Genetic analyses and dispersal patterns unveil the Amazonian origin of guava domestication

Guava (Psidium guajava L.) is a semi-domesticated fruit tree of moderate importance in the Neotropics, utilized for millennia due to its nutritional and medicinal benefits, but its origin of domestication remains unknown. In this study, we examine genetic diversity and population structure in 215 plants from 11 countries in Mesoamerica, the Andes, and Amazonia using 25 nuclear microsatellite loci to propose an origin of domestication. Genetic analyses reveal one gene pool in Mesoamerica (Mexico) and four in South America (Brazilian Amazonia, Peruvian Amazonia and Andes, and Colombia), indicating greater differentiation among localities, possibly due to isolation between guava populations, particularly in the Amazonian and Andean regions. Moreover, Mesoamerican populations show high genetic diversity, with moderate genetic structure due to gene flow from northern South American populations. Dispersal scenarios suggest that Brazilian Amazonia is the probable origin of guava domestication, spreading from there to the Peruvian Andes, northern South America, Central America, and Mexico. These findings present the first evidence of guava domestication in the Americas, contributing to a deeper understanding of its evolutionary history.

Archaeobotanical evidence supports indigenous cucurbit long-term use in the Mesoamerican Neotropics

The squash family (Cucurbitaceae) contains some of the most important crops cultivated worldwide and has played an important ecological, economic, and cultural role for millennia. In the American tropics, squashes were among the first cultivated crop species, but little is known about how their domestication unfolded. Here, we employ direct radiocarbon dating and morphological analyses of desiccated cucurbit seeds, rinds, and stems from El Gigante Rockshelter in Honduras to reconstruct human practices of selection and cultivation of Lagenaria siceraria, Cucurbita pepo, and Cucurbita moschata. Direct radiocarbon dating indicates that humans started using Lagenaria and wild Cucurbita starting ~ 10,950 calendar years before present (cal B.P.), primarily as watertight vessels and possibly as cooking and drinking containers. A rind directly dated to 11,150-10,765 cal B.P. represents the oldest known bottle gourd in the Americas. Domesticated C. moschata subsequently appeared ~ 4035 cal B.P., followed by domesticated C. pepo ~ 2190 cal B.P. associated with increasing evidence for their use as food crops. Multivariate statistical analysis of seed size and shape show that the archaeological C. pepo assemblage exhibits significant variability, representing at least three varieties: one similar to present-day zucchini, another like present-day vegetable marrow, and a native cultivar without modern analogs. Our archaeobotanical data supports the hypothesis that Indigenous cucurbit use started in the Early Holocene, and that agricultural complexity during the Late Holocene involved selective breeding that encouraged crop diversification.

The Evolution of Agrarian Landscapes in the Tropical Andes

Changes in land-use practices have been a central element of human adaptation to Holocene climate change. Many practices that result in the short-term stabilization of socio-natural systems, however, have longer-term, unanticipated consequences that present cascading challenges for human subsistence strategies and opportunities for subsequent adaptations. Investigating complex sequences of interaction between climate change and human land-use in the past-rather than short-term causes and effects-is therefore essential for understanding processes of adaptation and change, but this approach has been stymied by a lack of suitably-scaled paleoecological data. Through a high-resolution paleoecological analysis, we provide a 7000-year history of changing climate and land management around Lake Acopia in the Andes of southern Peru. We identify evidence of the onset of pastoralism, maize cultivation, and possibly cultivation of quinoa and potatoes to form a complex agrarian landscape by c. 4300 years ago. Cumulative interactive climate-cultivation effects resulting in erosion ended abruptly c. 2300 years ago. After this time, reduced sedimentation rates are attributed to the construction and use of agricultural terraces within the catchment of the lake. These results provide new insights into the role of humans in the manufacture of Andean landscapes and the incremental, adaptive processes through which land-use practices take shape.

Fatty Acids and Starch Identification within Minute Archaeological Fragments: Qualitative Investigation for Assessing Feasibility

Within the realm of archaeology, the analysis of biomolecules assumes significant importance in elucidating historical dietary patterns and their implications for contemporary contexts. To achieve this, knowledge and tools of both chemistry and archaeology are essential to yield objective outcomes and conduct analyses of archaeological materials for the detection of biomolecules. Usually, only minuscule remnants of ceramic fragments are retrieved from excavations, which limits the feasibility of comprehensive laboratory analysis. This study aimed to establish a protocol for analyzing fatty acids and starch from archaeological food utensils with minimal sample quantities. Various experiments were conducted to replicate preparations that might have occurred in archaeological vessels, aiming to establish the optimal protocol. The analyses were performed using clay griddles, subjecting vegetable oil to varying temperatures for fatty acid assessment. For starch analysis, a series of experiments encompassed diverse forms of potato preparations (pulp, chuño, tortilla, carbonization, and freeze-drying) and maize (flour, tortilla, and carbonization). The verification of the experiments was confirmed by conducting identical analyses, as developed in the current study, on authentic archaeological fragments. The principal outcomes of this investigation include the successful extraction of both types of biomolecules using only 0.25 g of the sample, obtained through direct scraping from the vessel. Soxhlet extraction was identified as the most efficient strategy to recover fatty acids. Additionally, a comprehensive protocol for the identification of starch extraction was developed. This study has, for the first time, elucidated two detailed methodologies for the extraction of fatty acids and starch in scenarios in which researchers can obtain limited quantities of archaeological food utensil fragments.

A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches

Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and Central America were analyzed using archaeogenomic and biochemical approaches. Here we show, for the first time, the widespread use of cacao in South America out of its native Amazonian area of origin, extending back 5000 years, likely supported by cultural interactions between the Amazon and the Pacific coast. We observed that strong genetic mixing between geographically distant cacao populations occurred as early as the middle Holocene, in South America, driven by humans, favoring the adaptation of T. cacao to new environments. This complex history of cacao domestication is the basis of today's cacao tree populations and its knowledge can help us better manage their genetic resources.

