel-Conde et al. [327] discovered that a substantial colonization of arbuscular mycorrhizal fungi (Glomeromycota) was associated with a native maize landrace (‘Negro’) in polyculture. Cabrera et al. [63] isolated a bacterial strain of the genus Amycolatopsis from a milpa polyculture that demonstrated antagonistic activity against Fusarium strains. Higdon et al. [328] identified 33 known taxa of diazotrophic bacteria in mucilage isolates from the aerial roots of the native Olotón maize landrace. Van Deynze et al. [329] had previously found that this landrace acquires 29–82% of its nitrogen from microbial communities growing in the mucilage secretion. Bennett et al. [330] proposed a model for the evolution of the association between nitrogen-fixing microbes and mucilage secreted by maize roots. They suggested that this process possibly originated from one of maize’s wild relatives (Zea mays subsp. mexicana). This knowledge must be further developed and effectively used to enhance milpa-based agriculture, reduce dependency on fertilizers, conserve agrobiodiversity, and strengthen the peasant economy.

8.2. Breeding

Milpa is a structured, long-standing polyculture that could serve as a foundational model for designing optimal crop mixtures and enhancing their functionality, complementarity, and productivity. As with crop mixtures, improving milpa polycultures requires transitioning from the ‘ideotype’ concept used in single-crop breeding [331] to the ‘mixeotype’ concept [47]. The latter, according to Litrico and Violle [47], involves designing, selecting, and optimizing crop mixtures across two fundamental groups of traits: agronomic traits, which are associated with yield, and interaction traits, which contribute to positive complementarity. In this regard, Litrico and Violle [47] proposed two strategies: (1) optimizing the means of the agronomic traits of the mixture by converging all genotypes to optimal values; and (2) maximizing the variance between components of the mixture for the interaction traits, while simultaneously minimizing the within-component variance. Optimizing interaction traits focuses on improving the functionality of the interactions, such as niche partitioning and facilitation, among species [332]. In contrast, optimizing agronomic traits focuses on selecting more cooperative genotypes within and between species to increase crop yields in combined populations (a ‘communal ideotype’), as proposed in kin selection theory [333].

Improving agronomic and interaction traits can be achieved through breeding schemes of recurrent selection for mixture performance of two or more crops. In this regard, it is important to consider that approaches such as the group selection procedure proposed by Griftin [334], particularly for identifying and selecting non-random diversity groups as departure for a breeding program. In polycultures, it is crucial to identify outstanding combinations of crops and incorporate them into specific recurrent selection schemes, such as the Reciprocal Mixture Ability selection scheme proposed by Wright [335] or the parallel improvement scheme of two populations for General Mixture Ability (GMA) proposed by Sampoux et al. [51], as well as the incorporation of the Producer/Associate (Pr/As) concept suggested by Haug et al. [336]. The scheme proposed by Wright [335] involves evaluating random pairs of crop species populations in mixtures or intercrops. The best populations of each species or the most effective pair of populations are selected from these pairs. These selected units of each crop are then intercrossed to produce a new set of units for subsequent evaluation in the next cycle. Thes scheme proposed by Sampoux et al. [51] allows for the expression of more pronounced GMA advantages (GMA of a given genetic unit is its average performance in mixture with any of the genetic units from the other species [51]). Sampoux et al.’s scheme consists of selecting candidates from progeny families of each species that are tested in a mixture with a balanced bulk of progeny families of all the other species’ candidates. The selected candidates from the best mixtures are then recombined to generate the n + 1 cycle. Finally, mixtures of pairs of progeny families from the best candidates could be formed for agricultural use [51]. Haug et al. [336] show that incorporating the Pr/As concept enables the characterizing of the contribution of genotypes to total mixture yield and describing biological interaction functions related to plant traits.

Other significant contributions stem from ecological theory and quantitative genetics, particularly regarding direct genetic effects (DGEs) and interspecific indirect genetic effects (IIGEs) [337]. These findings can assist in improving intercrops, which are considered as complex and productive plant communities [48,337]. Genomic approaches have also been proposed as tools to evaluate and improve intercrops [338]. However, it is also important to develop strategies for farmers that preserve the evolutionary process of maintaining and recreating sustainable crop communities, such as the milpa polyculture in Mesoamerica. This objective could be realized through the implementation of a comprehensive selection program targeting the crop community, following the optimization of agro-ecological traits related to productivity, functionality, and complementarity. Similarly, applying classical and even omic tools and strategies can help to achieve this goal by recovering and using valuable crop genetic resources, such as landraces, and by engaging various stakeholders through participatory breeding methodologies, as recently summarized and proposed by Santamarina et al. [339].

9. Conclusions

Milpa is a long-standing, emblematic polyculture formed and maintained in the Mesoamerican region (Mexico and Central America). It involves the management, domestication, and integration of the broad genetic diversity of maize, beans, and squash (some of the most important staple crops originating and domesticated in the Americas) in an agro-ecosystem. This system is known as milpa in this region. The milpa polyculture is a significant accomplishment in Mesoamerican agriculture. It involves the domestication of crops with contrasting functional traits in a distinctive arrangement that facilitates the expression and utilization of ecological, agronomic, and nutritional complementarities. In Mesoamerica and other regions of the Americas, various combinations, modalities and complexities of this polyculture system persist as an agro-ecological response to food production and as a risk-aversion strategy. The system conserves agrobiodiversity, ecosystem services, and culture, exemplifying multifunctionality and providing multiple values for farmers’ production units.

The average land equivalent ratio for milpa (LER) is 1.34, indicating that this polyculture has the potential to conserve up to 25% of land when compared to monocultures or binary intercrops. Its biomass production and yield are comparable to those of other intercrops that have been evaluated globally. When complemented by other agro-ecological strategies such as agroforestry, crop rotation, microbiome strengthening, and breeding its components as an assembly, this polyculture offers prospects for its improvement, evolution, and adaptation to contribute to sustainability in agriculture. To make progress in this area, it is important to understand the diversity, structure, management systems, and knowledge of milpa. It is also essential to leverage these attributes in conjunction with farmers to strengthen and expand the milpa’s capabilities and potential. This is particularly important because, like intercropping in general, the milpa presents limitations that must be overcome, such as a high workload, lack of mechanization, and limited scientific basis. This paper aims to contribute to this effort. Therefore, it is crucial to prioritize preserving and strengthening the milpa polyculture, and extending its research and development, especially in Mesoamerica, where it constitutes the core of a profound and enduring agricultural, economic, and biocultural heritage.