Inferring language dispersal patterns with velocity field estimation

Reconstructing the spatial evolution of languages can deepen our understanding of the demic diffusion and cultural spread. However, the phylogeographic approach that is frequently used to infer language dispersal patterns has limitations, primarily because the phylogenetic tree cannot fully explain the language evolution induced by the horizontal contact among languages, such as borrowing and areal diffusion. Here, we introduce the language velocity field estimation, which does not rely on the phylogenetic tree, to infer language dispersal trajectories and centre. Its effectiveness and robustness are verified through both simulated and empirical validations. Using language velocity field estimation, we infer the dispersal patterns of four agricultural language families and groups, encompassing approximately 700 language samples. Our results show that the dispersal trajectories of these languages are primarily compatible with population movement routes inferred from ancient DNA and archaeological materials, and their dispersal centres are geographically proximate to ancient homelands of agricultural or Neolithic cultures. Our findings highlight that the agricultural languages dispersed alongside the demic diffusions and cultural spreads during the past 10,000 years. We expect that language velocity field estimation could aid the spatial analysis of language evolution and further branch out into the studies of demographic and cultural dynamics.

A neotropical perspective on the uniqueness of the Holocene among interglacials

Understanding how tropical systems have responded to large-scale climate change, such as glacial-interglacial oscillations, and how human impacts have altered those responses is key to current and future ecology. A sedimentary record recovered from Lake Junín, in the Peruvian Andes (4085 m elevation) spans the last 670,000 years and represents the longest continuous and empirically-dated record of tropical vegetation change to date. Spanning seven glacial-interglacial oscillations, fossil pollen and charcoal recovered from the core showed the general dominance of grasslands, although during the warmest times some Andean forest trees grew above their modern limits near the lake. Fire was very rare until the last 12,000 years, when humans were in the landscape. Here we show that, due to human activity, our present interglacial, the Holocene, has a distinctive vegetation composition and ecological trajectory compared with six previous interglacials. Our data reinforce the view that modern vegetation assemblages of high Andean grasslands and the presence of a defined tree line are aspects of a human-modified landscape.

Crop adaptation to climate change: An evolutionary perspective

The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.

Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers

Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with up to millions of workers. Analogous to edible fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards-swollen hyphal cells called gongylidia that package metabolites and are consumed by ant farmers. Yet, little is known about how gongylidia form, and thus how fungal physiology and ant provisioning collectively govern farming performance. We explored the process of gongylidium formation using advanced microscopy to image the cultivar at scales of nanometers, and both in vitro experiments and in silico analyses to examine the mechanisms of gongylidia formation when isolated from ant farmers. We first used transmission electron, fluorescence, and confocal microscopy imaging to see inside hyphal cells. This imaging showed that the cultivar uses a process called autophagy to recycle its own cellular material (e.g. cytosol, mitochondria) and then shuttles the resulting metabolites into a vacuole whose continual expansion displaces other organelles and causes the gongylidium cell's bulging bulb-like appearance. We next used scanning electron microscopy and light microscopy to link this intracellular rearrangement to the external branching patterns of gongylidium cells as they clump together into edible bundles called staphyla. We next confirmed that autophagy plays a critical role in gongylidium formation both: (1) in vitro as gongylidium suppression occurred when isolated fungal cultures were grown on media with autophagy inhibitors, and (2) in silico as differential transcript expression (RNA-seq) analyses showed upregulation of multiple autophagy gene isoforms in gongylidia relative to undifferentiated hyphae. While autophagy is a ubiquitous and often highly derived process across the tree of life, our study reveals a new role for autophagy as a mechanism of functional integration between ant farmers and their fungal crop, and potentially as a signifier of higher-level homeostasis between uniquely life-time committed ectosymbionts.

Analysis of starch grains trapped in human dental calculus in Áspero, Peru during the Initial Formative Period (3000-1800 BCE)

The objective of this research is to identify the plants consumed and to determine their dietary importance in Áspero, an urban center on the coast of the Supe Valley, Peru. Consequently, starch grains trapped in the human dental calculus of nine individuals were recovered, while the results from one individual from the Sacred City of Caral, located in the interior of Supe Valley, are presented. Eight species of food plants were identified, among them C3 plants: sweet potato, squash, potato, chili pepper, algarrobo, manioc and bean and C4 plant: maize. Previous isotopic analysis indicates that C3 plants formed the foundation of the diet at Áspero and Caral. Our results indicate a high ubiquity of C3 plants like sweet potato (100%) and squash (90%) suggesting, with caution, that these taxa were an important C3 source in the menu. Maize, C4 plant, showed a similar ubiquity (100%) to sweet potato and squash, however, previous isotopic analysis indicate that maize was a marginal food in Áspero and Caral. These results support that the absence and abundance of starch grains cannot be employed to directly infer the frequency of intake of C3 and C4 plants within a small population, as suggested by previous studies.

Trans-Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras

El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human-environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100-2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.

Tracing the evolutionary history of hepatitis B virus genotype H endemic to Mexico

Hepatitis B virus (HBV) spreads efficiently among all human populations worldwide. HBV is classified into ten genotypes (A to J) with their geographic distribution and clinical features. In Mexico, HBV genotype H is the leading cause of hepatitis B and has been detected in indigenous populations, suggesting that HBV genotype H may be native to Mexico. However, little is known about the evolutionary history of HBV genotype H. Thus, we aimed to determine the age of HBV genotype H in Mexico using molecular dating techniques. Ninety-two HBV sequences of the reverse transcriptase (RT) domain of the polymerase gene (~1,251 bp) were analyzed; 48 were genotype H, 43 were genotype F, and the oldest HBV sequence from America was included as the root. All sequences were aligned, and the most recent common ancestor (TMRCA) time was calculated using the Bayesian Skyline Evolutionary Analysis. Our results estimate a TMRCA for the genotype H in Mexico of 2070.9 (667.5-4489.2) years before the present (YBP). We identified four major diversification events in genotype H, named H1, H2, H3, and H4. The TMRCA of H1 was 1213.0 (253.3-2638.3) YBP, followed by H2 1175.5 (557.5-2424.2) YBP, H3 949.6 (279.3-2105.0) YBP, and H4 1230.5 (336.3, 2756.7) YBP. We estimated that genotype H diverged from its sister genotype F around 8140.8 (1867.5-18012.8) YBP. In conclusion, this study found that genotype H in Mexico has an estimated age of 2070.9 (667.5-4489.2) YBP and has experienced at least four major diversification events since then.

CINWA (database of terminology for cultivated plants in indigenous languages of northwestern South America): introducing a resource for research in ethnobiology, anthropology, historical linguistics, and interdisciplinary research on the neolithic transition in South America

This article introduces CINWA, a freely accessible online database of terminology for cultivated plants in indigenous languages of South America based on FAIR principles for scientific data management and stewardship. In the pre-release version we present here, CINWA assembles more than 2700 terms from more than 60 indigenous languages of northwestern South America, and coverage will be continuously expanded. CINWA is primarily designed for use in historical linguistics to explore patterns of lexical borrowing that might be used as a proxy for tracing the pathways by which knowledge of individual cultivated plants and the associated know-how spread from speech community to speech community in pre-Columbian South America. In spite of intensifying research, this is still unclear for most cultivars as the locales of initial cultivation are heterogeneous and spatially diffuse. However, possible uses of the CINWA database are manifold and go beyond this research question. The database can be used as a resource for ethnobiological and comparative anthropological research on South American communities, South American agricultural ecosystems and practices, and for studies in lexical borrowing, language contact, and historical linguistics broadly.

Long‐term fire and vegetation change in northwestern Amazonia

Amazonian forest plots are used to quantify biodiversity and carbon sequestration, and provide the foundation for much of what is known about tropical ecology. Many plots are assumed to be undisturbed, but recent work suggests that past fire, forest openings, and cultivation created vegetation changes that have persisted for decades to centuries (ecological legacies). The Yasuní Forest Dynamics plot is one of the most biodiverse places on earth, yet its human history remains unknown. Here, we use charcoal and phytolith analysis to investigate the fire and vegetation history of the Yasuní forest plot, and compare results with nearby forest plots in Colombia (Amacayacu) and Peru (Medio Putumayo-Algodón [MPA]) to explore the spatial variability of past disturbances and ecological legacies in northwestern Amazonia. Three ¹⁴C dated charcoal fragments provided evidence for a modern (1956 CE) and a past fire event ca. 750 years ago at Yasuní, compared with fire ages of 1000-1600 years ago documented at Amacayacu and MPA. Small-scale disturbances and localized canopy openings also occurred in the Yasuní plot. Phytolith assemblages from Yasuní and Amacayacu showed more variability in past vegetation change than MPA. Low-intensity, non-continuous disturbances occurred at all three plots in the past, and our results highlight the variability of past human activities both in space and time in northwestern Amazonia. Our data also suggest that post-Columbian human disturbances from the Rubber Boom (AD 1850-1920) and subsequent oil exploration have likely left stronger ecological legacies than those left by pre-Columbian peoples in our studied regions.

Coupled and decoupled legumes and cereals in prehistoric northern and southern China

Legumes and cereals, which provide different nutrients, are cultivated as coupled crops in most centers of plant domestication worldwide. However, as the only legume domesticated in China, the spatio-temporal distribution of soybeans and its status in the millet- and rice-based agricultural system of the Neolithic and Bronze Ages remains elusive. Here, archaeobotanical evidence of soybeans (n=254), millet (n=462), rice (n=482), and zooarchaeological evidence of fish (n=138) were synthesized to elucidate the phenomenon of coupled or decoupled cereals and legumes in prehistoric China. During the Neolithic and Bronze Ages, soybeans was mostly confined to northern China and rarely found in southern China, serving as a companion to millet. In contrast, fish remains have been widely found in southern China, indicating a continuous reliance on fish as a staple food besides rice. Thus, an antipodal pattern of millet-soybeans and rice-fish agricultural systems may have been established in northern and southern China since the late Yangshao period (6000-5000 cal BP) respectively. These two agricultural systems were not only complementary in terms of diet, but they also exhibited positive interactions and feedback in the coculture system. Consequently, these two systems enabled the sustainable intensification of agriculture and served as the basis for the emergence of complex societies and early states in the Yellow and Yangtze Rivers.

Pre-Columbian cultivation of vegetatively propagated and fruit tree tropical crops in the Atacama Desert

South America is a megadiverse continent that witnessed the domestication, translocation and cultivation of various plant species from seemingly contrasting ecosystems. It was the recipient and supplier of crops brought to and from Mesoamerica (such as maize and cacao, respectively), and Polynesia to where the key staple crop sweet potato was exported. Not every instance of the trans-ecological expansion of cultivated plants (both domesticated and wild), however, resulted in successful farming. Here, we review the transregional circulation and introduction of five food tropical crops originated in the tropical and humid valleys of the eastern Andes—achira, cassava, ahipa, sweet potato, and pacay—to the hyper-arid coastal valleys of the Atacama Desert of northern Chile, where they have been found in early archeological sites. By means of an evaluation of the contexts of their deposition and supported by direct radiocarbon dating, stable isotopes analyses, and starch grain analysis, we evaluate different hypotheses for explaining their introduction and adaptation to the hyper-arid soils of northern Chile, by societal groups that after the introduction of cultigens still retained a strong dependence on marine hunting, gathering and fishing ways of life based on wide variety of marine coast resources. Many of the studied plants were part of a broader package of introduced goods and technological devices and procedures, linked to food, therapeutic medicine, social and ritual purposes that transformed previous hunter-gatherer social, economic, and ideological institutions. Based on archeological data, we discuss some of the possible socio-ecological processes involved in the development of agricultural landscapes including the adoption of tropical crops originated several hundred kilometers away from the Atacama Desert during the Late Holocene.

Human-Plant Coevolution: A modelling framework for theory-building on the origins of agriculture

The domestication of plants and the origin of agricultural societies has been the focus of much theoretical discussion on why, how, when, and where these happened. The ‘when’ and ‘where’ have been substantially addressed by different branches of archaeology, thanks to advances in methodology and the broadening of the geographical and chronological scope of evidence. However, the ‘why’ and ‘how’ have lagged behind, holding on to relatively old models with limited explanatory power. Armed with the evidence now available, we can return to theory by revisiting the mechanisms allegedly involved, disentangling their connection to the diversity of trajectories, and identifying the weight and role of the parameters involved. We present the Human-Plant Coevolution (HPC) model, which represents the dynamics of coevolution between a human and a plant population. The model consists of an ecological positive feedback system (mutualism), which can be reinforced by positive evolutionary feedback (coevolution). The model formulation is the result of wiring together relatively simple simulation models of population ecology and evolution, through a computational implementation in R. The HPC model captures a variety of potential scenarios, though which conditions are linked to the degree and timing of population change and the intensity of selective pressures. Our results confirm that the possible trajectories leading to neolithisation are diverse and involve multiple factors. However, simulations also show how some of those factors are entangled, what are their effects on human and plant populations under different conditions, and what might be the main causes fostering agriculture and domestication.

The Fits and Starts of Indian Rice Domestication: How the Movement of Rice Across Northwest India Impacted Domestication Pathways and Agricultural Stories

Rice is currently the staple food for over 3.5 billion people and is arguably the most important crop exploited by humans. Understanding how we came to the point where a single crop dominates the lives of almost half of the Earth’s population has major significance for our future, even more so given the climatic instability we face today, as rice is a cereal that is dependent on water to an extreme degree. In this study, the nature of early rice agriculture in South Asia is explored, looking at how this critical crop may have begun to be exploited, cultivated, and then brought under agricultural regimes during the long span between c.6500 and 1500 BC. There is now clear evidence for early Holocene cultivation of rice in the Middle Gangetic plains of northern India, but there is still considerable debate about the timing of when this cultivation began and whether it involved domestication of rice. By 3200 BC, however, rice agriculture was present outside the Ganges in the Indus Civilization. The data show accelerated domestication in the Indus environment and agricultural systems that played a part in later hybridization with the arrival of Chinese rice. Understanding how this move from its place of origin to a new environment may have become entangled in the domestication pathways of South Asia rice prior to the arrival of Chinese rice c.1500 BC are important to the overall rice story, as they play into modern concerns relating to biodiversity and different ways of growing and watering rice.

Maize dispersal patterns associated with different types of endosperm and migration of indigenous groups in lowland South America

BACKGROUND AND AIMS

The lowlands of South America appear to be remarkably important in the evolutionary history of maize, due to new evidence that suggests that maize dispersed from Mexico and arrived in this region in a state of partial domestication. This study aimed to identify dispersal patterns of maize genetic diversity in this part of the continent.

METHODS

A total of 170 maize accessions were characterized with 4398 single nucleotide polymorphisms (SNPs) and analysed to determine if maize dispersal was associated with types of endosperm and indigenous language families.

KEY RESULTS

Four genetic groups were identified in the discriminant analysis of principal components and five groups in the cluster analysis (neighbour-joining method). The groups were structured according to the predominance of endosperm types (popcorn, floury, flint/semi-flint). Spatial principal component analysis of genetic variation suggests different dispersal patterns for each endosperm type and can be associated with hypotheses of expansions of different indigenous groups.

CONCLUSIONS

From a possible origin in Southwestern Amazonia, different maize dispersal routes emerged: (1) towards Northern Amazonia, which continued towards the Caatinga and south-eastern Atlantic Forest (Floury); (2) towards Southern Brazil, passing through the Cerrado and Southern Atlantic Forest reaching the Pampa region (Floury); and (3) along the Atlantic Coast, following Tupi movements originating from two separate expansions: one (Tupinamba) from north to south, and the other (Guarani) in the opposite direction, from south to north (flint, floury and popcorn).

Early to mid-Holocene human activity exerted gradual influences on Amazonian forest vegetation

Humans have been present in Amazonia throughout the Holocene, with the earliest archaeological sites dating to 12 000 years ago. The earliest inhabitants began managing landscapes through fire and plant domestication, but the total extent of vegetation modification remains relatively unknown. Here, we compile palaeoecological records from lake sediments containing charcoal and from pollen analyses to understand how human land-use affected vegetation during the early to mid-Holocene, and place our results in the context of previous archaeological work. We identified gradual, rather than abrupt changes in forest openness, disturbance and enrichment, with useful species at almost all sites. Early human occupations occurred in peripheral sites of Amazonia, where natural fires are part of the vegetation dynamics, so human-made fires did not exert a novel form of disturbance. Synchronicity between evidence of the onset of human occupation in lake records and archaeological sites was found for eastern Amazonia. For southwestern and western Amazonia and the Guiana Shield, the timing of the onset of human occupation differed by thousands of years between lake records and archaeological sites. Plant cultivation showed a different spatio-temporal pattern, appearing ca 2000 years earlier in western Amazonia than in other regions. Our findings highlight the spatial-temporal heterogeneity of Amazonia and indicate that the region cannot be treated as one entity when assessing ecological or cultural history. This article is part of the theme issue 'Tropical forests in the deep human past'.

Tropical forests in the deep human past

Since Darwin, studies of human evolution have tended to give primacy to open 'savannah' environments as the ecological cradle of our lineage, with dense tropical forests cast as hostile, unfavourable frontiers. These perceptions continue to shape both the geographical context of fieldwork as well as dominant narratives concerning hominin evolution. This paradigm persists despite new, ground-breaking research highlighting the role of tropical forests in the human story. For example, novel research in Africa's rainforests has uncovered archaeological sites dating back into the Pleistocene; genetic studies have revealed very deep human roots in Central and West Africa and in the tropics of Asia and the Pacific; an unprecedented number of coexistent hominin species have now been documented, including Homo erectus, the 'Hobbit' (Homo floresiensis), Homo luzonensis, Denisovans, and Homo sapiens. Some of the earliest members of our own species to reach South Asia, Southeast Asia, Oceania and the tropical Americas have shown an unexpected rapidity in their adaptation to even some of the more 'extreme' tropical settings. This includes the early human manipulation of species and even habitats. This volume builds on these currently disparate threads and, for the first time, draws together a group of interdisciplinary, agenda-setting papers that firmly places a broader spectrum of tropical environments at the heart of the deep human past. This article is part of the theme issue 'Tropical forests in the deep human past'.

Potential distributions of pre-Columbian people in Tropical Andean landscapes

Much has yet to be learned of the spatial patterning of pre-Columbian people across the Tropical Andes. Using compiled archaeological data and a suite of environmental variables, we generate an ensemble species distribution model (SDM) that incorporates general additive models, random forest models and Maxent models to reconstruct spatial patterns of pre-Columbian people that inhabited the Tropical Andes east of the continental divide, within the modern countries of Bolivia, Peru and Ecuador. Within this region, here referred to as the eastern Andean flank, elevation, mean annual cloud frequency, distance to rivers and precipitation of the driest quarter are the environmental variables most closely related to human occupancy. Our model indicates that 11.04% of our study area (65 368 km²) was likely occupied by pre-Columbian people. Our model shows that 30 of 351 forest inventory plots, which are used to generate ecological understanding of Andean ecosystems, were likely occupied in the pre-Columbian period. In previously occupied sites, successional trajectories may still be shaping forest dynamics, and those forests may still be recovering from the ecological legacy of pre-Columbian impacts. Our ensemble SDM links palaeo- and neo-ecology and can also be used to guide both future archaeological and ecological studies. This article is part of the theme issue 'Tropical forests in the deep human past'.

South-to-north migration preceded the advent of intensive farming in the Maya region

The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.

The genetic prehistory of central America has not been well explored. Here, the authors find evidence from ancient DNA from twenty individuals who lived in Belize 9,600 to 3,700 years ago of a migration from the south that coincided with the first evidence for forest clearing and the spread of maize horticulture.

Looking inside Mexican Traditional Food as Sources of Synbiotics for Developing Novel Functional Products

Currently, emerging alimentary alternatives are growing, leading to the consumption of natural products including bio, fermented, and traditional foods. The studies over functional properties of food matrices and their derived compounds have resulted in the development of new functional alimentary items. However, most of the population still has limited access to, and information about, suitable foods. Analyzing traditional fermented products, we found fermented food matrices containing beneficial bacteria, with the possibility of exerting effects on different substrates enhancing the bioavailability of short-chain fatty acids (SFCAs), antioxidants, among other food-derived products. Maize (Zea mays L.), agave varieties, nopal (Opuntia ficus-indica), and beans (Phaseolus vulgaris L.) were key foods for the agricultural and nutritional development of Mesoamerica. We believe that the traditional Mexican diet has relevant ingredients with these functionalities and their association will allow us to develop functional food suitable for each population and their current needs. In this review, the functional properties of maize, agave, nopal, and frijol are detailed, and the functional food innovation and development opportunities for these food matrices are analyzed, which may be an important precedent for future basic and applied research.

Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent

Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).

Ingeniería genética contra estrés abiótico en cultivos neotropicales: osmolitos, factores de transcripción y CRISPR/Cas9

El neotrópico es sitio de origen de gran variedad de plantas que actualmente son cultivadas con éxito en diferentes regiones del mundo. Sin embargo, condiciones climáticas adversas, que se pueden ver acrecentadas por efectos del cambio climático antropogénico, pueden afectar su rendimiento y productividad debido a las situaciones de estrés abiótico que se pueden generar. Como alternativa para contrarrestar estos efectos, se ha experimentado con modificaciones genéticas, particularmente en genes relacionados con la producción de osmolitos y factores de transcripción que han llevado a que estas plantas, a nivel experimental, tengan mayor tolerancia a estrés oxidativo, altas y bajas temperaturas y fotoinhibición, sequía y salinidad, mediante la acumulación de osmoprotectores, la regulación en la expresión de genes y cambios en el fenotipo. En este trabajo se presentan y describen las estrategias metodológicas planteadas con estos fines y se complementan con ejemplos de trabajos realizados en cultivos de origen neotropical de importancia económica, como maíz, algodón, papa y tomate. Además, y debido a la novedad y potencial que ofrece la edición génica por medio del sistema CRISPR/Cas9, también se mencionan trabajos realizados en plantas con origen neotropical, enfocados en comprender e implementar mecanismos de tolerancia a sequía. Las metodologías aquí descritas podrían constituirse en opciones prácticas para mejorar la seguridad alimentaria con miras a contrarrestar las consecuencias negativas del cambio climático antropogénico.

Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas

The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.

Prebiotic potential and chemical characterization of the poly and oligosaccharides present in the mucilage of Opuntia ficus-indica and Opuntia joconostle

The mucilage extracted from the convection-dried cladodes of O. ficus-indica and O. joconostle, two species of economic importance, delivered three fractions after methanol precipitation. Two were composed of high molar mass polysaccharides, and one included water-soluble mono-, di-, and oligosaccharides. The large polysaccharides have a molar mass range of 4.0 × 10³ to 8.0 × 10⁵ g·mol^-1 and are consistently composed of galactose, arabinose, xylose, and rhamnose; however, the content of galacturonic acid was different between both fractions and species. Their fermentability by selected probiotics was relatively low, 11-27 % compared to glucose, and decreased with increasing levels of galacturonic acid in the molecules. In the third fraction, previously unreported oligosaccharides were found. These include simple- and complex-structured galactooligosaccharides with arabinosyl-, xylosyl- and galacturonosyl acid residues. Their fermentability by prebiotic species can be ascribed more to their structural characteristics and monosaccharide composition than their molecular dimensions.

Indigenous knowledge and the shackles of wilderness

The environmental crises currently gripping the Earth have been codified in a new proposed geological epoch: the Anthropocene. This epoch, according to the Anthropocene Working Group, began in the mid-20th century and reflects the "great acceleration" that began with industrialization in Europe [J. Zalasiewicz et al., Anthropocene 19, 55-60 (2017)]. Ironically, European ideals of protecting a pristine "wilderness," free from the damaging role of humans, is still often heralded as the antidote to this human-induced crisis [J. E. M. Watson et al., Nature, 563, 27-30 (2018)]. Despite decades of critical engagement by Indigenous and non-Indigenous observers, large international nongovernmental organizations, philanthropists, global institutions, and nation-states continue to uphold the notion of pristine landscapes as wilderness in conservation ideals and practices. In doing so, dominant global conservation policy and public perceptions still fail to recognize that Indigenous and local peoples have long valued, used, and shaped "high-value" biodiverse landscapes. Moreover, the exclusion of people from many of these places under the guise of wilderness protection has degraded their ecological condition and is hastening the demise of a number of highly valued systems. Rather than denying Indigenous and local peoples' agency, access rights, and knowledge in conserving their territories, we draw upon a series of case studies to argue that wilderness is an inappropriate and dehumanizing construct, and that Indigenous and community conservation areas must be legally recognized and supported to enable socially just, empowering, and sustainable conservation across scale.

The Taming of Psidium guajava: Natural and Cultural History of a Neotropical Fruit

Guava (Psidium guajava L., Myrtaceae) is a Neotropical fruit that is widely consumed around the world. However, its evolutionary history and domestication process are unknown. Here we examine available ecological, taxonomic, genetic, archeological, and historical evidence about guava. Guava needs full sunlight, warm temperatures, and well-distributed rainfall throughout the year to grow, but tolerates drought. Zoochory and anthropochory are the main forms of dispersal. Guava's phylogenetic relationships with other species of the genus Psidium are unclear. A group of six species that share several morphological characteristics are tentatively accepted as the Psidium guajava complex. DNA analyses are limited to the characterization of crop genetic diversity within localities and do not account for possible evolutionary and domestication scenarios. A significant amount of archeological information exists, with a greater number and older records in South America than in Mesoamerica, where there are also numerous historical records. From this information, we propose that: (1) the guava ancestor may have originated during the Middle or Late Miocene, and the savannas and semi-deciduous forests of South America formed during the Late Pleistocene would have been the most appropriate ecosystems for its growth, (2) the megafauna were important dispersers for guava, (3) dispersal by humans during the Holocene expanded guava's geographic range, including to the southwestern Amazonian lowlands, (4) where its domestication may have started, and (5) with the European conquest of the Neotropics, accompanied by their domestic animals, new contact routes between previously remote guava populations were established. These proposals could direct future research on the evolutionary and domestication process of guava.

‘Moving South’: Late Pleistocene Plant Exploitation and the Importance of Palm in the Colombian Amazon

The role of plants in early human migrations across the globe has received little attention compared to big game hunting. Tropical forests in particular have been seen as a barrier for Late Pleistocene human dispersals due to perceived difficulties in obtaining sufficient subsistence resources. Archaeobotanical data from the Cerro Azul rock outcrop in the Colombian Amazon details Late Pleistocene plant exploitation providing insight into early human subsistence in the tropical forest. The dominance of palm taxa in the assemblage, dating from 12.5 ka BP, allows us to speculate on processes of ecological knowledge transfer and the identification of edible resources in a novel environment. Following the hypothesis of Martin Jones from his 2009 work, “Moving North: archaeobotanical evidence for plant diet in Middle and Upper Paleolithic Europe”, we contend that the instantly recognizable and economically useful palm family (Arecaceae) provided a “gateway” to the unknown resources of the Amazon forest.

The effect of plant domestication on host control of the microbiota

Macroorganisms are colonized by microbial communities that exert important biological and ecological functions, the composition of which is subject to host control and has therefore been described as "an ecosystem on a leash". However, domesticated organisms such as crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the microbiota is influenced by domestication, in which a double leash acts from domesticator to host and host to microbes. We discuss how this framework applies to a plant compartment that has demonstrated remarkable phenotypic changes during domestication: the seed.

Let's go fishing: A quantitative analysis of subsistence choices with a special focus on mixed economies among small-scale societies

The transition to agriculture is regarded as a major turning point in human history. In the present contribution we propose to look at it through the lens of ethnographic data by means of a machine learning approach. More specifically, we analyse both the subsistence economies and the socioecological context of 1290 societies documented in the Ethnographic Atlas with a threefold purpose: (i) to better understand the variability and success of human economic choices; (ii) to assess the role of environmental settings in the configuration of the different subsistence economies; and (iii) to examine the relevance of fishing in the development of viable alternatives to cultivation. All data were extracted from the publicly available cross-cultural database D-PLACE. Our results suggest that not all subsistence combinations are viable, existing just a subset of successful economic choices that appear recurrently in specific ecological systems. The subsistence economies identified are classified as either primary or mixed economies in accordance with an information-entropy-based quantitative criterion that determines their degree of diversification. Remarkably, according to our results, mixed economies are not a marginal choice, as they constitute 25% of the cases in our data sample. In addition, fishing seems to be a key element in the configuration of mixed economies, as it is present across all of them.

The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Archaeogenomic distinctiveness of the Isthmo-Colombian area

The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.

Facing Change through Diversity: Resilience and Diversification of Plant Management Strategies during the Mid to Late Holocene Transition at the Monte Castelo Shellmound, SW Amazonia

Recent advances in the archaeology of lowland South America are furthering our understanding of the Holocene development of plant cultivation and domestication, cultural niche construction, and relationships between environmental changes and cultural strategies of food production. This article offers new data on plant and landscape management and mobility in Southwestern Amazonia during a period of environmental change at the Middle to Late Holocene transition, based on archaeobotanical analysis of the Monte Castelo shellmound, occupied between 6000 and 650 yr BP and located in a modern, seasonally flooded savanna–forest mosaic. Through diachronic comparisons of carbonized plant remains, phytoliths, and starch grains, we construct an ecology of resource use and explore its implications for the long-term history of landscape formation, resource management practices, and mobility. We show how, despite important changes visible in the archaeological record of the shellmound during this period, there persisted an ancient, local, and resilient pattern of plant management which implies a degree of stability in both subsistence and settlement patterns over the last 6000 years. This pattern is characterized by management practices that relied on increasingly diversified, rather than intensive, food production systems. Our findings have important implications in debates regarding the history of settlement permanence, population growth, and carrying capacity in the Amazon basin.

Ecological legacies of past human activities in Amazonian forests

In Amazonia, human activities that occurred hundreds of years ago in the pre-European era can leave long-lasting effects on the forests - termed ecological legacies. These legacies include the intentional or nonintentional enrichment or depletion of certain species. The persistence of these legacies through time varies by species, and creates complex long-term trajectories of post-disturbance succession that affect ecosystem processes for hundreds of years. Most of our knowledge of Amazonian biodiversity and carbon storage comes from a series of several hundred forest plots, and we only know the disturbance history of four of them. More empirical data are needed to determine the degree to which past human activities and their ecological legacies affect our current understanding of Amazonian forest ecology.

Disentangling Domestication from Food Production Systems in the Neotropics

The Neolithic Revolution narrative associates early-mid Holocene domestications with the development of agriculture that fueled the rise of late Holocene civilizations. This narrative continues to be influential, even though it has been deconstructed by archaeologists and geneticists in its homeland. To further disentangle domestication from reliance on food production systems, such as agriculture, we revisit definitions of domestication and food production systems, review the late Pleistocene–early Holocene archaeobotanical record, and quantify the use, management and domestication of Neotropical plants to provide insights about the past. Neotropical plant domestication relies on common human behaviors (selection, accumulation and caring) within agroecological systems that focus on individual plants, rather than populations—as is typical of agriculture. The early archaeobotanical record includes numerous perennial and annual species, many of which later became domesticated. Some of this evidence identifies dispersal with probable cultivation, suggesting incipient domestication by 10,000 years ago. Since the Pleistocene, more than 6500, 1206 and 6261 native plant species have been used in Mesoamerica, the Central Andes and lowland South America, respectively. At least 1555, 428 and 742 are managed outside and inside food production systems, and at least 1148, 428 and 600 are cultivated, respectively, suggesting at least incipient domestication. Full native domesticates are more numerous in Mesoamerica (251) than the Andes (124) and the lowlands (45). This synthesis reveals that domestication is more common in the Neotropics than previously recognized and started much earlier than reliance on food production systems. Hundreds of ethnic groups had, and some still have, alternative strategies that do involve domestication, although they do not rely principally on food production systems, such as agriculture.

Directly modelling population dynamics in the South American Arid Diagonal using 14C dates

Large anthropogenic ¹⁴C datasets are widely used to generate summed probability distributions (SPDs) as a proxy for past human population levels. However, SPDs are a poor proxy when datasets are small, bearing little relationship to true population dynamics. Instead, more robust inferences can be achieved by directly modelling the population and assessing the model likelihood given the data. We introduce the R package ADMUR which uses a continuous piecewise linear (CPL) model of population change, calculates the model likelihood given a ¹⁴C dataset, estimates credible intervals using Markov chain Monte Carlo, applies a goodness-of-fit test, and uses the Schwarz Criterion to compare CPL models. We demonstrate the efficacy of this method using toy data, showing that spurious dynamics are avoided when sample sizes are small, and true population dynamics are recovered as sample sizes increase. Finally, we use an improved ¹⁴C dataset for the South American Arid Diagonal to compare CPL modelling to current simulation methods, and identify three Holocene phases when population trajectory estimates changed from rapid initial growth of 4.15% per generation to a decline of 0.05% per generation between 10 821 and 7055 yr BP, then gently grew at 0.58% per generation until 2500 yr BP. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.

Phytoliths in selected broad-leaved trees in China

Broad-leaved trees are widely distributed from tropical to temperate zones in China, reference collections of phytoliths from these taxa are crucial for the precise reconstruction of paleoenvironments and the study of early plant resource exploitation. However, not much has been published on the phytoliths produced by modern broad-leaved trees. In this study, we collected samples of 110 species that cover the common species distributed in Northern and Southern China, and extracted phytoliths from leaves, twigs and fruits, in order to investigate the phytoliths types and production in these species. We found that only 58 species were phytoliths producers, and that 23 distinct phytoliths morphotypes could be recognized. The results showed that phytoliths types and production in Northern and Southern China could be similar in the two regions. Through analyzing previously published data and our data, Elongate brachiate geniculate, Polygonal tabular, Elongate facetate, Tracheary annulate/facetate geniculate and Tracheary annulate/facetate claviform have been proposed to be the potential diagnostic types for broad-leaved trees in general. This study provided a preliminary reference of phytoliths in modern broad-leaved trees, and could be used in the identification of phytoliths in sediments and archaeological contexts.

Exploring the chemotypes underlying important agronomic and consumer traits in cassava (Manihot esculenta crantz)

A broad diversity of phenotypes are available within the cassava germplasm collections. The phenotypes include improved nutritional, starch or culinary root quality as well as abiotic and biotic resistance properties. Some of these traits can be found naturally occurring in cassava landraces, whereas others are the result of targeted breeding efforts. For future breeding programmes it is important to know the underlying mechanisms of these desirable traits. Metabolomics can assist in the elucidation of these mechanisms by measuring the end products of the cellular processes conferring the traits of interest. The present study focused on the comparison of two or more variants of the same trait such as high and low culinary quality or resistance and susceptibility to thrips. Overall, eight different traits were assessed. Results showed that amino acids and umami compounds were associated with superior culinary attributes and the phenylpropanoid superpathway plays an important role in pest resistance. Furthermore, the data highlighted a low chemodiversity in African cassavas and that the source-sink relation was still active at the harvest stage.

Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology

Some of the World's most valuable crops, including watermelon, honey melon, cucumber, squash, zucchini and pumpkin, belong to the family Cucurbitaceae. We review insights on their domestication from new phylogenies, archaeology and genomic studies. Ancestral state estimation on the most complete Cucurbitaceae phylogeny to date suggests that an annual life cycle may have contributed to domestication. Domestication started c. 11 000 years ago in the New World and Asia, and apparently more recently in Africa. Some cucurbit crops were domesticated only once, others multiple times (e.g. melon from different Asian and African populations). Most wild cucurbit fruits are bitter and nonpalatable to humans, and nonbitterness of the pulp apparently was a trait favoured early during domestication, with genomic data showing how bitterness loss was achieved convergently. The genetic pathways underlying lycopene accumulation, red or orange pulp colour, and fruit size and shape are only just beginning to be understood. The study of cucurbit domestication in recent years has benefitted from the increasing integration of archaeological and genomic data with insights from herbarium collections, the most efficient way to understand species' natural geographic ranges and climate adaptations.

Exploring oral paleopathology in the Central Andes: A review

This targeted review of oral paleopathology in the Central Andes explores research that focuses on a set of interrelated, multifactorial processes: dental caries, macrowear, alveolar abscess, antemortem tooth loss (AMTL), periodontal disease, and the presence of dental calculus. These conditions help characterize oral health because they result from the culturally mediated interaction of individuals' oral cavity with their external environment. To better understand how osteologists working in the Central Andes have interpreted the frequencies of these conditions, I review the etiology of each, as well as discuss the important issues in their analyses. I then highlight studies that integrate of a number of oral paleopathological conditions, that examine associations between oral conditions and other skeletal indicators of health, or that use multivariate statistical techniques to analyze conditions. In the Central Andes, these proxies for oral health have generally focused on several key research themes including the introduction of domesticated foods may have occurred earlier than expected, but that populations may have maintained mixed subsistence strategies for a significant period. Researchers have also identified that changes accompanying Inca imperialism were likely not as detrimental to local populations as was Spanish colonialism. Finally, the long-practiced, culturally important, activity of chewing coca has been shown to create an identifiable pattern of oral paleopathological conditions.

Early isotopic evidence for maize as a staple grain in the Americas

Maize is a cultigen of global economic importance, but when it first became a staple grain in the Americas, was unknown and contested. Here, we report direct isotopic dietary evidence from 52 radiocarbon-dated human skeletons from two remarkably well-preserved rock-shelter contexts in the Maya Mountains of Belize spanning the past 10,000 years. Individuals dating before ~4700 calendar years before present (cal B.P.) show no clear evidence for the consumption of maize. Evidence for substantial maize consumption (~30% of total diet) appears in some individuals between 4700 and 4000 cal B.P. Isotopic evidence after 4000 cal B.P. indicates that maize became a persistently used staple grain comparable in dietary significance to later maize agriculturalists in the region (>70% of total diet). These data provide the earliest definitive evidence for maize as a staple grain in the Americas.

Early Holocene crop cultivation and landscape modification in Amazonia

The beginning of plant cultivation is one of the most important cultural transitions in human history^1–4. Based on molecular markers showing the genetic similarities between domesticated plants and wild relatives, south-western Amazonia has been proposed as one of the early centres of plant domestication^4–6. However, the nature of the early human occupation and the history of plant cultivation in south-western Amazonia are still little understood. Here, we document the cultivation of Cucurbita at ca. 10,250 cal yr BP, Manihot at ca. 10,350 cal yr BP and Zea mays at ca. 6,850 cal yr BP in the Llanos de Moxos. We show that, starting ca. 10,850 cal yr BP, pre-Columbians created an anthropic landscape made of approximately 4,700 artificial forest islands within a treeless seasonally flooded savannah. Our results confirm the Llanos de Moxos as a hotspot for early plant cultivation and demonstrate that ever since their arrival, humans have caused a profound alteration of Amazonian landscapes, with lasting repercussions for habitat heterogeneity and species conservation.

Tropical Trees as Time Capsules of Anthropogenic Activity

After the ice caps, tropical forests are globally the most threatened terrestrial environments. Modern trees are not just witnesses to growing contemporary threats but also legacies of past human activity. Here, we review the use of dendrochronology, radiocarbon analysis, stable isotope analysis, and DNA analysis to examine ancient tree management. These methods exploit the fact that living trees record information on environmental and anthropogenic selective forces during their own and past generations of growth, making trees living archaeological 'sites'. The applicability of these methods across prehistoric, historic, and industrial periods means they have the potential to detect evolving anthropogenic threats and can be used to set conservation priorities in rapidly vanishing environments.

The Call of the Wild: Rethinking Food Production in Ancient Amazonia

The Amazon basin is accepted as an independent center of plant domestication in the world. A variety of important plants were domesticated in the Amazon and its surroundings; however, the majority of plants cultivated today in the Amazon are not domesticated, if this descriptor is understood to convey substantial genetic and phenotypic divergence from wild varieties or species. Rather, many domesticates are trees and tubers that occupy an intermediate stage between wild and domesticated, which seems to be a prevailing pattern since at least the middle Holocene, 6,000 years ago. Likewise, basin-wide inventories of trees show a remarkable pattern where a few species, called hyperdominant, are overrepresented in the record, including many varieties that are economically and symbolically important to traditional societies. Cultivation practices among indigenous groups in the Amazon are embedded in other dimensions of meaning that go beyond subsistence, and such entanglement between nature and culture has long been noticed at the conceptual level by anthropologists. This principle manifests itself in ancient and dynamic practices of landscape construction and transformation, which are seriously threatened today by the risks posed by economic development and climate change to Amazonian traditional societies and biomes.